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| Publications of A. Jonathan Shaw :chronological alphabetical combined listing:
%% Books
@book{fds167042,
Author = {Anderson, L. E. and A. J. Shaw and B. Shaw},
Title = {Peatmosses (Sphagnum) of the southeastern United
States.},
Publisher = {New York Botanical Garden Press.},
Year = {2009},
Key = {fds167042}
}
@book{fds151717,
Author = {Goffinet, B. and A. J. Shaw},
Title = {Bryophyte Biology},
Publisher = {Cambridge University Press},
Year = {2009},
Key = {fds151717}
}
@book{fds230486,
Author = {Goffinet, B and Shaw, AJ},
Title = {Bryophyte biology, second edition},
Pages = {1-565},
Publisher = {Cambridge University Press},
Year = {2008},
Month = {January},
ISBN = {9780521872256},
url = {http://dx.doi.org/10.1017/CBO9780511754807},
Abstract = {Bryophyte Biology provides an extensive overview of the
hornworts, liverworts, and mosses; diverse groups of land
plants that occupy a great variety of habitats throughout
the world. This new edition covers essential aspects of
bryophyte biology, from morphology, physiological ecology
and conservation, to speciation, and genomics. Revised
classifications incorporate contributions from recent
phylogenetic studies. Six new chapters complement fully
updated chapters from the original book to provide a
completely up-to-date resource. New chapters focus on the
contributions of Physcomitrella to plant genomic research,
population ecology of bryophytes, mechanisms of drought
tolerance, a phylogenomic perspective on land plant
evolution, and problems and progress of bryophyte speciation
and conservation. Written by leaders in the field, this book
offers an authoritative treatment of bryophyte biology, with
rich citation of the current literature, suitable for
advanced students and researchers.},
Doi = {10.1017/CBO9780511754807},
Key = {fds230486}
}
%% Papers Published
@article{fds369316,
Author = {Healey, AL and Piatkowski, B and Lovell, JT and Sreedasyam, A and Carey,
SB and Mamidi, S and Shu, S and Plott, C and Jenkins, J and Lawrence, T and Aguero, B and Carrell, AA and Nieto-Lugilde, M and Talag, J and Duffy,
A and Jawdy, S and Carter, KR and Boston, L-B and Jones, T and Jaramillo-Chico, J and Harkess, A and Barry, K and Keymanesh, K and Bauer, D and Grimwood, J and Gunter, L and Schmutz, J and Weston, DJ and Shaw, AJ},
Title = {Newly identified sex chromosomes in the Sphagnum (peat moss)
genome alter carbon sequestration and ecosystem
dynamics.},
Journal = {Nature plants},
Volume = {9},
Number = {2},
Pages = {238-254},
Year = {2023},
Month = {February},
url = {http://dx.doi.org/10.1038/s41477-022-01333-5},
Abstract = {Peatlands are crucial sinks for atmospheric carbon but are
critically threatened due to warming climates. Sphagnum
(peat moss) species are keystone members of peatland
communities where they actively engineer hyperacidic
conditions, which improves their competitive advantage and
accelerates ecosystem-level carbon sequestration. To dissect
the molecular and physiological sources of this unique
biology, we generated chromosome-scale genomes of two
Sphagnum species: S. divinum and S. angustifolium. Sphagnum
genomes show no gene colinearity with any other reference
genome to date, demonstrating that Sphagnum represents an
unsampled lineage of land plant evolution. The genomes also
revealed an average recombination rate an order of magnitude
higher than vascular land plants and short putative U/V sex
chromosomes. These newly described sex chromosomes interact
with autosomal loci that significantly impact growth across
diverse pH conditions. This discovery demonstrates that the
ability of Sphagnum to sequester carbon in acidic peat bogs
is mediated by interactions between sex, autosomes and
environment.},
Doi = {10.1038/s41477-022-01333-5},
Key = {fds369316}
}
@article{fds374506,
Author = {Robinson, S. C. and M. Nieto-Lugilde and A. M. Duffy and K. M. Munoz and B. Aguero and A. Merced and K. Hassel and K. I. Flatberg and A. J.
Shaw. 2023},
Title = {The Sphagnum cuspidatum complex: phylogeny, specie
delimitation, and morphology},
Journal = {Biological Journal of the Linnean Society},
Volume = {https://doi.org/10.1093/biolinnean/blad1},
Year = {2023},
Key = {fds374506}
}
@article{fds374505,
Author = {Piatkowski, B. and D. J. Weston and B. Aguero and A. Duffy and K.
Imwattana, A. L. Healey and J. Schmutz and A. Jonathan
Shaw},
Title = {Divergent selection fuels genomic differentiation between
incipient species of Sphagnum (peat moss)},
Journal = {Annals of Botany},
Volume = {132},
Pages = {499–512},
Year = {2023},
Key = {fds374505}
}
@article{fds374502,
Author = {Shaw, A. J. and M. Nieto-Lugilde and B. Aguero and A. Duffy and B. T.
Piatkowski and J. Jaramillo-Chico and S. Robinson and K. Hassel and K.
I. Flatberg and D. J. Weston and S. Schuette and K. A.
Hicks},
Title = {Sphagnum diabolicum sp. nov. and S. magniae sp. nov.;
morphological variation and taxonomy of the “S.
magellanicum complex”},
Journal = {The Bryologist},
Volume = {126},
Pages = {69-89},
Year = {2023},
Key = {fds374502}
}
@article{fds374504,
Author = {Shaw, A. J. and A. Duffy and M. Nieto-Lugilde and B. Aguero and S.
Schuette, S. Robinson and J. Loveland and K. A. Hicks and D. Weston and B. Piatkowski and M. Kolton and J. Koska and A.
Healey},
Title = {Clonality, local population structure, and gametophyte sex
ratios in cryptic species of the Sphagnum magellanicum
complex},
Journal = {Annals of Botany},
Volume = {132},
Pages = {77–94},
Year = {2023},
Key = {fds374504}
}
@article{fds363287,
Author = {Carrell, AA and Lawrence, TJ and Cabugao, KGM and Carper, DL and Pelletier, DA and Lee, JH and Jawdy, SS and Grimwood, J and Schmutz, J and Hanson, PJ and Shaw, AJ and Weston, DJ},
Title = {Habitat-adapted microbial communities mediate Sphagnum
peatmoss resilience to warming.},
Journal = {The New phytologist},
Volume = {234},
Number = {6},
Pages = {2111-2125},
Year = {2022},
Month = {June},
url = {http://dx.doi.org/10.1111/nph.18072},
Abstract = {Sphagnum peatmosses are fundamental members of peatland
ecosystems, where they contribute to the uptake and
long-term storage of atmospheric carbon. Warming threatens
Sphagnum mosses and is known to alter the composition of
their associated microbiome. Here, we use a microbiome
transfer approach to test if microbiome thermal origin
influences host plant thermotolerance. We leveraged an
experimental whole-ecosystem warming study to collect
field-grown Sphagnum, mechanically separate the associated
microbiome and then transfer onto germ-free laboratory
Sphagnum for temperature experiments. Host and microbiome
dynamics were assessed with growth analysis, Chla
fluorescence imaging, metagenomics, metatranscriptomics and
16S rDNA profiling. Microbiomes originating from warming
field conditions imparted enhanced thermotolerance and
growth recovery at elevated temperatures. Metagenome and
metatranscriptome analyses revealed that warming altered
microbial community structure in a manner that induced the
plant heat shock response, especially the HSP70 family and
jasmonic acid production. The heat shock response was
induced even without warming treatment in the laboratory,
suggesting that the warm-microbiome isolated from the field
provided the host plant with thermal preconditioning. Our
results demonstrate that microbes, which respond rapidly to
temperature alterations, can play key roles in host plant
growth response to rapidly changing environments.},
Doi = {10.1111/nph.18072},
Key = {fds363287}
}
@article{fds363288,
Author = {Duffy, AM and Ricca, M and Robinson, S and Aguero, B and Johnson, MG and Stenøien, HK and Flatberg, KI and Hassel, K and Shaw,
AJ},
Title = {Heterogeneous genetic structure in eastern North American
peat mosses (Sphagnum)},
Journal = {Biological Journal of the Linnean Society},
Volume = {135},
Number = {4},
Pages = {692-707},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1093/biolinnean/blab175},
Abstract = {Bryophytes generally have broad geographical ranges that
suggest high dispersal ability. The aim of this study was to
test hypotheses about dispersal limitation, as indicated by
isolation by distance, in four spore-producing species of
the moss genus Sphagnum (Sphagnum carolinianum, Sphagnum
missouricum, Sphagnum macrophyllum and Sphagnum pylaesii)
and to assess whether plants in the southern USA harbour
high levels of unique alleles and/or other indicators of
exceptional genetic diversity. Isolation by distance was
detected in all four species, but regional patterns of
genetic structure were very species specific. Northern and
southern genotype groups were detected in S. carolinianum
and S. missouricum, but in S. pylaesii plants from the
Adirondack Mountains of New York were genetically distinct
from others to the north and south. One species, S.
macrophyllum, exhibited differentiation between northern and
southern genetic groups that appeared to reflect more
ancient phylogenetic diversification.},
Doi = {10.1093/biolinnean/blab175},
Key = {fds363288}
}
@article{fds363290,
Author = {Carrell, AA and Veličković, D and Lawrence, TJ and Bowen, BP and Louie, KB and Carper, DL and Chu, RK and Mitchell, HD and Orr, G and Markillie, LM and Jawdy, SS and Grimwood, J and Shaw, AJ and Schmutz, J and Northen, TR and Anderton, CR and Pelletier, DA and Weston,
DJ},
Title = {Novel metabolic interactions and environmental conditions
mediate the boreal peatmoss-cyanobacteria
mutualism.},
Journal = {The ISME journal},
Volume = {16},
Number = {4},
Pages = {1074-1085},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1038/s41396-021-01136-0},
Abstract = {Interactions between Sphagnum (peat moss) and cyanobacteria
play critical roles in terrestrial carbon and nitrogen
cycling processes. Knowledge of the metabolites exchanged,
the physiological processes involved, and the environmental
conditions allowing the formation of symbiosis is important
for a better understanding of the mechanisms underlying
these interactions. In this study, we used a cross-feeding
approach with spatially resolved metabolite profiling and
metatranscriptomics to characterize the symbiosis between
Sphagnum and Nostoc cyanobacteria. A pH gradient study
revealed that the Sphagnum-Nostoc symbiosis was driven by
pH, with mutualism occurring only at low pH. Metabolic
cross-feeding studies along with spatially resolved
matrix-assisted laser desorption/ionization mass
spectrometry imaging (MALDI-MSI) identified trehalose as the
main carbohydrate source released by Sphagnum, which were
depleted by Nostoc along with sulfur-containing
choline-O-sulfate, taurine and sulfoacetate. In exchange,
Nostoc increased exudation of purines and amino acids.
Metatranscriptome analysis indicated that Sphagnum host
defense was downregulated when in direct contact with the
Nostoc symbiont, but not as a result of chemical contact
alone. The observations in this study elucidated
environmental, metabolic, and physiological underpinnings of
the widespread plant-cyanobacterial symbioses with important
implications for predicting carbon and nitrogen cycling in
peatland ecosystems as well as the basis of general
host-microbe interactions.},
Doi = {10.1038/s41396-021-01136-0},
Key = {fds363290}
}
@article{fds363291,
Author = {Piatkowski, BT and Yavitt, JB and Turetsky, MR and Shaw,
AJ},
Title = {Natural selection on a carbon cycling trait drives ecosystem
engineering by Sphagnum (peat moss).},
Journal = {Proceedings. Biological sciences},
Volume = {288},
Number = {1957},
Pages = {20210609},
Year = {2021},
Month = {August},
url = {http://dx.doi.org/10.1098/rspb.2021.0609},
Abstract = {<i>Sphagnum</i> peat mosses have an extraordinary impact on
the global carbon cycle as they control long-term carbon
sequestration in boreal peatland ecosystems. <i>Sphagnum</i>
species engineer peatlands, which harbour roughly a quarter
of all terrestrial carbon, through peat accumulation by
constructing their own niche that allows them to outcompete
other plants. Interspecific variation in peat production,
largely resulting from differences in tissue
decomposability, is hypothesized to drive niche
differentiation along microhabitat gradients thereby
alleviating competitive pressure. However, little empirical
evidence exists for the role of selection in the creation
and maintenance of such gradients. In order to document how
niche construction and differentiation evolved in
<i>Sphagnum</i>, we quantified decomposability for 54
species under natural conditions and used phylogenetic
comparative methods to model the evolution of this carbon
cycling trait. We show that decomposability tracks the
phylogenetic diversification of peat mosses, that natural
selection favours different levels of decomposability
corresponding to optimum niche and that divergence in this
trait occurred early in the evolution of the genus prior to
the divergence of most extant species. Our results
demonstrate the evolution of ecosystem engineering via
natural selection on an extended phenotype, of a fundamental
ecosystem process, and one of the Earth's largest soil
carbon pools.},
Doi = {10.1098/rspb.2021.0609},
Key = {fds363291}
}
@article{fds357898,
Author = {Meleshko, O and Martin, MD and Korneliussen, TS and Schröck, C and Lamkowski, P and Schmutz, J and Healey, A and Piatkowski, BT and Shaw,
AJ and Weston, DJ and Flatberg, KI and Szövényi, P and Hassel, K and Stenøien, HK},
Title = {Extensive Genome-Wide Phylogenetic Discordance Is Due to
Incomplete Lineage Sorting and Not Ongoing Introgression in
a Rapidly Radiated Bryophyte Genus.},
Journal = {Molecular biology and evolution},
Volume = {38},
Number = {7},
Pages = {2750-2766},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.1093/molbev/msab063},
Abstract = {The relative importance of introgression for diversification
has long been a highly disputed topic in speciation research
and remains an open question despite the great attention it
has received over the past decade. Gene flow leaves traces
in the genome similar to those created by incomplete lineage
sorting (ILS), and identification and quantification of gene
flow in the presence of ILS is challenging and requires
knowledge about the true phylogenetic relationship among the
species. We use whole nuclear, plastid, and organellar
genomes from 12 species in the rapidly radiated,
ecologically diverse, actively hybridizing genus of peatmoss
(Sphagnum) to reconstruct the species phylogeny and quantify
introgression using a suite of phylogenomic methods. We
found extensive phylogenetic discordance among nuclear and
organellar phylogenies, as well as across the nuclear genome
and the nodes in the species tree, best explained by
extensive ILS following the rapid radiation of the genus
rather than by postspeciation introgression. Our analyses
support the idea of ancient introgression among the
ancestral lineages followed by ILS, whereas recent gene flow
among the species is highly restricted despite widespread
interspecific hybridization known in the group. Our results
contribute to phylogenomic understanding of how speciation
proceeds in rapidly radiated, actively hybridizing species
groups, and demonstrate that employing a combination of
diverse phylogenomic methods can facilitate untangling
complex phylogenetic patterns created by ILS and
introgression.},
Doi = {10.1093/molbev/msab063},
Key = {fds357898}
}
@article{fds353428,
Author = {Piatkowski, BT and Imwattana, K and Tripp, EA and Weston, DJ and Healey,
A and Schmutz, J and Shaw, AJ},
Title = {Phylogenomics reveals convergent evolution of red-violet
coloration in land plants and the origins of the anthocyanin
biosynthetic pathway.},
Journal = {Molecular phylogenetics and evolution},
Volume = {151},
Pages = {106904},
Year = {2020},
Month = {October},
url = {http://dx.doi.org/10.1016/j.ympev.2020.106904},
Abstract = {The flavonoids, one of the largest classes of plant
secondary metabolites, are found in lineages that span the
land plant phylogeny and play important roles in stress
responses and as pigments. Perhaps the most well-studied
flavonoids are the anthocyanins that have human health
benefits and help plants attract pollinators, regulate
hormone production, and confer resistance to abiotic and
biotic stresses. The canonical biochemical pathway
responsible for the production of these pigments is
well-characterized for flowering plants yet its conservation
across deep divergences in land plants remains debated and
poorly understood. Many early land plants such as mosses,
liverworts, and ferns produce flavonoid pigments, but their
biosynthetic origins and homologies to the anthocyanin
pathway remain uncertain. We conducted phylogenetic analyses
using full genome sequences representing nearly all major
green plant lineages to reconstruct the evolutionary history
of the anthocyanin biosynthetic pathway then test the
hypothesis that genes in this pathway are present in early
land plants. We found that the entire pathway was not intact
until the most recent common ancestor of seed plants and
that orthologs of many downstream enzymes are absent from
seedless plants including mosses, liverworts, and ferns. Our
results also highlight the utility of phylogenetic
inference, as compared to pairwise sequence similarity, in
orthology assessment within large gene families that have
complex duplication-loss histories. We suggest that the
production of red-violet flavonoid pigments widespread in
seedless plants, including the 3-deoxyanthocyanins, requires
the activity of novel, as-yet discovered enzymes, and
represents convergent evolution of red-violet coloration
across land plants.},
Doi = {10.1016/j.ympev.2020.106904},
Key = {fds353428}
}
@article{fds353429,
Author = {Duffy, AM and Aguero, B and Stenøien, HK and Flatberg, KI and Ignatov,
MS and Hassel, K and Shaw, AJ},
Title = {Phylogenetic structure in the Sphagnum recurvum complex
(Bryophyta) in relation to taxonomy and geography.},
Journal = {American journal of botany},
Volume = {107},
Number = {9},
Pages = {1283-1295},
Year = {2020},
Month = {September},
url = {http://dx.doi.org/10.1002/ajb2.1525},
Abstract = {<h4>Premise</h4>The Sphagnum recurvum complex comprises a
group of closely related peat mosses that are dominant
components of many northern wetland ecosystems. Taxonomic
hypotheses for the group range from interpreting the whole
complex as one polymorphic species to distinguishing 6-10
species. The complex occurs throughout the Northern
Hemisphere, and some of the putative species have
intercontinental ranges. Our goals were to delimit the
complex and assess its phylogenetic structure in relation to
morphologically defined species and intercontinental
geography.<h4>Methods</h4>RADseq analyses were applied to a
sample of 384 collections from Europe, North America, and
Asia. The data were subjected to maximum likelihood
phylogenetic analyses and analyses of genetic structure
using the software STRUCTURE and multivariate ordination
approaches.<h4>Results</h4>The S. recurvum complex includes
S. angustifolium, S. fallax, S. flexuosum, S. pacificum, and
S. recurvum as clades with little evidence of admixture. We
also resolved an unnamed clade that is referred to here as
S. "pseudopacificum." We confirm that S. balticum and S.
obtusum are nested within the complex. Species with bluntly
acute to obtuse stem leaf apices are sister to those with
acute to apiculate leaves. Most of the species exhibit some
differentiation between intraspecific population systems
disjunct on different continents.<h4>Conclusions</h4>We
recognize seven species in the amended S. recurvum complex,
including S. balticum and S. obtusum, in addition to the
informal clade S. "pseudopacificum." Although we detected
some geographically correlated phylogenetic structure within
widespread morphospecies, our RADseq data support the
interpretation that these species have intercontinental
geographic ranges.},
Doi = {10.1002/ajb2.1525},
Key = {fds353429}
}
@article{fds348449,
Author = {Bell, D and Lin, Q and Gerelle, WK and Joya, S and Chang, Y and Taylor, ZN and Rothfels, CJ and Larsson, A and Villarreal, JC and Li, F-W and Pokorny,
L and Szövényi, P and Crandall-Stotler, B and DeGironimo, L and Floyd,
SK and Beerling, DJ and Deyholos, MK and von Konrat, M and Ellis, S and Shaw, AJ and Chen, T and Wong, GK-S and Stevenson, DW and Palmer, JD and Graham, SW},
Title = {Organellomic data sets confirm a cryptic consensus on
(unrooted) land-plant relationships and provide new insights
into bryophyte molecular evolution.},
Journal = {American journal of botany},
Volume = {107},
Number = {1},
Pages = {91-115},
Year = {2020},
Month = {January},
url = {http://dx.doi.org/10.1002/ajb2.1397},
Abstract = {<h4>Premise</h4>Phylogenetic trees of bryophytes provide
important evolutionary context for land plants. However,
published inferences of overall embryophyte relationships
vary considerably. We performed phylogenomic analyses of
bryophytes and relatives using both mitochondrial and
plastid gene sets, and investigated bryophyte plastome
evolution.<h4>Methods</h4>We employed diverse
likelihood-based analyses to infer large-scale bryophyte
phylogeny for mitochondrial and plastid data sets. We tested
for changes in purifying selection in plastid genes of a
mycoheterotrophic liverwort (Aneura mirabilis) and a
putatively mycoheterotrophic moss (Buxbaumia), and compared
15 bryophyte plastomes for major structural
rearrangements.<h4>Results</h4>Overall land-plant
relationships conflict across analyses, generally weakly.
However, an underlying (unrooted) four-taxon tree is
consistent across most analyses and published studies.
Despite gene coverage patchiness, relationships within
mosses, liverworts, and hornworts are largely congruent with
previous studies, with plastid results generally better
supported. Exclusion of RNA edit sites restores cases of
unexpected non-monophyly to monophyly for Takakia and two
hornwort genera. Relaxed purifying selection affects
multiple plastid genes in mycoheterotrophic Aneura but not
Buxbaumia. Plastid genome structure is nearly invariant
across bryophytes, but the tufA locus, presumed lost in
embryophytes, is unexpectedly retained in several
mosses.<h4>Conclusions</h4>A common unrooted tree underlies
embryophyte phylogeny, [(liverworts, mosses), (hornworts,
vascular plants)]; rooting inconsistency across studies
likely reflects substantial distance to algal outgroups.
Analyses combining genomic and transcriptomic data may be
misled locally for heavily RNA-edited taxa. The Buxbaumia
plastome lacks hallmarks of relaxed selection found in
mycoheterotrophic Aneura. Autotrophic bryophyte plastomes,
including Buxbaumia, hardly vary in overall
structure.},
Doi = {10.1002/ajb2.1397},
Key = {fds348449}
}
@article{fds353430,
Author = {One Thousand Plant Transcriptomes Initiative},
Title = {One thousand plant transcriptomes and the phylogenomics of
green plants.},
Journal = {Nature},
Volume = {574},
Number = {7780},
Pages = {679-685},
Year = {2019},
Month = {October},
url = {http://dx.doi.org/10.1038/s41586-019-1693-2},
Abstract = {Green plants (Viridiplantae) include around 450,000-500,000
species<sup>1,2</sup> of great diversity and have important
roles in terrestrial and aquatic ecosystems. Here, as part
of the One Thousand Plant Transcriptomes Initiative, we
sequenced the vegetative transcriptomes of 1,124 species
that span the diversity of plants in a broad sense
(Archaeplastida), including green plants (Viridiplantae),
glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our
analysis provides a robust phylogenomic framework for
examining the evolution of green plants. Most inferred
species relationships are well supported across multiple
species tree and supermatrix analyses, but discordance among
plastid and nuclear gene trees at a few important nodes
highlights the complexity of plant genome evolution,
including polyploidy, periods of rapid speciation, and
extinction. Incomplete sorting of ancestral variation,
polyploidization and massive expansions of gene families
punctuate the evolutionary history of green plants. Notably,
we find that large expansions of gene families preceded the
origins of green plants, land plants and vascular plants,
whereas whole-genome duplications are inferred to have
occurred repeatedly throughout the evolution of flowering
plants and ferns. The increasing availability of
high-quality plant genome sequences and advances in
functional genomics are enabling research on genome
evolution across the green tree of life.},
Doi = {10.1038/s41586-019-1693-2},
Key = {fds353430}
}
@article{fds343423,
Author = {Piatkowski, BT and Shaw, AJ},
Title = {Functional trait evolution in Sphagnum peat mosses and its
relationship to niche construction.},
Journal = {The New phytologist},
Volume = {223},
Number = {2},
Pages = {939-949},
Year = {2019},
Month = {July},
url = {http://dx.doi.org/10.1111/nph.15825},
Abstract = {Species in the genus Sphagnum create, maintain, and dominate
boreal peatlands through 'extended phenotypes' that allow
these organisms to engineer peatland ecosystems and thereby
impact global biogeochemical cycles. One such phenotype is
the production of peat, or incompletely decomposed biomass,
that accumulates when rates of growth exceed decomposition.
Interspecific variation in peat production is thought to be
responsible for the establishment and maintenance of
ecological gradients such as the microtopographic
hummock-hollow gradient, along which sympatric species sort
within communities. This study investigated the mode and
tempo of functional trait evolution across 15 species of
Sphagnum using data from the most extensive studies of
Sphagnum functional traits to date and phylogenetic
comparative methods. We found evidence for phylogenetic
conservatism of the niche descriptor height-above-water-table
and of traits related to growth, decay and litter quality.
However, we failed to detect the influence of phylogeny on
interspecific variation in other traits such as shoot
density and suggest that environmental context can obscure
phylogenetic signal. Trait correlations indicate possible
adaptive syndromes that may relate to niche and its
construction. This study is the first to formally test the
extent to which functional trait variation among Sphagnum
species is a result of shared evolutionary
history.},
Doi = {10.1111/nph.15825},
Key = {fds343423}
}
@article{fds349972,
Author = {Nelson, J and Shaw, AJ},
Title = {Exploring the natural microbiome of the model liverwort:
fungal endophyte diversity in Marchantia polymorpha
L},
Journal = {Symbiosis},
Volume = {78},
Number = {1},
Pages = {45-59},
Year = {2019},
Month = {May},
url = {http://dx.doi.org/10.1007/s13199-019-00597-4},
Abstract = {Within their tissues, plants host diverse communities of
fungi, termed fungal endophytes. These fungi can affect
plant growth, competitiveness, and resistance to stressors,
thereby influencing plant community structure. Research
characterizing fungal endophyte communities has so far
mostly focused on seed plants, but information on the
endophytes of other plant lineages is needed to understand
how plant microbiomes impact whole ecosystems and how major
changes through land plant evolution have affected
plant-microbe relationships. In this study, we assess the
fungal endophyte community of the model liverwort Marchantia
polymorpha L. by both culturing and Illumina amplicon
sequencing methods. We detect a very diverse fungal
community that is distinct between M. polymorpha patches and
only shares a few core fungi between populations across the
United States. We also show low overlap in taxa detected by
the different methods. This study helps build a foundation
for using M. polymorpha and other Marchantia species as
models for the ecology and dynamics of bryophyte
microbiomes.},
Doi = {10.1007/s13199-019-00597-4},
Key = {fds349972}
}
@article{fds342429,
Author = {Liu, Y and Johnson, MG and Cox, CJ and Medina, R and Devos, N and Vanderpoorten, A and Hedenäs, L and Bell, NE and Shevock, JR and Aguero, B and Quandt, D and Wickett, NJ and Shaw, AJ and Goffinet,
B},
Title = {Resolution of the ordinal phylogeny of mosses using targeted
exons from organellar and nuclear genomes.},
Journal = {Nature communications},
Volume = {10},
Number = {1},
Pages = {1485},
Year = {2019},
Month = {April},
url = {http://dx.doi.org/10.1038/s41467-019-09454-w},
Abstract = {Mosses are a highly diverse lineage of land plants, whose
diversification, spanning at least 400 million years,
remains phylogenetically ambiguous due to the lack of
fossils, massive early extinctions, late radiations, limited
morphological variation, and conflicting signal among
previously used markers. Here, we present phylogenetic
reconstructions based on complete organellar exomes and a
comparable set of nuclear genes for this major lineage of
land plants. Our analysis of 142 species representing 29 of
the 30 moss orders reveals that relative average rates of
non-synonymous substitutions in nuclear versus plastid genes
are much higher in mosses than in seed plants, consistent
with the emerging concept of evolutionary dynamism in
mosses. Our results highlight the evolutionary significance
of taxa with reduced morphologies, shed light on the
relative tempo and mechanisms underlying major cladogenic
events, and suggest hypotheses for the relationships and
delineation of moss orders.},
Doi = {10.1038/s41467-019-09454-w},
Key = {fds342429}
}
@article{fds343791,
Author = {Kyrkjeeide, MO and Hassel, K and Aguero, B and Temsch, EM and Afonina,
OM and Shaw, AJ and Stenøien, HK and Flatberg, KI},
Title = {Sphagnum ×lydiae, the first allotriploid peatmoss in the
northern hemisphere},
Journal = {The Bryologist},
Volume = {122},
Number = {1},
Pages = {38-38},
Publisher = {American Bryological and Lichenological Society},
Year = {2019},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745-122.1.038},
Doi = {10.1639/0007-2745-122.1.038},
Key = {fds343791}
}
@article{fds345856,
Author = {Medina, R and Johnson, MG and Liu, Y and Wickett, NJ and Shaw, AJ and Goffinet, B},
Title = {Phylogenomic delineation of Physcomitrium (Bryophyta:
Funariaceae) based on targeted sequencing of nuclear exons
and their flanking regions rejects the retention of
Physcomitrella, Physcomitridium and Aphanorrhegma},
Journal = {Journal of Systematics and Evolution},
Volume = {57},
Number = {4},
Pages = {404-417},
Year = {2019},
Month = {January},
url = {http://dx.doi.org/10.1111/jse.12516},
Abstract = {Selection on spore dispersal mechanisms in mosses is thought
to shape the transformation of the sporophyte. The majority
of extant mosses develop a sporangium that dehisces through
the loss of an operculum, and regulates spore release
through the movement of articulate teeth, the peristome,
lining the capsule mouth. Such complexity was acquired by
the Mesozoic Era, but was lost in some groups during
subsequent diversification events, challenging the
resolution of the affinities for taxa with reduced
architectures. The Funariaceae are a cosmopolitan and
diverse lineage of mostly annual mosses, and exhibit
variable sporophyte complexities, spanning from long,
exerted, operculate capsules with two rings of
well-developed teeth, to capsules immersed among maternal
leaves, lacking a differentiated line of dehiscence (i.e.,
inoperculate) and without peristomes. The family underwent a
rapid diversification, and the relationships of taxa with
reduced sporophytes remain ambiguous. Here, we infer the
relationships of five taxa with highly reduced sporophytes
based on 648 nuclear loci (exons complemented by their
flanking regions), based on inferences from concatenated
data and concordance analysis of single gene trees.
Physcomitrellopsis is resolved as nested within one clade of
Entosthodon. Physcomitrella s. l., is resolved as a
polyphyletic assemblage and, along with its putative
relative Aphanorrhegma, nested within Physcomitrium. We
propose a new monophyletic delineation of Physcomitrium,
which accommodates species of Physcomitrella and
Aphanorrhegma. The monophyly of Physcomitrium s. l. is
supported by a small plurality of exons, but a majority of
trees inferred from exons and their adjacent non-coding
regions.},
Doi = {10.1111/jse.12516},
Key = {fds345856}
}
@article{fds339385,
Author = {Shaw, AJ and Carter, BE and Aguero, B and da Costa, DP and Crowl,
AA},
Title = {Range change evolution of peat mosses (Sphagnum) within and
between climate zones.},
Journal = {Global change biology},
Volume = {25},
Number = {1},
Pages = {108-120},
Year = {2019},
Month = {January},
url = {http://dx.doi.org/10.1111/gcb.14485},
Abstract = {Peat mosses (Sphagnum) hold exceptional importance in the
control of global carbon fluxes and climate because of the
vast stores of carbon bound up in partially decomposed
biomass (peat). This study tests the hypothesis that the
early diversification of Sphagnum was in the Northern
Hemisphere, with subsequent range expansions to tropical
latitudes and the Southern Hemisphere. A phylogenetic
analysis of 192 accessions representing the moss class
Sphagnopsida based on four plastid loci was conducted in
conjunction with biogeographic analyses using BioGeoBEARS to
investigate the tempo and mode of geographic range
evolution. Analyses support the hypothesis that the major
intrageneric clades of peat-forming species accounting for
>90% of peat moss diversity originated and diversified at
northern latitudes. The genus underwent multiple range
expansions into tropical and Southern Hemisphere regions.
Range evolution in peat mosses was most common within
latitudinal zones, attesting to the relative difficulty of
successfully invading new climate zones. Allopolyploidy in
Sphagnum (inferred from microsatellite heterozygosity) does
not appear to be biased with regard to geographic region nor
intrageneric clade. The inference that Sphagnum diversified
in cool-or cold-climate regions and repeatedly expanded its
range into tropical regions makes the genus an excellent
model for studying morphological, physiological, and genomic
traits associated with adaptation to warming
climates.},
Doi = {10.1111/gcb.14485},
Key = {fds339385}
}
@article{fds335270,
Author = {Laenen, B and Patiño, J and Hagborg, A and Désamoré, A and Wang, J and Shaw, AJ and Goffinet, B and Vanderpoorten, A},
Title = {Evolutionary origin of the latitudinal diversity gradient in
liverworts.},
Journal = {Molecular phylogenetics and evolution},
Volume = {127},
Pages = {606-612},
Year = {2018},
Month = {October},
url = {http://dx.doi.org/10.1016/j.ympev.2018.06.007},
Abstract = {A latitudinal diversity gradient towards the tropics appears
as one most recurrent patterns in ecology, but the
mechanisms underlying this pattern remain an area of
controversy. In angiosperms, the tropical conservatism
hypothesis proposes that most groups originated in the
tropics and are adapted to a tropical climatic regime, and
that relatively few species have evolved physiological
adaptations to cold, dry or unpredictable climates. This
mechanism is, however, unlikely to apply across land plants,
and in particular, to liverworts, a group of about 7500
species, whose ability to withstand cold much better than
their tracheophyte counterparts is at odds with the tropical
conservatism hypothesis. Molecular dating, diversification
rate analyses and ancestral area reconstructions were
employed to explore the evolutionary mechanisms that account
for the latitudinal diversity gradient in liverworts. As
opposed to angiosperms, tropical liverwort genera are not
older than their extra-tropical counterparts (median stem
age of tropical and extra-tropical liverwort genera of
24.35 ± 39.65 Ma and 39.57 ± 49.07 Ma,
respectively), weakening the 'time for speciation
hypothesis'. Models of ancestral area reconstructions with
equal migration rates between tropical and extra-tropical
regions outperformed models with asymmetrical migration
rates in either direction. The symmetry and intensity of
migrations between tropical and extra-tropical regions
suggested by the lack of resolution in ancestral area
reconstructions towards the deepest nodes are at odds with
the tropical niche conservatism hypothesis. In turn,
tropical genera exhibited significantly higher net
diversification rates than extra-tropical ones, suggesting
that the observed latitudinal diversity gradient results
from either higher extinction rates in extra-tropical
lineages or higher speciation rates in the tropics. We
discuss a series of experiments to help deciphering the
underlying evolutionary mechanisms.},
Doi = {10.1016/j.ympev.2018.06.007},
Key = {fds335270}
}
@article{fds335271,
Author = {Nelson, JM and Hauser, DA and Hinson, R and Shaw,
AJ},
Title = {A novel experimental system using the liverwort Marchantia
polymorpha and its fungal endophytes reveals diverse and
context-dependent effects.},
Journal = {The New phytologist},
Volume = {218},
Number = {3},
Pages = {1217-1232},
Year = {2018},
Month = {May},
url = {http://dx.doi.org/10.1111/nph.15012},
Abstract = {Fungal symbioses are ubiquitous in plants, but their effects
have mostly been studied in seed plants. This study aimed to
assess the diversity of fungal endophyte effects in a
bryophyte and identify factors contributing to the
variability of outcomes in these interactions. Fungal
endophyte cultures and axenic liverwort clones were isolated
from wild populations of the liverwort, Marchantia
polymorpha. These collections were combined in a gnotobiotic
system to test the effects of fungal isolates on the growth
rates of hosts under laboratory conditions. Under the
experimental conditions, fungi isolated from M. polymorpha
ranged from aggressively pathogenic to strongly
growth-promoting, but the majority of isolates caused no
detectable change in host growth. Growth promotion by
selected fungi depended on nutrient concentrations and was
inhibited by coinoculation with multiple fungi. The
M. polymorpha endophyte system expands the resources for
this model liverwort. The experiments presented here
demonstrate a wealth of diversity in fungal interactions
even in a host reported to lack standard mycorrhizal
symbiosis. In addition, they show that some known pathogens
of vascular plants live in M. polymorpha and can confer
benefits to this nonvascular host. This highlights the
importance of studying endophyte effects across the plant
tree of life.},
Doi = {10.1111/nph.15012},
Key = {fds335271}
}
@article{fds339386,
Author = {KYRKJEEIDE, MO and HASSEL, K and SHAW, B and SHAW, AJ and TEMSCH, EM and FLATBERG, KI},
Title = {Sphagnum incundum a new species in Sphagnum subg. Acutifolia
(Sphagnaceae) from boreal and arctic regions of North
America},
Journal = {Phytotaxa},
Volume = {333},
Number = {1},
Pages = {1-1},
Publisher = {Magnolia Press},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.11646/phytotaxa.333.1.1},
Abstract = {<jats:p>We describe Sphagnum incundum in Sphagnum subgenus
Acutifolia (Sphagnaceae, Bryophyta). We used both molecular
and morphological methods to describe the new species.
Molecular relationships with closely related species were
explored based on microsatellites and nuclear and plastid
DNA sequences. The morphological description is based on
qualitative examination of morphological characters and
measurements of leaves and hyalocysts. Morphological
characters are compared between closely related species. The
results from Feulgen densitometry and microsatellite
analysis show that S. incundum is gametophytically haploid.
Molecular analyses show that it is a close relative to S.
flavicomans, S. subfulvum and S. subnitens, but differs both
genetically and in morphological key characters, justifying
the description of S. incundum as a new species. The new
peatmoss is found in North America along the western coast
of Greenland, in Canada from Quebec and Northwest
Territories, and Alaska (United States). The new species has
a boreal to arctic distribution.</jats:p>},
Doi = {10.11646/phytotaxa.333.1.1},
Key = {fds339386}
}
@article{fds335272,
Author = {Weston, DJ and Turetsky, MR and Johnson, MG and Granath, G and Lindo, Z and Belyea, LR and Rice, SK and Hanson, DT and Engelhardt, KAM and Schmutz,
J and Dorrepaal, E and Euskirchen, ES and Stenøien, HK and Szövényi,
P and Jackson, M and Piatkowski, BT and Muchero, W and Norby, RJ and Kostka, JE and Glass, JB and Rydin, H and Limpens, J and Tuittila, E-S and Ullrich, KK and Carrell, A and Benscoter, BW and Chen, J-G and Oke, TA and Nilsson, MB and Ranjan, P and Jacobson, D and Lilleskov, EA and Clymo,
RS and Shaw, AJ},
Title = {The Sphagnome Project: enabling ecological and evolutionary
insights through a genus-level sequencing
project.},
Journal = {The New phytologist},
Volume = {217},
Number = {1},
Pages = {16-25},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1111/nph.14860},
Abstract = {Considerable progress has been made in ecological and
evolutionary genetics with studies demonstrating how genes
underlying plant and microbial traits can influence
adaptation and even 'extend' to influence community
structure and ecosystem level processes. Progress in this
area is limited to model systems with deep genetic and
genomic resources that often have negligible ecological
impact or interest. Thus, important linkages between genetic
adaptations and their consequences at organismal and
ecological scales are often lacking. Here we introduce the
Sphagnome Project, which incorporates genomics into a
long-running history of Sphagnum research that has
documented unparalleled contributions to peatland ecology,
carbon sequestration, biogeochemistry, microbiome research,
niche construction, and ecosystem engineering. The Sphagnome
Project encompasses a genus-level sequencing effort that
represents a new type of model system driven not only by
genetic tractability, but by ecologically relevant questions
and hypotheses.},
Doi = {10.1111/nph.14860},
Key = {fds335272}
}
@article{fds330487,
Author = {Yousefi, N and Hassel, K and Flatberg, KI and Kemppainen, P and Trucchi,
E and Shaw, AJ and Kyrkjeeide, MO and Szövényi, P and Stenøien,
HK},
Title = {Divergent evolution and niche differentiation within the
common peatmoss Sphagnum magellanicum.},
Journal = {American journal of botany},
Volume = {104},
Number = {7},
Pages = {1060-1072},
Year = {2017},
Month = {July},
url = {http://dx.doi.org/10.3732/ajb.1700163},
Abstract = {<h4>Premise of the study</h4>Populations with phenotypic
polymorphism in discrete characters may be good models for
investigating genome evolution and speciation. Sphagnum
magellanicum Brid. is found throughout the northern
hemisphere, and despite considerable variation in
morphological characters, it is considered one of the least
taxonomically controversial peatmoss species. We have
observed two main morphs of the species associated with
different microhabitats. Here we investigated the genomic
and environmental basis of this intraspecific morphological
variation.<h4>Methods</h4>We conducted transplant and common
garden experiments to test whether the two morphs are
genetically differentiated. We then used RAD-sequencing to
quantify the genomic divergence between the morphs and
approximate Bayesian computation (ABC) to infer the most
likely demographic scenario explaining the genome-wide
differentiation of the two morphs.<h4>Key results</h4>We
found that genomic differentiation between the two morphs is
unexpectedly high and that several of the differentiated
morphological characters have a genetic basis. Using
simulation approaches, we found support for a scenario of
ancient divergence followed by recent secondary
contact.<h4>Conclusions</h4>We show that the two morphs
represent the two main genetic clusters previously found
worldwide. Our results demonstrate that relatively minor
morphological differentiation in a presumed phenotypically
plastic peatmoss may be associated with massive divergence
across the genome.},
Doi = {10.3732/ajb.1700163},
Key = {fds330487}
}
@article{fds330488,
Author = {Carter, BE and Larraín, J and Manukjanová, A and Shaw, B and Shaw, AJ and Heinrichs, J and de Lange, P and Suleiman, M and Thouvenot, L and von
Konrat, M},
Title = {Species delimitation and biogeography of a southern
hemisphere liverwort clade, Frullania subgenus
Microfrullania (Frullaniaceae, Marchantiophyta).},
Journal = {Molecular phylogenetics and evolution},
Volume = {107},
Pages = {16-26},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1016/j.ympev.2016.10.002},
Abstract = {Frullania subgenus Microfrullania is a clade of ca. 15
liverwort species occurring in Australasia, Malesia, and
southern South America. We used combined nuclear and
chloroplast sequence data from 265 ingroup accessions to
test species circumscriptions and estimate the biogeographic
history of the subgenus. With dense infra-specific sampling,
we document an important role of long-distance dispersal in
establishing phylogeographic patterns of extant species. At
deeper time scales, a combination of phylogenetic analyses,
divergence time estimation and ancestral range estimation
were used to reject vicariance and to document the role of
long-distance dispersal in explaining the evolution and
biogeography of the clade across the southern Hemisphere. A
backbone phylogeny for the subgenus is proposed, providing
insight into evolution of morphological patterns and
establishing the basis for an improved sectional
classification of species within Microfrullania. Several
species complexes are identified, the presence of two
undescribed but genetically and morphologically distinct
species is noted, and previously neglected names are
discussed.},
Doi = {10.1016/j.ympev.2016.10.002},
Key = {fds330488}
}
@article{fds330489,
Author = {Patiño, J and Wang, J and Renner, MAM and Gradstein, SR and Laenen, B and Devos, N and Shaw, AJ and Vanderpoorten, A},
Title = {Range size heritability and diversification patterns in the
liverwort genus Radula.},
Journal = {Molecular phylogenetics and evolution},
Volume = {106},
Pages = {73-85},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1016/j.ympev.2016.09.020},
Abstract = {Why some species exhibit larger geographical ranges than
others, and to what extent does variation in range size
affect diversification rates, remains a fundamental, but
largely unanswered question in ecology and evolution. Here,
we implement phylogenetic comparative analyses and ancestral
area estimations in Radula, a liverwort genus of Cretaceous
origin, to investigate the mechanisms that explain
differences in geographical range size and diversification
rates among lineages. Range size was phylogenetically
constrained in the two sub-genera characterized by their
almost complete Australasian and Neotropical endemicity,
respectively. The congruence between the divergence time of
these lineages and continental split suggests that plate
tectonics could have played a major role in their present
distribution, suggesting that a strong imprint of vicariance
can still be found in extant distribution patterns in these
highly mobile organisms. Amentuloradula, Volutoradula and
Metaradula species did not appear to exhibit losses of
dispersal capacities in terms of dispersal life-history
traits, but evidence for significant phylogenetic signal in
macroecological niche traits suggests that niche
conservatism accounts for their restricted geographic
ranges. Despite their greatly restricted distribution to
Australasia and Neotropics respectively, Amentuloradula and
Volutoradula did not exhibit significantly lower
diversification rates than more widespread lineages, in
contrast with the hypothesis that the probability of
speciation increases with range size by promoting geographic
isolation and increasing the rate at which novel habitats
are encountered. We suggest that stochastic long-distance
dispersal events may balance allele frequencies across large
spatial scales, leading to low genetic structure among
geographically distant areas or even continents, ultimately
decreasing the diversification rates in highly mobile,
widespread lineages.},
Doi = {10.1016/j.ympev.2016.09.020},
Key = {fds330489}
}
@article{fds330490,
Author = {Boquete, MT and Fernández, JA and Aboal, JR and Shaw,
AJ},
Title = {Significance of the intraspecific morphological variability
in biomonitoring studies with mosses: Among-populations and
between-sexes approach},
Journal = {Environmental and Experimental Botany},
Volume = {130},
Pages = {106-112},
Publisher = {Elsevier BV},
Year = {2016},
Month = {October},
url = {http://dx.doi.org/10.1016/j.envexpbot.2016.05.013},
Abstract = {In this study we assessed for the first time the
intraspecific morphological variation in gametophytes of the
terrestrial moss Pseudoscleropodium purum in populations
growing naturally in areas affected by different levels of
atmospheric pollution (2 industrial and 2 unpolluted sites).
We also identified the sexes in each population and
evaluated the morphological variation in male, female and
non-expressing plants, together with the between-population
variation in levels of sex expression and the sex ratio
(female:male). Although sex expression levels and sex ratios
varied between populations, neither of these variables were
significantly correlated with the levels of pollution at any
of the four sites. We therefore conclude that the
reproductive traits of this species are not affected by the
pollution levels considered in the study. We observed
significant between-population variation in 8 of the 20
morphological traits considered, although the variation was
not associated with male, female or non-expressing plants.
The morphological traits were not significantly correlated
with the levels of heavy metals in the study sites. However,
the plants from the most polluted sites (the industrial
environments) were generally smaller (shorter plants with
fewer branches and smaller leaves) and therefore had less
surface area available for uptake of atmospheric pollutants
than the plants from the other sites. Irrespective of the
factors underlying the variation, mosses from some
populations can accumulate more pollutants than mosses from
other populations (consistent with their morphological
characteristics). This source of variation in the
concentrations of heavy metals measured in moss
biomonitoring studies has not previously been taken into
consideration.},
Doi = {10.1016/j.envexpbot.2016.05.013},
Key = {fds330490}
}
@article{fds324244,
Author = {Jonathan Shaw and A and Devos, N and Liu, Y and Cox, CJ and Goffinet, B and Flatberg, KI and Shaw, B},
Title = {Organellar phylogenomics of an emerging model system:
Sphagnum (peatmoss).},
Journal = {Annals of botany},
Volume = {118},
Number = {2},
Pages = {185-196},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1093/aob/mcw086},
Abstract = {<h4>Background and aims</h4>Sphagnum-dominated peatlands
contain approx. 30 % of the terrestrial carbon pool in the
form of partially decomposed plant material (peat), and, as
a consequence, Sphagnum is currently a focus of studies on
biogeochemistry and control of global climate. Sphagnum
species differ in ecologically important traits that scale
up to impact ecosystem function, and sequencing of the
genome from selected Sphagnum species is currently underway.
As an emerging model system, these resources for Sphagnum
will facilitate linking nucleotide variation to plant
functional traits, and through those traits to ecosystem
processes. A solid phylogenetic framework for Sphagnum is
crucial to comparative analyses of species-specific traits,
but relationships among major clades within Sphagnum have
been recalcitrant to resolution because the genus underwent
a rapid radiation. Herein a well-supported hypothesis for
phylogenetic relationships among major clades within
Sphagnum based on organellar genome sequences (plastid,
mitochondrial) is provided.<h4>Methods</h4>We obtained
nucleotide sequences (273 753 nucleotides in total) from the
two organellar genomes from 38 species (including three
outgroups). Phylogenetic analyses were conducted using a
variety of methods applied to nucleotide and amino acid
sequences. The Sphagnum phylogeny was rooted with sequences
from the related Sphagnopsida genera, Eosphagnum and
Flatbergium<h4>Key results</h4>Phylogenetic analyses of the
data converge on the following subgeneric relationships:
(Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum)
(Acutifolia))). All relationships were strongly supported.
Species in the two major clades (i.e. Subsecunda + Cuspidata
and Sphagnum + Acutifolia), which include >90 % of all
Sphagnum species, differ in ecological niches and these
differences correlate with other functional traits that
impact biogeochemical cycling. Mitochondrial intron
presence/absence are variable among species and genera of
the Sphagnopsida. Two new nomenclatural combinations are
made, in the genera Eosphagnum and Flatbergium<h4>Conclusions</h4>Newly
resolved relationships now permit phylogenetic analyses of
morphological, biochemical and ecological traits among
Sphagnum species. The results clarify long-standing
disagreements about subgeneric relationships and
intrageneric classification.},
Doi = {10.1093/aob/mcw086},
Key = {fds324244}
}
@article{fds330491,
Author = {Johnson, MG and Gardner, EM and Liu, Y and Medina, R and Goffinet, B and Shaw, AJ and Zerega, NJC and Wickett, NJ},
Title = {HybPiper: Extracting coding sequence and introns for
phylogenetics from high-throughput sequencing reads using
target enrichment.},
Journal = {Applications in plant sciences},
Volume = {4},
Number = {7},
Pages = {apps.1600016},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.3732/apps.1600016},
Abstract = {<h4>Premise of the study</h4>Using sequence data generated
via target enrichment for phylogenetics requires reassembly
of high-throughput sequence reads into loci, presenting a
number of bioinformatics challenges. We developed HybPiper
as a user-friendly platform for assembly of gene regions,
extraction of exon and intron sequences, and identification
of paralogous gene copies. We test HybPiper using baits
designed to target 333 phylogenetic markers and 125 genes of
functional significance in Artocarpus (Moraceae).<h4>Methods
and results</h4>HybPiper implements parallel execution of
sequence assembly in three phases: read mapping, contig
assembly, and target sequence extraction. The pipeline was
able to recover nearly complete gene sequences for all genes
in 22 species of Artocarpus. HybPiper also recovered more
than 500 bp of nontargeted intron sequence in over half of
the phylogenetic markers and identified paralogous gene
copies in Artocarpus.<h4>Conclusions</h4>HybPiper was
designed for Linux and Mac OS X and is freely available at
https://github.com/mossmatters/HybPiper.},
Doi = {10.3732/apps.1600016},
Key = {fds330491}
}
@article{fds330492,
Author = {Devos, N and Szövényi, P and Weston, DJ and Rothfels, CJ and Johnson,
MG and Shaw, AJ},
Title = {Analyses of transcriptome sequences reveal multiple ancient
large-scale duplication events in the ancestor of
Sphagnopsida (Bryophyta).},
Journal = {The New phytologist},
Volume = {211},
Number = {1},
Pages = {300-318},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1111/nph.13887},
Abstract = {The goal of this research was to investigate whether there
has been a whole-genome duplication (WGD) in the ancestry of
Sphagnum (peatmoss) or the class Sphagnopsida, and to
determine if the timing of any such duplication(s) and
patterns of paralog retention could help explain the rapid
radiation and current ecological dominance of peatmosses.
RNA sequencing (RNA-seq) data were generated for nine taxa
in Sphagnopsida (Bryophyta). Analyses of frequency plots for
synonymous substitutions per synonymous site (Ks ) between
paralogous gene pairs and reconciliation of 578 gene trees
were conducted to assess evidence of large-scale or
genome-wide duplication events in each transcriptome. Both
Ks frequency plots and gene tree-based analyses indicate
multiple duplication events in the history of the
Sphagnopsida. The most recent WGD event predates divergence
of Sphagnum from the two other genera of Sphagnopsida.
Duplicate retention is highly variable across species, which
might be best explained by local adaptation. Our analyses
indicate that the last WGD could have been an important
factor underlying the diversification of peatmosses and
facilitated their rise to ecological dominance in peatlands.
The timing of the duplication events and their significance
in the evolutionary history of peat mosses are
discussed.},
Doi = {10.1111/nph.13887},
Key = {fds330492}
}
@article{fds330493,
Author = {Kostka, JE and Weston, DJ and Glass, JB and Lilleskov, EA and Shaw, AJ and Turetsky, MR},
Title = {The Sphagnum microbiome: new insights from an ancient plant
lineage.},
Journal = {The New phytologist},
Volume = {211},
Number = {1},
Pages = {57-64},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1111/nph.13993},
Abstract = {57 I. 57 II. 58 III. 59 IV. 59 V. 61 VI. 62 63 References 63
SUMMARY: Peat mosses of the genus Sphagnum play a major role
in global carbon storage and dominate many northern peatland
ecosystems, which are currently being subjected to some of
the most rapid climate changes on Earth. A rapidly expanding
database indicates that a diverse community of
microorganisms is intimately associated with Sphagnum,
inhabiting the tissues and surface of the plant. Here we
summarize the current state of knowledge regarding the
Sphagnum microbiome and provide a perspective for future
research directions. Although the majority of the microbiome
remains uncultivated and its metabolic capabilities
uncharacterized, prokaryotes and fungi have the potential to
act as mutualists, symbionts, or antagonists of Sphagnum.
For example, methanotrophic and nitrogen-fixing bacteria may
benefit the plant host by providing up to 20-30% of Sphagnum
carbon and nitrogen, respectively. Next-generation
sequencing approaches have enabled the detailed
characterization of microbiome community composition in peat
mosses. However, as with other ecologically or economically
important plants, our knowledge of Sphagnum-microbiome
associations is in its infancy. In order to attain a
predictive understanding of the role of the microbiome in
Sphagnum productivity and ecosystem function, the mechanisms
of plant-microbiome interactions and the metabolic potential
of constituent microbial populations must be
revealed.},
Doi = {10.1111/nph.13993},
Key = {fds330493}
}
@article{fds330494,
Author = {Kyrkjeeide, MO and Hassel, K and Flatberg, KI and Shaw, AJ and Brochmann, C and Stenøien, HK},
Title = {Long-distance dispersal and barriers shape genetic structure
of peatmosses (Sphagnum) across the Northern
Hemisphere},
Journal = {Journal of Biogeography},
Volume = {43},
Number = {6},
Pages = {1215-1226},
Publisher = {WILEY},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1111/jbi.12716},
Abstract = {Aim: Disjunctly distributed peatmosses (Sphagnum) have been
found to exhibit little genetic structure over regional and
intercontinental scales, mainly caused by high ability for
transoceanic long-distance dispersal. Although, most
Northern Hemisphere peatmoss species have wide
circumboreal/nemoral ranges, little is known about the
magnitude and effects of long-distance dispersal and
barriers in shaping the genetic structure of such species.
We investigate whether high dispersal capacity has caused
genetic homogeneity across broad areas of the Northern
Hemisphere, or whether barriers act to shape genetic
structure across different species with similar
distributional ranges. Location: Northern Hemisphere.
Methods: We studied genetic variation and structure in six
Sphagnum species using 19 microsatellite loci. Results: Four
out of six species were genetically structured in similar
ways; with mainly one Beringian and one Atlantic group.
Overall, both the North American and Eurasian continents
seemed to act as a barrier to gene flow in several species.
However, the most abrupt breakpoint between genetic groups
was found in south-east Alaska. Main conclusions: We found
evidence for extensive gene flow between regions across the
Northern Hemisphere among peatmosses, with oceans seemingly
acting as weaker barriers to gene flow than landmasses.
Plants from the amphi-Atlantic and amphi-Beringian regions
of several species were genetically differentiated. Similar
genetic structuring across several species, indicate that
spore-producing species do not disperse freely across their
entire distributional range, but are likely limited by wind
directions, landmass barriers and/or habitat
availability.},
Doi = {10.1111/jbi.12716},
Key = {fds330494}
}
@article{fds332841,
Author = {Johnson, MG and Shaw, AJ},
Title = {The effects of quantitative fecundity in the haploid stage
on reproductive success and diploid fitness in the aquatic
peat moss Sphagnum macrophyllum.},
Journal = {Heredity},
Volume = {116},
Number = {6},
Pages = {523-530},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1038/hdy.2016.13},
Abstract = {A major question in evolutionary biology is how mating
patterns affect the fitness of offspring. However, in
animals and seed plants it is virtually impossible to
investigate the effects of specific gamete genotypes. In
bryophytes, haploid gametophytes grow via clonal propagation
and produce millions of genetically identical gametes
throughout a population. The main goal of this research was
to test whether gamete identity has an effect on the fitness
of their diploid offspring in a population of the aquatic
peat moss Sphagnum macrophyllum. We observed a heavily
male-biased sex ratio in gametophyte plants (ramets) and in
multilocus microsatellite genotypes (genets). There was a
steeper relationship between mating success (number of
different haploid mates) and fecundity (number of diploid
offspring) for male genets compared with female genets. At
the sporophyte level, we observed a weak effect of
inbreeding on offspring fitness, but no effect of brood size
(number of sporophytes per maternal ramet). Instead, the
identities of the haploid male and haploid female parents
were significant contributors to variance in fitness of
sporophyte offspring in the population. Our results suggest
that intrasexual gametophyte/gamete competition may play a
role in determining mating success in this
population.},
Doi = {10.1038/hdy.2016.13},
Key = {fds332841}
}
@article{fds331047,
Author = {Laenen, B and Machac, A and Gradstein, SR and Shaw, B and Patiño, J and Désamoré, A and Goffinet, B and Cox, CJ and Shaw, AJ and Vanderpoorten, A},
Title = {Increased diversification rates follow shifts to bisexuality
in liverworts.},
Journal = {The New phytologist},
Volume = {210},
Number = {3},
Pages = {1121-1129},
Year = {2016},
Month = {May},
url = {http://dx.doi.org/10.1111/nph.13835},
Abstract = {Shifts in sexual systems are one of the key drivers of
species diversification. In contrast to angiosperms,
unisexuality prevails in bryophytes. Here, we test the
hypotheses that bisexuality evolved from an ancestral
unisexual condition and is a key innovation in liverworts.
We investigate whether shifts in sexual systems influence
diversification using hidden state speciation and extinction
analysis (HiSSE). This new method compares the effects of
the variable of interest to the best-fitting latent
variable, yielding robust and conservative tests. We find
that the transitions in sexual systems are significantly
biased toward unisexuality, even though bisexuality is
coupled with increased diversification. Sexual systems are
strongly conserved deep within the liverwort tree but become
much more labile toward the present. Bisexuality appears to
be a key innovation in liverworts. Its effects on
diversification are presumably mediated by the interplay of
high fertilization rates, massive spore production and
long-distance dispersal, which may separately or together
have facilitated liverwort speciation, suppressed their
extinction, or both. Importantly, shifts in liverwort sexual
systems have the opposite effect when compared to
angiosperms, leading to contrasting diversification patterns
between the two groups. The high prevalence of unisexuality
among liverworts suggests, however, a strong selection for
sexual dimorphism.},
Doi = {10.1111/nph.13835},
Key = {fds331047}
}
@article{fds332842,
Author = {Johnson, MG and Malley, C and Goffinet, B and Shaw, AJ and Wickett,
NJ},
Title = {A phylotranscriptomic analysis of gene family expansion and
evolution in the largest order of pleurocarpous mosses
(Hypnales, Bryophyta).},
Journal = {Molecular phylogenetics and evolution},
Volume = {98},
Pages = {29-40},
Year = {2016},
Month = {May},
url = {http://dx.doi.org/10.1016/j.ympev.2016.01.008},
Abstract = {The pleurocarpous mosses (i.e., Hypnanae) are a species-rich
group of land plants comprising about 6,000 species that
share the development of female sex organs on short lateral
branches, a derived trait within mosses. Many of the
families within Hypnales, the largest order of pleurocarpous
mosses, trace their origin to a rapid radiation less than
100 million years ago, just after the rise of the
angiosperms. As a result, the phylogenetic resolution among
families of Hypnales, necessary to test evolutionary
hypotheses, has proven difficult using one or few loci. We
present the first phylogenetic inference from
high-throughput sequence data (transcriptome sequences) for
pleurocarpous mosses. To test hypotheses of gene family
evolution, we built a species tree of 21 pleurocarpous and
six acrocarpous mosses using over one million sites from 659
orthologous genes. We used the species tree to investigate
the genomic consequences of the shift to pleurocarpy and to
identify whether patterns common to other plant radiations
(gene family expansion, whole genome duplication, or changes
in the molecular signatures of selection) could be observed.
We found that roughly six percent of all gene families have
expanded in the pleurocarpous mosses, relative to
acrocarpous mosses. These gene families are enriched for
several gene ontology (GO) terms, including interaction with
other organisms. The increase in copy number coincident with
the radiation of Hypnales suggests that a process such as
whole genome duplication or a burst of small-scale
duplications occurred during the diversification. In over
500 gene families we found evidence of a reduction in
purifying selection. These gene families are enriched for
several terms in the GO hierarchy related to "tRNA metabolic
process." Our results reveal candidate genes and pathways
that may be associated with the transition to pleurocarpy,
illustrating the utility of phylotranscriptomics for the
study of molecular evolution in non-model
species.},
Doi = {10.1016/j.ympev.2016.01.008},
Key = {fds332842}
}
@article{fds330495,
Author = {Carter, BE and Shaw, B and Shaw, AJ},
Title = {Endemism in the moss flora of North America.},
Journal = {American journal of botany},
Volume = {103},
Number = {4},
Pages = {769-779},
Year = {2016},
Month = {April},
url = {http://dx.doi.org/10.3732/ajb.1500484},
Abstract = {<h4>Premise of the study</h4>Identifying regions of high
endemism is a critical step toward understanding the
mechanisms underlying diversification and establishing
conservation priorities. Here, we identified regions of high
moss endemism across North America. We also identified
lineages that contribute disproportionately to endemism and
document the progress of efforts to inventory the endemic
flora.<h4>Methods</h4>To understand the documentation of
endemic moss diversity in North America, we tabulated
species publication dates to document the progress of
species discovery across the continent. We analyzed
herbarium specimen data and distribution data from the Flora
of North America project to delineate major regions of moss
endemism. Finally, we surveyed the literature to assess the
importance of intercontinental vs. within-continent
diversification for generating endemic species.<h4>Key
results</h4>Three primary regions of endemism were
identified and two of these were further divided into a
total of nine subregions. Overall endemic richness has two
peaks, one in northern California and the Pacific Northwest,
and the other in the southern Appalachians. Description of
new endemic species has risen steeply over the last few
decades, especially in western North America. Among the few
studies documenting sister species relationships of
endemics, recent diversification appears to have played a
larger role in western North America, than in the
east.<h4>Conclusions</h4>Our understanding of bryophyte
endemism continues to grow rapidly. Large continent-wide
data sets confirm early views on hotspots of endemic
bryophyte richness and indicate a high rate of ongoing
species discovery in North America.},
Doi = {10.3732/ajb.1500484},
Key = {fds330495}
}
@article{fds330496,
Author = {Shaw, AJ and Schmutz, J and Devos, N and Shu, S and Carrell, AA and Weston,
DJ},
Title = {The Sphagnum Genome Project. A New Model for Ecological and
Evolutionary Genomics.},
Volume = {78},
Pages = {167-187},
Booktitle = {Advances in Botanical Research},
Publisher = {Elsevier},
Year = {2016},
Month = {January},
ISBN = {9780128011027},
url = {http://dx.doi.org/10.1016/bs.abr.2016.01.003},
Abstract = {The inception of the Sphagnum (peat moss) genome project
marks the first plant-based sequencing project aimed
specifically at carbon cycling genomics in a plant system
relevant to ecological and evolutionary genomics. Sphagnum
provides considerable intra- and interspecific variation at
the nucleotide level, and in physiology, morphology, net
production, decomposition and carbon accumulation (peat
formation). Because of the large number of peat moss
species, their diversity in mating systems, and clear
patterns of niche differentiation, Sphagnum provides an
exceptionally valuable complement to Physcomitrella patens
and Ceratodon purpureus as moss models for genomic research.
Here we review the organismal biology of Sphagnum including
phylogeny,. life cycle, mating systems, ecology and niche
differentiation. We include the current state of Sphagnum
genomic resources, in vitro methods and germplasm. A
use-case is provided to address questions concerning
epigenetics and reproduction. © 2016 Elsevier
Ltd.},
Doi = {10.1016/bs.abr.2016.01.003},
Key = {fds330496}
}
@article{fds330497,
Author = {Kyrkjeeide, MO and Hassel, K and Flatberg, KI and Shaw, AJ and Yousefi,
N and Stenøien, HK},
Title = {Spatial Genetic Structure of the Abundant and Widespread
Peatmoss Sphagnum magellanicum Brid.},
Journal = {PloS one},
Volume = {11},
Number = {2},
Pages = {e0148447},
Year = {2016},
Month = {January},
url = {http://dx.doi.org/10.1371/journal.pone.0148447},
Abstract = {Spore-producing organisms have small dispersal units
enabling them to become widespread across continents.
However, barriers to gene flow and cryptic speciation may
exist. The common, haploid peatmoss Sphagnum magellanicum
occurs in both the Northern and Southern hemisphere, and is
commonly used as a model in studies of peatland ecology and
peatmoss physiology. Even though it will likely act as a
rich source in functional genomics studies in years to come,
surprisingly little is known about levels of genetic
variability and structuring in this species. Here, we assess
for the first time how genetic variation in S. magellanicum
is spatially structured across its full distribution range
(Northern Hemisphere and South America). The morphologically
similar species S. alaskense was included for comparison. In
total, 195 plants were genotyped at 15 microsatellite loci.
Sequences from two plastid loci (trnG and trnL) were
obtained from 30 samples. Our results show that S. alaskense
and almost all plants of S. magellanicum in the northern
Pacific area are diploids and share the same gene pool.
Haploid plants occur in South America, Europe, eastern North
America, western North America, and southern Asia, and five
genetically differentiated groups with different
distribution ranges were found. Our results indicate that S.
magellanicum consists of several distinct genetic groups,
seemingly with little or no gene flow among them.
Noteworthy, the geographical separation of diploids and
haploids is strikingly similar to patterns found within
other haploid Sphagnum species spanning the Northern
Hemisphere. Our results confirm a genetic division between
the Beringian and the Atlantic that seems to be a general
pattern in Sphagnum taxa. The pattern of strong genetic
population structuring throughout the distribution range of
morphologically similar plants need to be considered in
future functional genomic studies of S. magellanicum.},
Doi = {10.1371/journal.pone.0148447},
Key = {fds330497}
}
@article{fds331048,
Author = {Kyrkjeeide, MO and Hassel, K and Stenøien, HK and Prestø, T and Boström, E and Shaw, AJ and Flatberg, KI},
Title = {The dark morph of Sphagnum fuscum (Schimp.) H. Klinggr. In
Europe is conspecific with the North American S.
beothuk},
Journal = {Journal of Bryology},
Volume = {37},
Number = {4},
Pages = {251-266},
Publisher = {Informa UK Limited},
Year = {2015},
Month = {December},
url = {http://dx.doi.org/10.1179/1743282015Y.0000000020},
Abstract = {Peat mosses (Sphagnum) are known to be difficult to
identify, especially in the field, because of extensive
morphological variation that can blur distinctions among
closely related species. The extent to which phenotypic
variation reflects genetic differentiation versus
environmentally induced plasticity is, however, poorly
understood. The common and widespread Sphagnum fuscum is
relatively easy to recognize, but two different colour
morphs, dark and pale brown, have been observed along the
western coast of Europe for some time. In this study, we
aimed to test whether the two colour morphs are genetically
differentiated, and assess their phylogenetic relationship
to the recently described S. beothuk from eastern North
America. We used a combination of morphological characters
and genetic markers (microsatellites and cpDNA sequences).
Our results indicate that the dark colour morph of S. fuscum
in Europe is conspecific with S. beothuk from eastern North
America. On the other hand, the pale morph of S. fuscum and
S. beothuk differ in morphology, are separated genetically,
and have different habitat preferences and distribution
ranges. The known occurrences of S. beothuk are restricted
to the oceanic regions along the North Atlantic coast. It is
one of few peat mosses restricted to the amphi-Atlantic
region. We show that by combining morphology, genetic data,
distributional information, and habitat knowledge, it is
possible to evaluate taxonomic uncertainties in Sphagnum. We
also epitypify the name S. fuscum.},
Doi = {10.1179/1743282015Y.0000000020},
Key = {fds331048}
}
@article{fds230482,
Author = {Shaw, AJ and Shaw, B and Johnson, MG and Devos, N and Stenøien, HK and Flatberg, KI and Carter, BE},
Title = {Phylogenetic structure and biogeography of the Pacific Rim
clade of Sphagnum subgen. Subsecunda: haploid and
allodiploid taxa},
Journal = {Biological journal of the Linnean Society. Linnean Society
of London},
Volume = {116},
Number = {2},
Pages = {295-311},
Publisher = {Oxford University Press (OUP)},
Year = {2015},
Month = {October},
ISSN = {0024-4066},
url = {http://dx.doi.org/10.1111/bij.12586},
Abstract = {Although it is an uncommon distribution in seed plants, many
bryophytes occur around the Pacific Rim of north‐western
North America and eastern Asia. This work focuses on a clade
of peatmosses (Sphagnum) that is distributed around the
Pacific Rim region, with some individual species found
across the total range. The goals were to infer divergent
phylogenetic relationships among haploid species in the
clade, assess parentage of allopolyploid taxa, and evaluate
alternative hypotheses about inter‐ and intraspecific
geographical range evolution. Multiple data sets and
analyses resolved an ‘Alaska’ clade, distributed across
western North America, eastern China and Japan, and an
‘Asia’ clade that includes western Chinese, Thai,
Korean, eastern Chinese and Japanese lineages.
Allopolyploids have arisen at least four times in the
Pacific Rim clade of Sphagnum subgen. Subsecunda; it appears
that all allopolyploid origins involved closely related
haploid parental taxa. Biogeographical inferences were
impacted by topological uncertainty and especially by the
biogeographical model utilized to reconstruct ancestral
areas. Most analyses converge on the conclusion that the
ancestor to this clade of Pacific Rim Sphagnum species was
widespread from Alaska south to eastern Asia, but a northern
origin for the Alaska subclade was supported by one of the
two biogeographical models we employed, under which it was
robust to phylogenetic uncertainty.},
Doi = {10.1111/bij.12586},
Key = {fds230482}
}
@article{fds322316,
Author = {Ye, W and Gradstein, SR and Shaw, AJ and Shaw, B and Ho, BC and Schäfer-Verwimp, A and Pócs, T and Heinrichs, J and Zhu,
RL},
Title = {Phylogeny and classification of Lejeuneaceae subtribe
Cheilolejeuneinae (Marchantiophyta) based on nuclear and
plastid molecular markers},
Journal = {Cryptogamie, Bryologie},
Volume = {36},
Number = {4},
Pages = {313-333},
Publisher = {BioOne},
Year = {2015},
Month = {October},
url = {http://dx.doi.org/10.7872/cryb/v36.iss4.2015.313},
Abstract = {Cheilolejeuneinae is an early diverging lineage of
Lejeuneaceae tribe Lejeuneeae with a pantropical
distribution. The current phylogeny and classification of
this subtribe is based on morphological and limited-sampling
molecular studies. Here we present a molecular phylogeny of
Cheilolejeuneinae and related lineages based on maximum
parsimony and maximum likelihood analyses, as well as
Bayesian inference of two chloroplast regions (trnL-F, trnG)
and the nuclear ribosomal ITS1-5.8S-ITS2 region, to test the
monophyly of this subtribe, and to re-evaluate the
infrageneric classification of Cheilolejeunea. The results
confirm the monophyly of Cheilolejeuneinae, which consists
of one single genus, Cheilolejeunea. Aureolejeunea and
Omphalanthus are nested in Cheilolejeunea and, consequently,
all species (11) and varieties (2) accepted in these two
genera are transferred to Cheilolejeunea. Based on
morphological and molecular evidence a new infrageneric
classification of Cheilolejeunea into nine sections is
proposed: sect. Anomalolejeunea, sect. Cheilolejeunea, sect.
Cyrtolejeunea, sect. Euosmolejeunea, sect. Leucolejeunea,
sect. Paroicae, sect. Omphalanthus, sect. Strepsilejeunea
and sect. Xenolejeunea. Cheilolejeunea decurviloba is
resolved in a sister relationship to Pycnolejeunea
densistipula and C. gaoi constitues a separate lineage
remote from Cheilolejeuneinae.},
Doi = {10.7872/cryb/v36.iss4.2015.313},
Key = {fds322316}
}
@article{fds230490,
Author = {Weston, DJ and Timm, CM and Walker, AP and Gu, L and Muchero, W and Schmutz, J and Shaw, AJ and Tuskan, GA and Warren, JM and Wullschleger,
SD},
Title = {Sphagnum physiology in the context of changing climate:
emergent influences of genomics, modelling and
host-microbiome interactions on understanding ecosystem
function.},
Journal = {Plant, cell & environment},
Volume = {38},
Number = {9},
Pages = {1737-1751},
Year = {2015},
Month = {September},
ISSN = {0140-7791},
url = {http://dx.doi.org/10.1111/pce.12458},
Abstract = {Peatlands harbour more than one-third of terrestrial carbon
leading to the argument that the bryophytes, as major
components of peatland ecosystems, store more organic carbon
in soils than any other collective plant taxa. Plants of the
genus Sphagnum are important components of peatland
ecosystems and are potentially vulnerable to changing
climatic conditions. However, the response of Sphagnum to
rising temperatures, elevated CO2 and shifts in local
hydrology have yet to be fully characterized. In this
review, we examine Sphagnum biology and ecology and explore
the role of this group of keystone species and its
associated microbiome in carbon and nitrogen cycling using
literature review and model simulations. Several issues are
highlighted including the consequences of a variable
environment on plant-microbiome interactions, uncertainty
associated with CO2 diffusion resistances and the
relationship between fixed N and that partitioned to the
photosynthetic apparatus. We note that the Sphagnum fallax
genome is currently being sequenced and outline potential
applications of population-level genomics and corresponding
plant photosynthesis and microbial metabolic modelling
techniques. We highlight Sphagnum as a model organism to
explore ecosystem response to a changing climate and to
define the role that Sphagnum can play at the intersection
of physiology, genetics and functional genomics.},
Doi = {10.1111/pce.12458},
Key = {fds230490}
}
@article{fds230489,
Author = {Patiño, J and Carine, M and Mardulyn, P and Devos, N and Mateo, RG and González-Mancebo, JM and Shaw, AJ and Vanderpoorten,
A},
Title = {Approximate Bayesian Computation Reveals the Crucial Role of
Oceanic Islands for the Assembly of Continental
Biodiversity.},
Journal = {Systematic biology},
Volume = {64},
Number = {4},
Pages = {579-589},
Year = {2015},
Month = {July},
ISSN = {1063-5157},
url = {http://dx.doi.org/10.1093/sysbio/syv013},
Abstract = {The perceived low levels of genetic diversity, poor
interspecific competitive and defensive ability, and loss of
dispersal capacities of insular lineages have driven the
view that oceanic islands are evolutionary dead ends.
Focusing on the Atlantic bryophyte flora distributed across
the archipelagos of the Azores, Madeira, the Canary Islands,
Western Europe, and northwestern Africa, we used an
integrative approach with species distribution modeling and
population genetic analyses based on approximate Bayesian
computation to determine whether this view applies to
organisms with inherent high dispersal capacities. Genetic
diversity was found to be higher in island than in
continental populations, contributing to mounting evidence
that, contrary to theoretical expectations, island
populations are not necessarily genetically depauperate.
Patterns of genetic variation among island and continental
populations consistently fitted those simulated under a
scenario of de novo foundation of continental populations
from insular ancestors better than those expected if islands
would represent a sink or a refugium of continental
biodiversity. We, suggest that the northeastern Atlantic
archipelagos have played a key role as a stepping stone for
transoceanic migrants. Our results challenge the traditional
notion that oceanic islands are the end of the colonization
road and illustrate the significant role of oceanic islands
as reservoirs of novel biodiversity for the assembly of
continental floras.},
Doi = {10.1093/sysbio/syv013},
Key = {fds230489}
}
@article{fds230487,
Author = {Johnson, MG and Shaw, AJ},
Title = {Genetic diversity, sexual condition, and microhabitat
preference determine mating patterns in Sphagnum
(Sphagnaceae) peat-mosses},
Journal = {Biological Journal of the Linnean Society},
Volume = {115},
Number = {1},
Pages = {96-113},
Publisher = {BLACKWELL PUBLISHING LTD},
Year = {2015},
Month = {May},
ISSN = {0024-4066},
url = {http://dx.doi.org/10.1111/bij.12497},
Abstract = {In bryophytes, the possibility of intragametophytic selfing
creates complex mating patterns that are not possible in
seed plants, although relatively little is known about
patterns of inbreeding in natural populations. In the
peat-moss genus Sphagnum, taxa are generally bisexual
(gametophytes produce both sperm and egg) or unisexual
(gametes produced by separate male and female plants). We
sampled populations of 14 species, aiming to assess
inbreeding variation and inbreeding depression in
sporophytes, and to evaluate correlations between sexual
expression, mating systems, and microhabitat preferences. We
sampled maternal gametophytes and their attached sporophytes
at 12-19 microsatellite loci. Bisexual species exhibited
higher levels of inbreeding than unisexual species but did
generally engage in some outcrossing. Inbreeding depression
did not appear to be common in either unisexual or bisexual
species. Genetic diversity was higher in populations of
unisexual species compared to populations of bisexual
species. We found a significant association between species
microhabitat preference and population genetic diversity:
species preferring hummocks (high above water table) had
populations with lower diversity than species inhabiting
hollows (at the water table). We also found a significant
interaction between sexual condition, microhabitat
preference, and inbreeding coefficients, suggesting a vital
role for species ecology in determining mating patterns in
Sphagnum populations.},
Doi = {10.1111/bij.12497},
Key = {fds230487}
}
@article{fds230483,
Author = {Jonathan Shaw and A and Shaw, B and Stenøien, HK and Karen Golinski and G and Hassel, K and Flatberg, KI and Carine, M},
Title = {Pleistocene survival, regional genetic structure and
interspecific gene flow among three northern peat‐mosses:
Sphagnum inexspectatum, S. orientale and
S. miyabeanum},
Journal = {Journal of biogeography},
Volume = {42},
Number = {2},
Pages = {364-376},
Publisher = {WILEY},
Editor = {Carine, M},
Year = {2015},
Month = {February},
ISSN = {0305-0270},
url = {http://dx.doi.org/10.1111/jbi.12399},
Abstract = {AIM: Arctic plant species are often characterized by a
complex genetic structure because of changes in their
population size, the fragmentation of metapopulation
systems, extensive hybridization and allopolyploidization,
and survival in disjunct refugia, historical features
associated with Pleistocene glaciation. We assessed the
biogeographical and genetic patterns in three closely
related northern species of peat‐moss (Sphagnum
inexspectatum, S. orientale and S. miyabeanum), especially
interspecific hybridization, infraspecific geographical
differentiation and Pleistocene survival in one or more
refugial areas. We tested alternative hypotheses of refugial
survival in three widely disjunct regions: eastern Asia,
Alaska and Greenland. LOCATION: North America (Canada,
western USA and Greenland), China, Japan and Russia.
METHODS: Four hundred and forty‐three plants were
genotyped at 12 microsatellite loci. Nucleotide sequences
from 130 accessions for two plastid and two nuclear loci
were used to reconstruct haplotype relationships. Population
genetic analyses produced estimates of genetic diversity,
levels of interspecific gene flow and rates of infraspecific
intercontinental migration. Approximate Bayesian computation
was used to test alternative biogeographical scenarios.
RESULTS: We found evidence of hybridization between two of
the three species, but phylogenetic patterns are
predominantly divergent rather than reticulate. Disjunct
populations of one species, S. orientale, in Greenland,
Alaska and China are genetically differentiated, but
migration has occurred among all three metapopulation
systems. Divergence‐time analyses strongly support the
hypothesis that S. orientale survived the Last Glacial
Maximum in Beringia and also in Greenland. MAIN CONCLUSIONS:
Our results indicate that Beringia served as a refugium for
peat‐mosses, and therefore peatlands, which are currently
extensive at high latitudes of the Northern Hemisphere.
Sphagnum orientale also appears to have survived the Last
Glacial Maximum in Greenland, indicating that the species
persisted in multiple Pleistocene refugia. Phylogenetic
patterns are relatively simple in these mosses compared with
those commonly encountered in Arctic angiosperms.},
Doi = {10.1111/jbi.12399},
Key = {fds230483}
}
@article{fds230488,
Author = {Shaw, B and Crandall-Stotler, B and Váňa, J and Stotler, RE and Von
Konrat, M and Engel, JJ and Davis, EC and Long, DG and Sova, P and Shaw,
AJ},
Title = {Phylogenetic Relationships and Morphological Evolution in a
Major Clade of Leafy Liverworts (Phylum Marchantiophyta,
Order Jungermanniales): Suborder Jungermanniineae},
Journal = {Systematic botany},
Volume = {40},
Number = {1},
Pages = {27-45},
Publisher = {American Society of Plant Taxonomists},
Year = {2015},
Month = {February},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364415x686314},
Abstract = {—The suborder Jungermanniineae of the Jungermanniales is a
major lineage of leafy liverworts, recognized in recent
classifications to include 15 families. Gametophytes within
the suborder are morphologically diverse, but commonly
anisophyllous to distichous, usually with succubous, rarely
transverse or incubuous, leaf insertions. Sporophytes are
frequently, but not universally, enclosed by stemderived
perigynia or coelocaules, often accompanied by perianth
reduction or loss and some level of geocauly or marsupial
development. We herein provide the first comprehensive
molecular phylogeny of this geographically widespread
suborder, using sequences generated from one nuclear (rpb2),
two mitochondrial (nad1 and rps3), and seven plastid (atpB,
psbA, psbT-H, rbcL, rps4, trnG and trnL) loci, sampled from
279 accessions representing 163 species in 57 genera.
Ancestral states were reconstructed for 14 morphological
characters generally considered taxonomically diagnostic for
families in the suborder. Our phylogenetic analyses support
the return of Leiomylia (=Mylia anomala) to the Myliaceae,
removal of Myliaceae from the Jungermanniineae, and
validation of the monogeneric suborder Myliineae subord.
nov. to house it. Eighteen families are recognized within
the Jungermanniineae, nine of which are monogeneric; namely,
Endogemmataceae, Harpanthaceae, Gyrothyraceae, Arnelliaceae,
Saccogynaceae, Geocalycaceae, Jackiellaceae, Notoscyphaceae
stat. nov., and Trichotemnomaceae. The generic compositions
of other families are modified as follows: Saccogynidium is
transferred from Geocalycaceae to a newly named subfamily of
Acrobolbaceae, Acrobolbaceae subf. Saccogynidioideae, and
one other subfamily of the Acrobolbaceae is validated,
Acrobolbaceae subf. Austrolophozioideae; Hygrobiella is
included in Antheliaceae (previously in Cephaloziaceae or
its own family); Jungermanniaceae is broadened to include
Mesoptychiaceae and Delavayellaceae; Cryptocoleopsis and
Nardia are transferred from Solenostomataceae to
Gymnomitriaceae; Gottschelia, Herzogobryum, and
Nothogymnomitrion are excluded from the Jungermanniineae;
Solenostomataceae is recognized to include Solenostoma,
Arctoscyphus, Cryptocolea, and Diplocolea. Additional
nomenclatural changes include recognizing Horikawaella as a
synonym of Solenostoma and Apomarsupella as a synonym of
Gymnomitrion, establishing two new subgenera of Solenostoma,
Solenostoma subg. Metasolenostoma and Solenostoma subg.
Eucalyx, and transferring Jungermannia conchata to
Cephalozia. Morphological character state reconstructions
identify dioecious inflorescences, gametangia on leading
stems, flagelliform or stoloniferous branches absent, dorsal
leaf insertions not overlapping the stem midline, large
underleaves, and lack of gemmae as ancestral within the
Jungermanniineae. All morphological characters appear to be
moderately to highly homoplasious within the
suborder.},
Doi = {10.1600/036364415x686314},
Key = {fds230488}
}
@article{fds230481,
Author = {Mikulášková, E and Hájek, M and Veleba, A and Johnson, MG and Hájek, T and Shaw, JA},
Title = {Local adaptations in bryophytes revisited: The genetic
structure of the calcium-tolerant peatmoss Sphagnum
warnstorfii along geographic and pH gradients},
Journal = {Ecology and Evolution},
Volume = {5},
Number = {1},
Pages = {229-242},
Publisher = {WILEY},
Year = {2015},
Month = {January},
ISSN = {2045-7758},
url = {http://dx.doi.org/10.1002/ece3.1351},
Abstract = {Bryophytes dominate some ecosystems despite their
extraordinary sensitivity to habitat quality. Nevertheless,
some species behave differently across various regions. The
existence of local adaptations is questioned by a high
dispersal ability, which is thought to redistribute genetic
variability among populations. Although Sphagnum warnstorfii
is an important ecosystem engineer in fen peatlands, the
causes of its rather wide niche along the pH/calcium
gradient are poorly understood. Here, we studied the genetic
variability of its global populations, with a detailed focus
on the wide pH/calcium gradient in Central Europe. Principal
coordinates analysis of 12 polymorphic microsatellite loci
revealed a significant gradient coinciding with water pH,
but independent of geography; even samples from the same
fens were clearly separated along this gradient. However,
most of the genetic variations remained unexplained,
possibly because of the introgression from phylogenetically
allied species. This explanation is supported by the small
heterogeneous cluster of samples that appeared when
populations morphologically transitional to S. subnites, S.
rubellum, or S. russowii were included into the analysis.
Alternatively, this unexplained variation might be
attributed to a legacy of glacial refugia with recently
dissolved ecological and biogeographic consequences.
Isolation by distance appeared at the smallest scale only
(up to 43 km). Negative spatial correlations occurred more
frequently, mainly at long distances (up to 950 km),
implying a genetic similarity among samples which are very
distant geographically. Our results confirm the high
dispersal ability of peatmosses, but simultaneously
suggested that their ability to cope with a high pH/calcium
level is at least partially determined genetically, perhaps
via specific physiological mechanisms or a hummock-forming
ability.},
Doi = {10.1002/ece3.1351},
Key = {fds230481}
}
@article{fds230493,
Author = {Johnson, MG and Granath, G and Tahvanainen, T and Pouliot, R and Stenøien, HK and Rochefort, L and Rydin, H and Shaw,
AJ},
Title = {Evolution of niche preference in Sphagnum peat
mosses.},
Journal = {Evolution; international journal of organic
evolution},
Volume = {69},
Number = {1},
Pages = {90-103},
Year = {2015},
Month = {January},
ISSN = {0014-3820},
url = {http://dx.doi.org/10.1111/evo.12547},
Abstract = {Peat mosses (Sphagnum) are ecosystem engineers-species in
boreal peatlands simultaneously create and inhabit narrow
habitat preferences along two microhabitat gradients: an
ionic gradient and a hydrological hummock-hollow gradient.
In this article, we demonstrate the connections between
microhabitat preference and phylogeny in Sphagnum. Using a
dataset of 39 species of Sphagnum, with an 18-locus DNA
alignment and an ecological dataset encompassing three large
published studies, we tested for phylogenetic signal and
within-genus changes in evolutionary rate of eight niche
descriptors and two multivariate niche gradients. We find
little to no evidence for phylogenetic signal in most
component descriptors of the ionic gradient, but
interspecific variation along the hummock-hollow gradient
shows considerable phylogenetic signal. We find support for
a change in the rate of niche evolution within the genus-the
hummock-forming subgenus Acutifolia has evolved along the
multivariate hummock-hollow gradient faster than the
hollow-inhabiting subgenus Cuspidata. Because peat mosses
themselves create some of the ecological gradients
constituting their own habitats, the classic microtopography
of Sphagnum-dominated peatlands is maintained by
evolutionary constraints and the biological properties of
related Sphagnum species. The patterns of phylogenetic
signal observed here will instruct future study on the role
of functional traits in peatland growth and
reconstruction.},
Doi = {10.1111/evo.12547},
Key = {fds230493}
}
@article{fds230492,
Author = {Wickett, NJ and Mirarab, S and Nguyen, N and Warnow, T and Carpenter, E and Matasci, N and Ayyampalayam, S and Barker, MS and Burleigh, JG and Gitzendanner, MA and Ruhfel, BR and Wafula, E and Der, JP and Graham,
SW and Mathews, S and Melkonian, M and Soltis, DE and Soltis, PS and Miles,
NW and Rothfels, CJ and Pokorny, L and Shaw, AJ and DeGironimo, L and Stevenson, DW and Surek, B and Villarreal, JC and Roure, B and Philippe,
H and dePamphilis, CW and Chen, T and Deyholos, MK and Baucom, RS and Kutchan, TM and Augustin, MM and Wang, J and Zhang, Y and Tian, Z and Yan,
Z and Wu, X and Sun, X and Wong, GK-S and Leebens-Mack,
J},
Title = {Phylotranscriptomic analysis of the origin and early
diversification of land plants.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {111},
Number = {45},
Pages = {E4859-E4868},
Year = {2014},
Month = {November},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1323926111},
Abstract = {Reconstructing the origin and evolution of land plants and
their algal relatives is a fundamental problem in plant
phylogenetics, and is essential for understanding how
critical adaptations arose, including the embryo, vascular
tissue, seeds, and flowers. Despite advances in molecular
systematics, some hypotheses of relationships remain weakly
resolved. Inferring deep phylogenies with bouts of rapid
diversification can be problematic; however, genome-scale
data should significantly increase the number of informative
characters for analyses. Recent phylogenomic reconstructions
focused on the major divergences of plants have resulted in
promising but inconsistent results. One limitation is sparse
taxon sampling, likely resulting from the difficulty and
cost of data generation. To address this limitation,
transcriptome data for 92 streptophyte taxa were generated
and analyzed along with 11 published plant genome sequences.
Phylogenetic reconstructions were conducted using up to 852
nuclear genes and 1,701,170 aligned sites. Sixty-nine
analyses were performed to test the robustness of
phylogenetic inferences to permutations of the data matrix
or to phylogenetic method, including supermatrix, supertree,
and coalescent-based approaches, maximum-likelihood and
Bayesian methods, partitioned and unpartitioned analyses,
and amino acid versus DNA alignments. Among other results,
we find robust support for a sister-group relationship
between land plants and one group of streptophyte green
algae, the Zygnematophyceae. Strong and robust support for a
clade comprising liverworts and mosses is inconsistent with
a widely accepted view of early land plant evolution, and
suggests that phylogenetic hypotheses used to understand the
evolution of fundamental plant traits should be
reevaluated.},
Doi = {10.1073/pnas.1323926111},
Key = {fds230492}
}
@article{fds230491,
Author = {Liu, Y and Ah-Peng, C and Wilding, N and Bardat, J and Devos, N and Carter,
B and Shaw, AJ},
Title = {Population structure in the tropical peatmoss, Sphagnum
tumidulum Besch. (Sphagnaceae)},
Journal = {Bryologist},
Volume = {117},
Number = {4},
Pages = {329-335},
Publisher = {American Bryological and Lichenological Society},
Year = {2014},
Month = {October},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-117.4.329},
Abstract = {Sphagnum and Sphagnum-dominated peatlands have long provided
a model for analyses of community structure, and recent work
has elucidated the genetic structure of various Sphagnum
species in the boreal zone. We report here analyses of
genetic variation and population differentiation in a
tropical species, S. tumidulum, from Réunion Island.
Forty-eight plants (including one sample from Madagascar)
were genotyped at 10 microsatellite loci. The species is
highly variable on Réunion Island and approximately 22% of
the total variation is partitioned among populations.
Thirty-one multilocus genotypes could be distinguished and
clones represented by more than one gametophyte stem were
restricted to individual populations. Our results suggest
the occurrence of sexual reproduction on Réunion Island,
although sporophytes have not been observed there. Gene flow
among most populations appears to be very
limited.},
Doi = {10.1639/0007-2745-117.4.329},
Key = {fds230491}
}
@article{fds230494,
Author = {Laenen, B and Shaw, B and Schneider, H and Goffinet, B and Paradis, E and Désamoré, A and Heinrichs, J and Villarreal, JC and Gradstein, SR and McDaniel, SF and Long, DG and Forrest, LL and Hollingsworth, ML and Crandall-Stotler, B and Davis, EC and Engel, J and Von Konrat and M and Cooper, ED and Patiño, J and Cox, CJ and Vanderpoorten, A and Shaw,
AJ},
Title = {Extant diversity of bryophytes emerged from successive
post-Mesozoic diversification bursts.},
Journal = {Nature communications},
Volume = {5},
Pages = {5134},
Year = {2014},
Month = {October},
url = {http://dx.doi.org/10.1038/ncomms6134},
Abstract = {Unraveling the macroevolutionary history of bryophytes,
which arose soon after the origin of land plants but exhibit
substantially lower species richness than the more recently
derived angiosperms, has been challenged by the scarce
fossil record. Here we demonstrate that overall estimates of
net species diversification are approximately half those
reported in ferns and ∼30% those described for
angiosperms. Nevertheless, statistical rate analyses on
time-calibrated large-scale phylogenies reveal that mosses
and liverworts underwent bursts of diversification since the
mid-Mesozoic. The diversification rates further increase in
specific lineages towards the Cenozoic to reach, in the most
recently derived lineages, values that are comparable to
those reported in angiosperms. This suggests that low
diversification rates do not fully account for current
patterns of bryophyte species richness, and we hypothesize
that, as in gymnosperms, the low extant bryophyte species
richness also results from massive extinctions.},
Doi = {10.1038/ncomms6134},
Key = {fds230494}
}
@article{fds230495,
Author = {Gradstein, SR and Laenen, B and Frahm, JP and Schwarz, U and Crandall-Stotler, BJ and Engel, JJ and von Konrat, M and Stotler, RE and Shaw, B and Jonathan Shaw and A},
Title = {On the taxonomic status of the enigmatic Phycolepidoziaceae
(Marchantiophyta: Jungermanniales) with description of a new
species, Phycolepidozia indica},
Journal = {Taxon},
Volume = {63},
Number = {3},
Pages = {498-508},
Publisher = {International Association for Plant Taxonomy},
Year = {2014},
Month = {June},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.12705/633.17},
Abstract = {The monospecific Phycolepidoziaceae with the single
neotropical species Phycolepidozia exigua is a highly
specialized leafy liverwort without vegetative leaves. The
extreme reduction of morphological and anatomical characters
of Phycolepidozia has caused uncertainties as to the
systematic position of the genus and family. In 2012, a
second species of Phycolepidozia was detected in the Western
Ghats, South India. The Indian plant differs from P. exigua
in several respects and is described here as P. (subg.
Metaphycolepidozia) indica Gradst., J.-P.Frahm & U.Schwarz.
Differences include the massive stem of P. indica, the
larger perianth with a crenate, 3-lobed mouth, and the
epidermis of the capsule wall made up of non-tiered cells
with nodular thickenings on both longitudinal and transverse
walls. A phylogenetic analysis using four different
chloroplast regions (psbA, psbT, rps4, rbcL) of P. indica
and putatively related groups shows that Phycolepidozia is
nested within the leafy liverwort family Cephaloziellaceae.
Consequently, Phycolepidoziaceae is placed in the synonymy
of Cephaloziellaceae. The discovery of P. indica adds a
further example to the list of amphi-Pacific tropical
disjunctions in bryophytes. © International Association for
Plant Taxonomy (IAPT) 2014.},
Doi = {10.12705/633.17},
Key = {fds230495}
}
@article{fds230498,
Author = {Szövényi, P and Devos, N and Weston, DJ and Yang, X and Hock, Z and Shaw,
JA and Shimizu, KK and McDaniel, SF and Wagner, A},
Title = {Efficient purging of deleterious mutations in plants with
haploid selfing.},
Journal = {Genome biology and evolution},
Volume = {6},
Number = {5},
Pages = {1238-1252},
Year = {2014},
Month = {May},
url = {http://dx.doi.org/10.1093/gbe/evu099},
Abstract = {In diploid organisms, selfing reduces the efficiency of
selection in removing deleterious mutations from a
population. This need not be the case for all organisms.
Some plants, for example, undergo an extreme form of selfing
known as intragametophytic selfing, which immediately
exposes all recessive deleterious mutations in a parental
genome to selective purging. Here, we ask how effectively
deleterious mutations are removed from such plants.
Specifically, we study the extent to which deleterious
mutations accumulate in a predominantly selfing and a
predominantly outcrossing pair of moss species, using
genome-wide transcriptome data. We find that the selfing
species purge significantly more nonsynonymous mutations, as
well as a greater proportion of radical amino acid changes
which alter physicochemical properties of amino acids.
Moreover, their purging of deleterious mutation is
especially strong in conserved regions of protein-coding
genes. Our observations show that selfing need not impede
but can even accelerate the removal of deleterious
mutations, and do so on a genome-wide scale.},
Doi = {10.1093/gbe/evu099},
Key = {fds230498}
}
@article{fds230496,
Author = {Stenøien, HK and Hassel, K and Segreto, R and Gabriel, R and Karlin,
EF and Shaw, AJ and Flatberg, KI},
Title = {High morphological diversity in remote island populations of
the peat moss Sphagnum palustre: Glacial refugium, adaptive
radiation or just plasticity?},
Journal = {Bryologist},
Volume = {117},
Number = {2},
Pages = {95-109},
Publisher = {American Bryological and Lichenological Society},
Year = {2014},
Month = {January},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-117.2.095},
Abstract = {Many islands are characterized by high biological diversity,
and both adaptive and non-adaptive factors have been found
to contribute to island richness. Here we study extensive
color morph variability in the allopolyploid peat moss
Sphagnum palustre on the Azores Islands. By comparing
genetic diversity patterns in island and mainland
populations we evaluate various hypotheses for the high
diversity observed within and between islands. We conclude
that the diversity observed cannot be explained by Azores
Islands having acted as refugia for morphotypes during
Pleistocene glacial periods. Furthermore, high island
diversity is not the result of past or ongoing adaptive
radiations. Lack of genetic differentiation and free
reproduction among morphs growing closely together is not
consistent with adaptive differentiation in space or time to
changing environmental conditions. We conclude that high
island diversity in this species likely reflects phenotypic
plasticity, possibly in response to unfavourable
microenvironmental conditions. Evolution of phenotypic
plasticity is expected in organisms with extensive gene
flow, and island diversity in the highly dispersive S.
palustre is probably the result of either higher
environmental variability in island than mainland
populations, or perhaps more likely, selection for increased
plasticity in colonizers of variable and stressful island
environments. © 2014 The American Bryological and
Lichenological Society, Inc.},
Doi = {10.1639/0007-2745-117.2.095},
Key = {fds230496}
}
@article{fds230497,
Author = {Karlin, EF and Temsch, EM and Bizuru, E and Marino, J and Boles, SB and Devos, N and Shaw, AJ},
Title = {Invisible in plain sight: Recurrent double allopolyploidy in
the African Sphagnum ×planifolium (Sphagnaceae)},
Journal = {Bryologist},
Volume = {117},
Number = {2},
Pages = {187-201},
Publisher = {American Bryological and Lichenological Society},
Year = {2014},
Month = {January},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-117.2.187},
Abstract = {Microsatellites, nucleotide sequences, and flow cytometry
were used to determine if two sympatricAfrican peat mosses
(Sphagnum ×planifolium and S. ×slooveri) had a history of
inter-subgeneric hybridization and to assess their
phylogenetic relationship. Both species had previously not
been considered to be hybrids. Sphagnum ×slooveri was found
to be gametophytically allodiploid. Its maternal parent was
S. recurvum (or a closely related species) of subg.
Cuspidata and its paternal parent was an unidentified
species from the S. africanum complex of subg. Subsecunda.
Sphagnum ×planifolium was found to be a cryptic species
complex of gametophytic allotriploids, with recurrent double
allopolyploidy resulting in at least two evolutionarily
distinct lineages. The maternal parent of both lineages was
S. ×slooveri. The paternal parent of one lineage (S.
×planifolium I) was an unidentified haploid associated with
the S. capense complex of subgenus Subsecunda while the
paternal parent of the second lineage (S. ×planifolium II)
was S. cuspidatum (or a closely related species) of subg.
Cuspidata. Four species having a history of double
allopolyploidy are now documented in bryophytes; all are
gametophytically allotriploid, all are in Sphagnum, and all
had an allodiploid parent having a history of
inter-subgeneric hybridization. It is postulated that a high
genetic divergence between subgenomes may facilitate double
allopolyploidy in Sphagnum. Genetic analyses reveal that S.
pulchricoma, S. recurvum and S. sancto-josephense form a
complex of non-hybrid and hybrid plants in the Neotropics,
with the hybrids having a history of hybridization between
S. cuspidatum and S. recurvum. Reticulate evolution needs
more attention in bryophyte studies and this requires
experimental designs sufficiently robust to detect it. ©
2014 The American Bryological and Lichenological Society,
Inc.},
Doi = {10.1639/0007-2745-117.2.187},
Key = {fds230497}
}
@article{fds230502,
Author = {Shaw, AJ and Golinski, GK and Clark, EG and Shaw, B and Stenøien, HK and Flatberg, KI},
Title = {Intercontinental genetic structure in the amphi-Pacific
peatmoss Sphagnum miyabeanum (Bryophyta:
Sphagnaceae)},
Journal = {Biological Journal of the Linnean Society},
Volume = {111},
Number = {1},
Pages = {17-37},
Year = {2014},
Month = {January},
ISSN = {0024-4066},
url = {http://dx.doi.org/10.1111/bij.12200},
Abstract = {Unlike seed plants where global biogeographical patterns
typically involve interspecific phylogenetic history,
spore-producing bryophyte species often have
intercontinental distributions that are best understood from
a population genetic perspective. We sought to understand
how reproductive processes, especially dispersal, have
contributed to the intercontinental 'Pacific Rim'
distribution of Sphagnum miyabeanum. In total, 295
gametophyte plants from western North America (California,
Oregon, British Columbia, Alaska), Russia, Japan, and China
were genotyped at 12 microsatellite loci. Nucleotide
sequences were obtained for seven anonymous nuclear loci
plus two plastid regions from 21 plants of S.miyabeanum and
two outgroup species. We detected weak but significant
genetic differentiation among plants from China, Japan,
Alaska, British Columbia, and the western USA. Alaskan
plants are genetically most similar to Asian plants, and
British Columbian plants are most similar to those in the
western USA. There is detectable migration between regions,
with especially high levels between Alaska and Asia (China
and Japan). Migration appears to be recent and/or ongoing,
and more or less equivalent in both directions. There is
weak (but significant) isolation-by-distance within
geographical regions, and the slope of the regression of
genetic on geographical distance differs for Asian versus
North American plants. A distinctive Vancouver Island
morphotype is very weakly differentiated, and does not
appear to be reproductively isolated from plants of the
normal morphotype. The intercontinental geographical range
of S.miyabeanum reflects recent and probably ongoing
migration, facilitated by the production of tiny spores
capable of effective long distance dispersal. The results of
the present study are consistent with Pleistocene survival
of S.miyabeanum in unglaciated Beringia, although we cannot
eliminate the possibility that the species recolonized
Alaska from Asia more recently. © 2013 The Linnean Society
of London.},
Doi = {10.1111/bij.12200},
Key = {fds230502}
}
@article{fds322317,
Author = {Matasci, N and Hung, L-H and Yan, Z and Carpenter, EJ and Wickett, NJ and Mirarab, S and Nguyen, N and Warnow, T and Ayyampalayam, S and Barker,
M and Burleigh, JG and Gitzendanner, MA and Wafula, E and Der, JP and dePamphilis, CW and Roure, B and Philippe, H and Ruhfel, BR and Miles,
NW and Graham, SW and Mathews, S and Surek, B and Melkonian, M and Soltis,
DE and Soltis, PS and Rothfels, C and Pokorny, L and Shaw, JA and DeGironimo, L and Stevenson, DW and Villarreal, JC and Chen, T and Kutchan, TM and Rolf, M and Baucom, RS and Deyholos, MK and Samudrala,
R and Tian, Z and Wu, X and Sun, X and Zhang, Y and Wang, J and Leebens-Mack,
J and Wong, GK-S},
Title = {Data access for the 1,000 Plants (1KP) project.},
Journal = {GigaScience},
Volume = {3},
Pages = {17},
Year = {2014},
Month = {January},
url = {http://dx.doi.org/10.1186/2047-217x-3-17},
Abstract = {The 1,000 plants (1KP) project is an international
multi-disciplinary consortium that has generated
transcriptome data from over 1,000 plant species, with
exemplars for all of the major lineages across the
Viridiplantae (green plants) clade. Here, we describe how to
access the data used in a phylogenomics analysis of the
first 85 species, and how to visualize our gene and species
trees. Users can develop computational pipelines to analyse
these data, in conjunction with data of their own that they
can upload. Computationally estimated protein-protein
interactions and biochemical pathways can be visualized at
another site. Finally, we comment on our future plans and
how they fit within this scalable system for the
dissemination, visualization, and analysis of large
multi-species data sets.},
Doi = {10.1186/2047-217x-3-17},
Key = {fds322317}
}
@article{fds230500,
Author = {Li, F and Villarreal, JC and Kelly, S and Rothfels, CJ and Melkonian, M and Frangedakis, E and Ruhsam, M and Sigel, EM and Der, JP and Pittermann,
J},
Title = {Horizontal transfer of an adaptive chimeric photoreceptor
from bryophytes to ferns},
Journal = {Proceedings of the National Academy of Sciences},
Volume = {111},
Number = {18},
Pages = {6672-6677},
Publisher = {National Academy of Sciences},
Year = {2014},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1319929111},
Abstract = {Ferns are well known for their shade-dwelling habits. Their
ability to thrive under low-light conditions has been linked
to the evolution of a novel chimeric photoreceptor--neochrome--that
fuses red-sensing phytochrome and blue-sensing phototropin
modules into a single gene, thereby optimizing phototropic
responses. Despite being implicated in facilitating the
diversification of modern ferns, the origin of neochrome has
remained a mystery. We present evidence for neochrome in
hornworts (a bryophyte lineage) and demonstrate that ferns
acquired neochrome from hornworts via horizontal gene
transfer (HGT). Fern neochromes are nested within hornwort
neochromes in our large-scale phylogenetic reconstructions
of phototropin and phytochrome gene families. Divergence
date estimates further support the HGT hypothesis, with fern
and hornwort neochromes diverging 179 Mya, long after the
split between the two plant lineages (at least 400 Mya). By
analyzing the draft genome of the hornwort Anthoceros
punctatus, we also discovered a previously unidentified
phototropin gene that likely represents the ancestral
lineage of the neochrome phototropin module. Thus, a
neochrome originating in hornworts was transferred
horizontally to ferns, where it may have played a
significant role in the diversification of modern
ferns.},
Doi = {10.1073/pnas.1319929111},
Key = {fds230500}
}
@article{fds230501,
Author = {Câmara, PEAS and Shaw, J},
Title = {A molecular phylogeny of the moss genus Taxithelium
(Pylaisiadelphaceae) based on plastid, mitochondrial and
nuclear markers},
Journal = {Systematic Botany},
Volume = {38},
Number = {4},
Pages = {861-868},
Publisher = {American Society of Plant Taxonomists},
Year = {2013},
Month = {December},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364413X674832},
Abstract = {To test infrageneric classification and species delimitation
within the pantropical moss genus Taxithelium
(Pylaisiadelphaceae), we constructed a molecular phylogeny
using three chloroplast loci (trnL, psbT and rps4), three
mitochondrial loci (rps3, nad5 and nad4-5) and the nuclear
marker ho1. Analyses of each locus separately and in various
combinations, all support the monophyly of Taxithelium. Two
major clades corresponding to taxonomically recognized
subgenera were resolved within the genus. The first clade is
composed of at least five smaller groups, four of which only
include Southeast Asian plants and one is from the Americas
and Africa; the latter is nested within the Southeast Asian
groups. The second group appears to have a Southeast Asian
origin with two dispersal events into America. Taxithelium
is highly variable morphologically and includes plants with
pluripapillose leaf cells as well as plants that lack
papillae. Our data show that species T. nepalense, T.
leptosigmatum, T. concavum, T. instratum, T. lindbergii and
T. isocladum are each demonstrably monophyletic. On the
other hand, T. planum and T. kerianum as circumscribed today
are polyphyletic. The ho1 nuclear locus is used for the
first time, with promising results for moss phylogenetic
investigation. © Copyright 2013 by the American Society of
Plant Taxonomists.},
Doi = {10.1600/036364413X674832},
Key = {fds230501}
}
@article{fds230504,
Author = {Karlin, EF and Buck, WR and Seppelt, RD and Boles, SB and Jonathan Shaw,
A},
Title = {The double allopolyploid Sphagnum × falcatulum
(Sphagnaceae) in Tierra del Fuego, a Holantarctic
perspective},
Journal = {Journal of Bryology},
Volume = {35},
Number = {3},
Pages = {157-172},
Publisher = {Informa UK Limited},
Year = {2013},
Month = {September},
ISSN = {0373-6687},
url = {http://dx.doi.org/10.1179/1743282013Y.0000000066},
Abstract = {A Holantarctic species, the inter-subgeneric allopolyploid
Sphagnum ×falcatulum s.l. is a cryptic species complex
composed of allodiploid and allotriploid cytotypes. The
allotriploid plants are double allopolyploids (one of just
two reported for bryophytes), with the allodiploid cytotype
being one parent. Using a combination of microsatellites,
nucleotide sequences, and morphological characters,
allotriploid S. ×falcatulum is shown to be the most
widespread Sphagnum species in the Holantarctic, with
genetically documented populations in South America (Tierra
del Fuego), New Zealand (South Island), and Australia
(Macquarie Island, Tasmania). It is further concluded that
six Sphagnum species described from the Tierra del Fuego
Archipelago (TDF) of South America and a seventh described
from South Island, New Zealand are synonymous with the
allotriploid cytotype of S. ×falcatulum. The synonymized
species include five named by Heikki Roivainen in 1937, S.
×ehyalinum, and S. subditivum. Allotriploid S. ×falcatulum
is the predominant, perhaps the only, subgenus Cuspidata
species present in TDF and immediate vicinity. The
combination of low genetic diversity and an apparent absence
of sexual reproduction indicate that the TDF population of
the dioicous allotriploid S. ×falcatulum was likely founded
by one or a limited number of individuals. The same is
apparently the case for Macquarie I. and Tasmanian
populations of allotriploid S. ×falcatulum. Several lines
of evidence, including high genetic diversity, frequent
sporophyte production, and the occurrence of the allodiploid
parent, suggest that allotriploid S. ×falcatulum likely
evolved in New Zealand. © British Bryological Society
2013.},
Doi = {10.1179/1743282013Y.0000000066},
Key = {fds230504}
}
@article{fds230499,
Author = {Szövényi, P and Ricca, M and Hock, Z and Shaw, JA and Shimizu, KK and Wagner, A},
Title = {Selection is no more efficient in haploid than in diploid
life stages of an angiosperm and a moss.},
Journal = {Molecular biology and evolution},
Volume = {30},
Number = {8},
Pages = {1929-1939},
Year = {2013},
Month = {August},
ISSN = {0737-4038},
url = {http://dx.doi.org/10.1093/molbev/mst095},
Abstract = {The masking hypothesis predicts that selection is more
efficient in haploids than in diploids, because dominant
alleles can mask the deleterious effects of recessive
alleles in diploids. However, gene expression breadth and
noise can potentially counteract the effect of masking on
the rate at which genes evolve. Land plants are ideal to ask
whether masking, expression breadth, or expression noise
dominate in their influence on the rate of molecular
evolution, because they have a biphasic life cycle in which
the duration and complexity of the haploid and diploid phase
varies among organisms. Here, we generate and compile
genome-wide gene expression, sequence divergence, and
polymorphism data for Arabidopsis thaliana and for the moss
Funaria hygrometrica to show that the evolutionary rates of
haploid- and diploid-specific genes contradict the masking
hypothesis. Haploid-specific genes do not evolve more slowly
than diploid-specific genes in either organism. Our data
suggest that gene expression breadth influence the
evolutionary rate of phase-specific genes more strongly than
masking. Our observations have implications for the role of
haploid life stages in the purging of deleterious mutations,
as well as for the evolution of ploidy.},
Doi = {10.1093/molbev/mst095},
Key = {fds230499}
}
@article{fds230506,
Author = {Shaw, AJ and Shaw, B and Johnson, MG and Higuchi, M and Arikawa, T and Ueno, T and Devos, N},
Title = {Origins, genetic structure, and systematics of the narrow
endemic peatmosses (Sphagnum): S. guwassanense and S.
triseriporum (Sphagnaceae).},
Journal = {American journal of botany},
Volume = {100},
Number = {6},
Pages = {1202-1220},
Year = {2013},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23720430},
Abstract = {<h4>Unlabelled</h4><h4>Premise of the study</h4>Sphagnum
dominates vast expanses of wetland habitats throughout the
northern hemisphere and species delimitation within the
genus is important because floristic changes associated with
a warming global climate may have measureable impacts on
large-scale ecological processes. Most northern hemisphere
peatmoss species (Sphagnum) have circumboreal ranges, but
the Japanese species generally known as S. calymmatophyllum
is endemic to Honshu Island. This prompted a population
genetic and phylogenetic analysis to resolve the origin(s),
population structure, and phylogenetic relationships of this
morphologically variable species. •<h4>Methods</h4>Sixty
plants collected from Mt. Gassan and Mt. Hakkoda were
genotyped for 12 microsatellite loci. Two plastid loci and
three anonymous nuclear loci were sequenced in a subset of
the plants, plus representatives from 10 closely related
species. •<h4>Key results</h4>Gametophytes exhibited fixed
or nearly fixed heterozygosity at 9-10 of the 12
microsatellite loci. Two genetic groups were resolved by the
microsatellite data, individuals showed no evidence of
admixture, and the two groups of plants differ in
morphology. They are heterozygous for different sets of
alleles. The two taxa share plastid DNA sequences with two
species that are common in Alaska. •<h4>Conclusions</h4>Two
taxa were distinguished: S. guwassanense and S.
triseriporum. Both are allopolyploids; they originated
independently from different but closely related
progenitors. The maternal progenitor was likely either S.
orientale or S. inexspectatum. The two allopolyploid taxa
are heterozygous for (different) private microsatellite
alleles, and one progenitor could be extinct.},
Doi = {10.3732/ajb.1200630},
Key = {fds230506}
}
@article{fds230503,
Author = {Shaw, AJ and Golinski, GK and Clark, EG and Shaw, B and Stenøien, HK and Flatberg, KI},
Title = {Intercontinental genetic structure in the amphi-Pacific
peatmoss Sphagnum miyabeanum (Bryophyta:
Sphagnaceae)},
Journal = {Biological Journal of the Linnean Society},
Volume = {111},
Number = {1},
Pages = {17-37},
Publisher = {Oxford University Press (OUP)},
Year = {2013},
ISSN = {0024-4066},
url = {http://dx.doi.org/10.1111/bij.12200},
Doi = {10.1111/bij.12200},
Key = {fds230503}
}
@article{fds230574,
Author = {Szövényi, P and Sundberg, S and Shaw, AJ},
Title = {Long-distance dispersal and genetic structure of natural
populations: an assessment of the inverse isolation
hypothesis in peat mosses.},
Journal = {Molecular ecology},
Volume = {21},
Number = {22},
Pages = {5461-5472},
Year = {2012},
Month = {November},
ISSN = {0962-1083},
url = {http://dx.doi.org/10.1111/mec.12055},
Abstract = {It is well accepted that the shape of the dispersal kernel,
especially its tail, has a substantial effect on the genetic
structure of species. Theory predicts that dispersal by
fat-tailed kernels reshuffles genetic material, and thus,
preserves genetic diversity during colonization. Moreover,
if efficient long-distance dispersal is coupled with random
colonization, an inverse isolation effect is predicted to
develop in which increasing genetic diversity per colonizer
is expected with increasing distance from a genetically
variable source. By contrast, increasing isolation leads to
decreasing genetic diversity when dispersal is via
thin-tailed kernels. Here, we use a well-established model
group for dispersal biology (peat mosses: genus Sphagnum)
with a fat-tailed dispersal kernel, and the natural
laboratory of the Stockholm archipelago to study the
validity of the inverse isolation hypothesis in
spore-dispersed plants in island colonization. Population
genetic structure of three species (Sphagnum fallax,
Sphagnum fimbriatum and Sphagnum palustre) with contrasting
life histories and ploidy levels were investigated on a set
of islands using microsatellites. Our data show (ϕ'(st),
amova, IBD) that dispersal of the two most abundant species
can be well approximated by a random colonization model. We
find that genetic diversity per colonizer on islands
increases with distance from the mainland for S. fallax and
S. fimbriatum. By contrast, S. palustre deviates from this
pattern, owing to its restricted distribution in the region,
affecting its source pool strength. Therefore, the inverse
isolation effect appears to hold in natural populations of
peat mosses and, likely, in other organisms with small
diaspores.},
Doi = {10.1111/mec.12055},
Key = {fds230574}
}
@article{fds230578,
Author = {Ho, BC and Pokorny, L and Tan, BC and Frahm, JP and Shaw, AJ and Quandt,
D},
Title = {Molecular evolution and diversification of the moss family
Daltoniaceae (Hookeriales, Bryophyta) with emphasis on the
unravelling of the phylogeny of Distichophyllum and its
allies},
Journal = {Botanical Journal of the Linnean Society},
Volume = {170},
Number = {2},
Pages = {157-175},
Publisher = {Oxford University Press (OUP)},
Year = {2012},
Month = {October},
ISSN = {0024-4074},
url = {http://dx.doi.org/10.1111/j.1095-8339.2012.01279.x},
Abstract = {Phylogenetic relationships in Daltoniaceae (∼200 species
in 14 genera) are inferred from nucleotide sequences from
five genes, representing all genomic compartments, using
parsimony, likelihood and Bayesian methods. Alternative
classifications for Daltoniaceae have favoured traits from
either sporophytes or gametophytes; phylogenetic transitions
in gametophytic leaf limbidia and sporophytic exostome
ornamentation were evaluated using ancestral state
reconstruction to assess the levels of conflict between
these generations. Elimbate leaves and the cross-striate
exostome are reconstructed as plesiomorphic states. Limbate
leaves and papillose exostomes evolved at least two and six
times, respectively, without reversals. The evolution of
leaf limbidia is relatively conserved, but exostome
ornamentation is highly homoplasious, indicating that
superficial similarity in peristomes gives unreliable
approximations of phylogenetic relatedness. Our phylogenetic
analyses show that Achrophyllum and Calyptrochaeta are
reciprocally monophyletic. Within core Daltoniaceae,
relationships among taxa with elimbate leaves are generally
well understood. However, taxa with limbate leaves form a
monophyletic group, but resolved subclades correspond to
biogeographical entities, rather than to traditional
concepts of genera. Daltonia (∼21 species),
Distichophyllum (∼100 species) and Leskeodon (∼20
species) are polyphyletic. Seven nomenclatural changes are
proposed here. As the current taxonomy of Daltoniaceae lacks
phylogenetic consistency, critical generic revisions are
needed. © 2012 The Linnean Society of London.},
Doi = {10.1111/j.1095-8339.2012.01279.x},
Key = {fds230578}
}
@article{fds230573,
Author = {Pokorny, L and Ho, B-C and Frahm, J-P and Quandt, D and Shaw,
AJ},
Title = {Phylogenetic analyses of morphological evolution in the
gametophyte and sporophyte generations of the moss order
Hookeriales (Bryopsida).},
Journal = {Molecular phylogenetics and evolution},
Volume = {63},
Number = {2},
Pages = {351-364},
Year = {2012},
Month = {May},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22266481},
Abstract = {Morphological characters from the gametophyte and sporophyte
generations have been used in land plants to infer
relationships and construct classifications, but sporophytes
provide the vast majority of data for the systematics of
vascular plants. In bryophytes both generations are well
developed and characters from both are commonly used to
classify these organisms. However, because morphological
traits of gametophytes and sporophytes can have different
genetic bases and experience different selective pressures,
taxonomic emphasis on one generation or the other may yield
incongruent classifications. The moss order Hookeriales has
a controversial taxonomic history because previous
classifications have focused almost exclusively on either
gametophytes or sporophytes. The Hookeriales provide a model
for comparing morphological evolution in gametophytes and
sporophytes, and its impact on alternative classification
systems. In this study we reconstruct relationships among
mosses that are or have been included in the Hookeriales
based on sequences from five gene regions, and reconstruct
morphological evolution of six sporophyte and gametophyte
traits that have been used to differentiate families and
genera. We found that the Hookeriales, as currently
circumscribed, are monophyletic and that both sporophyte and
gametophyte characters are labile. We documented parallel
changes and reversals in traits from both generations. This
study addresses the general issue of morphological reversals
to ancestral states, and resolves novel relationships in the
Hookeriales.},
Doi = {10.1016/j.ympev.2012.01.005},
Key = {fds230573}
}
@article{fds230582,
Author = {Johnson, MG and Shaw, B and Zhou, P and Shaw, AJ},
Title = {Genetic analysis of the peatmoss Sphagnum cribrosum
(Sphagnaceae) indicates independent origins of an extreme
infra-specific morphology shift},
Journal = {Biological Journal of the Linnean Society},
Volume = {106},
Number = {1},
Pages = {137-153},
Publisher = {Oxford University Press (OUP)},
Year = {2012},
Month = {May},
ISSN = {0024-4066},
url = {http://dx.doi.org/10.1111/j.1095-8312.2012.01842.x},
Abstract = {Within Sphagnum cribrosum, a dioicous aquatic peatmoss, a
unique morphological variant (the 'waveform'), found at only
two lakes in North Carolina, has a branching architecture
that is extremely differentiated from anything otherwise
known in Sphagnum, although the plants are microscopically
indistinguishable from S. cribrosum. At one site where the
two morphologies co-occur, 60 years of field observations
demonstrate the persistence of each morphology, even where
the two forms grow intermixed. We conducted a reciprocal
transplant experiment in which waveform and normal plants
maintained their divergent morphologies for 8 months. We
sampled populations throughout the range and conducted
genetic and phylogenetic analyses with microsatellite
markers and DNA sequences to investigate the genetic context
of the waveform morphology within S. cribrosum. Haplotype
networks from DNA sequences showed the two waveform
populations are separated by 11 substitutions across three
loci. Microsatellite analyses using nonparametric clustering
and admixture models also indicated genetic dissimilarity
between genotypes with waveform morphology at the two lakes.
Both molecular datasets suggest that the waveform morphology
had at least two independent origins, despite the proximity
of the two lakes where it occurs uniquely. Given the clonal
nature of the waveform, it is unlikely to form a cohesive
evolutionary lineage deserving of taxonomic status. The
analysis also revealed a genetically diverse population in
Georgia as the potential source of variation found in all
other populations of S. cribrosum. © 2012 The Linnean
Society of London.},
Doi = {10.1111/j.1095-8312.2012.01842.x},
Key = {fds230582}
}
@article{fds230576,
Author = {Karlin, EF and Hotchkiss, SC and Boles, SB and Stenøien, HK and Hassel,
K and Flatberg, KI and Shaw, AJ},
Title = {High genetic diversity in a remote island population system:
sans sex.},
Journal = {The New phytologist},
Volume = {193},
Number = {4},
Pages = {1088-1097},
Year = {2012},
Month = {March},
ISSN = {0028-646X},
url = {http://dx.doi.org/10.1111/j.1469-8137.2011.03999.x},
Abstract = {It has been proposed that long-distance dispersal of mosses
to the Hawaiian Islands rarely occurs and that the Hawaiian
population of the allopolyploid peat moss Sphagnum palustre
probably resulted from a single dispersal event. Here, we
used microsatellites to investigate whether the Hawaiian
population of the dioicous S. palustre had a single founder
and to compare its genetic diversity to that found in
populations of S. palustre in other regions. The genetic
diversity of the Hawaiian population is comparable to that
of larger population systems. Several lines of evidence,
including a lack of sporophytes and an apparently restricted
natural distribution, suggest that sexual reproduction is
absent in the Hawaiian plants. In addition, all samples of
Hawaiian S. palustre share a genetic trait rare in other
populations. Time to most recent ancestor (TMRCA) analysis
indicates that the Hawaiian population was probably founded
49-51 kyr ago. It appears that all Hawaiian plants of S.
palustre descend from a single founder via vegetative
propagation. The long-term viability of this clonal
population coupled with the development of significant
genetic diversity suggests that vegetative propagation in a
moss does not necessarily preclude evolutionary success in
the long term.},
Doi = {10.1111/j.1469-8137.2011.03999.x},
Key = {fds230576}
}
@article{fds230577,
Author = {Heinrichs, J and Bombosch, A and Feldberg, K and Kreier, H-P and Hentschel, J and Eckstein, J and Long, D and Zhu, R-L and Schäfer-Verwimp, A and Schmidt, AR and Shaw, B and Shaw, AJ and Váňa,
J},
Title = {A phylogeny of the northern temperate leafy liverwort genus
Scapania (Scapaniaceae, Jungermanniales).},
Journal = {Molecular phylogenetics and evolution},
Volume = {62},
Number = {3},
Pages = {973-985},
Year = {2012},
Month = {March},
ISSN = {1055-7903},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000300275300017&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Scapania is a northern temperate genus with a few
disjunctions in the south. Despite receiving considerable
attention, the supraspecific classification of this genus
remains unsatisfactorily solved. We use three molecular
markers (nrITS, cpDNA trnL-F region, atpB-rbcL spacer) and
175 accessions belonging to 50 species (plus eight outgroup
taxa) to estimate the phylogeny and to test current
classification systems. Our data support the classification
of Scapania into six rather than three subgenera,
rearrangements within numerous sections, and inclusion of
Macrodiplophyllum microdontum. Scapania species with a
plicate perianth form three early diverging lineages; the
most speciose subgenus, Scapania s.str., represents a
derived clade. Most morphological species concepts are
supported by the molecular topologies but classification of
sect. Curtae requires further study. Southern lineages are
nested in northern hemispheric clades. Palearctic-Nearctic
distribution ranges are supported for several
species.},
Doi = {10.1016/j.ympev.2011.11.029},
Key = {fds230577}
}
@article{fds230579,
Author = {Shaw, AJ and Shaw, B and Ricca, M and Flatberg, KI},
Title = {A phylogenetic monograph of the Sphagnum subsecundum complex
(Sphagnaceae) in eastern North America},
Journal = {Bryologist},
Volume = {115},
Number = {1},
Pages = {128-152},
Publisher = {American Bryological and Lichenological Society},
Year = {2012},
Month = {March},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-115.1.128},
Abstract = {A taxonomic treatment based on field studies, examination of
herbarium collections, and previously published molecular
data is provided for the North American species of the
Sphagnum subsecundum complex. Sphagnum platyphyllum, S.
contortum, S. lescurii, and S. subsecundum are
gametophytically haploid. Sphagnum missouricum and S.
carolinianum are gametophytically allodiploid. A single
allodiploid population of S. platyphyllum and a homoploid
(haploid) hybrid between S. contortum and S. subscundum,
previously documented genetically, are described and
illustrated (but neither distinguished taxonomically).
Epitypes are designated from (haploid) S. lescurii and
(allodiploid) S. missouricum because the ploidal level of
the original type material cannot be determined
unambiguously. In North America, S. subsecundum is
restricted to the eastern part of the continent, as western
plants named this species are not conspecific. North
American plants named S. inundatum are considered synonymous
with either S. lescurii (when haploid) or S. missouricum
(when diploid). © 2012 by The American Bryological and
Lichenological Society, Inc.},
Doi = {10.1639/0007-2745-115.1.128},
Key = {fds230579}
}
@article{fds230580,
Author = {Shaw, AJ and Shaw, B and Higuchi, M and Arikawa, T and Hirayama, Y and Devos, N},
Title = {Climacium (Climaciaceae): Species relationships and
biogeographic implications},
Journal = {Bryologist},
Volume = {115},
Number = {1},
Pages = {23-30},
Publisher = {American Bryological and Lichenological Society},
Year = {2012},
Month = {March},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745.115.1.23},
Abstract = {Climacium is a small but morphologically distinctive genus
("tree mosses") with four species distributed primarily in
the Northern Hemisphere. Climacium dendroides occurs around
the globe at northern latitudes with disjunct populations in
Mexico and New Zealand, whereas C. americanum and C.
kindbergii are endemic to eastern North America and C.
japonicum is limited to eastern Asia. Using nucleotide
sequence data from five plastid loci plus the nuclear
ribosomal ITS region we assessed evidence for monophyly of
taxonomic species and tested the hypothesis that C.
americanum and C. kindbergii from eastern North America have
a sister group relationship with C. japonicum from eastern
Asia. Climacium japonicum is resolved as sister to a clade
containing the circumboreal C. dendroides, C. americanum,
and C. kindbergii. Climacium americanum and C. kindbergii
were not resolved as monophyletic based on sequence data but
together they composed the sister lineage to C. dendroides.
Geographically disjunct populations of C. dendroides in
Asia, Mexico, the United States, and Canada vary at only a
few polymorphic nucleotide sites across the three loci. The
disjunctive New Zealand plants of C. dendroides are related
to Asian accessions. © 2012 by The American Bryological and
Lichenological Society, Inc.},
Doi = {10.1639/0007-2745.115.1.23},
Key = {fds230580}
}
@article{fds230572,
Author = {Huttunen, S and Bell, N and Bobrova, VK and Buchbender, V and Buck, WR and Cox, CJ and Goffinet, B and Hedenäs, L and Ho, BC and Ignatov, MS and Krug, M and Kuznetsova, O and Milyutina, IA and Newton, A and Olsson, S and Pokorny, L and Shaw, JA and Stech, M and Troitsky, A and Vanderpoorten,
A and Quandt, D},
Title = {Disentangling knots of rapid evolution: Origin and
diversification of the moss order Hypnales},
Journal = {Journal of Bryology},
Volume = {34},
Number = {3},
Pages = {187-211},
Publisher = {Informa UK Limited},
Year = {2012},
Month = {January},
ISSN = {0373-6687},
url = {http://dx.doi.org/10.1179/1743282012Y.0000000013},
Abstract = {The Hypnales are the largest order of mosses comprising
approximately 4200 species. Phylogenetic reconstruction
within the group has proven to be difficult due to rapid
radiation at an early stage of evolution and, consequently,
relationships among clades have remained poorly resolved. We
compiled data from four sequence regions, namely, nuclear
ITS1-5.8S-ITS2, plastid trnL-F and rps4, and mitochondrial
nad5, for 122 hypnalean species and 34 species from closely
related groups. Tree topologies from both Bayesian and
parsimony analyses resolve the order as monophyletic.
Although inferences were made from fastevolving genes, and
despite strong phylogenetic signal in the nuclear
ITS1-5.8S-ITS2 data, monophyly, as well as backbone nodes
within the Hypnales, remains rather poorly supported except
under Bayesian inferences. Ancestral distribution based on
Bayesian dispersal-vicariance analysis supports a Gondwanan
origin of the Hypnales and subsequent geographical radiation
in the area of the former Laurasian supercontinent.
Reconstruction of historical biogeography is congruent with
mainly tropical and Gondwanan distributions in the sister
groups Hypnodendrales, Ptychomniales, and Hookeriales, and
with the dating for the oldest pleurocarp and hypnalean
fossils. We contrast groupings in the phylogenetic tree with
recent classifications and other phylogenetic inferences
based on molecular data, and summarise current knowledge on
the evolutionary history of, and relationships among, the
Hypnales. © British Bryological Society
2012.},
Doi = {10.1179/1743282012Y.0000000013},
Key = {fds230572}
}
@article{fds230575,
Author = {Ellis, LT and Alegro, A and Bansal, P and Nath, V and Cykowska, B and Bednarek-Ochyra, H and Ochyra, R and Dulin, MV and Erzberger, P and Garcia, C and Sérgio, C and Claro, D and Stow, S and Hedderson, TA and Hodgetts, NG and Hugonnot, V and Kucěra, J and Lara, F and Pertierra,
L and Lebouvier, M and Liepina, L and Mežaka, A and Strazdiņa, L and Madžule, L and Reriha, I and Mazooji, A and Natcheva, R and Phephu, N and Philippov, DA and Plášek, V and Číhal, L and Pócs, T and Porley,
RD and Sabovljević, M and Salimpour, F and Motlagh, MB and Sharifnia,
F and Darzikolaei, SA and Schäfer-Verwimp, A and Šegota, V and Shaw,
AJ and Sim-Sim, M and Sollman, P and Spitale, D and Hölzer, A and Stebel,
A and Váňa, J and van Rooy, J and Vončina, G},
Title = {New national and regional bryophyte records,
32},
Journal = {Journal of Bryology},
Volume = {34},
Number = {3},
Pages = {231-246},
Publisher = {Informa UK Limited},
Year = {2012},
Month = {January},
ISSN = {0373-6687},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000309047100006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.1179/1743282012Y.0000000019},
Key = {fds230575}
}
@article{fds318047,
Author = {Shaw, AJ and Flatberg, KI and Szövényi, P and Ricca, M and Johnson,
MG and Stenøien, HK and Shaw, B},
Title = {Systematics of the Sphagnum fimbriatum complex: Phylogenetic
relationships, morphological variation, and
allopolyploidy},
Journal = {Systematic Botany},
Volume = {37},
Number = {1},
Pages = {15-30},
Publisher = {American Society of Plant Taxonomists},
Year = {2012},
Month = {January},
url = {http://dx.doi.org/10.1600/036364412X616585},
Abstract = {The application of genetic tools for studying species
delimitation and relationships in Sphagnum (peatmosses) has
demonstrated that evolutionary patterns are complex and
include homoploid hybridization and multiple taxa of
allopolyploid origin. We investigated evolutionary
relationships in the so-called S. fimbriatum complex and
tested hypotheses of species delimitation derived from
patterns of morphological variation, and determined the
origin of one species with diploid gametophytes. Plastid DNA
sequences resolve a single haplotype shared by one described
species, S. concinnum, and a morphotype that we had
hypothesized to be another species (referred to informally
as S. "diskoense"). All samples of the polyploid, S.
tescorum, share an identical haplotype with most samples of
S. girgensohnii. Sphagnum fimbriatum and S. girgensohnii
share several plastid DNA haplotypes, and also share
haplotypes with two other morphotypes that we had
hypothesized to be distinct species (S. "obscurum" and S.
"ubertum"). Fixed or nearly fixed heterozygosity at ten
microsatellite loci show that S. tescorum is an
allopolyploid. Genetic admixture analyses and computation of
hybrid indices from microsatellite data, in combination with
sequences from the plastid genome, support the hypothesis
that S. fimbriatum and S. girgensohnii are progenitors of S.
tescorum, with S. girgensohnii as the maternal parent. Data
from 14 microsatellite loci demonstrate that S. concinnum,
S. fimbriatum, S. girgensohnii, and S. tescorum are
genetically distinct but the same data do not support
separation of S. "diskoense," S. "obscurum," and S.
"ubertum." Homoploid hybridization between S. fimbriatum and
S. girgensohnii is strongly suggested by genetic data and
phylogenetic analyses. © Copyright 2012 by the American
Society of Plant Taxonomists.},
Doi = {10.1600/036364412X616585},
Key = {fds318047}
}
@article{fds230581,
Author = {Shaw, AJ and Flatberg, KI and Szövényi, P and Ricca, M and Johnson,
MG and Stenøien, HK and Shaw, B},
Title = {Systematics of the Sphagnum fimbriatum complex: phylogenetic
relationships, morphological variation, and
allopolyploidy},
Journal = {Systematic Botany},
Volume = {63},
Number = {1},
Pages = {351-364},
Year = {2012},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364412X616585},
Abstract = {The application of genetic tools for studying species
delimitation and relationships in Sphagnum (peatmosses) has
demonstrated that evolutionary patterns are complex and
include homoploid hybridization and multiple taxa of
allopolyploid origin. We investigated evolutionary
relationships in the so-called S. fimbriatum complex and
tested hypotheses of species delimitation derived from
patterns of morphological variation, and determined the
origin of one species with diploid gametophytes. Plastid DNA
sequences resolve a single haplotype shared by one described
species, S. concinnum, and a morphotype that we had
hypothesized to be another species (referred to informally
as S. "diskoense"). All samples of the polyploid, S.
tescorum, share an identical haplotype with most samples of
S. girgensohnii. Sphagnum fimbriatum and S. girgensohnii
share several plastid DNA haplotypes, and also share
haplotypes with two other morphotypes that we had
hypothesized to be distinct species (S. "obscurum" and S.
"ubertum"). Fixed or nearly fixed heterozygosity at ten
microsatellite loci show that S. tescorum is an
allopolyploid. Genetic admixture analyses and computation of
hybrid indices from microsatellite data, in combination with
sequences from the plastid genome, support the hypothesis
that S. fimbriatum and S. girgensohnii are progenitors of S.
tescorum, with S. girgensohnii as the maternal parent. Data
from 14 microsatellite loci demonstrate that S. concinnum,
S. fimbriatum, S. girgensohnii, and S. tescorum are
genetically distinct but the same data do not support
separation of S. "diskoense," S. "obscurum," and S.
"ubertum." Homoploid hybridization between S. fimbriatum and
S. girgensohnii is strongly suggested by genetic data and
phylogenetic analyses. © Copyright 2012 by the American
Society of Plant Taxonomists.},
Doi = {10.1600/036364412X616585},
Key = {fds230581}
}
@article{fds230586,
Author = {Hutsemékers, V and Szövényi, P and Shaw, AJ and González-Mancebo,
J-M and Muñoz, J and Vanderpoorten, A},
Title = {Oceanic islands are not sinks of biodiversity in
spore-producing plants.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {108},
Number = {47},
Pages = {18989-18994},
Year = {2011},
Month = {November},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1109119108},
Abstract = {Islands have traditionally been considered as migratory and
evolutionary dead ends for two main reasons: island
colonizers are typically assumed to lose their dispersal
power, and continental back colonization has been regarded
as unlikely because of niche preemption. The hypothesis that
islands might actually represent dynamic refugia and
migratory stepping stones for species that are effective
dispersers, and in particular, for spore-producing plants,
is formally tested here, using the archipelagos of the
Azores, Canary Islands, and Madeira, as a model. Population
genetic analyses based on nuclear microsatellite variation
indicate that dispersal ability of the moss Platyhypnidium
riparioides does not decrease in the island setting. The
analyses further show that, unlike island populations,
mainland (southwestern Europe and North Africa) populations
underwent a severe bottleneck during the last glacial
maximum (LGM). Our results thus refute the traditional view
of islands as the end of the colonization road and point to
a different perception of North Atlantic archipelagos as
major sources of biodiversity for the postglacial
recolonization of Europe by spore-producing
plants.},
Doi = {10.1073/pnas.1109119108},
Key = {fds230586}
}
@article{fds230590,
Author = {Devos, N and Renner, MAM and Gradstein, R and Shaw, AJ and Laenen, B and Vanderpoorten, A},
Title = {Evolution of sexual systems, dispersal strategies and
habitat selection in the liverwort genus
Radula.},
Journal = {The New phytologist},
Volume = {192},
Number = {1},
Pages = {225-236},
Year = {2011},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21649662},
Abstract = {• Shifts in sexual systems are among the most common and
important transitions in plants and are correlated with a
suite of life-history traits. The evolution of sexual
systems and their relationships to gametophyte size, sexual
and asexual reproduction, and epiphytism are examined here
in the liverwort genus Radula. • The sequence of trait
acquisition and the phylogenetic correlations between those
traits was investigated using comparative methods. •
Shifts in sexual systems recurrently occurred from dioecy to
monoecy within facultative epiphyte lineages. Production of
specialized asexual gemmae was correlated to neither dioecy
nor strict epiphytism. • The significant correlations
among life-history traits related to sexual systems and
habitat conditions suggest the existence of evolutionary
trade-offs. Obligate epiphytes do not produce gemmae more
frequently than facultative epiphytes and disperse by whole
gametophyte fragments, presumably to avoid the sensitive
protonemal stage in a habitat prone to rapid changes in
moisture availability. As dispersal ranges correlate with
diaspore size, this reinforces the notion that epiphytes
experience strong dispersal limitations. Our results thus
provide the evolutionary complement to metapopulation,
metacommunity and experimental studies demonstrating
trade-offs between dispersal distance, establishment
ability, and life-history strategy, which may be central to
the evolution of reproductive strategies in
bryophytes.},
Doi = {10.1111/j.1469-8137.2011.03783.x},
Key = {fds230590}
}
@article{fds230587,
Author = {Heinrichs, J and Kreier, H-P and Feldberg, K and Schmidt, AR and Zhu,
R-L and Shaw, B and Shaw, AJ and Wissemann, V},
Title = {Formalizing morphologically cryptic biological entities: new
insights from DNA taxonomy, hybridization, and biogeography
in the leafy liverwort Porella platyphylla
(Jungermanniopsida, Porellales).},
Journal = {American journal of botany},
Volume = {98},
Number = {8},
Pages = {1252-1262},
Year = {2011},
Month = {August},
ISSN = {0002-9122},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000293513400015&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {<h4>Premise of the study</h4>Recognition and formalization
of morphologically cryptic species is a major challenge to
modern taxonomy. An extreme example in this regard is the
Holarctic Porella platyphylla s.l. (P. platyphylla plus P.
platyphylloidea). Earlier studies demonstrated the presence
of three isozyme groups and two molecular lineages. The
present investigation was carried out to elucidate the
molecular diversity of P. platyphylla s.l. and the
distribution of its main clades, and to evaluate evidence
for the presence of one vs. several species.<h4>Methods</h4>We
obtained chloroplast (atpB-rbcL, trnL-trnF) and nuclear
ribosomal (ITS) DNA sequences from 101 Porella accessions
(P. platyphylla s.l., P. × baueri, P. cordaeana, P.
bolanderi, plus outgroup species) to estimate the phylogeny
using parsimony and likelihood analyses. To facilitate the
adoption of Linnean nomenclature for molecular lineages, we
chose a DNA voucher as epitype.<h4>Key results</h4>Phylogenies
derived from chloroplast vs. nuclear data were congruent
except for P. platyphylla s.l., including a North American
lineage that was placed sister to P. cordaeana in the
chloroplast DNA phylogeny but sister to the Holarctic P.
platyphylla s.str. in the nuclear DNA phylogeny. European
and North American accessions of P. cordaeana and P.
platyphylla form sister clades.<h4>Conclusions</h4>The
genetic structure of P. platyphylla s.l. reflects
morphologically cryptic or near cryptic speciation into
Holarctic P. platyphylla s.str. and North American P.
platyphylloidea. The latter species is possibly an ancient
hybrid resulting from crossings of P. cordaeana and P.
platyphylla s.str. and comprises several distinct molecular
entities.},
Doi = {10.3732/ajb.1100115},
Key = {fds230587}
}
@article{fds230594,
Author = {Ricca, M and Szövényi, P and Temsch, EM and Johnson, MG and Shaw,
AJ},
Title = {Interploidal hybridization and mating patterns in the
Sphagnum subsecundum complex.},
Journal = {Molecular ecology},
Volume = {20},
Number = {15},
Pages = {3202-3218},
Year = {2011},
Month = {August},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21722226},
Abstract = {Polyploidization is thought to result in instant sympatric
speciation, but several cases of hybrid zones between one of
the parental species and its polyploid derivative have been
documented. Previous work showed that diploid Sphagnum
lescurii is an allopolyploid derived from the haploids S.
lescurii (maternal progenitor) and S. subsecundum (paternal
progenitor). Here, we report the results from analyses of a
population where allodiploid and haploid S. lescurii
co-occur and produce sporophytes. We tested (i) whether
haploids and diploids form hybrid triploid sporophytes; (ii)
how hybrid and nonhybrid sporophytes compare in fitness;
(iii) whether hybrid sporophytes form viable spores; (iv)
the ploidy of any viable gametophyte offspring from hybrid
sporophytes; (v) the relative viability of sporelings
derived from hybrid and nonhybrid sporophytes; and (vi) if
interploidal hybridization results in introgression between
the allopolyploid and its haploid progenitor. We found that
triploid hybrid sporophytes do occur and are larger than
nonhybrid sporophytes, but exhibit very low germination
percentages and produce sporelings that develop more slowly
than those from nonhybrid sporophytes. All sporophytes
attached to haploid gametophytes were triploid and were
sired by diploid males, but all sporophytes attached to
diploid gametophytes were tetraploid. This asymmetric
pattern of interploidal hybridization is related to an
absence of haploid male gametophytes in the population.
Surprisingly, all sporelings from triploid sporophytes were
triploid, yet were genetically variable, suggesting some
form of aberrant meiosis that warrants further study. There
was limited (but some) evidence of introgression between
allodiploid and haploid S. lescurii.},
Doi = {10.1111/j.1365-294x.2011.05170.x},
Key = {fds230594}
}
@article{fds230595,
Author = {Pokorny, L and Oliván, G and Shaw, AJ},
Title = {Phylogeographic patterns in two Southern Hemisphere species
of calyptrochaeta (Daltoniaceae, Bryophyta)},
Journal = {Systematic Botany},
Volume = {36},
Number = {3},
Pages = {542-553},
Publisher = {American Society of Plant Taxonomists},
Year = {2011},
Month = {July},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364411X583529},
Abstract = {To better understand biogeographic patterns in the Southern
Hemisphere, infraspecific molecular patterns were compared
in two species of the moss genus Calyptrochaeta with
contrasting distributions. One, C. apiculata, has a disjunct
distribution encompassing South America and Australasia, and
the other, C. asplenioides, occurs from South Africa
northward to Rwanda and eastward into the Indian Ocean
Islands. Nucleotide sequence data from two plastid loci
(trnL-F and trnG) and nuclear ribosomal DNA (ITS12) were
gathered from 62 samples representing the genera
Calyptrochaeta and Daltonia (the latter as an outgroup), and
subjected to phylogenetic analyses using maximum likelihood
and Bayesian inference. The phylogenetic analyses revealed
strong, geographically correlated structure within C.
asplenioides in which populations from southern Africa are
sister to those from eastern Africa, Madagascar, and the
other Indian Ocean islands. Continental plants are further
differentiated from island plants to the east. Divergence
times suggest that C. asplenioides diversified in a time
frame that does not support vicariance associated with
continental drift, but rather dispersal, to explain the
disjunct distribution of this species. Sequences of C.
apiculata disjunct between Chile and Australia are nearly
identical, which strongly suggests recent and/or ongoing
gene flow. Our dating suggests that the South
American-Australian disjunction of C. apiculata is also not
old enough to reflect vicariance associated with continental
drift. Thus, in both cases, recent long distance dispersal
best explains their distributions in the Southern
Hemisphere. © 2011 by the American Society of Plant
Taxonomists.},
Doi = {10.1600/036364411X583529},
Key = {fds230595}
}
@article{fds230592,
Author = {Cooper, ED and Shaw, AJ and Shaw, B and Henwood, MJ and Heslewood, MM and Brown, EA},
Title = {A multi-locus molecular phylogeny of the Lepidoziaceae:
laying the foundations for a stable classification.},
Journal = {Molecular phylogenetics and evolution},
Volume = {59},
Number = {2},
Pages = {489-509},
Year = {2011},
Month = {May},
ISSN = {1055-7903},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000290358800023&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {The Lepidoziaceae, with over 700 species in 30 genera, is
one of the largest leafy liverwort families. Despite
receiving considerable attention, the composition of
subfamilies and genera remains unsatisfactorily resolved. In
this study, 10 loci (one nuclear 26S, two mitochondrial nad1
and rps3, and seven chloroplast atpB, psbA, psbT-psbH, rbcL,
rps4, trnG and trnL-trnF) are used to estimate the phylogeny
of 93 species of Lepidoziaceae. These molecular data provide
strong evidence against the monophyly of three subfamilies;
Lepidozioideae, Lembidioideae and Zoopsidoideae, and seven
of the 20 sampled genera; Lepidozia, Telaranea, Kurzia,
Zoopsis, Lembidium, Paracromastigum and Chloranthelia.
Several robust clades are recognised that might provide the
basis for a revised subfamily circumscription including a
narrower circumscription of the Lepidozioideae and a more
inclusive Lembidioideae. Neogrollea notabilis is returned to
the Lepidoziaceae and Megalembidium insulanum is placed in
the Lembidioideae.},
Doi = {10.1016/j.ympev.2011.02.006},
Key = {fds230592}
}
@article{fds230583,
Author = {Stenøien, HK and Shaw, AJ and Shaw, B and Hassel, K and Gunnarsson,
U},
Title = {North American origin and recent European establishments of
the amphi-Atlantic peat moss Sphagnum angermanicum.},
Journal = {Evolution; international journal of organic
evolution},
Volume = {65},
Number = {4},
Pages = {1181-1194},
Year = {2011},
Month = {April},
ISSN = {0014-3820},
url = {http://dx.doi.org/10.1111/j.1558-5646.2010.01191.x},
Abstract = {Genetic and morphological similarity between populations
separated by large distances may be caused by frequent
long-distance dispersal or retained ancestral polymorphism.
The frequent lack of differentiation between disjunct
conspecific moss populations on different continents has
traditionally been explained by the latter model, and has
been cited as evidence that many or most moss species are
extremely ancient and slowly diverging. We have studied
intercontinental differentiation in the amphi-Atlantic peat
moss Sphagnum angermanicum using 23 microsatellite markers.
Two major genetic clusters are found, both of which occur
throughout the distributional range. Patterns of genetic
structuring and overall migration patterns suggest that the
species probably originated in North America, and seems to
have been established twice in Northern Europe during the
past 40,000 years. We conclude that similarity between S.
angermanicum populations on different continents is not the
result of ancient vicariance and subsequent stasis. Rather,
the observed pattern can be explained by multiple
long-distance dispersal over limited evolutionary time. The
genetic similarity can also partly be explained by
incomplete lineage sorting, but this appears to be caused by
the short time since separation. Our study adds to a growing
body of evidence suggesting that Sphagnum, constituting a
significant part of northern hemisphere biodiversity, may be
more evolutionary dynamic than previously
assumed.},
Doi = {10.1111/j.1558-5646.2010.01191.x},
Key = {fds230583}
}
@article{fds230591,
Author = {Laenen, B and Désamoré, A and Devos, N and Shaw, AJ and González-Mancebo, JM and Carine, MA and Vanderpoorten,
A},
Title = {Macaronesia: A source of hidden genetic diversity for
post-glacial recolonization of western Europe in the leafy
liverwort Radula lindenbergiana},
Journal = {Journal of Biogeography},
Volume = {38},
Number = {4},
Pages = {631-639},
Publisher = {WILEY},
Year = {2011},
Month = {April},
ISSN = {0305-0270},
url = {http://dx.doi.org/10.1111/j.1365-2699.2010.02440.x},
Abstract = {Aim Bryophytes exhibit apparently low rates of endemism in
Macaronesia and differ from angiosperms in their diversity
patterns by the widespread occurrence of endemics within and
among archipelagos. This paper investigates the
phylogeography of the leafy liverwort Radula lindenbergiana
to determine: (1) whether or not morphologically cryptic
diversification has occurred in Macaronesia, and (2) the
relationships between Macaronesian and continental
populations. Location Macaronesia, Europe, Africa. Methods
Eighty-four samples were collected across the species'
distribution range and sequenced at four chloroplast DNA
(cpDNA) loci (atpB-rbcL, trnG, trnL and rps4). Phylogenetic
reconstructions and Bayesian ancestral area reconstructions
were used in combination with population genetics statistics
(H, NST, FST) to describe the pattern of present genetic
diversity in R. lindenbergiana and infer its biogeographic
history. Results Patterns of genetic diversity in R.
lindenbergiana exhibit a striking westwards gradient,
wherein haplotype (0.90) and nucleotide (0.0038±0.0019)
diversity peak in Macaronesia, with a substantial endemic
component. We found 20.9% of the genetic variance between
biogeographic regions, and most pairwise FST comparisons
between regions are significantly different from zero. The
global NST (0.78) is significantly higher than the global
FST (0.20), providing evidence for the presence of
phylogeographic signal in the data. Ancestral area
reconstructions suggest that the haplotypes currently found
in western Europe share a Macaronesian common ancestor. Main
conclusions The haplotype diversification exhibited by R.
lindenbergiana in Macaronesia is comparable to that reported
for many angiosperm groups at the species level. The
apparent lack of radiation among Macaronesian bryophytes may
thus reflect the reduced morphology of bryophytes in
comparison with angiosperms. The high diversity found among
Macaronesian haplotypes, especially in Madeira and the
Canary Islands, and the significant NST/FST ratio between
Macaronesia and all the other biogeographic regions (an
indication that mutation rate exceeds dispersal rates)
suggest that Macaronesian archipelagos could have served as
a refugium during the Quaternary glaciations. Many
haplotypes currently found in Europe share a Macaronesian
common ancestor, and this further suggests that Macaronesia
might have played a key role in the back-colonization of the
continent. © 2010 Blackwell Publishing Ltd.},
Doi = {10.1111/j.1365-2699.2010.02440.x},
Key = {fds230591}
}
@article{fds304313,
Author = {Shaw, AJ and Szövényi, P and Shaw, B},
Title = {Bryophyte diversity and evolution: windows into the early
evolution of land plants.},
Journal = {American journal of botany},
Volume = {98},
Number = {3},
Pages = {352-369},
Year = {2011},
Month = {March},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21613131},
Abstract = {The "bryophytes" comprise three phyla of plants united by a
similar haploid-dominant life cycle and unbranched
sporophytes bearing one sporangium: the liverworts
(Marchantiophyta), mosses (Bryophyta), and hornworts
(Anthocerophyta). Combined, these groups include some 20000
species. As descendents of embryophytes that diverged before
tracheophytes appeared, bryophytes offer unique windows into
the early evolution of land plants. We review insights into
the evolution of plant life cycles, in particular the
elaboration of the sporophyte generation, the major lineages
within bryophyte phyla, and reproductive processes that
shape patterns of bryophyte evolution. Recent transcriptomic
work suggests extensive overlap in gene expression in
bryophyte sporophytes vs. gametophytes, but also novel
patterns in the sporophyte, supporting Bower's antithetic
hypothesis for origin of alternation of generations. Major
lineages of liverworts, mosses, and hornworts have been
resolved and general patterns of morphological evolution can
now be inferred. The life cycles of bryophytes, arguably
more similar to those of early embryophytes than are those
in any other living plant group, provide unique insights
into gametophyte mating patterns, sexual conflicts, and the
efficacy and effects of spore dispersal during early land
plant evolution.},
Doi = {10.3732/ajb.1000316},
Key = {fds304313}
}
@article{fds230585,
Author = {Karlin, EF and Andrus, RE and Boles, SB and Shaw,
AJ},
Title = {One haploid parent contributes 100% of the gene pool for a
widespread species in northwest North America.},
Journal = {Molecular ecology},
Volume = {20},
Number = {4},
Pages = {753-767},
Year = {2011},
Month = {February},
ISSN = {0962-1083},
url = {http://dx.doi.org/10.1111/j.1365-294x.2010.04982.x},
Abstract = {The monoicous peatmoss Sphagnum subnitens has a tripartite
distribution that includes disjunct population systems in
Europe (including the Azores), northwestern North America
and New Zealand. Regional genetic diversity was highest in
European S. subnitens but in northwestern North America, a
single microsatellite-based multilocus haploid genotype was
detected across 16 sites ranging from Coos County, Oregon,
to Kavalga Island in the Western Aleutians (a distance of
some 4115 km). Two multilocus haploid genotypes were
detected across 14 sites on South Island, New Zealand. The
microsatellite-based regional genetic diversity detected in
New Zealand and North American S. subnitens is the lowest
reported for any Sphagnum. The low genetic diversity
detected in both of these regions most likely resulted from
a founder event associated with vegetative propagation and
complete selfing, with one founding haploid plant in
northwest North America and two in New Zealand. Thus, one
plant appears to have contributed 100% of the gene pool for
the population systems of S. subnitens occurring in
northwest North America, and this is arguably the most
genetically uniform group of plants having a widespread
distribution yet detected. Although having a distribution
spanning 12.5° of latitude and 56° of longitude, there was
no evidence of any genetic diversification in S. subnitens
in northwest North America. No genetic structure was
detected among the three regions, and it appears that
European plants of S. subnitens provided the source for New
Zealand and northwest North American populations.},
Doi = {10.1111/j.1365-294x.2010.04982.x},
Key = {fds230585}
}
@article{fds230602,
Author = {Stenøien, HK and Shaw, AJ and Stengrundet, K and Flatberg,
KI},
Title = {The narrow endemic Norwegian peat moss Sphagnum
troendelagicum originated before the last glacial
maximum.},
Journal = {Heredity},
Volume = {106},
Number = {2},
Pages = {370-382},
Year = {2011},
Month = {February},
ISSN = {0018-067X},
url = {http://dx.doi.org/10.1038/hdy.2010.96},
Abstract = {It is commonly found that individual hybrid, polyploid
species originate recurrently and that many polyploid
species originated relatively recently. It has been
previously hypothesized that the extremely rare
allopolyploid peat moss Sphagnum troendelagicum has
originated multiple times, possibly after the last glacial
maximum in Scandinavia. This conclusion was based on low
linkage disequilibrium in anonymous genetic markers within
natural populations, in which sexual reproduction has never
been observed. Here we employ microsatellite markers and
chloroplast DNA (cpDNA)-encoded trnG sequence data to test
hypotheses concerning the origin and evolution of this
species. We find that S. tenellum is the maternal progenitor
and S. balticum is the paternal progenitor of S.
troendelagicum. Using various Bayesian approaches, we
estimate that S. troendelagicum originated before the
Holocene but not before c. 80,000 years ago (median expected
time since speciation 40 000 years before present). The
observed lack of complete linkage disequilibrium in the
genome of this species suggests cryptic sexual reproduction
and recombination. Several lines of evidence suggest
multiple origins for S. troendelagicum, but a single origin
is supported by approximate Bayesian computation analyses.
We hypothesize that S. troendelagicum originated in a
peat-dominated refugium before last glacial maximum, and
subsequently immigrated to central Norway by means of spore
flow during the last thousands of years.},
Doi = {10.1038/hdy.2010.96},
Key = {fds230602}
}
@article{fds230505,
Author = {Ye, W and Zhu, RL and Jonathan Shaw and A and Robbert Gradstein,
S},
Title = {(1999) Proposal to conserve the name Cheilolejeunea against
Omphalanthus (Lejeuneaceae)},
Journal = {Taxon},
Volume = {60},
Number = {2},
Pages = {588-589},
Year = {2011},
Month = {January},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.1002/tax.602030},
Doi = {10.1002/tax.602030},
Key = {fds230505}
}
@article{fds230551,
Author = {Karlin, EF and Boles, SB and Seppelt, RD and Terracciano, S and Shaw,
AJ},
Title = {The peat moss sphagnum cuspidatum in Australia:
Microsatellites provide a global perspective},
Journal = {Systematic Botany},
Volume = {36},
Number = {1},
Pages = {22-32},
Publisher = {American Society of Plant Taxonomists},
Year = {2011},
Month = {January},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364411X553090},
Abstract = {The distribution of Sphagnum cuspidatum has been subject to
controversy. Although historically reported from all
continents except Antarctica recent authors consider S.
cuspidatum to be endemic to Europe and eastern North
America. Microsatellites from Australian plants
morphologically identified as S. cuspidatum were compared to
microsatellites of plants morphologically identified as S.
cuspidatum collected from other regions. The species was
found to occur in Australia as well as on every continent
except Antarctica. The sample most closely related to the
Australian plants was collected in the Philippines, and
samples from Australia, the Philippines, Colombia, and
Equatorial Guinea formed a subclade within S. cuspidatum.
Microsatellites further show that S. cuspidatum is one of
the parental species of the double allopolyploid S.
falcatulum, a Holantarctic species which is reported from
Tasmania, New Zealand, and Chile. © Copyright 2011 by the
American Society of Plant Taxonomists.},
Doi = {10.1600/036364411X553090},
Key = {fds230551}
}
@article{fds230552,
Author = {Devos, N and Renner, MAM and Robbert Gradstein and S and Shaw, J and Vanderpoorten, A},
Title = {Molecular data challenge traditional subgeneric divisions in
the leafy liverwort radula},
Journal = {Taxon},
Volume = {60},
Number = {6},
Pages = {1623-1632},
Year = {2011},
Month = {January},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.1002/tax.606007},
Abstract = {With approximately 200 species, the genus Radula is one of
the most speciose genera of leafy liverworts. Although the
genus is well delimited, its subdivision into subgenera and
sections has been controversial. None of the subgeneric
subdivisions have been the subject of an explicit test of
internal consistency or monophyly based on molecular data
and a comprehensive view of evolutionary relationships
within the genus is thus still lacking. In the present paper
we propose, based on a molecular phylogeny of the genus, a
new subgeneric classification for Radula, and create three
new subgenera. While the reconstructions of ancestral
gametophytic characters allow for a morphological
description of each of the seven lineages identified in our
phylogeny, synapomorphies for these lineages are mostly
lacking. Uncertainty of morphological state reconstructions
at the deepest nodes of the phylogeny, which point to a
rapid morphological diversification of the genus in its
early history, do not allow for pinpointing when
morphological changes occurred. The classification scheme
proposed here is therefore mostly based on molecular
features.},
Doi = {10.1002/tax.606007},
Key = {fds230552}
}
@article{fds230589,
Author = {Szövényi, P and Rensing, SA and Lang, D and Wray, GA and Shaw,
AJ},
Title = {Generation-biased gene expression in a bryophyte model
system.},
Journal = {Molecular biology and evolution},
Volume = {28},
Number = {1},
Pages = {803-812},
Year = {2011},
Month = {January},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20855429},
Abstract = {The evolution of land plants is tightly linked to the
evolution of the alternation of generations. Because
alternating ploidal generations share their genomes,
investigating generation-biased gene expression can give
insight into the evolution of life cycles in land plants.
Toward this end, we describe gene expression differences
associated with the alternation of isogenic sporophyte and
gametophyte generations in bryophytes, extant
representatives of early diverging land plants, using a moss
model system (Funaria hygrometrica). We found that
differentiation in gene expression between the sporophyte
and gametophyte generations is weaker in the bryophyte model
system than in Arabidopsis thaliana. This is in line with
the basal phylogenetic position of bryophytes and with the
origin of alternating generations from a purely haplontic
life cycle. Comparative analysis of F. hygrometrica and A.
thaliana gene expression data shows that there is limited
conservation of generation-biased gene expression across
land plants. However, genes showing shared sporophyte-biased
expression in both F. hygrometrica and A. thaliana appear to
be enriched for biological pathways representing critical
molecular adaptations to terrestrial life. Comparative
analyses of the expression of F. hygrometrica and A.
thaliana regulatory genes suggest that conserved regulatory
networks may be involved in growth and reproductive tissue
development of the angiosperm and bryophyte sporophyte
generations despite their morphological divergence. This
study represents the first attempt to describe
generation-biased gene expression in a plant with a
well-developed sporophyte and gametophyte generations, and
as such it lays the foundation for future targeted research
on the developmental mechanisms underlying evolutionary
diversification of plant sporophytes.},
Doi = {10.1093/molbev/msq254},
Key = {fds230589}
}
@article{fds230584,
Author = {Fuselier, LC and Shaw, B and Engel, JJ and von Konrat, M and Costa, DP and Devos, N and Shaw, AJ},
Title = {The status and phylogeography of the liverwort genus
Apometzgeria Kuwah. (Metzgeriaceae)},
Journal = {Bryologist},
Volume = {114},
Number = {1},
Pages = {92-101},
Publisher = {American Bryological and Lichenological Society},
Year = {2011},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-114.1.92},
Abstract = {Three species have been formerly segregated from Metzgeria
in the genus Apometzgeria. One of the species, A.
frontipilis, is endemic to South America but the second, A.
pubescens, is currently understood as having a bipolar range
with populations across the Holarctic and in southern South
America. The third species, A. longifrondis, was described
from China (and is not included in this study). Species of
bryophytes that range across continents and have little or
no morphological variation among populations may
nevertheless harbor morphologically cryptic genetic
lineages. We used nuclear and plastid sequence data to
examine the phylogenetic relationship between Apometzgeria
and Metzgeria, and phylogeographic patterns in taxa assigned
to Apometzgeria. Two species often assigned to Apometzgeria
are phylogenetically embedded within Metzgeria in two
separate clades, one comprising all Holarctic A. pubescens
and a second with A. pubescens from South America and all
accessions of A. frontipilis. Phylogenetic and haplotype
analyses reveal a lack of phylogeographic structure among A.
pubescens plants from throughout its Holarctic distribution.
However, A. pubescens in South America is more closely
related to A. frontipilis and species of Metzgeria from
South America than to any A. pubescens from the Northern
Hemisphere. Thus, A. pubescens is Holarctic in distribution
and morphologically similar plants form a divergent lineage
in South America. Our results do not support Apometzgeria as
a separate genus in the Metzgeriaceae. © 2011 by the
American Bryological and Lichenological Society,
Inc.},
Doi = {10.1639/0007-2745-114.1.92},
Key = {fds230584}
}
@article{fds230593,
Author = {Shaw, AJ and Szövényi, P and Shaw, B},
Title = {Bryophyte diversity and evolution: windows into the early
evolution of land plants},
Journal = {American Journal of Botany},
Volume = {98},
Number = {3},
Pages = {1-18},
Year = {2011},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21613131},
Abstract = {The "bryophytes" comprise three phyla of plants united by a
similar haploid-dominant life cycle and unbranched
sporophytes bearing one sporangium: the liverworts
(Marchantiophyta), mosses (Bryophyta), and hornworts
(Anthocerophyta). Combined, these groups include some 20000
species. As descendents of embryophytes that diverged before
tracheophytes appeared, bryophytes offer unique windows into
the early evolution of land plants. We review insights into
the evolution of plant life cycles, in particular the
elaboration of the sporophyte generation, the major lineages
within bryophyte phyla, and reproductive processes that
shape patterns of bryophyte evolution. Recent transcriptomic
work suggests extensive overlap in gene expression in
bryophyte sporophytes vs. gametophytes, but also novel
patterns in the sporophyte, supporting Bower's antithetic
hypothesis for origin of alternation of generations. Major
lineages of liverworts, mosses, and hornworts have been
resolved and general patterns of morphological evolution can
now be inferred. The life cycles of bryophytes, arguably
more similar to those of early embryophytes than are those
in any other living plant group, provide unique insights
into gametophyte mating patterns, sexual conflicts, and the
efficacy and effects of spore dispersal during early land
plant evolution.},
Doi = {10.3732/ajb.1000316},
Key = {fds230593}
}
@article{fds230550,
Author = {Bombosch, A and Wieneke, A and Busch, A and Yonas, R and Hentschel, J and Kreier, H-P and Shaw, B and Shaw, AJ and Heinrichs,
J},
Title = {Narrow species concepts in the Frullania
dilatata-appalachiana-eboracensis complex (Porellales,
Jungermanniopsida): evidence from nuclear and chloroplast
DNA markers},
Journal = {Plant systematics and evolution = Entwicklungsgeschichte und
Systematik der Pflanzen},
Volume = {290},
Number = {1-4},
Pages = {151-158},
Publisher = {Springer Nature},
Year = {2010},
Month = {December},
ISSN = {0378-2697},
url = {http://dx.doi.org/10.1007/s00606-010-0357-3},
Abstract = {We investigated the phylogeny of a Holarctic-Asian group of
Frullania species, the Frullania dilatata-F. appalachiana-F.
eboracensis complex, using multiple accessions of
morphologically circumscribed taxa and three molecular
markers (nrITS region, cp DNA trnL-F and atpB-rbcL regions).
Maximum parsimony and likelihood analyses indicated
monophyly of morphologically defined taxa. Our phylogenies
support a species rather than a subspecies concept within
the complex, with four species in North America (F.
appalachiana, F. eboracensis, F. parvistipula and F.
virginica), and two species in Europe (F. dilatata and F.
parvistipula). Accessions of F. dilatata from Southeast
Europe and Asia are separated from other European
accessions, indicating a former disjunct range of the
species.},
Doi = {10.1007/s00606-010-0357-3},
Key = {fds230550}
}
@article{fds230597,
Author = {Kreier, H-P and Feldberg, K and Mahr, F and Bombosch, A and Schmidt, AR and Zhu, R-L and von Konrat, M and Shaw, B and Shaw, AJ and Heinrichs,
J},
Title = {Phylogeny of the leafy liverwort Ptilidium: cryptic
speciation and shared haplotypes between the Northern and
Southern Hemispheres.},
Journal = {Molecular phylogenetics and evolution},
Volume = {57},
Number = {3},
Pages = {1260-1267},
Year = {2010},
Month = {December},
ISSN = {1055-7903},
url = {http://dx.doi.org/10.1016/j.ympev.2010.10.002},
Abstract = {The small, phylogenetically isolated liverwort genus
Ptilidium has been regarded as of cool-Gondwanic origin with
the bipolar, terrestrial Ptilidium ciliare giving rise to
the Northern Hemisphere epiphytes Ptilidium pulcherrimum and
Ptilidium californicum. This hypothesis is examined using a
dataset including three chloroplast DNA regions from 134
Ptilidium accessions and one accession each of its closest
relatives Trichocoleopsis and Neotrichocolea. Maximum
likelihood and parsimony analyses point to a close
relationship between P. ciliare and P. pulcherrimum, whereas
P. californicum is placed sister to the remainder of the
genus, separated by a long branch. Haplotype analysis and
our phylogeny indicate the presence of Southern Hemisphere
haplotypes of P. ciliare in the Northern Hemisphere, and
shared haplotypes of P. ciliare and P. pulcherrimum between
Europe and North America. Based on our findings, we reject
the Gondwana-scenario and propose recent long distance
dispersal as an explanation for the bipolar disjunct range.
Ptilidium ciliare is resolved as paraphyletic with P.
pulcherrimum nested within it. An isolated Ptilidium lineage
with the morphology of P. ciliare from the Himalaya region
likely represents a hitherto unrecognized cryptic species.
Ptilidium pulcherrimum splits into a Japanese clade and a
clade with accessions from Europe and North
America.},
Doi = {10.1016/j.ympev.2010.10.002},
Key = {fds230597}
}
@article{fds230549,
Author = {Shaw, AJ},
Title = {Erratum to Newly resolved relationships in an early land
plant lineage: Bryophyta class Sphagnopsida (peat
mosses)(American Journal of Botany, (2010), 97, 9,
(1511-1531))},
Journal = {American Journal of Botany},
Volume = {97},
Number = {10},
Pages = {105},
Year = {2010},
Month = {October},
ISSN = {0002-9122},
Key = {fds230549}
}
@article{fds230598,
Author = {Ramaiya, M and Johnson, MG and Shaw, B and Heinrichs, J and Hentschel,
J and von Konrat, M and Davison, PG and Shaw, AJ},
Title = {Morphologically cryptic biological species within the
liverwort Frullania asagrayana.},
Journal = {American journal of botany},
Volume = {97},
Number = {10},
Pages = {1707-1718},
Year = {2010},
Month = {October},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21616804},
Abstract = {<h4>Unlabelled</h4><h4>Premise of the study</h4>The
Frullania tamarisci complex includes eight Holarctic
liverwort species. One of these, F. asagrayana, is
distributed broadly throughout eastern North America from
Canada to the Gulf Coast. Preliminary genetic data suggested
that the species includes two groups of populations. This
study was designed to test whether the two groups are
reproductively isolated biological species.
•<h4>Methods</h4>Eighty-eight samples from across the
range of F. asagrayana, plus 73 samples from one population,
were genotyped for 13 microsatellite loci. Sequences for two
plastid loci and nrITS were obtained from 13 accessions.
Genetic data were analyzed using coalescent models and
Bayesian inference. •<h4>Key results</h4>Frullania
asagrayana is sequence-invariant at the two plastid loci and
ITS2, but two clear groups were resolved by microsatellites.
The two groups are largely reproductively isolated, but
there is a low level of gene flow from the southern to the
northern group. No gene flow was detected in the other
direction. A local population was heterogeneous but
displayed strong genetic structure. •<h4>Conclusions</h4>The
genetic structure of F. asagrayana in eastern North America
reflects morphologically cryptic differentiation between
reproductively isolated groups of populations, near-panmixis
within groups, and clonal propagation at local scales.
Reproductive isolation between groups that are invariant at
the level of nucleotide sequences shows that caution must be
exercised in making taxonomic and evolutionary inferences
from reciprocal monophyly (or lack thereof) between putative
species.},
Doi = {10.3732/ajb.1000171},
Key = {fds230598}
}
@article{fds230599,
Author = {Vanderpoorten, A and Shaw, AJ},
Title = {The application of molecular data to the phylogenetic
delimitation of species in bryophytes: A note of
caution},
Journal = {PHYTOTAXA},
Volume = {9},
Pages = {229-237},
Publisher = {MAGNOLIA PRESS},
Year = {2010},
Month = {September},
ISSN = {1179-3155},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000294423600010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds230599}
}
@article{fds230600,
Author = {Cox, CJ and Goffinet, B and Wickett, NJ and Boles, SB and Shaw,
AJ},
Title = {Moss diversity: A molecular phylogenetic analysis of
genera},
Journal = {PHYTOTAXA},
Volume = {9},
Pages = {175-195},
Publisher = {MAGNOLIA PRESS},
Year = {2010},
Month = {September},
ISSN = {1179-3155},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000294423600008&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds230600}
}
@article{fds339387,
Author = {Von Konrat and M and Shaw, AJ and Renzaglia, KS},
Title = {A special issue of Phytotaxa dedicated to Bryophytes: The
closest living relatives of early land plants},
Journal = {PHYTOTAXA},
Volume = {9},
Pages = {5-10},
Publisher = {MAGNOLIA PRESS},
Year = {2010},
Month = {September},
Key = {fds339387}
}
@article{fds230601,
Author = {Shaw, AJ and Cox, CJ and Buck, WR and Devos, N and Buchanan, AM and Cave,
L and Seppelt, R and Shaw, B and Larraín, J and Andrus, R and Greilhuber,
J and Temsch, EM},
Title = {Newly resolved relationships in an early land plant lineage:
Bryophyta class Sphagnopsida (peat mosses).},
Journal = {American journal of botany},
Volume = {97},
Number = {9},
Pages = {1511-1531},
Year = {2010},
Month = {September},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21616905},
Abstract = {<h4>Unlabelled</h4><h4>Premise of the study</h4>The
Sphagnopsida, an early-diverging lineage of mosses (phylum
Bryophyta), are morphologically and ecologically unique and
have profound impacts on global climate. The Sphagnopsida
are currently classified in two genera, Sphagnum (peat
mosses) with some 350-500 species and Ambuchanania with one
species. An analysis of phylogenetic relationships among
species and genera in the Sphagnopsida were conducted to
resolve major lineages and relationships among species
within the Sphagnopsida. •<h4>Methods</h4>Phylogenetic
analyses of nucleotide sequences from the nuclear, plastid,
and mitochondrial genomes (11 704 nucleotides total) were
conducted and analyzed using maximum likelihood and Bayesian
inference employing seven different substitution models of
varying complexity. •<h4>Key results</h4>Phylogenetic
analyses resolved three lineages within the Sphagnopsida:
(1) Sphagnum sericeum, (2) S. inretortum plus Ambuchanania
leucobryoides, and (3) all remaining species of Sphagnum.
Sister group relationships among these three clades could
not be resolved, but the phylogenetic results indicate that
the highly divergent morphology of A. leucobryoides is
derived within the Sphagnopsida rather than plesiomorphic. A
new classification is proposed for class Sphagnopsida, with
one order (Sphagnales), three families, and four genera.
•<h4>Conclusions</h4>The Sphagnopsida are an old lineage
within the phylum Bryophyta, but the extant species of
Sphagnum represent a relatively recent radiation. It is
likely that additional species critical to understanding the
evolution of peat mosses await discovery, especially in the
southern hemisphere.},
Doi = {10.3732/ajb.1000055},
Key = {fds230601}
}
@article{fds230604,
Author = {Heinrichs, J and Hentschel, J and Bombosch, A and Fiebig, A and Reise,
J and Edelmann, M and Kreier, H-P and Schäfer-Verwimp, A and Caspari,
S and Schmidt, AR and Zhu, R-L and von Konrat, M and Shaw, B and Shaw,
AJ},
Title = {One species or at least eight? Delimitation and distribution
of Frullania tamarisci (L.) Dumort. s. l.
(Jungermanniopsida, Porellales) inferred from nuclear and
chloroplast DNA markers.},
Journal = {Molecular phylogenetics and evolution},
Volume = {56},
Number = {3},
Pages = {1105-1114},
Year = {2010},
Month = {September},
ISSN = {1055-7903},
url = {http://dx.doi.org/10.1016/j.ympev.2010.05.004},
Abstract = {Frullania tamarisci is usually regarded as a polymorphic,
holarctic-Asian liverwort species with four allopatric
subspecies [subsp. asagrayana, moniliata, nisquallensis and
tamarisci]. This hypothesis is examined using a dataset
including sequences of the nuclear internal transcribed
spacer region and the plastid trnL-trnF and atpB-rbcL
regions of 88 accessions of F. tamarisci and putatively
related taxa. Maximum parsimony and maximum likelihood
analyses indicate the presence of at least eight main
lineages within F. tamarisci s. l. The long branches leading
to the tip nodes of the different F. tamarisci s. l. clades
and their partly sympatric distribution reinforce species
rank. Within F. tamarisci s. l. we recognize the Asian F.
moniliata, the western North American F. californica and F.
nisquallensis, the eastern North American F. asagrayana, the
eastern North American-European F. tamarisci s. str., the
Macaronesian F. sergiae, and two newly identified European
lineages assigned to as F. calcarifera and F. tamarisci var.
azorica. The considerable sequence differences are not
reflected in conspicuous morphological disparities,
rendering F. tamarisci s. l. the most explicit example of a
complex of semi-cryptic and cryptic liverwort species. The
temperate Frullania clades of this study likely went through
recent extinction and expansion processes as indicated by
the bottleneck pattern of genetic diversity. Species from
tropical regions or regions with an Atlantic climate usually
contain several geographical lineages. Our findings support
frequent short-distance migration, rare successful
long-distance dispersal events, extinction and
recolonization as an explanation for the range formation in
these Frullania species.},
Doi = {10.1016/j.ympev.2010.05.004},
Key = {fds230604}
}
@article{fds230605,
Author = {Shaw, AJ and Devos, N and Cox, CJ and Boles, SB and Shaw, B and Buchanan,
AM and Cave, L and Seppelt, R},
Title = {Peatmoss (Sphagnum) diversification associated with Miocene
Northern Hemisphere climatic cooling?},
Journal = {Molecular phylogenetics and evolution},
Volume = {55},
Number = {3},
Pages = {1139-1145},
Year = {2010},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20102745},
Abstract = {Global climate changes sometimes spark biological radiations
that can feed back to effect significant ecological impacts.
Northern Hemisphere peatlands dominated by living and dead
peatmosses (Sphagnum) harbor almost 30% of the global soil
carbon pool and have functioned as a net carbon sink
throughout the Holocene, and probably since the late
Tertiary. Before that time, northern latitudes were
dominated by tropical and temperate plant groups and
ecosystems. Phylogenetic analyses of mosses (phylum
Bryophyta) based on nucleotide sequences from the plastid,
mitochondrial, and nuclear genomes indicate that most
species of Sphagnum are of recent origin (ca. <20 Ma).
Sphagnum species are not only well-adapted to boreal
peatlands, they create the conditions that promote
development of peatlands. The recent radiation that gave
rise to extant diversity of peatmosses is temporally
associated with Miocene climatic cooling in the Northern
Hemisphere. The evolution of Sphagnum has had profound
influences on global biogeochemistry because of the unique
biochemical, physiological, and morphological features of
these plants, both while alive and after
death.},
Doi = {10.1016/j.ympev.2010.01.020},
Key = {fds230605}
}
@article{fds230608,
Author = {Feldberg, K and Váňa, J and Long, DG and Shaw, AJ and Hentschel, J and Heinrichs, J},
Title = {A phylogeny of Adelanthaceae (Jungermanniales,
Marchantiophyta) based on nuclear and chloroplast DNA
markers, with comments on classification, cryptic speciation
and biogeography.},
Journal = {Molecular phylogenetics and evolution},
Volume = {55},
Number = {1},
Pages = {293-304},
Year = {2010},
Month = {April},
ISSN = {1055-7903},
url = {http://dx.doi.org/10.1016/j.ympev.2009.11.009},
Abstract = {Adelanthaceae (including Jamesoniellaceae) represent a major
lineage of jungermannialean liverworts that is characterized
by ventral-intercalary, often flagelliform branches,
succubous leaves, ovoid to cylindrical, plicate perianths
with a contracted mouth, often connate bracts and
bracteoles, and 4-7 stratose capsule walls. Here we present
the first comprehensive molecular phylogeny of Adelanthaceae
using five markers (rbcL, psbA, trnL-trnF region, atpB-rbcL
spacer, nrITS1-5.8S-ITS2) and 108 accessions from throughout
the geographic range of the family. The molecular data
support the separation of subfamilies Adelanthoideae and
Jamesonielloideae. The Adelanthoideae include the genera
Adelanthus, Pseudomarsupidium and Wettsteinia. The
Jamesonielloideae include representatives of the genera
Anomacaulis, Cryptochila, Cuspidatula, Jamesoniella, and
Syzygiella in five main clades. The monophyly of taxa in
current morphological classification schemes of
Jamesonielloideae is not supported by the molecular data.
Based on the outcome of the molecular phylogenetic analyses
we propose to include Anomacaulis and Jamesoniella kirkii in
Cuspidatula, and to place Cryptochila, Roivainenia, and
Jamesoniella in the synonymy of Syzygiella. Molecular data
support intercontinental ranges for several species and a
range formation of Adelanthaceae by frequent short-distance
dispersal, rare long-distance dispersal, extinction, and
diversification. Disjunct distribution patterns within the
Adelanthaceae cannot be explained by Gondwanan
vicariance.},
Doi = {10.1016/j.ympev.2009.11.009},
Key = {fds230608}
}
@article{fds304319,
Author = {Karlin, EF and Giusti, MM and Lake, RA and Boles, SB and Shaw,
AJ},
Title = {Microsatellite analysis of Sphagnum centrale, S. henryense,
and S. palustre (Sphagnaceae)},
Journal = {Bryologist},
Volume = {113},
Number = {1},
Pages = {90-98},
Publisher = {American Bryological and Lichenological Society},
Year = {2010},
Month = {March},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-113.1.90},
Abstract = {This study provides the first report that Sphagnum centrale
and S. henryense are allopolyploids. Microsatellites show S.
henryense and S. palustre to be conspecific. In contrast,
they show S. centrale to be genetically distinct from S.
palustre s.l. In addition to differences in alleles and
allele frequencies, the patterns of observed heterozygosity
across 17 microsatellite markers also differed between S.
centrale and S. palustre s.l. This represents a dimension of
genetic differentiation that is not detected or addressed by
statistical approaches such as AMOVA or Principal
Coordinates Analysis. The patterns of microsatellites
further provide preliminary evidence suggesting that S.
centrale and S. palustre have one parental taxon in common
and differ in the second. © 2010 by The American
Bryological and Lichenological Society, Inc.},
Doi = {10.1639/0007-2745-113.1.90},
Key = {fds304319}
}
@article{fds304320,
Author = {Karlin, EF and Gardner, GP and Lukshis, K and Boles, S and Shaw,
AJ},
Title = {Allopolyploidy in Sphagnum mendocinum and S. papillosum
(Sphagnaceae)},
Journal = {Bryologist},
Volume = {113},
Number = {1},
Pages = {114-119},
Publisher = {American Bryological and Lichenological Society},
Year = {2010},
Month = {March},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-113.1.114},
Abstract = {This study provides the first report that Sphagnum
mendocinum (Sphagnum section Cuspidata) and S. papillosum
(Sphagnum section Sphagnum) are allopolyploids. Sphagnum
mendocinum is an intersectional allopolyploid, with parental
species from Sphagnum sections Cuspidata and Subsecunda. It
is the third intersectional alloploid species reported for
Sphagnum. The gametophytically allodiploid cytotype of S.
papillosum was detected in Europe, North America, and Japan.
It appears to be the predominant, if not the only, cytotype
for this species. Our results may warrant re-examination of
the report of a haploid (n = x) cytotype for S. papillosum.
© 2010 by The American Bryological and Lichenological
Society, Inc.},
Doi = {10.1639/0007-2745-113.1.114},
Key = {fds304320}
}
@article{fds230508,
Author = {Renner, MAM and Devos, N and Jonathan Shaw and A},
Title = {Radula splendida sp. nov. (Radulaceae: Marchantiophyta), a
polymorphic species from New Zealand},
Journal = {Nova Hedwigia},
Volume = {90},
Number = {1-2},
Pages = {105-122},
Publisher = {Schweizerbart},
Year = {2010},
Month = {February},
ISSN = {0029-5035},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000275843900005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {We describe Radula splendida, a new species endemic to New
Zealand. Radula splendida is most similar to Radula
physoloba in size, colour, and habitat, but differs in
producing microphyllous and amentulose branches, reflexed
lobule exterior margin, lobules as wide as long with a
deeply arched keel, and by amentulose branches dislocating
as cladia. Radula splendida is the first Radula species
reported to produce cladia. This species is surprising in
two ways, firstly individual propensity to produce cladia
differs, and secondly the propensity to produce cladia is
correlated with differences in lobule shape. This
correlation is confirmed by geometric morphometric analysis
of sexually and asexually reproducing plants within one
North Island population where individuals differing in their
tendency to asexual reproduction were observed. We present a
key to New Zealand species of Radula with amentulose or
microphyllous axes, which leads us to reinstate Radula
multiamentula for Australasia. © 2010 J. Cramer in der
Gebrüder Borntraeger Verlagsbuchhandlung.},
Doi = {10.1127/0029-5035/2010/0090-0105},
Key = {fds230508}
}
@article{fds230603,
Author = {Hutsemekers, V and Hardy, OJ and Mardulyn, P and Shaw, AJ and Vanderpoorten, A},
Title = {Macroecological patterns of genetic structure and diversity
in the aquatic moss Platyhypnidium riparioides.},
Journal = {The New phytologist},
Volume = {185},
Number = {3},
Pages = {852-864},
Year = {2010},
Month = {February},
ISSN = {0028-646X},
url = {http://dx.doi.org/10.1111/j.1469-8137.2009.03094.x},
Abstract = {Genetic diversity and structure are described in the aquatic
moss Platyhypnidium riparioides to assess its dispersal
ability at a regional scale and to determine whether
patterns of genetic differentiation correlate with
environmental variation. Variation at six nuclear
microsatellite loci from 50 populations in southern Belgium
was investigated through Mantel tests, partial Mantel tests
and spatial analysis of molecular variance. Overall patterns
of genotypic variation showed strong differentiation among
populations at a regional scale (F(ST) = 0.57). The high
values of F(IS) observed within populations at both the
ramet and genet levels, and the higher proportion of ramets
with the same genotype than expected by chance, all point to
a strongly clonal or selfing mating system. A genetic
discontinuity was identified between northern and southern
groups of populations. Within each group, F(ST) and
geographical distances were significantly correlated.
Partial Mantel tests suggest that genetic and ecological
distances are significantly correlated in the southern
group. The results point to strong dispersal limitation at
the landscape scale and suggest that the southern and
northern groups experienced different histories. Within the
former, the correlation between genetic and ecological
variation is suggestive of reproductive isolation among
ecotypes.},
Doi = {10.1111/j.1469-8137.2009.03094.x},
Key = {fds230603}
}
@article{fds230606,
Author = {Yu, J and Devos, N and Majestyk, P and Jonathan Shaw,
A},
Title = {Intercontinentally disjunct species are derived rather than
relictual in the moss genus Daltonia (Bryophyta)},
Journal = {Taxon},
Volume = {59},
Number = {2},
Pages = {459-465},
Year = {2010},
Month = {January},
ISSN = {0040-0262},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000276617400011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {We present a phylogenetic analysis of the moss genus
Daltonia based on nucleotide sequences from three plastid
loci (psbT, trnL, trnG) plus the nuclear ribosomal RNA gene
(ITS), including 9 of 21 species in this genus. Of the nine
species, seven are well-supported as monophyletic, even when
multiple accessions came from different continents. Early
diverging species in the genus have relatively restricted
ranges that are limited to a single continent, whereas most
or all later-diverging species have broad intercontinental
distributions. The observation that intercontinental
distributions are repeated in multiple monophyletic species
suggests that a key innovation underlying enhanced abilities
for long dispersal evolved within Daltonia, and that this
potential was inherited among derived species from their
common ancestor. The nature of this (these) innovation(s)
remains ob- scure, but may be related to both relaxation of
ecological limitations on establishment, and to effective
dispersal of spores per se.},
Doi = {10.1002/tax.592011},
Key = {fds230606}
}
@article{fds230609,
Author = {Ricca, M and Shaw, AJ},
Title = {Allopolyploidy and homoploid hybridization in the Sphagnum
subsecundum complex (Sphagnaceae: Bryophyta)},
Journal = {Biological Journal of the Linnean Society},
Volume = {99},
Number = {1},
Pages = {135-151},
Publisher = {Oxford University Press (OUP)},
Year = {2010},
Month = {January},
ISSN = {0024-4066},
url = {http://dx.doi.org/10.1111/j.1095-8312.2009.01340.x},
Abstract = {Several complexes of species in Sphagnum (peat mosses)
originated through hybridization and allopolyploidy,
suggesting that these processes have played a major
evolutionary role in this genus. The Sphagnum subsecundum
complex includes gametophytically haploid and diploid
species in North America. Analyses of 12 microsatellite loci
and sequences from two plastid DNA markers show that the
evolutionary history of this group is substantially more
complex than previously thought. Two taxonomic species,
Sphagnum lescurii and Sphagnum inundatum, include both
haploid and diploid populations. Within each ploidal level,
S. lescurii and S. inundatum are not genetically
differentiated. The diploid taxa show patterns of fixed
heterozygosity for the microsatellite markers, consistent
with an allopolyploid origin. Diploid S. lescurii is an
allopolyploid between haploid S. lescurii and (haploid) S.
subsecundum. Sphagnum carolinianum is an allopolyploid
between haploid S. lescurii and an unknown parent. We
detected homoploid hybridization between the haploids
Sphagnum contortum and S. subsecundum. Finally, we report
three samples of diploid Sphagnum platyphyllum (otherwise
haploid) that have an allopolyploid origin involving
north-eastern haploid S. platyphyllum and an unidentified
taxon. © 2010 The Linnean Society of London.},
Doi = {10.1111/j.1095-8312.2009.01340.x},
Key = {fds230609}
}
@article{fds183571,
Author = {Fuselier, L. and P. G. Davison and M. Clements and B. Shaw and N. Devos and J. Heinrichs and J. Hentschel and M. Sabovljevic and P. Szövényi and S. Schuette and W. Hofbauer. and A. J. Shaw},
Title = {Phylogeographic analyses reveal distinct lineages of
Metzgeria furcata (L.) Dumort. and M. conjugata Lindb.
(Metzgeriaceae) in Europe and North America},
Journal = {Biological Journal of the Linnaean Society},
Volume = {98},
Pages = {745-756},
Year = {2010},
Key = {fds183571}
}
@article{fds230596,
Author = {Szövényi, P and Rensing, SA and Lang, D and Wray, GA and Shaw,
AJ},
Title = {Generation-biased gene expression in a bryophyte model
system: implications for the evolution of the embryophyte
sporophyte},
Journal = {Molecular Biology and Evolution},
Volume = {doi: 10.1093/molbev/msq254},
Year = {2010},
Key = {fds230596}
}
@article{fds230607,
Author = {Karlin, EF and Gardner, GP and Lukshis, K and Boles, SB and Shaw,
AJ},
Title = {Allopolyploidy in Sphagnum mendocinum and S. papillosum
(Sphagnaceae)},
Journal = {Bryologis},
Volume = {113},
Number = {1},
Pages = {90-98},
Year = {2010},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-113.1.114},
Abstract = {This study provides the first report that Sphagnum
mendocinum (Sphagnum section Cuspidata) and S. papillosum
(Sphagnum section Sphagnum) are allopolyploids. Sphagnum
mendocinum is an intersectional allopolyploid, with parental
species from Sphagnum sections Cuspidata and Subsecunda. It
is the third intersectional alloploid species reported for
Sphagnum. The gametophytically allodiploid cytotype of S.
papillosum was detected in Europe, North America, and Japan.
It appears to be the predominant, if not the only, cytotype
for this species. Our results may warrant re-examination of
the report of a haploid (n = x) cytotype for S. papillosum.
© 2010 by The American Bryological and Lichenological
Society, Inc.},
Doi = {10.1639/0007-2745-113.1.114},
Key = {fds230607}
}
@article{fds230610,
Author = {FUSELIER, LINDA and Davison, PG and CLEMENTS, MARIAH and Shaw, B and DEVOS, NICOLAS and Heinrichs, J and HENTSCHEL, J and SABOVLJEVIC,
MARKO and SZÖVÉNYI, P and SCHUETTE, SCOTT and Hofbauer, W and SHAW,
AJ},
Title = {Phylogeographic analyses reveal distinct lineages of the
liverworts Metzgeria furcata (L.) Dumort. and Metzgeria
conjugata Lindb. (Metzgeriaceae) in Europe and North
America},
Journal = {Biological journal of the Linnean Society. Linnean Society
of London},
Volume = {98},
Number = {4},
Pages = {745-756},
Publisher = {Oxford University Press (OUP)},
Year = {2009},
Month = {December},
ISSN = {0024-4066},
url = {http://dx.doi.org/10.1111/j.1095-8312.2009.01319.x},
Abstract = {Seed plant genera often exhibit intercontinental
disjunctions where different species are found on different
continents. Many morphologically circumscribed bryophyte
species exhibit similar disjunctions. We used nucleotide
sequences from the plastid and nuclear genomes to test
hypotheses of phylogeography within representatives of the
genus Metzgeria: Metzgeria furcata, Metzgeria conjugata, and
Metzgeria myriopoda. The first two species have sexual and
asexual populations, exhibit disjunctions between North
America and Europe, and have been split into separate
species, numerous subspecies or varieties. The third species
occurs in eastern North America but is not reported from
Europe. Phylogenetic analyses resolved three distinct
lineages within the morphologically defined species, M.
furcata: one in North America, and two in Europe. Similarly,
three morphologically cryptic clades of M. conjugata were
resolved by the molecular data: northern North America,
Europe, and south-eastern North America. For both species,
molecular divergence among taxa occurred in the absence of
morphological change. In the case of M. myriopoda, all
plants from eastern North America were both morphologically
uniform and genetically homogeneous (although not
identical). The present study provides significant insight
into a plant group with complex taxonomy, and indicates that
these liverwort taxa with wide distributions, extreme sex
ratios, and continental disjunctions harbor cryptic
lineages.},
Doi = {10.1111/j.1095-8312.2009.01319.x},
Key = {fds230610}
}
@article{fds339388,
Author = {Goffinet, B and Buck, WR and Shaw, AJ},
Title = {Addenda to the classification of mosses. I. Andreaeophytina
stat. nov. and Andreaeobryophytina stat.
nov},
Journal = {The Bryologist},
Volume = {112},
Number = {4},
Pages = {856-857},
Publisher = {American Bryological and Lichenological Society},
Year = {2009},
Month = {December},
url = {http://dx.doi.org/10.1639/0007-2745-112.4.856},
Doi = {10.1639/0007-2745-112.4.856},
Key = {fds339388}
}
@article{fds230611,
Author = {Szövényi, P and Ricca, M and Shaw, AJ},
Title = {Multiple paternity and sporophytic inbreeding depression in
a dioicous moss species.},
Journal = {Heredity},
Volume = {103},
Number = {5},
Pages = {394-403},
Year = {2009},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19623211},
Abstract = {Multiple paternity (polyandry) frequently occurs in
flowering plants and animals and is assumed to have an
important function in the evolution of reproductive traits.
Polyandry in bryophytes may occur among multiple sporophytes
of a female gametophyte; however, its occurrence and extent
is unknown. In this study we investigate the occurrence and
extent of multiple paternity, spatial genetic structure, and
sporophytic inbreeding depression in natural populations of
a dioicous bryophyte species, Sphagnum lescurii, using
microsatellite markers. Multiple paternity is prevalent
among sporophytes of a female gametophyte and male genotypes
exhibit significant skew in paternity. Despite significant
spatial genetic structure in the population, suggesting
frequent inbreeding, the number of inbred and outbred
sporophytes was balanced, resulting in an average fixation
coefficient and population level selfing rate of zero. In
line with the prediction of sporophytic inbreeding
depression sporophyte size was significantly correlated with
the level of heterozygosity. Furthermore, female
gametophytes preferentially supported sporophytes with
higher heterozygosity. These results indicate that polyandry
provides the opportunity for postfertilization selection in
bryophytes having short fertilization distances and
spatially structured populations facilitating inbreeding.
Preferential maternal support of the more heterozygous
sporophytes suggests active inbreeding avoidance that may
have significant implications for mating system evolution in
bryophytes.},
Doi = {10.1038/hdy.2009.82},
Key = {fds230611}
}
@article{fds230613,
Author = {Szövényi, P and Hock, Z and Korpelainen, H and Shaw,
AJ},
Title = {Spatial pattern of nucleotide polymorphism indicates
molecular adaptation in the bryophyte Sphagnum
fimbriatum.},
Journal = {Molecular phylogenetics and evolution},
Volume = {53},
Number = {1},
Pages = {277-286},
Year = {2009},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19539771},
Abstract = {In organisms with haploid-dominant life cycles, natural
selection is expected to be especially effective because
genetic variation is exposed directly to selection. However,
in spore-producing plants with high dispersal abilities,
among-population migration may counteract local adaptation
by continuously redistributing genetic variability. In this
study, we tested for adaptation at the molecular level by
comparing nucleotide polymorphism in two genes (GapC and
Rpb2) in 10 European populations of the peatmoss species,
Sphagnum fimbriatum with variability at nine microsatellite
loci assumed to be selectively neutral. In line with
previous results, the GapC and Rpb2 genes showed strikingly
different patterns of nucleotide polymorphism. Neutrality
tests and comparison of population differentiation based on
the GapC and Rpb2 genes with neutrally evolving
microsatellites using coalescent simulations supported
non-neutral evolution in GapC, but neutral evolution in the
Rpb2 gene. These observations and the positions of the
replacement mutations in the GAPDH enzyme (coded by GapC)
indicate a significant impact of replacement mutations on
enzyme function. Furthermore, the geographic distribution of
alternate GapC alleles and/or linked genomic regions
suggests that they have had differential success in the
recolonization of Europe following the Last Glacial
Maximum.},
Doi = {10.1016/j.ympev.2009.06.007},
Key = {fds230613}
}
@article{fds230546,
Author = {Shaw, AJ},
Title = {Mielichhoferia shevockii, comb. Nov. (mielichhoferiaceae)},
Journal = {Bryologist},
Volume = {112},
Number = {3},
Pages = {605},
Publisher = {American Bryological and Lichenological Society},
Year = {2009},
Month = {September},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-112.3.605},
Abstract = {The California endemic species described as Schiymenium
shevockii A. J. Shaw is transferred to the genus
Mielichhoferia because phylogenetic analyses have shown that
peristome structure (exostomial versus endostomial) is not a
reliable character for distinguishing these two genera.
Copyright © 2009 by The American Bryological and
Lichenological Society, Inc.},
Doi = {10.1639/0007-2745-112.3.605},
Key = {fds230546}
}
@article{fds230612,
Author = {Dias, E and Mendes, C and Shaw, J},
Title = {Sphagnum recurvum P.Beauv. On Terceira, Azores, new to
Macaronesia-Europe},
Journal = {Journal of Bryology},
Volume = {31},
Number = {3},
Pages = {199-201},
Publisher = {Informa UK Limited},
Year = {2009},
Month = {September},
ISSN = {0373-6687},
url = {http://dx.doi.org/10.1179/174328209X458458},
Doi = {10.1179/174328209X458458},
Key = {fds230612}
}
@article{fds230614,
Author = {Hentschel, J and von Konrat, MJ and Pócs, T and Schäfer-Verwimp, A and Jonathan Shaw and A and Schneider, H and Heinrichs,
J},
Title = {Molecular insights into the phylogeny and subgeneric
classification of Frullania Raddi (Frullaniaceae,
Porellales).},
Journal = {Molecular phylogenetics and evolution},
Volume = {52},
Number = {1},
Pages = {142-156},
Year = {2009},
Month = {July},
ISSN = {1055-7903},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000266692800013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {With an estimated 300-375 species, Frullania is the largest
genus of Porellales and forms a major clade of leafy
liverworts. The cosmopolitan genus includes mostly epiphytes
and represents an important component of the cryptogamic
vegetation in various, especially tropical, habitats. There
have been abundant changes and modifications to the
infrageneric classification of Frullania, with up to fifteen
subgenera and numerous sections solely based on morphology.
Here we present the first molecular phylogeny of Frullania
using four markers (rbcL, psbA, trnL-trnF region of cp DNA,
nr5.8S-ITS-2 region) and 171 accessions from throughout the
range. The molecular data provide evidence for the monophyly
of several subgenera and support intercontinental ranges of
these clades. Previous subgeneric assignment for a suite of
taxa based on morphological evidence is not supported by the
molecular data. Representatives of the genera Amphijubula,
Neohattoria and Schusterella are nested in robust subclades
of Frullania. Basal relationships within Frullania are
largely unsupported. Based on the outcome of the
phylogenetic analyses we present a revised supraspecific
classification and provide evidence for the monophyly of
some morphological species. Disjunct distributional patterns
within Frullania cannot be explained by Gondwanan
vicariance.},
Doi = {10.1016/j.ympev.2008.12.021},
Key = {fds230614}
}
@article{fds230615,
Author = {Karlin, EF and Boles, SB and Ricca, M and Temsch, EM and Greilhuber, J and Shaw, AJ},
Title = {Three-genome mosses: complex double allopolyploid origins
for triploid gametophytes in Sphagnum.},
Journal = {Molecular ecology},
Volume = {18},
Number = {7},
Pages = {1439-1454},
Year = {2009},
Month = {April},
ISSN = {0962-1083},
url = {http://dx.doi.org/10.1111/j.1365-294x.2009.04113.x},
Abstract = {This paper documents the occurrence of allotriploidy (having
three differentiated genomes) in gametophytes of two
Southern Hemisphere Sphagnum species (S. australe, S.
falcatulum). The pattern of microsatellite alleles indicates
that both species are composed of a complex of allodiploid
and allotriploid gametophytes, with the latter resulting
from two allopolyploidization events. No haploid (n = x)
gametophytes were found for either species. The ploidal
levels suggested by the pattern of microsatellite alleles
were confirmed by flow cytometry and Feulgen DNA image
densitometry. For both S. australe and S. falcatulum, the
respective allodiploid plants (or their ancestors) are one
of the parent species of the allotriploid plants. This is
the first report of triploidy in Sphagnum gametophytes
occurring in nature and also the first report of the
presence of three differentiated genomes in any bryophyte.
It is also the first report of intersectional allopolyploidy
in Sphagnum, with S. australe appearing to have parental
species from Sphagnum sections Rigida and Sphagnum, and S.
falcatulum having parental species from Sphagnum sections
Cuspidata and Subsecunda. In both species, the allotriploid
cytotypes were the most prevalent cytotype on the South
Island of New Zealand. The pattern of microsatellite alleles
shows the presence of two genetically distinct populations
of allodiploid S. australe, possibly indicating multiple
origins of polyploidy for that allodiploid cytotype.
Morphological evidence is also highly indicative of
recurrent polyploidy in the allotriploid cytotype of S.
falcatulum. Allopolyploidy has clearly played a major
evolutionary role in these two Southern Hemisphere taxa.
This study, in conjunction with other recent research,
indicates that allopolyploidy is a common, if not the
predominant, form of polyploidy in Sphagnum.},
Doi = {10.1111/j.1365-294x.2009.04113.x},
Key = {fds230615}
}
@article{fds230544,
Author = {Shaw, AJ and Toren, D},
Title = {Pohlia flexuosa (Mielichhoferiaceae) in North
America},
Journal = {Bryologist},
Volume = {112},
Number = {1},
Pages = {178-183},
Publisher = {American Bryological and Lichenological Society},
Year = {2009},
Month = {March},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745-112.1.178},
Abstract = {Pohlia flexuosa is reported from a single California site as
new for the North American moss flora. This species is
otherwise found in central and eastern Asia, where it is one
of the most common gemmiferous Pohlia species, and in
western Europe. A key is provided for the six gemmiferous
species of Pohlia currently known from California. Copyright
©2009 by The American Bryological and Lichenological
Society, Inc.},
Doi = {10.1639/0007-2745-112.1.178},
Key = {fds230544}
}
@article{fds304318,
Author = {Shaw, BLANKA and Terracciano, STEFANO and Shaw,
AJONATHAN},
Title = {A Genetic Analysis of Two Recently Described Peat Moss
Species, Sphagnum atlanticum and S. bergianum
(Sphagnaceae).},
Journal = {Systematic botany},
Volume = {34},
Number = {1},
Pages = {6-12},
Publisher = {American Society of Plant Taxonomists},
Year = {2009},
Month = {January},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364409787602212},
Abstract = {Microsatellite markers were used to test whether two
recently described species of Sphagnum (Bryophyta), S.
atlanticum R.E. Andrus and S. bergianum R.E. Andrus,
represent distinct gene pools. The first species is
considered endemic to eastern North America while the second
species has been reported from Alaska and Newfoundland. The
results indicate that S. atlanticum does not differ
genetically from the closely related species, S. torreyanum,
also restricted to eastern North America. In fact, some
samples that are identical across all 15 micro-satellite
loci have been distinguished morphologically as these two
species. Plants of S. bergianum from Alaska are closely
related genetically to Alaskan plants of the similar
species, S. subfulvum, whereas Newfoundland plants of S.
bergianum are more closely related to Newfoundland plants of
S. subfulvum. Alaskan versus Newfoundland plants of S.
subfulvum s.l. (including S. bergianum) are differentiated
at microsatellite loci. Another closely related species, S.
subnitens, is distinct from S. subfulvum and S. bergianum.
Sphagnum atlanticum is synonymized under S. torreyanum and
S. bergianum is synonymized under S. subfulvum.},
Doi = {10.1600/036364409787602212},
Key = {fds304318}
}
@article{fds167055,
Author = {J. Shaw},
Title = {Pseudoditrichaceae},
Booktitle = {Flora of North America, Bryophytes.},
Year = {2009},
url = {http://http://www.mobot.org/plantscience/bfna/V2/Pseudoditrichaceae.htm},
Key = {fds167055}
}
@article{fds167056,
Author = {J. Shaw},
Title = {Mielichhoferiaceae},
Booktitle = {Flora of North America, Bryophytes.},
Year = {2009},
url = {//http://www.mobot.org/plantscience/bfna/V2/MielMielichhoferiaceae.htm},
Key = {fds167056}
}
@article{fds230616,
Author = {Shaw, and B, and Terracciano, S and Shaw, AJ},
Title = {A genetic analysis of two recently described peat moss
species, Sphagnum atlanticum and S. bergianum
(Sphagnaceae).},
Journal = {Systematic Botany},
Volume = {34},
Number = {1},
Pages = {1-9},
Year = {2009},
ISSN = {0363-6445},
Abstract = {Microsatellite markers were used to test whether two
recently described species of Sphagnum (Bryophyta), S.
atlanticum R.E. Andrus and S. bergianum R.E. Andrus,
represent distinct gene pools. The first species is
considered endemic to eastern North America while the second
species has been reported from Alaska and Newfoundland. The
results indicate that S. atlanticum does not differ
genetically from the closely related species, S. torreyanum
, also restricted to eastern North America. In fact, some
samples that are identical across all 15 microsatellite loci
have been distinguished morphologically as these two
species. Plants of S. bergianum from Alaska are closely
related genetically to Alaskan plants of the similar
species, S. subfulvum , whereas Newfoundland plants of S.
bergianum are more closely related to Newfoundland plants of
S. subfulvum . Alaskan versus Newfoundland plants of S.
subfulvum s.l. (including S. bergianum ) are differentiated
at microsatellite loci. Another closely related species, S.
subnitens , is distinct from S. subfulvum and S. bergianum .
Sphagnum atlanticum is synonymized under S. torreyanum and
S. bergianum is synonymized under S. subfulvum © Copyright
2009.},
Key = {fds230616}
}
@article{fds230617,
Author = {Szövényi, P and Terracciano, S and Ricca, M and Giordano, S and Shaw,
AJ},
Title = {Recent divergence, intercontinental dispersal and shared
polymorphism are shaping the genetic structure of
amphi-Atlantic peatmoss populations.},
Journal = {Molecular ecology},
Volume = {17},
Number = {24},
Pages = {5364-5377},
Year = {2008},
Month = {December},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19121003},
Abstract = {Several lines of evidence suggest that recent long-distance
dispersal may have been important in the evolution of
intercontinental distribution ranges of bryophytes. However,
the absolute rate of intercontinental migration and its
relative role in the development of certain distribution
ranges is still poorly understood. To this end, the genetic
structure of intercontinental populations of six peatmoss
species showing an amphi-Atlantic distribution was
investigated using microsatellite markers. Methods relying
on the coalescent were applied (IM and MIGRATE) to
understand the evolution of this distribution pattern in
peatmosses. Intercontinental populations of the six peatmoss
species were weakly albeit significantly differentiated
(average F(ST) = 0.104). This suggests that the North
Atlantic Ocean is acting as a barrier to gene flow even in
bryophytes adapted to long-range dispersal. The im analysis
suggested a relatively recent split of intercontinental
populations dating back to the last two glacial periods
(9000-289,000 years ago). In contrast to previous
hypotheses, analyses indicated that both ongoing migration
and ancestral polymorphism are important in explaining the
intercontinental genetic similarity of peatmoss populations,
but their relative contribution varies with species.
Migration rates were significantly asymmetric towards
America suggesting differential extinction of genotypes on
the two continents or invasion of the American continent by
European lineages. These results indicate that low genetic
divergence of amphi-Atlantic populations is a general
pattern across numerous flowering plants and bryophytes.
However, in bryophytes, ongoing intercontinental gene flow
and retained shared ancestral polymorphism must both be
considered to explain the genetic similarity of
intercontinental populations.},
Doi = {10.1111/j.1365-294x.2008.04003.x},
Key = {fds230617}
}
@article{fds304317,
Author = {Ricca, M and Beecher, FW and Boles, SB and Temsch, E and Greilhuber, J and Karlin, EF and Shaw, AJ},
Title = {Cytotype variation and allopolyploidy in North American
species of the Sphagnum subsecundum complex
(Sphagnaceae).},
Journal = {American journal of botany},
Volume = {95},
Number = {12},
Pages = {1606-1620},
Year = {2008},
Month = {December},
ISSN = {0002-9122},
url = {http://dx.doi.org/10.3732/ajb.0800148},
Abstract = {Allopolyploid speciation is likely the predominant mode of
sympatric speciation in plants. The Sphagnum subsecundum
complex includes six species in North America. Three have
haploid gametophytes, and three are thought to have diploid
gametophytes. Microsatellite analyses indicated that some
plants of S. inundatum and S. lescurii are heterozygous at
most loci, but others have only one allele at each locus.
Flow cytometry and Feulgen staining showed that heterozygous
plants have twice the genome size as plants with one allele
per locus; thus, microsatellite patterns can be used to
survey the distribution and abundance of haploid and diploid
gametophytes. Microsatellite analyses also revealed that S.
carolinianum is consistently diploid, but S. lescurii and S.
inundatum include both haploid and diploid populations. The
frequency of diploid plants in S. lescurii increases with
latitude. In an analysis of one population of S. lescurii,
both cytotypes co-occurred but were genetically
differentiated with no evidence of interbreeding. The degree
of genetic differentiation showed that the diploids were not
derived from simple genome duplication of the local
haploids. Heterozygosity appears to be fixed or nearly so in
diploids, strongly suggesting that although morphologically
indistinguishable from the haploids, they are derived by
allopolyploidy.},
Doi = {10.3732/ajb.0800148},
Key = {fds304317}
}
@article{fds230622,
Author = {Shaw, AJ and Pokorny, L and Shaw, B and Ricca, M and Boles, S and Szövényi, P},
Title = {Genetic structure and genealogy in the Sphagnum subsecundum
complex (Sphagnaceae: Bryophyta).},
Journal = {Molecular phylogenetics and evolution},
Volume = {49},
Number = {1},
Pages = {304-317},
Year = {2008},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18634892},
Abstract = {Allopolyploidy is probably the most extensively studied mode
of plant speciation and allopolyploid species appear to be
common in the mosses (Bryophyta). The Sphagnum subsecundum
complex includes species known to be gametophytically
haploid or diploid, and it has been proposed that the
diploids (i.e., with tetraploid sporophytes) are
allopolyploids. Nucleotide sequence and microsatellite
variation among haploids and diploids from Newfoundland and
Scandinavia indicate that (1) the diploids exhibit fixed or
nearly fixed heterozygosity at the majority of loci sampled,
and are clearly allopolyploids, (2) diploids originated
independently in North America and Europe, (3) the European
diploids appear to have the haploid species, S. subsecundum,
as the maternal parent based on shared chloroplast DNA
haplotypes, (4) the North American diploids do not have the
chloroplast DNA of any sampled haploid, (5) both North
American and European diploids share nucleotide and
microsatellite similarities with S. subsecundum, (6) the
diploids harbor more nucleotide and microsatellite diversity
than the haploids, and (7) diploids exhibit higher levels of
linkage disequilibrium among microsatellite loci. An
experiment demonstrates significant artifactual
recombination between interspecific DNAs coamplified by PCR,
which may be a complicating factor in the interpretation of
sequence-based analyses of allopolyploids.},
Doi = {10.1016/j.ympev.2008.06.009},
Key = {fds230622}
}
@article{fds303166,
Author = {Hutsemékers, V and Risterucci, AM and Ricca, M and Boles, S and Hardy,
OJ and Shaw, AJ and Vanderpoorten, A},
Title = {Identification and characterization of nuclear
microsatellite loci in the aquatic moss Platyhypnidium
riparioides (Brachytheciaceae).},
Journal = {Molecular ecology resources},
Volume = {8},
Number = {5},
Pages = {1130-1132},
Year = {2008},
Month = {September},
ISSN = {1755-098X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21585992},
Abstract = {Eight microsatellite loci from the aquatic moss
Platyhypnidium riparioides were identified using the method
of microsatellite-enriched libraries. Polymorphism was
assessed in a sample of four populations of 20 individuals
each from four streams of the Meuse hydrographic basin in
southern Belgium. The markers amplified three to seven
alleles per locus. Comparison of observed and expected
heterozygosities as well as F-statistics (F(ST) = 0.62)
reveals a significant genetic differentiation among
populations. These markers will be useful for further
investigation of population genetic structure and diversity
at different nested spatial scales.},
Doi = {10.1111/j.1755-0998.2008.02193.x},
Key = {fds303166}
}
@article{fds230623,
Author = {Davis, EC and Shaw, AJ},
Title = {Biogeographic and phylogenetic patterns in diversity of
liverwort-associated endophytes.},
Journal = {American journal of botany},
Volume = {95},
Number = {8},
Pages = {914-924},
Year = {2008},
Month = {August},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21632414},
Abstract = {Liverworts harbor diverse fungi, including endophytes, in
their healthy tissues. To address whether patterns of
endophyte diversity are correlated with host phylogeny or
geography, we designed a broad geographic survey with
controlled phylogenetic host sampling. We collected
liverworts in North Carolina, Washington, Idaho, British
Columbia, Germany, and New Zealand and identified endophytes
using culture-based and molecular methods. Of the major
lineages of filamentous ascomycetes recovered, 53-88%
belonged to the Xylariales. Endophyte accumulation curves
did not saturate, and singleton sequences were dominant in
each region, suggesting that liverwort endophyte communities
are diverse. There was no significant difference in species
richness between regional endophyte communities; however,
total richness estimators indicated that North Carolina and
New Zealand have richer communities than do Germany and the
Pacific Northwest. This pattern reflects lower per-host
endophyte density and prevalence of a common, shared
sequence group in Germany and the Pacific Northwest.
Although species richness was relatively low in the Pacific
Northwest, the greatest phylogenetic diversity of endophytes
was recovered there. Tests for regional and host specificity
revealed that endophyte floras of hosts within a geographic
area are more similar to one another than to those of
closely related hosts. Geographic distance, not host
phylogeny, best explains differences among
communities.},
Doi = {10.3732/ajb.2006463},
Key = {fds230623}
}
@article{fds230619,
Author = {McDaniel, SF and Willis, JH and Shaw, AJ},
Title = {The genetic basis of developmental abnormalities in
interpopulation hybrids of the moss Ceratodon
purpureus.},
Journal = {Genetics},
Volume = {179},
Number = {3},
Pages = {1425-1435},
Year = {2008},
Month = {July},
ISSN = {0016-6731},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18562651},
Abstract = {Divergent populations are intrinsically reproductively
isolated when hybrids between them either fail to develop
properly or do not produce viable offspring. Intrinsic
isolation may result from Dobzhansky-Muller (DM)
incompatibilities, in which deleterious interactions among
genes or gene products lead to developmental problems or
underdominant chromosome structure differences between the
parents. These mechanisms can be tested by studying marker
segregation patterns in a hybrid mapping population. Here we
examine the genetic basis of abnormal development in hybrids
between two geographically distant populations of the moss
Ceratodon purpureus. Approximately half of the hybrid
progeny exhibited a severely reduced growth rate in early
gametophyte development. We identified four unlinked
quantitative trait loci (QTL) that interacted asymmetrically
to cause the abnormal development phenotype. This pattern is
consistent with DM interactions. We also found an excess of
recombination between three marker pairs in the abnormally
developing progeny, relative to that estimated in the normal
progeny. This suggests that structural differences in these
regions contribute to hybrid breakdown. Two QTL coincided
with inferred structural differences, consistent with recent
theory suggesting that rearrangements may harbor population
divergence alleles. These observations suggest that multiple
complex genetic factors contribute to divergence among
populations of C. purpureus.},
Doi = {10.1534/genetics.107.086314},
Key = {fds230619}
}
@article{fds230624,
Author = {Shaw, AJ and Andrus, RICHARDE and Shaw, BLANKA},
Title = {Sphagnum Beringiense sp. nov. (bryophyta) from Arctic
Alaska, Based on Morphological and Molecular
Data.},
Journal = {Systematic botany},
Volume = {33},
Number = {3},
Pages = {469-477},
Publisher = {American Society of Plant Taxonomists},
Year = {2008},
Month = {July},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364408785679842},
Abstract = {A new species of Sphagnum section Subsecunda, S. beringiense
, is described from arctic Alaska from the vicinity of
Barrow along the northern coast. The species is
distinguished morphologically by the light, yellow-green
color of the gametophytes, multistratose stem cortex with
2-4 layers of enlarged thin-walled cells, round, medium-size
(ca. 5 μm diameter) outer branch leaf pores, scattered
inner branch leaf pores, typically few outer stem leaf
pores, and abundant, round to elliptic inner stem leaf
pores. Two unique plastid DNA haplotypes occur among Barrow
area plants of S. beringiense , and these differ by a
minimum of three nucleotide substitutions from those of
other Alaskan Sphagnum species in the section Subsecunda.
Microsatellite markers show that S. beringiense is
genetically variable despite the fact that all plants were
sampled from within an area of a few km2 and neither
gametangia nor sporophytes have been observed. A key to the
six Alaskan species of Sphagnum section Subsecunda is
provided.},
Doi = {10.1600/036364408785679842},
Key = {fds230624}
}
@article{fds230541,
Author = {Shaw, AJ and Boles, S and Shaw, B},
Title = {A phylogenetic delimitation of the "Sphagnum subsecundum
complex" (Sphagnaceae, Bryophyta).},
Journal = {American journal of botany},
Volume = {95},
Number = {6},
Pages = {731-744},
Year = {2008},
Month = {June},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21632399},
Abstract = {A seemingly obvious but sometimes overlooked premise of any
evolutionary analysis is delineating the group of taxa under
study. This is especially problematic in some bryophyte
groups because of morphological simplicity and convergence.
This research applies information from nucleotide sequences
for eight plastid and nuclear loci to delineate a group of
northern hemisphere peat moss species, the so-called
Sphagnum subsecundum complex, which includes species known
to be gametophytically haploid or diploid (i.e.,
sporophytically diploid-tetraploid). Despite the fact that
S. subsecundum and several species in the complex have been
attributed disjunct ranges that include all major
continents, phylogenetic analyses suggest that the group is
actually restricted to Europe and eastern North America.
Plants from western North America, from California to
Alaska, which are morphologically similar to species of the
S. subsecundum complex in eastern N. America and Europe,
actually belong to a different deep clade within Sphagnum
section Subsecunda. One species often considered part of the
S. subsecundum complex, S. contortum, likely has a
reticulate history involving species in the two deepest
clades within section Subsecunda. Nucleotide sequences have
a strong geographic structure across the section Subsecunda,
but shallow tip clades suggest repeated long-distance
dispersal in the section as well.},
Doi = {10.3732/ajb.0800048},
Key = {fds230541}
}
@article{fds230634,
Author = {Vanderpoorten, A and Devos, N and Goffinet, B and Hardy, OJ and Shaw,
AJ},
Title = {The barriers to oceanic island radiation in bryophytes:
Insights from the phylogeography of the moss Grimmia
montana},
Journal = {Journal of Biogeography},
Volume = {35},
Number = {4},
Pages = {654-663},
Publisher = {WILEY},
Year = {2008},
Month = {April},
ISSN = {0305-0270},
url = {http://dx.doi.org/10.1111/j.1365-2699.2007.01802.x},
Abstract = {Aim: In contrast to angiosperms, bryophytes do not appear to
have radiated in Macaronesia and the western Mediterranean.
We evaluate if: (1) the apparent lack of radiation in
bryophytes reflects our failure to recognize cryptic endemic
species; (2) bryophytes are characterized by extremely low
evolutionary rates; or (3) bryophytes have a high dispersal
ability, which prevents genetic isolation. Location:
Worldwide, with a special emphasis on Macaronesia and the
western Mediterranean. Methods: Three chloroplast regions
were sequenced from samples of the moss Grimmia montana from
its entire distribution range. Network analyses, Fst and Nst
statistics were used to describe and interpret the
phylogeographical signal in the data. Results: Despite
significant phylogeographical signal in the chloroplast
genome, which demonstrates limits to gene flow at the
continental scale, repeated sister group relationships
observed among accessions from different geographical areas
suggest recurrent colonization patterns. These observations
are consistent with mounting evidence that intercontinental
distributions exhibited by many bryophyte species result
from long-distance dispersal rather than continental drift.
Madeiran and western Mediterranean island haplotypes are
either shared by, or closely related to, European and North
American ones. Fst values between Madeira, western
Mediterranean islands, North America and Europe are not
significantly different from zero, and suggest that Madeira
and the south-western Mediterranean are subject to strong
transatlantic gene flow. By contrast, haplotypes found in
the Canary Islands are shared or closely related to those of
populations from south-western Europe or southern Africa.
Main conclusions: Multiple origins and colonization events
are not consistent with the hypothesis of a relictual origin
of the Macaronesian moss flora. One possible reason for the
failure of taxa that experienced multiple colonization
events to radiate is niche pre-emption. We suggest that
strong gene flow, coupled with the occupancy of all suitable
niches, either by earlier conspecific colonizers or by other
species, could be the mechanism preventing island radiation
in G. montana and other cryptogams with high long-distance
dispersal abilities. © 2007 The Authors.},
Doi = {10.1111/j.1365-2699.2007.01802.x},
Key = {fds230634}
}
@article{fds230625,
Author = {Shaw, AJ and Holz, I and Cox, CJ and Goffinet, B},
Title = {Phylogeny, character evolution, and biogeography of the
gondwanic moss family Hypopterygiaceae (Bryophyta)},
Journal = {Systematic Botany},
Volume = {33},
Number = {1},
Pages = {21-30},
Publisher = {American Society of Plant Taxonomists},
Year = {2008},
Month = {March},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364408783887311},
Abstract = {Phylogenetic relationships among the seven genera of the
Hypopterygiaceae, represented by 14 of the 21 species
recognized in the family, were reconstructed based on
variation in nucleotide sequences of six nuclear,
mitochondrial, and plastid loci. Monophyly of the
Hypopterygiaceae is strongly supported, whereas the genera
Cyathophorum and Dendrohypopterygium are unambiguously
polyphyletic. Cyathophorum bulbosum and C. adiantum make up
a lineage sister to the remainder of the family. A lineage
comprising four monotypic genera (Arbusculohypopterygium,
Canalohypopterygium, Catharomnion, and Dendrocyathophorum)
is sister to Lopidium plus a heterogenous clade that
includes Dendrohypopterygium, Hypopterygium, Cyathophorum
hookerianum, and C. parvifolium. The later two species are
transferred to Hypopterygium as H. hookerianum and H.
parvifolium. The Hypopterygiaceae are distinguished from
their sister family, the Hookeriaceae, by their anisophylly,
and by a border of two or more differentiated cells on
lateral leaves, although this character also occurs in some
Hookeriaceae and has been lost at least twice in the
Hypopterygiaceae. Intermediate cells in the axillary hairs
arose early in the evolution of the family but are lacking
in the two species of Cyathophorum that form a sister group
to the remainder of the Hypopterygiaceae. © Copyright 2008
by the American Society of Plant Taxonomists.},
Doi = {10.1600/036364408783887311},
Key = {fds230625}
}
@article{fds230484,
Author = {Shaw, AJ},
Title = {Bryophyte species and speciation},
Pages = {445-486},
Booktitle = {Bryophyte Biology, Second Edition},
Publisher = {Cambridge University Press},
Year = {2008},
Month = {January},
ISBN = {9780521872256},
url = {http://dx.doi.org/10.1017/CBO9780511754807.013},
Abstract = {Introduction The three lineages of bryophytes, mosses,
liverworts, and hornworts, compose successful groups of
early embryophytes. The mosses are estimated to include some
12 700 species (Crosby et al. 2000), the liverworts
approximately 6000–8000 extant species (Crandall-Stotler &
Stotler 2000, Chapter 1, this volume), and the hornworts
about 100–150 species (Chapter 3, this volume). Mosses are
comparable in species richness to the monilophytes, which
are estimated to include about 11 500 species (Pryer et al.
2004). Among the extant land plants, therefore, only the
angiosperms are currently more species-rich than are the
bryophytes. I. is often stated that bryophytes are most
diverse in the tropics and fit the general pattern found in
many groups of organisms, with increasing species richness
toward the equator (Rosenzweig 1995). However, a
quantitative analysis of latitudinal diversity patterns in
the mosses failed to detect any such latitudinal gradient,
except perhaps a weak one in the Americas (Shaw et al.
2005a). I. appears that liverwort diversity is highest at
moderate to high latitudes of the Southern Hemisphere,
although one family, the Lejeuneaceae, is hyperdiverse in
wet tropical forests of both the New and Old Worlds
(Gradstein 1979). The fossil record for mosses, liverworts,
and hornworts is too incomplete to assess whether these
groups were more or less diverse in the geological past
(Miller 1984, Oostendorp 1987).},
Doi = {10.1017/CBO9780511754807.013},
Key = {fds230484}
}
@article{fds230485,
Author = {Goffinet, B and Buck, WR and Shaw, AJ},
Title = {Morphology, anatomy, and classification of the
bryophyta},
Pages = {55-138},
Booktitle = {Bryophyte Biology, Second Edition},
Publisher = {Cambridge University Press},
Year = {2008},
Month = {January},
ISBN = {9780521872256},
url = {http://dx.doi.org/10.1017/CBO9780511754807.003},
Abstract = {With approximately 13 000 species, the Bryophyta compose the
second most diverse phylum of land plants. Mosses share with
the Marchantiophyta and Anthocerotophyta a haplodiplobiontic
life cycle that marks the shift from the haploid-dominated
life cycle of the algal ancestors of embryophytes to the
sporophyte-dominated life cycle of vascular plants. The
gametophyte is free-living, autotrophic, and almost always
composed of a leafy stem. Following fertilization a
sporophyte develops into an unbranched axis bearing a
terminal spore-bearing capsule. The sporophyte remains
physically attached to the gametophyte and is at least
partially physiologically dependent on the maternal plant.
Recent phylogenetic reconstructions suggest that three
lineages of early land plants compose an evolutionary grade
that spans the transition to land and the origin of plants
with branched sporophytes (see Chapter 4). The Bryophyta
seem to occupy an intermediate position: their origin
predates the divergence of the ancestor to the hornworts and
vascular plants but evolved from a common ancestor with
liverworts (Qiu et al. 2006). The origin of the earliest
land plants can be traced back to the Ordovician and maybe
the Cambrian (Strother et al. 2004). Although unambiguous
fossils of mosses have only been recovered from sediments
dating from younger geological periods (Upper
Carboniferous), divergence time estimates based on molecular
phylogenies suggest that the origin of mosses dates back to
the Ordovician (Newton et al. 2007) and thus that their
unique evolutionary history spans at least 400 million
years.},
Doi = {10.1017/CBO9780511754807.003},
Key = {fds230485}
}
@article{fds230628,
Author = {Karlin, EF and Boles, SB and Shaw, AJ},
Title = {Resolving boundaries between species in Sphagnum section
Subsecunda using microsatellite markers},
Journal = {Taxon},
Volume = {57},
Number = {4},
Pages = {1189-1200},
Year = {2008},
Month = {January},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.1002/tax.574012},
Abstract = {Populations and species of Sphagnum section Subsecunda are
morphologically variable and it is often difficult from
studying field-collected plants and herbarium specimens to
delimit species. Allelic patterns at 20 microsatellite loci
indicate that three distinguishable gene pools can be
identified among plants from Australia and New Zealand. All
three species are morphologically variable along a moisture
gradient and this appears to be largely plastic, without
genetic differentiation among species specific morphotypes.
Sphagnum novozelandicum and S. comosum appear to have
monoploid gametophytes, are closely related, and are endemic
to Australia and New Zealand. The former usually occurs at
or above water level and the latter is an aquatic plant with
extensive morphological variation, ranging from simplex to
branched morphotypes. Sphagnum fuscovinosum and S. simplex
are synonyms of S. comosum. The third species is a highly
disjunct population of the S. auriculatum/S. inundatum
complex of Europe, which has not previously been reported
for Australia and New Zealand. These plants appear to be
polyploid and are genetically and morphologically distinct
from both S. novo-zelandicum and S. comosum. All three
species had duplicated loci amplified by one of the
microsatellite primer pairs. Ten Sphagnum species are now
reported for Australia and New Zealand, with three of these
being endemic.},
Doi = {10.1002/tax.574012},
Key = {fds230628}
}
@article{fds230629,
Author = {Karlin, EF and Boles, SB and Shaw, AJ},
Title = {Systematics of sphagnum section sphagnum in New Zealand: A
microsatellite-based analysis},
Journal = {New Zealand Journal of Botany},
Volume = {46},
Number = {2},
Pages = {105-118},
Publisher = {Informa UK Limited},
Year = {2008},
Month = {January},
ISSN = {0028-825X},
url = {http://dx.doi.org/10.1080/00288250809509758},
Abstract = {The systematics of Sphagnum section Sphagnum in New Zealand
has been controversial. Two species are currently recognised
in the New Zealand flora, S. cristatum and S. perichaetiale,
but the presence of the widespread S. magellanicum has been
debated. An analysis of 16 microsatellite loci shows that
the gametophytes of Sphagnum perichaetiale appear to have
one monoploid set of chromosomes (i.e., are haploid). Fixed
heterozygosity at 10 loci indicates that S. cristatum is an
alloploid. A red morphotype of S. cristatum, similar in
macroappearance to S. magellanicum, is not genetically
differentiated from the more common brown-green morphotypes
of S. cristatum. Although analysis of the microsatellite
data for S. cristatum showed most of the genetic variation
to be within populations, significant variation did occur
among populations within regions and also between regions.
© 2008 Taylor & Francis Group, LLC.},
Doi = {10.1080/00288250809509758},
Key = {fds230629}
}
@article{fds230618,
Author = {Shevock, JR and Norris, DH and Shaw, AJ},
Title = {Identification, distribution and family placement of the
pleurocarpous moss Bestia longipes},
Journal = {Madronõ},
Volume = {56},
Pages = {1-9},
Year = {2008},
Key = {fds230618}
}
@article{fds230620,
Author = {Hutsenmékers, and Risterucci, VAM and Ricca, M and Boles, S and Hardy,
OJ and Shaw, AJ and Vanderpoorten, A},
Title = {Identification and characterization of nuclear
microsatellite loci in the aquatic moss Platyhypnidium
riparioides (Brachytheciaceae)},
Journal = {Molecular Ecology Resources},
Volume = {8},
Number = {5},
Pages = {1120-1132},
Year = {2008},
ISSN = {1755-098X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21585992},
Abstract = {Eight microsatellite loci from the aquatic moss
Platyhypnidium riparioides were identified using the method
of microsatellite-enriched libraries. Polymorphism was
assessed in a sample of four populations of 20 individuals
each from four streams of the Meuse hydrographic basin in
southern Belgium. The markers amplified three to seven
alleles per locus. Comparison of observed and expected
heterozygosities as well as F-statistics (F(ST) = 0.62)
reveals a significant genetic differentiation among
populations. These markers will be useful for further
investigation of population genetic structure and diversity
at different nested spatial scales.},
Doi = {10.1111/j.1755-0998.2008.02193.x},
Key = {fds230620}
}
@article{fds230621,
Author = {Ricca, M and Beecher, FW and Boles, SB and Temsch, E and Greilhuber, J and Karlin, EF and Shaw, AJ},
Title = {Cytotype variation and allopolyploidy in North American
species of the},
Journal = {American Journal of Botany},
Volume = {95},
Number = {12},
Pages = {1-16},
Year = {2008},
ISSN = {0002-9122},
url = {http://dx.doi.org/10.3732/ajb.0800148},
Abstract = {Allopolyploid speciation is likely the predominant mode of
sympatric speciation in plants. The Sphagnum subsecundum
complex includes six species in North America. Three have
haploid gametophytes, and three are thought to have diploid
gametophytes. Microsatellite analyses indicated that some
plants of S. inundatum and S. lescurii are heterozygous at
most loci, but others have only one allele at each locus.
Flow cytometry and Feulgen staining showed that heterozygous
plants have twice the genome size as plants with one allele
per locus; thus, microsatellite patterns can be used to
survey the distribution and abundance of haploid and diploid
gametophytes. Microsatellite analyses also revealed that S.
carolinianum is consistently diploid, but S. lescurii and S.
inundatum include both haploid and diploid populations. The
frequency of diploid plants in S. lescurii increases with
latitude. In an analysis of one population of S. lescurii,
both cytotypes co-occurred but were genetically
differentiated with no evidence of interbreeding. The degree
of genetic differentiation showed that the diploids were not
derived from simple genome duplication of the local
haploids. Heterozygosity appears to be fixed or nearly so in
diploids, strongly suggesting that although morphologically
indistinguishable from the haploids, they are derived by
allopolyploidy.},
Doi = {10.3732/ajb.0800148},
Key = {fds230621}
}
@article{fds230626,
Author = {Shaw, and J, A and Cao, T and Wang, L-S and Flatberg, KI and Flatberg, B and Shaw, B and Zhou, P and Boles, SB and B, S and Terraccino, and S},
Title = {Genetic variation in three Chinese peat mosses (Sphagnum)
based on microsatellite markers, with primer information and
analysis of ascertainment bias},
Journal = {Bryologist},
Volume = {111},
Number = {2},
Pages = {271-281},
Publisher = {American Bryological and Lichenological Society},
Year = {2008},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745(2008)111[271:GVITCP]2.0.CO;2},
Abstract = {Primer sequences are provided for amplification of 21
microsatellite- containing loci in Sphagnum. Although these
primers were developed for species in Sphagnum section
Subsecunda, they amplify microsatellite loci in most species
that have been tested across the genus Sphagnum. Results are
described from a survey of genetic variation in three
species of Sphagnum collected in China: S. junghuhnianum in
section Acutifolia, and S. palustre and S. imbricatum in
section Sphagnum. Six and eight multilocus genotypes were
detected within one population each of S. junghuhnianum and
S. palustre, respectively. Four populations of S. imbricatum
were sampled; they vary substantially in allele frequencies
and in the amount of genetic diversity detected; overall,
approximately 40% of the genetic variation sampled within S.
imbricatum could be attributed to differentiation among
populations. Microsatellite profiles indicate that S.
palustre gametophytes are diploid whereas those of S.
junghuhnianum and S. imbricatum are haploid. Copyright
©2008 by The American Bryological and Lichenological
Society, Inc.},
Doi = {10.1639/0007-2745(2008)111[271:GVITCP]2.0.CO;2},
Key = {fds230626}
}
@article{fds230627,
Author = {Shaw, AJ and Boles, SB and Shaw, B},
Title = {A phylogenetic delineation of the “Sphagnum subsecundum
complex” (Bryophyta)},
Journal = {American Journal of Botany},
Volume = {95},
Number = {731-744},
Year = {2008},
Key = {fds230627}
}
@article{fds230630,
Author = {McDaniel, SF and Willis, JH and Shaw, AJ},
Title = {A linkage map reveals a complex basis for segregation
distortion in an interpopulation cross in the moss Ceratodon
purpureus.},
Journal = {Genetics},
Volume = {176},
Number = {4},
Pages = {2489-2500},
Year = {2007},
Month = {August},
ISSN = {0016-6731},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17603096},
Abstract = {We report the construction of a linkage map for the moss
Ceratodon purpureus (n = 13), based on a cross between
geographically distant populations, and provide the first
experimental confirmation of maternal chloroplast
inheritance in bryophytes. From a mapping population of 288
recombinant haploid gametophytes, genotyped at 121
polymorphic AFLP loci, three gene-based nuclear loci, one
chloroplast marker, and sex, we resolved 15 linkage groups
resulting in a map length of approximately 730 cM. We
estimate that the map covers more than three-quarters of the
C. purpureus genome. Approximately 35% of the loci were sex
linked, not including those in recombining pseudoautosomal
regions. Nearly 45% of the loci exhibited significant
segregation distortion (alpha = 0.05). Several pairs of
unlinked distorted loci showed significant deviations from
multiplicative genotypic frequencies, suggesting that
distortion arises from genetic interactions among loci. The
distorted autosomal loci all exhibited an excess of the
maternal allele, suggesting that these interactions may
involve nuclear-cytoplasmic factors. The sex ratio of the
progeny was significantly male biased, and the pattern of
nonrandom associations among loci indicates that this
results from interactions between the sex chromosomes. These
results suggest that even in interpopulation crosses,
multiple mechanisms act to influence segregation
ratios.},
Doi = {10.1534/genetics.107.075424},
Key = {fds230630}
}
@article{fds230631,
Author = {Zhou, P and Menzel, F and Shaw, AJ},
Title = {Systematics and population genetics of Sphagnum macrophyllum
and S. cribrosum (Sphagnaceae)},
Journal = {Systematic Botany},
Volume = {32},
Number = {3},
Pages = {493-503},
Publisher = {American Society of Plant Taxonomists},
Year = {2007},
Month = {July},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364407782250698},
Abstract = {To clarify long-standing disagreements about the taxonomic
and phylogenetic status of Sphagnum macrophyllum and S.
cribrosum, twenty-five samples of S. macrophyllum and
twenty-four of S. cribrosum, including the rare wave-form
morphotype, were sampled from ten states of the eastern
United States. The data set included intensive sampling from
three populations in North Carolina. Three anonymous genomic
regions (rapdA, rapdB and rapdF) were sequenced for all the
samples; two (nuclear) LEAFY introns (LEAFY1 and LEAFY2) and
one chloroplast locus (trnG) were sequenced for all the
samples excluding the twenty-two within-population North
Carolina samples. The results showed that S. macrophyllum
and S. cribrosum are reciprocally monophyletic with maximum
parsimony bootstrap support and significant Bayesian
posterior probabilities. Genetic analyses based on neutral
coalescence models suggest that the simplest allopatric
speciation model - the isolation model with no subsequent
gene flow and constant population sizes - cannot be
rejected. Nevertheless, some topological conflicts among
loci suggest the possibility of limited interspecific
hybridization. This study also showed that the
morphologically distinctive wave-form is nested within S.
cribrosum and wave-form samples from Singletary Lake make up
a clade of nearly identical plants. Interestingly, S.
macrophyllum and S. cribrosum are morphologically highly
similar but are reciprocally monophyletic and highly
differentiated, whereas the unique and morphologically
divergent wave-form is genealogically derived from within
normal S. cribrosum. © Copyright 2007 by the American
Society of Plant Taxonomists.},
Doi = {10.1600/036364407782250698},
Key = {fds230631}
}
@article{fds230540,
Author = {Shaw, J},
Title = {A molecular phylogenetic approach to the evolution of
bryophytes},
Journal = {Bryologist},
Volume = {110},
Number = {2},
Pages = {178},
Publisher = {American Bryological and Lichenological Society},
Year = {2007},
Month = {June},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745(2007)110[178:AMPATT]2.0.CO;2},
Abstract = {Bryophytes comprise the root from which the green plant
Tree-of-Life developed. Molecular methods have been applied
to a range of evolutionary problems in bryophytes including
phylogenetic relationships among the major lineages,
delimination of families and genera, infraspecific
geographic patterns and speciation. This symposium
encompasses molecular phylogenetic analyses at various
levels of organization. Presentations include overviews of
where we stand on resolving relationships within the three
divisions: Bryophyta (mosses), Marchantiophyta (liverworts)
and Anthocerophyta (hornworts). Other presentations address
the evolution of development in early land plants, the use
of characters describing gene and genome structure in
phylogenetic analyses and infra-specific,
geographically-correlated molecular variation in bryophytes.
Copyright ©2007 by the American Bryological and
Lichenological Society, Inc.},
Doi = {10.1639/0007-2745(2007)110[178:AMPATT]2.0.CO;2},
Key = {fds230540}
}
@article{fds230632,
Author = {Renzaglia, KS and Schuette, S and Duff, RJ and Ligrone, R and Shaw, AJ and Mishler, BD and Duckett, JG},
Title = {Bryophyte phylogeny: Advancing the molecular and
morphological frontiers},
Journal = {Bryologist},
Volume = {110},
Number = {2},
Pages = {179-213},
Publisher = {American Bryological and Lichenological Society},
Year = {2007},
Month = {June},
ISSN = {0007-2745},
url = {http://dx.doi.org/10.1639/0007-2745(2007)110[179:BPATMA]2.0.CO;2},
Abstract = {Revolutionary new concepts of bryophyte relationships have
emerged from molecular phylogenetic analyses conducted since
the onset of the 21st century. For example, sequence data
contradict the historical notion that isophylly in leafy
liverworts is plesiomorphic and that simple thalloid
liverworts are monophyletic. Also contrary to traditional
views are the concepts that Leiosporoceros is genetically
distinct from other hornworts and that Oedipodium is sister
to the peristomate mosses. Substantial increases in
ultrastructural and anatomical data likewise have provided
new insights on interrelationships. Because of this recent
deluge in evolutionary studies on bryophytes, it is an
opportune time to co-examine contemporary morphological
knowledge and novel molecular hypotheses. An understanding
of bryophyte evolution and biology is essential to identify
structural innovations that accompanied early land
colonization and to illuminate the evolution of more
complicated body plans in tracheophytes. In this review, we
examine the progress that has been made since the 1999
International Botanical Congress in clarifying the
evolutionary history of the three groups of bryophytes. The
state of our knowledge on interrelationships is discussed,
with poorly-known, genetically divergent taxa illustrated
for each group. Our review of bryophyte evolution includes a
reëvaluation of the evolution of sperm cells, sporogenesis,
stomata, symbioses, conducting cells and chloroplast
ultrastructure in hornworts. We explore the prospects for
future discoveries and advances with an emphasis on
fundamental evolutionary problems that remain and the
challenges that must be met to resolve them. Copyright
©2007 by the American Bryological and Lichenological
Society, Inc.},
Doi = {10.1639/0007-2745(2007)110[179:BPATMA]2.0.CO;2},
Key = {fds230632}
}
@article{fds230633,
Author = {Goffinet, B and Wickett, NJ and Werner, O and Ros, RM and Shaw, AJ and Cox,
CJ},
Title = {Distribution and phylogenetic significance of the 71-kb
inversion in the plastid genome in Funariidae
(Bryophyta).},
Journal = {Annals of botany},
Volume = {99},
Number = {4},
Pages = {747-753},
Year = {2007},
Month = {April},
ISSN = {0305-7364},
url = {http://dx.doi.org/10.1093/aob/mcm010},
Abstract = {<h4>Background and aims</h4>The recent assembly of the
complete sequence of the plastid genome of the model taxon
Physcomitrella patens (Funariaceae, Bryophyta) revealed that
a 71-kb fragment, encompassing much of the large single copy
region, is inverted. This inversion of 57% of the genome is
the largest rearrangement detected in the plastid genomes of
plants to date. Although initially considered diagnostic of
Physcomitrella patens, the inversion was recently shown to
characterize the plastid genome of two species from related
genera within Funariaceae, but was lacking in another member
of Funariidae. The phylogenetic significance of the
inversion has remained ambiguous.<h4>Methods</h4>Exemplars
of all families included in Funariidae were surveyed. DNA
sequences spanning the inversion break ends were amplified,
using primers that anneal to genes on either side of the
putative end points of the inversion. Primer combinations
were designed to yield a product for either the inverted or
the non-inverted architecture.<h4>Key results</h4>The survey
reveals that exemplars of eight genera of Funariaceae, the
sole species of Disceliaceae and three generic
representatives of Encalyptales all share the 71-kb
inversion in the large single copy of the plastid genome. By
contrast, the plastid genome of Gigaspermaceae (Funariales)
is characterized by a gene order congruent with that
described for other mosses, liverworts and hornworts, and
hence it does not possess this inversion.<h4>Conclusions</h4>The
phylogenetic distribution of the inversion in the gene order
supports a hypothesis only weakly supported by inferences
from sequence data whereby Funariales are paraphyletic, with
Funariaceae and Disceliaceae sharing a common ancestor with
Encalyptales, and Gigaspermaceae sister to this combined
clade. To reflect these relationships, Gigaspermaceae are
excluded from Funariales and accommodated in their own
order, Gigaspermales order nov., within Funariideae.},
Doi = {10.1093/aob/mcm010},
Key = {fds230633}
}
@article{fds230635,
Author = {Gunnarsson, U and Shaw, AJ and Lönn, M},
Title = {Local-scale genetic structure in the peatmoss Sphagnum
fuscum.},
Journal = {Molecular ecology},
Volume = {16},
Number = {2},
Pages = {305-312},
Year = {2007},
Month = {January},
ISSN = {0962-1083},
url = {http://dx.doi.org/10.1111/j.1365-294x.2006.03144.x},
Abstract = {Sphagnum (peatmoss) dominates huge areas of the Northern
Hemisphere and acts as a significant carbon sink on a global
scale, yet little is known about the genetic structure of
Sphagnum populations. We investigated genetic structure
within a population of the common peatmoss Sphagnum fuscum,
to assess local patterns of genetic diversity and the
spatial extent of clones. One hundred seventeen shoots were
sampled from five transects in Fuglmyra, central Norway, and
sequenced for three anonymous DNA regions. Five
neighbourhood patches were marked along each transect, and
from each patch, five stems were sampled for molecular
analyses. Seventeen haplotypes could be distinguished and
two major groups of haplotypes differed by 12 mutational
steps. The two major haplotype groups differed significantly
in microhabitat association along the distance to
groundwater table and the pH gradients, indicating
microhabitat differentiation. The haplotypes within these
groups were all genetically similar, differing by one or two
mutations. The most common haplotype occurred in four
transects separated by 250-m distance. Most of the molecular
variation in the population was found among transects, and
within patches. Large dominating clones within each transect
resulted in low variation explained by the
among-patch-within-transect component of spatial structure.
Mutation appears to account for a larger proportion of the
population variation than recombination. Within the
population, vegetative growth and asexual reproduction from
gametophyte fragments dominate as the main reproductive
mode.},
Doi = {10.1111/j.1365-294x.2006.03144.x},
Key = {fds230635}
}
@article{fds140588,
Author = {Gunnarsson, U. and M. Lönn and A. J. Shaw},
Title = {Local-scale genetic structure in the peatmoss, Sphagnum
fuscum.},
Journal = {Molecular Ecology},
Volume = {16},
Pages = {305-312},
Year = {2007},
Key = {fds140588}
}
@article{fds230636,
Author = {Zartman, CE and McDaniel, SF and Shaw, AJ},
Title = {Experimental habitat fragmentation increases linkage
disequilibrium but does not affect genetic diversity or
population structure in the Amazonian liverwort Radula
flaccida.},
Journal = {Molecular ecology},
Volume = {15},
Number = {9},
Pages = {2305-2315},
Year = {2006},
Month = {August},
ISSN = {0962-1083},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16842407},
Abstract = {Habitat fragmentation increases the migration distances
among remnant populations, and is predicted to play a
significant role in altering both demographic and genetic
processes. Nevertheless, few studies have evaluated the
genetic consequences of habitat fragmentation in light of
information about population dynamics in the same set of
organisms. In a 10,000-km(2) experimentally fragmented
landscape of rainforest reserves in central Amazonia, we
examine patterns of genetic variation (amplified fragment
length polymorphisms, AFLPs) in the epiphyllous (e.g.
leaf-inhabiting) liverwort Radula flaccida Gott. Previous
demographic work indicates that colonization rates in this
species are significantly reduced in small forest reserves.
We scored 113 polymorphic loci in 86 individuals
representing five fragmented and five experimentally
unmanipulated populations. Most of the variation (82%) in
all populations was harboured at the smallest (400 m(2))
sampling unit. The mean ((+/-) SD) within-population genetic
diversity (Nei's), of forest remnants (0.412 +/- 0.2) was
indistinguishable from continuous (0.413 +/- 0.2) forests.
Similarly, F(ST) was identical among small (1- and 10-ha)
and large (> or = 100-ha) reserves (0.19 and 0.18,
respectively), but linkage disequilibrium between pairs of
loci was significantly elevated in fragmented populations
relative to those in continuous forests. These results
illustrate that inferences regarding the long-term viability
of fragmented populations based on neutral marker data alone
must be viewed with caution, and underscore the importance
of jointly evaluating information on both genetic structure
and demography. Second, multilocus analyses may be more
sensitive to the effects of fragmentation in the short term,
although the effects of increasing linkage disequilibrium on
population viability remain uncertain.},
Doi = {10.1111/j.1365-294x.2006.02929.x},
Key = {fds230636}
}
@article{fds230637,
Author = {Shaw, AJ},
Title = {A revision of the moss genus Pohlia Hedw. (Mniaceae) in
Australia},
Journal = {Systematic Botany},
Volume = {31},
Number = {2},
Pages = {247-257},
Publisher = {American Society of Plant Taxonomists},
Year = {2006},
Month = {July},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364406777585694},
Abstract = {The moss genus Pohlia is most diverse in the Northern
Hemisphere, but ten species occur in Australia, mostly in
New South Wales and Tasmania. One species, P. clavaeformis,
is endemic to Australia; P. tenuifolia is disjunct between
Australia and South America; P. flexousa is widespread in
southern Asia, and P. inflexa is high-latitude,
circum-Antarctic. The remaining six species are more or less
widespread in the Northern Hemisphere. Keys, descriptions,
synonomy, and illustrations are provided. Pohlia
mielichoferia and P. turgens are newly synonymized with P.
clavaeformis; P. flexuosa and P. inflexa are newly reported
from Australia. © Copyright 2006 by the American Society of
Plant Taxonomists.},
Doi = {10.1600/036364406777585694},
Key = {fds230637}
}
@article{fds230638,
Author = {Zartman, CE and Shaw, AJ},
Title = {Metapopulation extinction thresholds in rain forest
remnants.},
Journal = {The American naturalist},
Volume = {167},
Number = {2},
Pages = {177-189},
Year = {2006},
Month = {February},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16670979},
Abstract = {Although habitat fragmentation is a major threat to global
biodiversity, the demographic mechanisms underlying species
loss from tropical forest remnants remain largely
unexplored. In particular, no studies at the landscape scale
have quantified fragmentation's impacts on colonization,
extinction, and local population growth simultaneously. In
central Amazonia, we conducted a multiyear demographic
census of 292 populations of two leaf-inhabiting (i.e.,
epiphyllous) bryophyte species transplanted from continuous
forest into a network of 10 study sites ranging from 1, 10,
and 100 to > 10,000 ha in size. All populations experienced
significantly positive local growth (lambda > 1) and a
nearly constant per-generational extinction probability
(15%). However, experimental leaf patches in reserves of >
or = 100 ha experienced nearly double (48%) the colonization
probability observed in small reserves (27%), suggesting
that the proximate cause of epiphyll species loss in small
fragments (< or = 10 ha) is reduced colonization.
Nonetheless, populations of small fragments exhibit rates of
colonization above patch extinction, positive local growth,
and low temporal variation, which are features that should
theoretically reduce the probability of extinction. This
result suggests that for habitat-tracking metapopulations
subject to frequent and stochastic turnover events,
including epiphylls, colonization/extinction ratios must be
maintained well above unity to ensure metapopulation
persistence.},
Doi = {10.1086/499376},
Key = {fds230638}
}
@article{fds230640,
Author = {Shaw, AJ and Cox, CJ},
Title = {Variation in "biodiversity value" of peatmoss species in
Sphagnum section Acutifolia (Sphagnaceae).},
Journal = {American journal of botany},
Volume = {92},
Number = {11},
Pages = {1774-1783},
Year = {2005},
Month = {November},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21646095},
Abstract = {Species are the most common currency by which biodiversity
is measured, but species are not equivalent in "biodiversity
value" because of differences in phylogenetic history and
current population processes. Morphologically defined
species in Sphagnum section Acutifolia (Bryophyta) were
compared with regard to how phylogenetically distinct each
is from its sister species and how much nucleotide variation
each encompasses. Comparisons were based on sequence
variation at seven nuclear and chloroplast loci. Assignment
of collections to morphospecies accounted for about 57-75%
of the overall nucleotide variation at the seven loci, but
morphospecies differed greatly in how much nucleotide
diversity they encompass. In addition, morphospecies varied
widely in their genetic distinctiveness, estimated as the
length of the stem branch from the most recent common
ancestor and numbers of differentially fixed and shared
polymorphic nucleotides among taxa. Levels of molecular
diversity within morphospecies were not correlated with
their degree of isolation. Factors that affected the
biodiversity value of species include age, mode of origin,
demographic history, and reproductive biology.},
Doi = {10.3732/ajb.92.11.1774},
Key = {fds230640}
}
@article{fds230639,
Author = {Buryová, B and Shaw, AJ},
Title = {Phenotypic plasticity in Philonotis fontana (Bryopsida:
Bartramiaceae)},
Journal = {Journal of Bryology},
Volume = {27},
Number = {1},
Pages = {13-22},
Publisher = {Informa UK Limited},
Year = {2005},
Month = {April},
url = {http://dx.doi.org/10.1179/174328205X40545},
Abstract = {Gametophytes from six populations of the moss Philonotis
fontana (Hedw.) Brid. were grown under two light and two
water regimes in order to assess the effects of these
environmental factors on gametophytic architecture and leaf
and leaf-cell dimensions. Both light and water affected
growth, but the light treatments had a greater effect, and
on more characters, than did the water treatments.
Significant population effects under common garden
conditions point to genetic variation for several traits,
and population x environmental treatment interactions
demonstrated genetic variation for patterns of phenotypic
plasticity, i.e. plants differed in their 'norms of
reaction'. Variation among populations in leaf dimensions
tended to have a strong genetic component (20-30% of the
total variation), whereas cell dimensions showed relatively
little genetic variation (<10% of the total). © British
Bryological Society 2005.},
Doi = {10.1179/174328205X40545},
Key = {fds230639}
}
@article{fds230539,
Author = {McDaniel, SF and Shaw, AJ},
Title = {Selective sweeps and intercontinental migration in the
cosmopolitan moss Ceratodon purpureus (Hedw.)
Brid.},
Journal = {Molecular ecology},
Volume = {14},
Number = {4},
Pages = {1121-1132},
Year = {2005},
Month = {April},
ISSN = {0962-1083},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15773940},
Abstract = {The moss Ceratodon purpureus has long been used as a model
system in plant development and physiology. However, the
molecular population genetics of the species remains
virtually unexplored. In this study, we used population
genetic analyses of DNA sequence data from three unlinked
loci (atpB-rbcL spacer, adk, and phy2) to examine
biogeographical patterns in a global sample of this species.
The three loci differed significantly in mutation frequency
spectra and implied population structure. Pairs of
haplotypes from single populations were frequently more
divergent than haplotypes sampled from widely disjunct
populations. In the atpB-rbcL spacer and adk samples,
Australasian haplotypes were more closely related to
Northern Hemisphere haplotypes than to haplotypes found in
the equatorial regions. In contrast, the phy2 sample showed
that the north and south temperate regions were genetically
divergent, with the equatorial regions intermediate.
Maximum-likelihood estimates (MLE) of the rates of migration
between the two hemispheres were significantly different for
the two nuclear genes. The frequency spectra of mutations
indicated that differences in implied population structure
among the three loci resulted from directional selection on
the chloroplast genome and on the chromosomal segment
containing adk. Collectively, these data suggest that
long-distance migration within the Northern Hemisphere and
Australasian regions is common (relative to the mutation
rate) and that migration between these two regions,
potentially via equatorial populations, is more frequent
than migration among equatorial populations.},
Doi = {10.1111/j.1365-294x.2005.02484.x},
Key = {fds230539}
}
@article{fds230642,
Author = {Ryall, K and Whitton, J and Schofield, W and Ellis, S and Shaw,
AJ},
Title = {Molecular phylogenetic study of interspecific variation in
the moss Isothecium (Brachytheciaceae)},
Journal = {Systematic Botany},
Volume = {30},
Number = {2},
Pages = {242-247},
Publisher = {American Society of Plant Taxonomists},
Year = {2005},
Month = {April},
url = {http://dx.doi.org/10.1600/0363644054223567},
Abstract = {Isothecium myosuroides is an abundant and taxonomically
problematic moss that occurs in Europe and on the west and
east coasts of North America. It has sometimes been split
into two taxa, I. myosuroides on the east coast of North
America and in Europe, and I. stoloniferum on the west coast
of North America. Isothecium stoloniferum has four distinct
morphological types known as the ordinary, julaceous,
coarse, and pinnate morphs. The degree to which the
morphotypes are genetically distinct versus ecologically
determined has been debated as has the distinction between
I. stoloniferum and I. myosuroides, resulting in conflicting
taxonomic treatments. This study uses phylogenetic analyses
of the trnL-trnf and trnG regions of the chloroplast genome
to examine relationships among the two species and four
morphotypes. Molecular phylogenetic analyses reveal that
there is some genetic basis to the morphs of I.
stoloniferum, and that I. stoloniferum is paraphyletic.
Accessions of I. myosuroides form a trans-Atlantic
monophyletic group. The remaining samples form two distinct
groups that each include samples of two morphotypes within
I. stoloniferum. Populations of julaceous and ordinary
morphotypes form a monophyletic group. Populations of coarse
and pinnate morphotypes form an unresolved polytomy at the
base of the clade that includes accessions of I.
myosuroides. © Copyright 2005 by the American Society of
Plant Taxonomists.},
Doi = {10.1600/0363644054223567},
Key = {fds230642}
}
@article{fds230641,
Author = {Shaw, AJ and Melosik, I and Cox, CJ and Boles, SB},
Title = {Divergent and reticulate evolution in closely related
species of Sphagnum section Subsecunda},
Journal = {Bryologist},
Volume = {108},
Number = {3},
Pages = {363-376},
Publisher = {American Bryological and Lichenological Society},
Year = {2005},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2005)108[0363:DAREIC]2.0.CO;2},
Abstract = {The Sphagnum subsecundum complex includes a group of closely
related, morphologically intergrading species in section
Subsecunda. Nucleotide sequences from six genes (four
nuclear and two chloroplast) were obtained from 74
populations representing all the putative species in this
complex (S. denticulatum, S. inundatum, S. lescurii, S.
subsecundum) to determine if the morphologically-defined
taxa represent genetically distinct units. Sampling included
populations from North America, Europe, and Asia. Parsimony
analyses resolved two major groups of populations, one
containing only North American plants (plus one from
northern Russia) and the other containing all but two of the
European samples, a few from North America, and one from
Japan. Two of the four morphospecies occurred in both
groups. Shimodaira-Hasegawa (SH) tests indicate that
monophyly of S. inundatum, S. subsecundum, and S. lescurii
can be rejected, whereas monophyly of S. denticulatum cannot
be rejected with our data. Intragenic recombination was
detected in both groups of populations, but was
substantially higher in the "American" group. Because
recombination calls into question the applicability of
character-based phylogenetic methods, including parsimony,
molecular similarity among populations was estimated using
neighbor-joining. Neighbor-joining also resolved
geographically correlated groups and corroborated the
conclusion that morphologically defined species do not form
genetically coherent groups. Groups oj populations more
closely reflect geographic than morphological patterns.
Copyright © 2005 by the American Bryological and
Lichenological Society, Inc.},
Doi = {10.1639/0007-2745(2005)108[0363:DAREIC]2.0.CO;2},
Key = {fds230641}
}
@article{fds230643,
Author = {Shevock, JR and Shaw, AJ},
Title = {Pohlia robertsonii and P. rabunbaldensis (Bryopsida,
Mniaceae), two new species from the western and eastern
United States},
Journal = {Bryologist},
Volume = {108},
Number = {2},
Pages = {177-182},
Publisher = {American Bryological and Lichenological Society},
Year = {2005},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2005)108[0177:PRAPRB]2.0.CO;2},
Abstract = {Pohlia robertsonii is newly described from central
California. Plants with polysetous sporophytes immediately
separate this species from all other members of the genus
Pohlia in North America. Pohlia robertsonii is further
characterized by firm, but not thickened leaf cells,
paroicous inflorescences, long, narrowly cylindric capsules,
and irregular peristomes in which the endostome segments
equal or exceed the exostome teeth, and lack cilia. The
peristomial formula is 4:2:2-4. Pohlia rabunbaldensis is
described from the southern Appalachian Mountains of Georgia
and North Carolina. The slender gametophytes bear single
bud-like gemmae in upper leaf axils. The dull leaves that
are somewhat shriveled on drying resemble those of P.
annotina, but the large single gemmae with flexuose, broadly
laminate leaf primordia resemble those of P. drummondii. The
conspicuously decurrent leaves distinguish P. rabunbaldensis
from both previously known species. Copyright © 2005 by the
American Bryological and Lichenological Society,
Inc.},
Doi = {10.1639/0007-2745(2005)108[0177:PRAPRB]2.0.CO;2},
Key = {fds230643}
}
@article{fds230644,
Author = {Goffinet, B and Wickett, NJ and Shaw, AJ and Cox,
CJ},
Title = {Phylogenetic significance of the rpoA loss in the
chloroplast genome of mosses},
Journal = {Taxon},
Volume = {54},
Number = {2},
Pages = {353-360},
Publisher = {WILEY},
Year = {2005},
Month = {January},
url = {http://dx.doi.org/10.2307/25065363},
Abstract = {A recent survey of arthrodontous mosses revealed that their
chloroplast genome lacks the gene encoding the alpha subunit
of the RNA polymerase (i.e., rpoA), and that at least in
Physcomitrella patens the gene has been transferred to the
nuclear genome. Subsequently the gene was recorded from the
cytoplasmic genome in Takakia and Sphagnum. Here we extend
the survey to representatives of all major lineages of
mosses to determine when in the evolutionary history of the
Bryophyta the loss took place. Amplifications using primers
annealing to the flanking regions of the rpoA gene yield a
product that contains the gene in Takakia, Sphagnum,
Andreaea, Oedipodium, Polytrichaceae, and Buxbaumia. The
gene is lacking in all arthrodontous mosses, including
Diphyscium but also in both species of Tetraphis.
Reconstruction of the transfer on the phylogeny of mosses
suggests (a) that the rpoA gene was lost twice and (b) that
the gene was lost after the divergence of Buxbaumiidae and
prior to the divergence of Diphyscium from the remaining
Bryopsida.},
Doi = {10.2307/25065363},
Key = {fds230644}
}
@article{fds230645,
Author = {Shaw, AJ and Cox, CJ and Goffinet, B},
Title = {Global patterns of moss diversity: Taxonomic and molecular
inferences},
Journal = {Taxon},
Volume = {54},
Number = {2},
Pages = {337-352},
Publisher = {WILEY},
Year = {2005},
Month = {January},
url = {http://dx.doi.org/10.2307/25065362},
Abstract = {Taxonomic and molecular data were utilized to test the
hypothesis that moss diversity is greatest near the equator.
Species richness estimates from 86 taxonomic checklists
representing global moss diversity do not support the
hypothesis that, in general, mosses are more species-rich in
the tropics than at higher latitudes. A significant
latitudinal gradient was, however, detected for North,
Central, and South American samples when analyzed alone.
Taxonomic estimates of biodiversity patterns were compared
to molecular estimates based on standing nucleotide
diversity, and on phylogenetic diversity, the latter taking
into account the historical information contained in a
molecular phylogenetic tree for the mosses. Molecular
estimates suggest that moss diversity is highest in the
Southern Hemisphere and lowest in the Northern Hemisphere,
with the tropics having an intermediate level. The
differences, however, are slight, and analyses of molecular
variance (AMOVA) indicate that there is virtually no
generalized differentiation between major latitudinal zones.
These results reflect the fact that virtually all moss
lineages have representatives in all three latitudinal
zones. At the nucleotide level, mosses best fit the pattern
of "everything is everywhere".},
Doi = {10.2307/25065362},
Key = {fds230645}
}
@article{fds304316,
Author = {Shaw, AJ and Cox, CJ and Boles, SB},
Title = {Phylogeny, species delimitation, and recombination in
Sphagnum section Acutifolia},
Journal = {Systematic Botany},
Volume = {30},
Number = {1},
Pages = {16-33},
Publisher = {American Society of Plant Taxonomists},
Year = {2005},
Month = {January},
url = {http://dx.doi.org/10.1600/0363644053661823},
Abstract = {Nucleotide sequences for six nuclear loci and one
chloroplast region were used to reconstruct phylogenetic
relationships in Sphagnum section Acutifolia. The combined
data matrix, which includes 136 accessions (129 ingroup taxa
and seven outgroups) and 5126 nucleotide sites, was analyzed
using Bayesian inference. Most of the individual
morphospecies commonly recognized in the section were
represented by multiple populations, in some cases by up to
16 accessions from throughout the Northern Hemisphere.
Results of the combined seven-locus analysis resolved many
of the species as monophyletic, but the deeper nodes were
generally without support. Separate analyses of single-locus
data sets revealed significant conflicts, indicating gene
flow among both closely and more distantly related species
within the section. The sequence data allowed likely
parentage to be identified for several species of hybrid
origin, and identified individual accessions that appear to
be genetic admixtures. Taxonomic conclusions that can be
made from the analyses include: 1. Sphagnum wulfianum and S.
aongstroemii should both be included in section Acutifolia,
2. S. subtile cannot be separated from S. capillifolium, and
the two should be synonymized, 3. S. capillifolium and S.
rubellum each contain a monophyletic core of populations and
should be retained as separate species, but 4. S. rubellum
cannot be separated from S. andersonianum and S.
bartlettianum and the three should be merged, 5. S. tenerum
is highly differentiated from S. capillifolium and should be
treated as a separate species, 6. interspecific mixed
ancestry is demonstrated for S. russowii (a likely
allopolyploid), S. skyense, S. arcticum, and S. olafii.
Interspecific recombination appears to be rather common in
section Acutifolia, yet species, for the most part, maintain
cohesiveness. © Copyright 2005 by the American Society of
Plants Taxonomists.},
Doi = {10.1600/0363644053661823},
Key = {fds304316}
}
@article{fds230646,
Author = {Shaw, AJ and Cox, CJ and Boles, SB},
Title = {Phylogeny, species delimitation, and interspecific
hybridization in Sphagnum section Acutifolia.},
Journal = {Syst. Bot},
Volume = {30},
Number = {1},
Pages = {16-33},
Year = {2005},
url = {http://dx.doi.org/10.1600/0363644053661823},
Abstract = {Nucleotide sequences for six nuclear loci and one
chloroplast region were used to reconstruct phylogenetic
relationships in Sphagnum section Acutifolia. The combined
data matrix, which includes 136 accessions (129 ingroup taxa
and seven outgroups) and 5126 nucleotide sites, was analyzed
using Bayesian inference. Most of the individual
morphospecies commonly recognized in the section were
represented by multiple populations, in some cases by up to
16 accessions from throughout the Northern Hemisphere.
Results of the combined seven-locus analysis resolved many
of the species as monophyletic, but the deeper nodes were
generally without support. Separate analyses of single-locus
data sets revealed significant conflicts, indicating gene
flow among both closely and more distantly related species
within the section. The sequence data allowed likely
parentage to be identified for several species of hybrid
origin, and identified individual accessions that appear to
be genetic admixtures. Taxonomic conclusions that can be
made from the analyses include: 1. Sphagnum wulfianum and S.
aongstroemii should both be included in section Acutifolia,
2. S. subtile cannot be separated from S. capillifolium, and
the two should be synonymized, 3. S. capillifolium and S.
rubellum each contain a monophyletic core of populations and
should be retained as separate species, but 4. S. rubellum
cannot be separated from S. andersonianum and S.
bartlettianum and the three should be merged, 5. S. tenerum
is highly differentiated from S. capillifolium and should be
treated as a separate species, 6. interspecific mixed
ancestry is demonstrated for S. russowii (a likely
allopolyploid), S. skyense, S. arcticum, and S. olafii.
Interspecific recombination appears to be rather common in
section Acutifolia, yet species, for the most part, maintain
cohesiveness. © Copyright 2005 by the American Society of
Plants Taxonomists.},
Doi = {10.1600/0363644053661823},
Key = {fds230646}
}
@article{fds230648,
Author = {Shaw, J and Renzaglia, K},
Title = {Phylogeny and diversification of bryophytes},
Journal = {American Journal of Botany},
Volume = {91},
Number = {10},
Pages = {1557-1581},
Publisher = {WILEY},
Year = {2004},
Month = {October},
ISSN = {0002-9122},
url = {http://dx.doi.org/10.3732/ajb.91.10.1557},
Abstract = {The bryophytes comprise three phyla of embryophytes that are
well established to occupy the first nodes among extant
lineages in the land-plant tree of life. The three bryophyte
groups (hornworts, liverworts, mosses) may not form a
monophyletic clade, but they share life history features
including dominant free-living gametophytes and matrotrophic
monosporangiate sporophytes. Because of their unique
vegetative and reproductive innovations and their critical
position in embryophyte phylogeny, studies of bryophytes are
crucial to understanding the evolution of land plant
morphology and genomes. This review focuses on phylogenetic
relationships within each of the three divisions of
bryophytes and relates morphological diversity to new
insights about those relationships. Most previous work has
been on the mosses, but progress on understanding the
phylogeny of hornworts and liverworts is advancing at a
rapid pace. Multilocus multigenome studies have been
successful at resolving deep relationships within the mosses
and liverworts, whereas single-gene analyses have advanced
understanding of hornwort evolution.},
Doi = {10.3732/ajb.91.10.1557},
Key = {fds230648}
}
@article{fds230650,
Author = {Goffinet, B and Shaw, AJ and Cox, CJ},
Title = {Phylogenetic inferences in the dung-moss family Splachnaceae
from analyses of cpDNA sequence data and implications for
the evolution of entomophily.},
Journal = {American journal of botany},
Volume = {91},
Number = {5},
Pages = {748-759},
Year = {2004},
Month = {May},
ISSN = {0002-9122},
url = {http://dx.doi.org/10.3732/ajb.91.5.748},
Abstract = {The moss family Splachnaceae is characterized by half of its
members relying on insects for spore dispersal. These
species grow on dung or other animal substrates. They
produce small and aggregated spores, and their capsule is
modified to attract coprophilous insects or carrion flies
using olfactory and visual cues. Systematic concepts and
implicit evolutionary inferences have relied much on
variation in characters associated with the spore dispersal
syndrome. Phylogenetic reconstructions based on sequence
variation of two chloroplast loci (trnL-trnF region and the
rps4 gene) suggest that most supraspecific taxa are poly- or
paraphyletic. Transformations in morphological characters
associated to the syndrome thus offer little if any
phylogenetically informative signal. Brachymitrion is
resolved in a nested position within Tayloria. A new
combination, Tayloria immersa (Goffinet) Goffinet, Shaw &
Cox is proposed for B. immersum. Only one of the five
subgenera of Tayloria (subg. Orthodon) is potentially
monophyletic. Voitia shares a common ancestor with
Tetraplodon and is thus nested within the Splachnoideae. The
affinities of Aplodon remain ambiguous. Reconstruction of
shifts between wind and insect spore dispersal syndromes
suggests that entomophily arose more than once and may have
been followed by a reversal to the generalist strategy in
two lineages.},
Doi = {10.3732/ajb.91.5.748},
Key = {fds230650}
}
@article{fds230673,
Author = {Vanderpoorten, A and Shaw, AJ and Cox, CJ},
Title = {Evolution of multiple paralogous adenosine kinase genes in
the moss genus Hygroamblystegium: phylogenetic
implications.},
Journal = {Molecular phylogenetics and evolution},
Volume = {31},
Number = {2},
Pages = {505-516},
Year = {2004},
Month = {May},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15062791},
Abstract = {Maximum likelihood analyses of DNA sequences from two
chloroplast regions, trnL-trnF and atpB-rbcL, and the
internal transcribed spacers of 18S-5.8S-26S rRNA gene
array, were performed to resolve species relationships
within the moss genus Hygroamblystegium. Constraining
morphospecies to monophyly resulted in significantly less
likely trees for H. tenax, but not for the other species.
The lack of support for most clades and the partial
incongruence among topologies necessitated the use of
another independent, more variable region, namely the
adenosine kinase gene (adk). Sequences for adk were
polymorphic but were present as multiple copies within
individuals, making parology a problem for phylogenetic
analyses. Adk evolution was reconstructed using a reconciled
gene tree approach in which duplications and losses were
minimized in the context of an estimate of the species tree
derived from the analysis of the cp and nrDNA sequence data.
Additional resolution of the species tree was then obtained
by searching for reconstructions that further reduced adk
duplications and losses. All the traditionally recognized
morphospecies appeared to be polyphyletic in the resulting
tree. Together with previous data from different molecular
markers, the results support the interpretation that
Hygroamblystegium represents a recent radiation in which
molecular and morphological evolution have been
uncoupled.},
Doi = {10.1016/j.ympev.2003.09.020},
Key = {fds230673}
}
@article{fds230649,
Author = {Cox, CJ and Goffinet, B and Jonathan Shaw and A and Boles,
SB},
Title = {Phylogenetic relationships among the mosses based on
heterogeneous Bayesian analysis of multiple genes from
multiple genomic compartments},
Journal = {Systematic Botany},
Volume = {29},
Number = {2},
Pages = {234-250},
Publisher = {American Society of Plant Taxonomists},
Year = {2004},
Month = {April},
ISSN = {0363-6445},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000221661400002&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Nucleotide sequences from eight nuclear, chloroplast, and
mitochondrial genes were obtained from 30 mosses (plus four
outgroup liverworts) in order to resolve phylogenetic
relationships among the major clades of division Bryophyta.
Phylogenetic analyses were conducted using maximum
parsimony, maximum likelihood (ML), and Bayesian inference.
Inferences were compared from Bayesian analyses using
homogeneous and several heterogeneous models. Estimates of
clade confidence were based on bootstrap analyses, posterior
probabilities (in Bayesian analyses) and novel combined
approaches. Most ingroup relationships were congruent among
analyses, but support for individual clades depended on the
analytical approach. Increasingly parameterized models of
nucleotide substitution in the likelihood analyses provided
significantly higher goodness-of-fit to the data. The
results suggest that 1) the Bryophyta, including Sphagnum
and Takakia, are monophyletic, 2) Andreaea and Andreaeobryum
form a monophyletic group, 3) Oedipodium griffithianum is
sister to all other operculate taxa, 4) mosses with
nematodontous peristomes are paraphyletic and basal to
arthrodontous mosses, 5) Diphyscium is sister to all other
arthrodontous mosses, 6) Encalypta is sister to the
Funariaceae, and 6) mosses with diplolepideous-alternate
peristomes form a monophyletic group. Implications of the
phylogenetic hypothesis for morphological evolution in
mosses include 1) a pseudopodium has arisen independently in
Sphagnum and Andreaea, 2) the mucilage hairs of
Andreaeobryum and Takakia are non-homologous, 3) the stomata
found in Sphagnum are not homologous to those of other
mosses, and 4) that stomata were absent in the ancestor of
all mosses.},
Doi = {10.1600/036364404774195458},
Key = {fds230649}
}
@article{fds230537,
Author = {Rams, S and Ros, RM and Werner, O and Shaw, AJ},
Title = {Pohlia bolanderi from Sierra Nevada, Spain, new to the
European bryophyte flora},
Journal = {Bryologist},
Volume = {107},
Number = {3},
Pages = {312-315},
Publisher = {American Bryological and Lichenological Society},
Year = {2004},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2004)107[0312:PBFSNS]2.0.CO;2},
Abstract = {Pohlia bolanderi (Lesq.) Broth. is reported for the first
time for Europe from the south of Spain (Sierra Nevada
range). A description from European material is provided and
differences from closely related species, with which it has
been confused, are discussed. It is also known from alpine
regions in western North America, including British
Columbia, Washington, Oregon, California, and
Nevada.},
Doi = {10.1639/0007-2745(2004)107[0312:PBFSNS]2.0.CO;2},
Key = {fds230537}
}
@article{fds230651,
Author = {Shaw, J and Cox, CJ and Boles, SB},
Title = {Phylogenetic relationships among Sphagnum sections:
Hemitheca, Isocladus, and Subsecunda},
Journal = {Bryologist},
Volume = {107},
Number = {2},
Pages = {189-196},
Publisher = {American Bryological and Lichenological Society},
Year = {2004},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2004)107[0189:PRASSH]2.0.CO;2},
Abstract = {Sphagnum macrophyllum, S. pylaesii, and S. cyclophyllum are
morphologically atypical in the genus Sphagnum and their
systematic placement has been a source of controversy. The
first is generally classified in the mono-specific section
Isocladus, and the second as section Hemitheca. Sphagnum
cyclophyllum is classified in the section Subsecunda, but
several authors have hypothesized a close relationship
between all three species. Nucleotide sequences from eight
nuclear and chloroplast loci were obtained to test
hypotheses about relationships among these taxa.
Phylogenetic analyses resolve these species (along with S.
microcarpum, closely related to S. cyclophyllum) in a
well-supported monophyletic group within the section
Subsecunda. Sphagnum macrophyllum is sister to S.
cyclophyllum, S. microcarpum, and S. pylaesii. Sphagnum
cyclophyllum and S. microcarpum form a clade that is sister
to S. pylaesii. Two mutually monophyletic groups of
populations are resolved within S. pylaesii, one including
the European populations and the other including populations
from eastern North America and South America. The European
populations are almost identical at the nucleotide sequence
level whereas the American populations are genetically
diverse. Short, delicate pseudopodia; exceptionally large
opercula; and an absence or near absence of pseudostomata
appear to be synapomorphies for the clade containing S.
macrophyllum, S. microcarpum, S. cyclophyllum, and S.
pylaesii.},
Doi = {10.1639/0007-2745(2004)107[0189:PRASSH]2.0.CO;2},
Key = {fds230651}
}
@article{fds339389,
Author = {Shaw, AJ and Cox, CJ and Melosik, I},
Title = {Diversification of peatmosses: A phylogenetic
approach},
Journal = {MOLECULAR SYSTEMATICS OF BRYOPHYTES},
Volume = {98},
Series = {Monographs in Systematic Botany from the Missouri Botanical
Garden},
Pages = {240-254},
Booktitle = {Molecular systematics of bryophytes: progress, problems &
perspectives},
Publisher = {MISSOURI BOTANICAL GARDEN},
Editor = {Goffinet, B and Hollowell, V and Magill, R},
Year = {2004},
Month = {January},
ISBN = {1-930723-38-5},
Key = {fds339389}
}
@article{fds230647,
Author = {Buck, WR and Cox, CJ and Shaw, AJ and Goffinet, B},
Title = {Ordinal relationships of pleurocarpous mosses, with special
emphasis on the Hookeriales},
Journal = {Systematics and Biodiversity},
Volume = {2},
Number = {2},
Pages = {121-145},
Publisher = {Informa UK Limited},
Year = {2004},
url = {http://dx.doi.org/10.1017/S1477200004001410},
Abstract = {Sequence data from four DNA regions, namely, chloroplast
trnl-trn? and rps4, mitochondrial nad$, and nuclear 26S
rDNA, were surveyed from 89 taxa traditionally associated
with the Hookeriales, five Hypnales and five outgroups.
Phylogenetic reconstruction was performed using the maximum
parsimony and maximum likelihood optimality criteria and by
Bayesian phylogenetic inference. Thirteen morphological
characters were optimized on the resulting phytogeny using
maximum likelihood. Inferences of character evolution based
on the molecular phytogeny suggest that (1) the core of
pleurocarpous mosses (i.e. the Hypnanae) is best defined and
thus distinguished from the Ptychomnianae by smooth rather
than furrowed capsules, (2) a synapomorphy for the
Ptychomnianae is the short and double (or absent) costa and
(3) the Hookeriales are defined by undifferentiated alar
cells. The Ptychomniaceae plus Garovagliaceae are recognized
as a single family in its own order, the Ptychomniales ord.
nov. and superorder, the Ptychomnianae, superord. nov. This
superorder is sister to the combined Hypnales and
Hookeriales, i.e. the Hypnanae. The Hookeriales are
interpreted as consisting of seven families, the
Hy-popterygiaceae, Saulomataceae fam. nov., Daltoniaceae,
Schimperobryaceae fam. nov., Hookeriaceae, Leucomiaceae and
Pilotrichaceae. The Adelotheciaceae are embedded within the
Daltoniaceae and considered synonymous with that family.
Within the Ptychomniaceae, Ptychomniella is raised from a
subgenus of Ptychomnion to generic status. Euptychium
setigerum and its monospecific section, Crassisubulata, are
transferred to Garovaglia. Callicostella diatomophila is
transferred to Diploneuron. Additional alterations at the
generic level await more data. © 2004, Taylor & Francis
Group, LLC. All rights reserved.},
Doi = {10.1017/S1477200004001410},
Key = {fds230647}
}
@article{fds230670,
Author = {Shaw, AJ and Cox, CJ and Boles, SB},
Title = {Polarity of peatmoss (Sphagnum) evolution: who says
bryophytes have no roots?},
Journal = {American journal of botany},
Volume = {90},
Number = {12},
Pages = {1777-1787},
Year = {2003},
Month = {December},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21653354},
Abstract = {The class Sphagnopsida (Bryophyta) includes two genera:
Ambuchanania and Sphagnum. Ambuchanania contains just one
rare species known from two Tasmanian localities, but
Sphagnum comprises a speciose clade of mosses that dominates
many wetland ecosystems, especially in the boreal zone of
the Northern Hemisphere. Recent phylogenetic analyses have
resolved well-supported clades within Sphagnum, but
polarizing Sphagnum evolution has been problematic because
the genus is so isolated that it is difficult to determine
homologies between morphological and/or molecular traits
within Sphagnum with those of any potential outgroup. DNA
sequences from 16 genomic regions representing the
mitochondrial, chloroplast, and nuclear genomes (ca. 16
kilobases) were obtained from 24 species of Sphagnum plus
one species each from Takakia and Andreaea in order to
resolve a rooted phylogeny. Two tropical species, S.
sericeum and S. lapazense, were resolved as sister to the
rest of the genus and are extremely divergent from all other
sphagna. The main Sphagnum lineage consists of two clades;
one includes the sections Sphagnum, Rigida, and Cuspidata,
and the other includes Subsecunda, Acutifolia, and
Squarrosa. The placement of section Subsecunda is weakly
supported, but other nodes are strongly supported by maximum
parsimony, maximum likelihood, and Bayesian analyses. In
addition to homogeneous Bayesian analyses, heterogeneous
models were employed to account for different patterns of
nucleotide substitution among genomic regions.},
Doi = {10.3732/ajb.90.12.1777},
Key = {fds230670}
}
@article{fds230671,
Author = {Davis, EC and Franklin, JB and Shaw, AJ and Vilgalys,
R},
Title = {Endophytic Xylaria (Xylariaceae) among liverworts and
angiosperms: phylogenetics, distribution, and
symbiosis.},
Journal = {American journal of botany},
Volume = {90},
Number = {11},
Pages = {1661-1667},
Year = {2003},
Month = {November},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21653342},
Abstract = {Nuclear ribosomal 18S and internal transcribed spacer (ITS)
sequence data were used to identify endophytic fungi
cultured from six species of liverworts collected in Jamaica
and North Carolina. Comparisons with other published fungal
sequences and phylogenetic analyses yielded the following
conclusions: (1) the endophytes belong to the ascomycete
families Xylariaceae, Hypocreaceae, and Ophiostomataceae,
and (2) liverwort endophytes in the genus Xylaria are
closely related to each other and to endophytes isolated
from angiosperms in China, Puerto Rico, and Europe.
Liverwort endophytes are expected to be foragers or
endophytic specialists, although little is known about the
role of these fungi in symbioses. Features that may indicate
a mutualistic role for these endophytes are
discussed.},
Doi = {10.3732/ajb.90.11.1661},
Key = {fds230671}
}
@article{fds230536,
Author = {Vanderpoorten, A and Boles, S and Shaw, AJ},
Title = {Patterns of Molecular and Morphological Variation in
Leucobryum albidum, L. glaucum, and L. juniperoideum
(Bryopsida)},
Journal = {Systematic Botany},
Volume = {28},
Number = {4},
Pages = {651-656},
Year = {2003},
Month = {October},
Abstract = {Restriction digest patterns from 18S-26S nuclear ribosomal
DNA internal transcribed spacers (ITS) were employed to
investigate delineation between the morphologically similar
moss species Leucobryum glaucum, L. juniperoideum, and L.
albidum. Discriminant analysis allowed assignment of
specimens to haplotypes based on their morphological
features and supported the recognition of L. glaucum and L.
albidum. In contrast, L. albidum and L. juniperoideum both
corresponded to the same haplotype. Many populations could
be readily assigned to either L. glaucum or L. albidum by
their morphological features. However, morphological
variation between these two species was continuous and one
of the ITS haplotypes could not be unambiguously
characterized by its morphology. Genetically and
morphologically identifiable specimens of L. albidum were
sampled in Europe and North America, in contrast to the
traditional interpretation of L. albidum as a North American
endemic. Although L. albidum seems to have a more
southern-Atlantic distribution pattern than L. glaucum, the
two species occupy broadly overlapping geographic ranges and
were sometimes found intermixed.},
Key = {fds230536}
}
@article{fds230672,
Author = {Shaw, AJ and Cox, CJ and Boles, SB},
Title = {Global patterns in peatmoss biodiversity.},
Journal = {Molecular ecology},
Volume = {12},
Number = {10},
Pages = {2553-2570},
Year = {2003},
Month = {October},
ISSN = {0962-1083},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12969461},
Abstract = {DNA sequence data from the nuclear ribosomal internal
transcribed spacers (ITS) and the trnL-trnF chloroplast DNA
regions were used to quantify geographical partitioning of
global biodiversity in peatmosses (Sphagnum), and to compare
patterns of molecular diversity with patterns of species
richness. Molecular diversity was estimated for boreal,
tropical, Neotropical, nonboreal (tropical plus Southern
Hemisphere), Old World and New World partitions, based on a
total of 436 accessions. Diversity was partitioned among
geographical regions in terms of combined nuclear and
chloroplast sequence data and separately for the ITS and
trnL-trnF data sets. Levels of variation were estimated
using phylogenetic diversity (PD), which incorporates branch
lengths from a phylogenetic tree, and the number of
polymorphic nucleotide sites. Estimates of species richness
suggest that peatmoss diversity is higher in New World than
Old World regions, and that the Neotropics constitute a
"hotspot" of diversity. Molecular estimates, in contrast,
indicate that peatmoss biodiversity is almost evenly divided
between New and Old World regions, and that the Neotropics
account for only 20-35% of global peatmoss diversity. In
general, levels of tropical and boreal peatmoss molecular
diversity were comparable. Two species, S. sericeum from the
Old World tropics and S. lapazense from Bolivia, are
remarkably divergent in nucleotide sequences from all other
Sphagna and together account for almost 20% of all peatmoss
diversity, although they are represented by only three of
the 436 accessions (0.7%). These species clearly demonstrate
the nonequivalence of species biodiversity
value.},
Doi = {10.1046/j.1365-294x.2003.01929.x},
Key = {fds230672}
}
@article{fds230674,
Author = {Shaw, AJ and Cox, CJ and Goffinet, B and Buck, WR and Boles,
SB},
Title = {Phylogenetic evidence of a rapid radiation of pleurocarpous
mosses (Bryophyta).},
Journal = {Evolution; international journal of organic
evolution},
Volume = {57},
Number = {10},
Pages = {2226-2241},
Year = {2003},
Month = {October},
ISSN = {0014-3820},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14628911},
Abstract = {Pleurocarpous mosses, characterized by lateral female
gametangia and highly branched, interwoven stems, comprise
three orders and some 5000 species, or almost half of all
moss diversity. Recent phylogenetic analyses resolve the
Ptychomniales as sister to the Hypnales plus Hookeriales.
Species richness is highly asymmetric with approximately 100
Ptychomniales, 750 Hookeriales, and 4400 Hypnales.
Chloroplast DNA (cpDNA) sequences were obtained to compare
partitioning of molecular diversity among the orders with
estimates of species richness, and to test the hypothesis
that either the Hookeriales or Hypnales underwent a period
(or periods) of exceptionally rapid diversification. Levels
of biodiversity were quantified using explicitly historical
"phylogenetic diversity" and non-historical estimates of
standing sequence diversity. Diversification rates were
visualized using lineage-through-time (LTT) plots, and
statistical tests of alternative diversification models were
performed using the methods of Paradis (1997). The effects
of incomplete sampling on the shape of LTT plots and
performance of statistical tests were investigated using
simulated phylogenies with incomplete sampling. Despite a
much larger number of accepted species, the Hypnales contain
lower levels of (cpDNA) biodiversity than their sister
group, the Hookeriales, based on all molecular measures.
Simulations confirm previous results that incomplete
sampling yields diversification patterns that appear to
reflect a decreasing rate through time, even when the true
phylogenies were simulated with constant rates. Comparisons
between simulated results and empirical data indicate that a
constant rate of diversification cannot be rejected for the
Hookeriales. The Hypnales, however, appear to have undergone
a period of exceptionally rapid diversification for the
earliest 20% of their history.},
Doi = {10.1111/j.0014-3820.2003.tb00235.x},
Key = {fds230674}
}
@article{fds230675,
Author = {Vanderpoorten, A and Goffinet, B and Hedenäs, L and Cox, CJ and Shaw,
AJ},
Title = {A taxonomic reassessment of the Vittiaceae (Hypnales,
Bryopsida): Evidence from phylogenetic analyses of combined
chloroplast and nuclear sequence data},
Journal = {Plant Systematics and Evolution},
Volume = {241},
Number = {1-2},
Pages = {1-12},
Publisher = {Springer Nature},
Year = {2003},
Month = {October},
url = {http://dx.doi.org/10.1007/s00606-003-0032-z},
Abstract = {The Vittiaceae are a small family of aquatic mosses that are
defined based on gametophytic traits whose interpretation
has led to conflicting taxonomic arrangements. Phylogenetic
analyses of two cpDNA regions, trnL-trnF and atpB-rbcL,
indicate that Vittia is nested within the Amblystegiaceae s.
str., suggesting that the family Vittiaceae should not be
recognized. Platylomella lescurii appears nested within the
Thuidiaceae/Leskeaceae. This suggests that the series of
character states shared by Vittia and Platylomella,
including a differentiated leaf border, short laminal cells,
stiff stems, and a thick costa, are convergent features that
arose independently in unrelated lineages of aquatic
Hypnales. Within the Amblystegiaceae, phylogenetic analyses
of the two cpDNA regions combined with ITS sequence data
show that Hypnobartlettia, Vittia elimbata spec. nov., V.
pachyloma, and V. salina, despite their strong morphological
similarity to aquatic Amblystegium species, form a clade
that is sister to the Drepanocladus/Pseudocalliergon
complex. This combined clade is unresolved at a polytomy
that includes Amblystegium serpens and a clade including all
the other Amblystegium species. The occurrence of A. serpens
outside the strongly supported clade including other
Amblystegium species suggests that A. serpens may be better
accommodated in a distinct genus. Amblystegium serpens is
the type species of Amblystegium and thus retains the name.
The other species are accommodated in their own genus,
Hygroamblystegium, including H. fluviatile, H. humile comb.
nov., H. noterophyllum, H. tenax, and H.
varium.},
Doi = {10.1007/s00606-003-0032-z},
Key = {fds230675}
}
@article{fds230535,
Author = {Werner, O and Ros, RM and Guerra, J and Shaw, AJ},
Title = {Molecular data confirm the presence of Anacolia menziesii
(Bartramiaceae, Musci) in Southern Europe and its separation
from Anacolia webbii},
Journal = {Systematic Botany},
Volume = {28},
Number = {3},
Pages = {483-489},
Year = {2003},
Month = {July},
Abstract = {ISSR (Inter-Simple Sequence Repeat) fingerprint data and
nrITS sequences confirm the presence of Anacolia menziesii
in Europe. The species is more variable genetically in North
America than in Europe. The data show only minor
differentiation between the North American and European
populations of A. menziesii. Anacolia webbii is
morphologically and genetically very similar to Anacolia
menziesii, but can be separated from Anacolia menziesii with
high confidence based on the ITS and ISSR data. Long
distance dispersal is the most likely explanation for the
disjunction of Anacolia menziesii between North America and
Europe.},
Key = {fds230535}
}
@article{fds230677,
Author = {Shaw, AJ and Werner, O and Ros, RM},
Title = {Intercontinental Mediterranean disjunct mosses:
morphological and molecular patterns.},
Journal = {American journal of botany},
Volume = {90},
Number = {4},
Pages = {540-550},
Year = {2003},
Month = {April},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21659147},
Abstract = {This study focused on three species that occur disjunctly
between western North America and the Mediterranean region
of southern Europe, northern Africa, and western Asia,
forming the so-called Madrean-Tethyan distribution pattern.
Quantitative morphological characters were measured in New
and Old World plants to find any subtle phenotypic
differentiation between the disjunct populations. Sequences
from the nuclear ribosomal internal transcribed spacer
region were obtained from the same populations to assess
differentiation at the molecular level and to compare
molecular diversity with patterns of morphological
similarity among plants. Little or no morphological
differentiation existed between New and Old World plants in
any of the species, but internal transcribed spacer (ITS)
sequences revealed some phylogeographic structure. Patterns
of morphological similarity in all three species were
incongruent with phylogeographic structure revealed by
sequence data. New World populations were more variable than
Old World populations at the molecular level in the three
species. Despite some evidence for differentiation between
disjunct plants, no plausible mutation rate would date the
divergence at ≥20 million years ago (MYA), as implied by
the Madrean-Tethyan hypothesis. Recent long-distance
dispersal is a more likely explanation for intercontinental
disjunctions in these species.},
Doi = {10.3732/ajb.90.4.540},
Key = {fds230677}
}
@article{fds230676,
Author = {McDaniel, SF and Shaw, AJ},
Title = {Phylogeographic structure and cryptic speciation in the
trans-Antarctic moss Pyrrhobryum mnioides.},
Journal = {Evolution; international journal of organic
evolution},
Volume = {57},
Number = {2},
Pages = {205-215},
Year = {2003},
Month = {Fall},
ISSN = {0014-3820},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12683518},
Abstract = {Many bryophyte species have distributions that span multiple
continents. The hypotheses historically advanced to explain
such distributions rely on either long-distance spore
dispersal or slow rates of morphological evolution following
ancient continental vicariance events. We use phylogenetic
analyses of DNA sequence variation at three chloroplast loci
(atpB-rbcL spacer, rps4 gene, and trnL intron and 3' spacer)
to examine these two hypotheses in the trans-Antarctic moss
Pyrrhobryum mnioides. We find: (1) reciprocal monophyly of
Australasian and South American populations, indicating a
lack of intercontinental dispersal; (2) shared haplotypes
between Australia and New Zealand, suggesting recent or
ongoing migration across the Tasman Sea; and (3) reciprocal
monophyly among Patagonian and neotropical populations,
suggesting no recent migration along the Andes. These
results corroborate experimental work suggesting that spore
features may be critical determinants of species range. We
use the mid-Miocene development of the Atacama Desert, 14
million years ago, to calibrate a molecular clock for the
tree. The age of the trans-Antarctic disjunction is
estimated to be 80 million years ago, consistent with
Gondwanan vicariance, making it among the most ancient
documented cases of cryptic speciation. These data are in
accord with niche conservatism, but whether the
morphological stasis is a product of stabilizing selection
or phylogenetic constraint is unknown.},
Doi = {10.1111/j.0014-3820.2003.tb00256.x},
Key = {fds230676}
}
@article{fds230533,
Author = {Vanderpoorten, A and Hedenäs, L and Cox, CJ and Shaw,
AJ},
Title = {Erratum: Circumscription, classification, and taxonomy of
the Amblystegiaceae (Bryopsida) inferred from nuclear and
chloroplast DNA sequence data and morphology (Taxon (2002)
51:1 (115-122))},
Journal = {Taxon},
Volume = {51},
Number = {3},
Pages = {633},
Publisher = {INT ASSOC PLANT TAXONOMY},
Year = {2002},
Month = {August},
ISSN = {0040-0262},
Key = {fds230533}
}
@article{fds230653,
Author = {La Farge and C and Shaw, AJ and Vitt, DH},
Title = {The circumscription of the Dicranaceae (Bryopsida) based on
the chloroplast regions trnL - trnF and rps4},
Journal = {Systematic Botany},
Volume = {27},
Number = {3},
Pages = {435-452},
Year = {2002},
Month = {July},
ISSN = {0363-6445},
Abstract = {The Dicranaceae have been classified as one of the largest,
most heterogeneous families of the moss subclass Dicranidae.
Circumscriptions of the family have varied, with some
studies excluding selected subfamilies and recognizing them
at the familial rank, whereas others have retained a broader
familial concept. As well, classifications have varied in
their generic circumscriptions of the subfamilies.
Chloroplast DNA sequence data (trnL (UAA) - trnF (GAA) and
rps4) were used to examine the monophyly of the family and
phylogenetic relationships among the subfamilial and generic
taxa. Special emphasis was given to subfamily Dicranoideae,
with 18 of the 23 genera sampled. Seventy-four trnL-F and
rps4 sequences formed a matrix of 1161 aligned base pairs
(bp). Phylogenetic analyses using MP and ML criteria were
based on 983 bp (333 parsimony informative) after ambiguous
data were removed. Our results support the following
inferences: 1) Dicranaceae as traditionally defined are
polyphyletic; 2) subfamilies Campylopodioideae,
Dicranelloideae, Rhabdoweisioideae, and Trematodontoideae
are excluded from a robust monophyletic concept of the
Dicranaceae; 3) subfamily Dicranoideae is polyphyletic
unless 16 genera are excluded from the subfamily, seven of
which are transferred to the Rhabdoweisiaceae; 3) subfamily
Paraleucobryoideae is polyphyletic with Brothera resolved in
the Leucobryaceae clade and Paraleucobryum nested within
subfamily Dicranoideae; 4) Dicnemonaceae (including Mesotus)
and Wardiaceae are nested within traditional members of the
Dicranaceae; and 5) four clades - Dicranoideae, Mesotoideae,
Dicranoloma group plus Wardia, and the Leucoloma group, form
a robust monophyletic taxon, considered here as a restricted
concept of Dicranaceae (sensu stricto). This circumscription
excludes 18 genera that have previously been included in the
Dicranaceae.},
Key = {fds230653}
}
@article{fds230668,
Author = {Goffinet, B and Shaw, AJ},
Title = {Independent origins of cleistocarpy in the splachnaceae:
Analyses of cpDNA sequences and polyphyly of the Voitioideae
(Bryophyta)},
Journal = {Systematic Botany},
Volume = {27},
Number = {2},
Pages = {203-208},
Year = {2002},
Month = {June},
ISSN = {0363-6445},
Abstract = {Many dung mosses (Splachnaceae) are characterized by
insect-mediated spore dispersal. All of the entomophilous
species are coprophilous, whereas anemophilous species are
humicolous or epiphytic. The three species of the
Voitioideae are coprophilous but are distinguished from
other members of the family by sporangia that remain closed
(cleistocarpous) and lack a peristome. Spores are released
when the sporangial wall disintegrates. Phylogenetic
analyses of nucleotide sequences of the trnL-trnF region and
the rps4 locus (cpDNA) for 25 species of Splachnaceae
suggest that this combination of characters arose twice
within the Splachnaceae and that Voitia grandis is more
closely related to species of Tayloria subgenus Tayloria
rather to the other species of Voitia, which are nested
within the genus Tetraplodon. Hence the new combination
Tayloria grandis (Long) Goffinet & Shaw is made. Although
the optimal trees were left unrooted, our results resolve
the Voitioideae (i.e., the genus Voitia) as nested within
the Splachnoideae. Tile phylogenetic significance of
sporophytic characters within the family Splachnaceae is
briefly discussed.},
Key = {fds230668}
}
@article{fds230667,
Author = {Vanderpoorten, A and Hedenäs, L and Cox, CJ and Shaw,
AJ},
Title = {Phylogeny and morphological evolution of the amblystegiaceae
(Bryopsida).},
Journal = {Molecular phylogenetics and evolution},
Volume = {23},
Number = {1},
Pages = {1-21},
Year = {2002},
Month = {April},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12182399},
Abstract = {To circumscribe the moss family Amblystegiaceae, we
performed a broad-scale analysis of trnL-trnF spacer
sequence data for 168 species of the Hypnales and 11 species
of the Hookeriales and additional analyses of trnL-trnF and
atpB-rbcL (chloroplast DNA), one nuclear region, the
internal transcribed spacers of 18S-26S rDNA, and 68
morphological characters for a reduced data set of 54
species of Hypnales. The traditionally circumscribed
Amblystegiaceae are polyphyletic and include the
Amblystegiaceae s. str. and the Calliergonaceae fam. nov.,
plus several taxa closely related to other Hypnalean
families. Generic relationships within the redefined
Amblystegiaceae were investigated by analyzing data from the
three DNA regions and morphology as used in the broader
analysis. Reconstruction of morphological evolution was
evaluated using maximum-parsimony and maximum-likelihood.
Numerous independent character-state transitions implied by
the phylogeny suggest that morphological characters that
have traditionally been used to delineate the
Amblystegiaceae are homoplastic. Sporophytic traits, which
are generally given primacy over gametophytic traits in moss
classification, are more labile than previously thought, and
many characters that are related to sporophyte
specializations are strongly correlated with habitat
conditions. The evolution of several gametophyte features
previously thought to be reliable for delineating the family
are also strongly correlated with habitat. These
observations help to explain the instability of the
Amblystegiaceae in previous taxonomic and phylogenetic
analyses based on morphology.},
Doi = {10.1006/mpev.2001.1067},
Key = {fds230667}
}
@article{fds230652,
Author = {Buck, WR and Shaw, AJ and Cox, CJ},
Title = {A new species of Leskeodon (Daltoniaceae) from
Ecuador},
Journal = {Brittonia},
Volume = {54},
Number = {3},
Pages = {178-180},
Publisher = {Springer Nature},
Year = {2002},
Month = {January},
url = {http://dx.doi.org/10.1663/0007-196X(2002)054[0178:ANSOLD]2.0.CO;2},
Abstract = {Leskeodon caducifolius is described from recent collections
made at a single site in a cloud forest in southern Ecuador.
The species is distinctive in its small, caducous leaves and
elongate, porose exothecial cells.},
Doi = {10.1663/0007-196X(2002)054[0178:ANSOLD]2.0.CO;2},
Key = {fds230652}
}
@article{fds230654,
Author = {Shaw, AJ and McDaniel, SF and Werner, O and Ros, RM},
Title = {Invited essay: New frontiers in bryology and lichenology.
Phylogeography and phylodemography},
Journal = {Bryologist},
Volume = {105},
Number = {3},
Pages = {373-383},
Publisher = {American Bryological and Lichenological Society},
Year = {2002},
Month = {January},
ISSN = {0007-2745},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000177962700010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Phylogenetic analyses of infraspecific molecular data in
relation to geographic and ecological information has come
to be known as phylogeography. Bryophytes offer fertile
material for such analyses, which can help clarify long
standing biogeographic questions that were intractable
before molecular data became available. In particular,
molecular data can help distinguish between dispersal and
fragmentation explanations for disjunct distributions that
characterize many bryophytes at the specific as well as
higher levels. Phylodemography is the application of
molecular data and phylogenetic analyses to infer past
changes in population size within species. Grounded in
coalescence theory from population genetics, this new field
could be fruitfully applied to bryophytes. Combining
phylogeography and phylodemography yields a powerful
strategy for elucidating evolutionary processes.},
Doi = {10.1639/0007-2745(2002)105[0373:pap]2.0.co;2},
Key = {fds230654}
}
@article{fds230669,
Author = {Vanderpoorten, A and Hedenäs, L and Cox, CJ and Shaw,
AJ},
Title = {Circumscription, classification, and taxonomy of
Amblystegiaceae (Bryopsida) inferred from nuclear and
chloroplast DNA sequence data and morphology},
Journal = {Taxon},
Volume = {51},
Number = {1},
Pages = {115-122},
Publisher = {WILEY},
Year = {2002},
Month = {January},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.2307/1554968},
Abstract = {Results from a previous broad-scale analysis employing
trnL-trnF sequence data for 168 Hypnalean and 11
Hookerialean taxa, and an analysis employing two chloroplast
regions, trnL-trnF and atpB-rbcL, one nuclear region, the
internal transcribed spacers of 18S-26S rDNA, plus 68
morphological characters for a reduced data set of 54
Hypnalean taxa, were used to circumscribe Amblystegiaceae.
The analyses provided two well-supported main clades
including taxa traditionally included in Amblystegiaceae
s.l. and recognized as Amblystegiaceae s.str. [Anacamptodon,
Amblystegium, Campyliadelphus, Campylium, Cratoneuron,
Cratoneuropsis, Drepanocladus s.str., Gradsteinia,
Hygrohypnum s.str. (including the type species, H. luridum,
but excluding a number of other species previously
accommodated in the genus), Hypnobartlettia, Leptodictyum,
Palustriella, Pseudo-calliergon, and Serpoleskea] and
Calliergonaceae stat. nov. (Calliergon, Hamatocaulis,
Loeskypnum, Straminergon, and Warnstorfia). Scorpidium and
"Hygrohypnum" ochraceum were closely related to
Calliergonaceae but were not included in the family because
of the lack of support. All these genera but Anacamptodon
have previously been included in Amblystegiaceae s.l. The
sporophytic features of Anacamptodon, which contrast with
those of all the other members of Amblystegiaceae, are
interpreted as adaptations to an epiphytic habitat and
suggest, together with other recent taxonomic works in
Hookeriales, that characters related to sporophytic
specializations are among the most homoplastic. Several
other taxa (Calliergonella, Campylophyllum, Conardia,
Donrichardsia, "Hygrohypnum" smithii, Platydictya,
Sanionia), previously included in Amblystegiaceae s.l.,
appeared more closely related to other Hypnalean families.
Recircumscribed Amblystegiaceae, and several clades within
the family, have no identifiable morphological
synapomorphies. A new system of classification for
recircumscribed Amblystegiaceae, including morphological
delimitation of presented clades based on maximum likelihood
reconstruction of ancestral character states, is proposed
and appropriate nomenclatural changes made.},
Doi = {10.2307/1554968},
Key = {fds230669}
}
@article{fds230531,
Author = {Shaw, AJ},
Title = {Antagonistic pleiotropy and the evolution of alternate
generations.},
Journal = {The New phytologist},
Volume = {152},
Number = {3},
Pages = {365-368},
Publisher = {WILEY},
Year = {2001},
Month = {December},
url = {http://dx.doi.org/10.1046/j.0028-646x.2001.00286.x},
Abstract = {The simple (but elegant) series of experiments performed by
McHaffie et al. (see pp. 491-500 in this issue) - involving
studies of segregation from field-collected sporophytes,
sporophytic progeny of selfed gametophytes, and the
morphology of sporophytes from reciprocal crosses -
conclusively demonstrates the genetic basis of the
intervarietal morphological differences. These differences
are further conditioned by one gene and two alleles, with
the 'distentifolium allele' (A ) dominant over the 'flexile
allele' (A ). Did the authors also achieve their goal of
determining those factors that might help explain how
flexile is maintained within populations? The issue is
complex. Gametophytes of the flexile type seem to have a
consistent growth advantage, and it might be that this
translates into a reproductive advantage. In the sporophyte
generation, pleiotropic effects of the A allele appear to
confer an advantage in terms of frond number and fertility
to the flexile form at high nutrient concentrations, whereas
at the same high nutrient levels the A (distentifolium)
allele is associated with larger fronds. From this, the
authors hypothesize 'antagonistic pleiotropy' for the
maintenance of the A allele in Scottish populations of A.
distentifolium. Whether or not this is correct, they have
provided new information about this fern that has
implications for both conservation and basic evolutionary
biology. D F F D F},
Doi = {10.1046/j.0028-646x.2001.00286.x},
Key = {fds230531}
}
@article{fds230665,
Author = {Vanderpoorten, A and Shaw, AJ and Goffinet, B},
Title = {Testing controversial alignments in Amblystegium and related
genera (Amblystegiaceae: Bryopsida). Evidence from rDNA ITS
sequences},
Journal = {Systematic Botany},
Volume = {26},
Number = {3},
Pages = {470-479},
Year = {2001},
Month = {October},
ISSN = {0363-6445},
Abstract = {The Amblystegiaceae include pleurocarpous mosses typical of
moist, wet, or aquatic habitats. Sporophytes are uniform,
and genera are distinguished by the habit, arrangement, and
anatomy of leaves, leaf cell shape, and costal structure.
Generic limits are controversial. Species have been shifted
from genus to genus, sometimes in or out of other related
families. Nucleotide sequences from the Internal Transcribed
Spacer region of nuclear ribosomal DNA repeat from 39
accessions were analyzed to test monophyly of the genera
Amblystegium, Campylium, and Drepanocladus. Reconstructions
constrained to support monophyly of each genus were
significantly less parsimonious and less likely than from
unconstrained searches. ITS sequences support previous
suggestions based on morphology that Campylophyllum halleri
is not closely related to Campylium stellatum or
Campyliadelphus chrysophyllus. Our results also support
previous treatments that divide Drepanocladus into two or
more segregate genera. Leptodictyum riparium appears more
closely related to Campylium stellatum and Campyliadelphus
chrysophyllus than to Amblystegium species. Some, but not
all, populations of A. humile, Hygroamblystegium tenax, H.
fluviatile, and H. varium form a strongly supported
clade.},
Key = {fds230665}
}
@article{fds304315,
Author = {Goffinet, B and Cox, CJ and Shaw, AJ and Hedderson,
TAJ},
Title = {The Bryophyta (Mosses): Systematic and Evolutionary
Inferences from an rps4 Gene (cpDNA) Phylogeny.},
Journal = {Annals of botany},
Volume = {87},
Number = {2},
Pages = {191-208},
Publisher = {Oxford University Press (OUP)},
Year = {2001},
Month = {February},
ISSN = {0305-7364},
url = {http://dx.doi.org/10.1006/anbo.2000.1318},
Abstract = {Phylogenetic analyses of nucleotide and amino acid sequences
of the chloroplast protein coding gene rps4 were performed
for 225 species of mosses, representing 84% of families
recognized by Vitt (1984. In: Schuster RM, ed. New manual of
bryology , vol 2 . Nichinan: Hattori Botanical Laboratory),
under the criterion of maximum parsimony with Takakia and
Sphagnum as outgroups. Most parsimonious topologies converge
to a scenario wherein the Andreaeidae are monophyletic and
sister to the Bryidae (peristomate mosses), the
Nematodonteae and the Buxbaumiaceae form a monophyletic
lineage, the Diphysciaceae are sister to the Arthrodonteae
and, within the latter, the Funarineae-Encalyptineae-Timmiaceae-Haplolepideae
compose a monophyletic clade sister to remaining
diplolepideous mosses. This hypothesis suggests that early
in the evolution of the Arthrodonteae, two major lineages
diverged, with opposite and alternate peristomes,
respectively. Bootstrap support for the deep dichotomies is
poor or lacking but increases when protein translations of
rps 4 sequences are included in the analysis. Several novel
systematic hypotheses are raised, including ( a ) a
diplolepideous rather than haplolepideous origin of the
Pleurophascaceae; ( b ) an affinity of the Catascopiaceae
with the Funariineae rather than the Bryineae; and ( c ) a
close relationship of the Calomniaceae and Mitteniaceae to
the Rhizgoniaceae. The advantages and disadvantages of a
single gene phylogeny are discussed with respect to the
identification of polyphyletic familial or suprafamilial
taxa.},
Doi = {10.1006/anbo.2000.1318},
Key = {fds304315}
}
@article{fds230507,
Author = {Jonathan Shaw and A},
Title = {Biogeographic patterns and cryptic speciation in
bryophytes},
Journal = {Journal of Biogeography},
Volume = {28},
Number = {2},
Pages = {253-261},
Publisher = {WILEY},
Year = {2001},
Month = {January},
ISSN = {0305-0270},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000169547000009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Bryophytes (mosses, liverworts, hornworts) typically have
broad geographical distributions that span two or more
continents. Many species show classic patterns of
disjunction that are similar to those found in many other
groups of organisms (e.g. eastern Asia-eastern North
America), and which are thought to result from fragmentation
of previously continuous ranges (i.e. vicariance). However,
in the bryophytes, these disjunctions often occur at the
infra-specific level and suggest that morphological
uniformity may belie complex underlying genetic structure.
Recent demonstrations of cryptic speciation, revealed by
analyses of isozymes and DNA sequence variation, support the
interpretation that genetic subdivision has occurred within
some morphologically uniform species. Evidence for cryptic
or nearly cryptic speciation exists for seven species of
liverworts and seven mosses. In most (but not all) cases,
cryptic species have broadly overlapping geographical
ranges, although many are ecologically differentiated.
Future work should focus on species that display 'classic'
patterns of disjunction at higher taxonomic levels in other
organisms (e.g. eastern North America-eastern Asia, eastern
or western North America-Europe, Gondwanic), and should
utilize explicitly phylogenetic approaches.},
Doi = {10.1046/j.1365-2699.2001.00530.x},
Key = {fds230507}
}
@article{fds230666,
Author = {Goffinet, B and Cox, CJ and Shaw, AJ and Hedderson,
TA},
Title = {Pylogeny of bryophytes: inferenes from chloroplast-encoded
rps4 nucleotide sequences},
Journal = {Annals of Botany},
Volume = {87},
Number = {2},
Pages = {191-208},
Year = {2001},
ISSN = {0305-7364},
url = {http://dx.doi.org/10.1006/anbo.2000.1318},
Abstract = {Phylogenetic analyses of nucleotide and amino acid sequences
of the chloroplast protein coding gene rps4 were performed
for 225 species of mosses, representing 84 % of families
recognized by Vitt (1984. In: Schuster RM, ed. New manual of
bryology, vol 2. Nichinan: Hattori Botanical Laboratory),
under the criterion of maximum parsimony with Takakia and
Sphagnum as outgroups. Most parsimonious topologies converge
to a scenario wherein the Andreaeidae are monophyletic and
sister to the Bryidae (peristomate mosses), the
Nematodonteae and the Buxbaumiaceae form a monophyletic
lineage, the Diphysciaceae are sister to the Arthrodonteae
and, within the latter, the Funarineae-Encalyptineae-Timmiaceae-Haplolepideae
compose a monophyletic clade sister to remaining
diplolepideous mosses. This hypothesis suggests that early
in the evolution of the Arthrodonteae, two major lineages
diverged, with opposite and alternate peristomes,
respectively. Bootstrap support for the deep dichotomies is
poor or lacking but increases when protein translations of
rps4 sequences are included in the analysis. Several novel
systematic hypotheses are raised, including (a) a
diplolepideous rather than haplolepideous origin of the
Pleurophascaceae; (b) an affinity of the Catascopiaceae with
the Funariineae rather than the Bryineae; and (c) a close
relationship of the Calomniaceae and Mitteniaceae to the
Rhizgoniaceae. The advantages and disadvantages of a single
gene phylogeny are discussed with respect to the
identification of polyphyletic familial or suprafamilial
taxa. © 2001 Annals of Botany Company.},
Doi = {10.1006/anbo.2000.1318},
Key = {fds230666}
}
@article{fds230659,
Author = {Buck, WR and Goffinet, B and Shaw, AJ},
Title = {Testing morphological concepts of orders of pleurocarpous
mosses (Bryophyta) using phylogenetic reconstructions based
on TRNL-TRNF and RPS4 sequences.},
Journal = {Molecular phylogenetics and evolution},
Volume = {16},
Number = {2},
Pages = {180-198},
Year = {2000},
Month = {August},
url = {http://dx.doi.org/10.1006/mpev.2000.0805},
Abstract = {The ordinal classification of pleurocarpous mosses rests on
characters such as branching mode and architecture of the
peristome teeth that line the mouth of the capsule. The
Leucodontales comprise mainly epiphytic taxa, characterized
by sympodial branching and reduced peristomes, whereas the
Hypnales are primarily terricolous and monopodially
branching. The third order, the Hookeriales, is defined by a
unique architecture of the endostome. We sampled 78 exemplar
taxa representing most families of these orders and
sequenced two chloroplast loci, the trnL-trnF region and the
rps4 gene, to test the monophyly and relationships of these
orders of pleurocarpous mosses. Estimates of levels of
saturation suggest that the trnL-trnF spacer and the third
codon position of the rps4 gene have reached saturation, in
at least the transitions. Analyses of the combined data set
were performed under three optimality criteria with
different sets of assumptions, such as excluding
hypervariable positions, downweighting the most likely
transformations, and indirect weighting of rps4 codon
positions by including amino acid translations. Multiple
parallelism in nonsynonymous mutations led to little or no
improvement in various indices upon inclusion of amino acid
sequences. Trees obtained under likelihood were
significantly better under likelihood than the trees derived
from the same matrix under parsimony. Our phylogenetic
analyses suggest that (1) the pleurocarpous mosses, with the
exception of the Cyrtopodaceae, form a monophyletic group
which is here given formal recognition as the Hypnidae; (2)
the Leucodontales are at least paraphyletic; and (3) the
Hypnales form, with most members of the Leucodontalean
grade, a monophyletic group sister to a Hookerialean
lineage. The Hypopterygiaceae, Hookeriales, and a clade
composed of Neorutenbergia, Pseudocryphaea, and Trachyloma
likely represent a basal clade or grade within the Hypnidae.
These results suggest that mode of branching and reduced
peristomes are homoplastic at the ordinal level in
pleurocarpous mosses.},
Doi = {10.1006/mpev.2000.0805},
Key = {fds230659}
}
@article{fds230660,
Author = {Shaw, AJ and Allen, B},
Title = {Phylogenetic relationships, morphological incongruence, and
geographic speciation in the fontinalaceae
(Bryophyta).},
Journal = {Molecular phylogenetics and evolution},
Volume = {16},
Number = {2},
Pages = {225-237},
Year = {2000},
Month = {August},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10942609},
Abstract = {Nuclear ribosomal DNA (internal transcribed spacer region)
and chloroplast DNA (trnL-trnF region) were sequenced from
40 samples representing all three genera (Brachelyma,
Dichelyma, and Fontinalis) and 18 species of the aquatic
moss family, Fontinalaceae. Phylogenetic reconstructions
recovered from separate and combined analyses were used to
test the hypotheses that Fontinalis and Dichelyma are
monophyletic (Brachelyma is monotypic), that groups of
species within Fontinalis based on leaf morphology (keeled,
concave, plane) form monophyletic groups, and that species
delineation based on morphological characters within
Fontinalis are congruent with nr- and cpDNA gene trees.
Using Brachelyma subulata to root the tree, both Dichelyma
and Fontinalis are monophyletic and patristically divergent
(each united by >15 synapomorphic mutations). Groups of
species within Fontinalis defined by leaf morphology are
polyphyletic and it is clear that leaf morphology is labile
in the genus. As defined morphologically, species of
Fontinalis are nonmonophyletic for both nr- and cpDNA
sequences and populations of some morphological taxa are
separated in widely divergent clades. Molecular evidence
suggests that at least some morphospecies are artificial,
defined by convergent leaf forms. The weight of the evidence
indicates that F. antipyretica is positively paraphyletic,
with European populations more closely related to (i.e.,
share a more recent common ancestor with) European endemic
species than to North American populations that are
morphologically conspecific. North American populations are
more closely related to North American endemic
species.},
Doi = {10.1006/mpev.2000.0786},
Key = {fds230660}
}
@article{fds230569,
Author = {Shaw, J and Brody, S},
Title = {Circadian rhythms in Neurospora: a new measurement, the
reset zone.},
Journal = {Journal of biological rhythms},
Volume = {15},
Number = {3},
Pages = {225-240},
Year = {2000},
Month = {June},
url = {http://dx.doi.org/10.1177/074873040001500304},
Abstract = {The authors define a new feature of a circadian rhythm, the
reset zone, and point out its usefulness for predictions
concerning oscillator behavior. The reset zone measures the
responses of a circadian system to resetting pulses. It can
be easily determined from a phase transition curve (PTC),
which is simply a phase response curve (PRC) replotted as
new phase versus old phase (Winfree's format). The reset
zone is the range of new phases seen in such a plot and has
two potentially useful characteristics: its size and its
midpoint. A series of experiments with Neurospora involving
temperature pulses indicated that the size of the reset zone
changed in a nonlinear way in response to both the duration
of 40 degrees C pulses and to the magnitude of temperature
change for 3-h pulses. Other existing data are replotted to
show how the reset zone size varies with growth temperature
and with the period of different clock mutants. Employing
exclusively reset zone data within the framework of a limit
cycle displacement model, an equation is formulated that
predicts the relative changes in the values of state
variables of the oscillator for changes in any given
environmental condition, such as temperature. Examples are
also drawn from other organisms, such as hamsters,
Gonyalaux, Kalanchoe, and Drosophila, illustrating the
usefulness of the reset zone measurement. It can be used as
a numerical scale for assessing the strength of a pulse, for
comparing the relative effects of a given pulse applied to
different organisms or mutants, for determining the
directionality of the changes in state variables produced by
various types of pulses, and possibly for measuring clock
amplitude.},
Doi = {10.1177/074873040001500304},
Key = {fds230569}
}
@article{fds230657,
Author = {Shaw, AJ},
Title = {Molecular phylogeography and cryptic speciation in the
mosses, Mielichhoferia elongata and M. mielichhoferiana
(Bryaceae).},
Journal = {Molecular ecology},
Volume = {9},
Number = {5},
Pages = {595-608},
Year = {2000},
Month = {May},
ISSN = {0962-1083},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10792702},
Abstract = {Nucleotide sequence variation in the ITS1-5.8S-ITS2 region
of nuclear ribosomal DNA (nrDNA) from 70 populations of
Mielichhoferia elongata and M. mielichhoferiana, plus two
outgroup species, was analysed using maximum parsimony and
maximum likelihood methods. High levels of nucleotide
substitution and numerous insertion-deletion events were
detected within and between the two species. M. elongata is
monophyletic with regard to nrDNA variation, but M.
mielichhoferiana is paraphyletic. (M. elongata is nested
within it.) A clade within M. mielichhoferiana provides
evidence of vicariance, with North American and Scandinavian
sister groups of populations. Two major clades are resolved
in M. elongata by sequence data that are completely
congruent with previous isozyme work. One clade includes
populations from both North America and Europe whereas the
other is strictly North American. These two clades, resolved
by multiple independent loci, clearly represent cryptic
species within the morphologically uniform M. elongata.
Certain geographical areas, most notably southwestern
Colorado in Ouray and San Juan Counties, harbour diverse
populations of M. elongata with distinct phylogenetic and
phylogeographical histories. Morphologically
indistinguishable but phylogenetically distant populations
were detected a few metres apart at one site. In contrast,
all populations collected over hundreds of kilometres in
California belong to a single clade. Arctic North American
populations belong to a clade that includes disjunct
populations in Alaska, northern Ellesmere Island, and the
northeastern USA, but not subarctic Swedish populations,
which are more closely related to plants from the Rocky
Mountains. Morphological uniformity belies complex
infraspecific phylogenetic patterns within M. elongata and
M. mielichhoferiana.},
Doi = {10.1046/j.1365-294x.2000.00907.x},
Key = {fds230657}
}
@article{fds230567,
Author = {Shaw, AJ and Anderson, LE and Mishler, BD},
Title = {Paedomorphic sporophyte development in Bruchia flexuosa
(Bruchiaceae)},
Journal = {Bryologist},
Volume = {103},
Number = {1},
Pages = {147-155},
Publisher = {American Bryological and Lichenological Society},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2000)103[0147:PSDIBF]2.0.CO;2},
Abstract = {Cleistocarpous mosses, those lacking a differentiated
operculum and having the capsule dehisce irregularly, are
generally thought to have evolved via reduction from
stegocarpous ancestors. Bruchia (Bruchiaceae), a
cleistocarpous genus of approximately 15 species, shares
gametophytic similarities with the genus Trematodon, which
has a functional annulus and dehiscent capsule. The sequence
of cell divisions characterizing the sporophyte of Bruchia
flexuosa shows that development is typically haplolepideous
up to the stage in which the peristomial formula is 4:2:2.
Whereas other haplolepideous species, including Trematodon
longicollis, complete development with a 4:2:3 peristomial
formula, the last set of anticlinal divisions in the Inner
Peristomial Layer do not occur in B. flexuosa, which
therefore appears to mature at what is an immature stage in
related stegocarpous taxa. This pattern of development is
consistent with an origin of the cleistocarpous capsules of
Bruchia through paedomorphosis from a Trematodon-like
(haplopideous) ancestor.},
Doi = {10.1639/0007-2745(2000)103[0147:PSDIBF]2.0.CO;2},
Key = {fds230567}
}
@article{fds230655,
Author = {Shaw, AJ and Goffinet, B},
Title = {Molecular evidence of reticulate evolution in the peatmosses
(Sphagnum), including S. ehyalinum sp. nov.},
Journal = {Bryologist},
Volume = {103},
Number = {2},
Pages = {357-374},
Publisher = {American Bryological and Lichenological Society},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2000)103[0357:MEOREI]2.0.CO;2},
Abstract = {Phylogenetic analyses of nuclear and chloroplast DNA
sequences resolve four major clades within the peatmosses,
and these lineages correspond to sections that have
traditionally been recognized based on morphology. The
sectional placement of most species is unambiguous, but four
taxa combine the nuclear sequences of one section with the
chloroplast sequences of another. A hypothesis of past
reticulate evolution is favored over lineage sorting to
account for this incongruence, because single genome
analyses (nuclear vs. chloroplast) indicate that the species
are derived within their respective sections. Sphagnum
mendocinum, from the Pacific coast of North America, has the
nuclear DNA of section Subsecunda, but the chloroplast DNA
of section Cuspidata. Sphagnum cuculliforme, from Ecuador,
has the nuclear sequences of section Subsecunda, but the
chloroplast sequences of section Sphagnum. Sphagnum
falcatulum and S. ehyalinum, both from temperate Southern
Hemisphere, have the nuclear sequences of section Cuspidata,
but the chloroplast sequences of section Subsecunda. While
morphological evidence alone would not be sufficient to
hypothesize past reticulations, at least three of the four
species are atypical and ambiguous with regard to sectional
placement. Sphagnum mendocinum is morphologically
intermediate between the Subsecunda and Cuspidata, S.
cuculliforme has previously been classified in its own
monotypic section because of a unique combination of
morphological characters, and S. ehyalinum is highly unusual
because of a near absence of differentiated chlorophyllose
and hyaline cells in the branch leaves. S. ehyalinum is
described as new in this paper. Sphagnum falcatulum is
morphologically typical of the section Cuspidata, to which
it appears to belong based on nuclear DNA sequences. These
inferences of reticulation between widely divergent taxa add
to growing evidence of hybridization in the
peatmosses.},
Doi = {10.1639/0007-2745(2000)103[0357:MEOREI]2.0.CO;2},
Key = {fds230655}
}
@article{fds230661,
Author = {Cox, CJ and Goffinet, B and Newton, AE and Shaw, AJ and Hedderson,
TAJ},
Title = {Phylogenetic relationships among the diplolepideous-alternate
mosses (Bryidae) inferred from nuclear and chloroplast DNA
sequences},
Journal = {Bryologist},
Volume = {103},
Number = {2},
Pages = {224-241},
Publisher = {American Bryological and Lichenological Society},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2000)103[0224:PRATDA]2.0.CO;2},
Abstract = {The diplolepideous-alternate peristome, when most highly
developed, has endostome segments attached to a basal
membrane and positioned alternate to the outer exostome
teeth, with cilia often present between the segments. This
peristome type defines the Bryidae (sensu Vitt et al. 1998),
which includes four orders: the Bryales, Leucodontales,
Hypnales, and Hookeriales, of which the latter three are
mainly pleurocarpous in their growth form. Chloroplast
(rbcL, rps4, and trnL-trnF) and nuclear (18S rRNA) gene
sequences have been analyzed using the parsimony optimality
criterion to elucidate relationships among the Bryidae. The
analyses strongly support the paraphyly of the Bryidae, with
the Splachnidae, and possibly the Orthotrichidae, having
arisen from ancestors within the Bryidae. The Leucodontales,
Hypnales, and Hookeriales form a monophyletic group, as do
the pleurocarpous members of the Bryidae. However, the two
pleurocarpous clades are not resolved as sister groups,
although their non-monophyly is not supported by the
bootstrap. The phylogenetic hypothesis provides a context in
which to infer evolutionary transitions in some key
morphological characters relating to the peristome and the
transition from the acrocarpous to pleurocarpous growth
forms.},
Doi = {10.1639/0007-2745(2000)103[0224:PRATDA]2.0.CO;2},
Key = {fds230661}
}
@article{fds230663,
Author = {La Farge and C and Mishler, BD and Wheeler, JA and Wall, DP and Johannes,
K and Schaffer, S and Shaw, AJ},
Title = {Phylogenetic relationships within the haplolepideous
mosses},
Journal = {Bryologist},
Volume = {103},
Number = {2},
Pages = {257-276},
Publisher = {American Bryological and Lichenological Society},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2000)103[0257:PRWTHM]2.0.CO;2},
Abstract = {Mosses with haplolepideous peristomes form a major lineage
within the arthrodontous taxa, the Dicranidae. Relationships
among lineages within the Dicranidae are explored using
three cpDNA regions: rbcL, rps4, and the region spanning
trnL(UAA)- trnF(GAA). Maximum parsimony analyses of combined
data sets support robust clades that correspond to
traditionally recognized families. Phylogenetic
relationships of 71 exemplar taxa rooted with five outgroup
taxa identify 13 major clades within the Dicranidae.
Predominantly the monophyly of these groups is strongly
supported, although relationships among the clades are
ambiguous. The phylogenetic implications of the current
taxon sampling include 1) the Dicranidae are monophyletic,
2) the Pottiales are polyphyletic with the Calymperaceae and
Octoblepharaceae cladistically distant from the Pottiaceae,
and these two former families should be transferred to the
Dicranales, 3) the Dicranales are polyphyletic, with
Ditrichaceae and Rhabdoweisiaceae more closely related to
the Pottiaceae than other members of the Dicranales, 4) the
Fissidentaceae are nested within the Dicranales, 5) the
Rhachitheciaceae and Erpodiaceae are nested within the
Dicranidae and sister to the Pottiaceae, 6) Amphidium is
sister to the pottiaceous clade, 7) the Seligeriaceae form a
well supported sister relationship to the Grimmiales, and 8)
Scouleria aquatica, Bryoxiphium norvegicum, Ditrichum
flexicaule, and Timmiella crassinervis appear to form basal
lineages within the Dicranidae.},
Doi = {10.1639/0007-2745(2000)103[0257:PRWTHM]2.0.CO;2},
Key = {fds230663}
}
@article{fds230664,
Author = {Buck, WR and Goffinet, B and Shaw, AJ},
Title = {Novel relationships in pleurocarpous mosses as revealed by
cpDNA sequences},
Journal = {Bryologist},
Volume = {103},
Number = {4},
Pages = {774-789},
Publisher = {American Bryological and Lichenological Society},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2000)103[0774:NRIPMAR]2.0.CO;2},
Abstract = {As a result of a project using two chloroplast loci, the
trnL-trnF region and the rps4 gene, to test the monophyly of
pleurocarpous mosses as a group and the traditional three
orders contained in it, several novel generic alliances were
revealed. Of particular interest are the inclusion of the
Ptychomniaceae and Garovagliaceae in the Hookeriales, as
well as generic inclusions in the Anomodontaceae,
Brachytheciaceae, Amblystegiaceae sensu lato, and
Sematophyllaceae.},
Doi = {10.1639/0007-2745(2000)103[0774:NRIPMAR]2.0.CO;2},
Key = {fds230664}
}
@article{fds304314,
Author = {Shaw, AJ},
Title = {Phylogeny of the sphagnopsida based on chloroplast and
nuclear DNA sequences},
Journal = {Bryologist},
Volume = {103},
Number = {2},
Pages = {277-306},
Publisher = {American Bryological and Lichenological Society},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2000)103[0277:POTSBO]2.0.CO;2},
Abstract = {Most reconstructions of basal land plant relationships
derived from morphological or molecular data suggest that
the Sphagnopsida form a critical clade at or near the base
of the mosses (Bryophyta s.s.). The Sphagnopsida include two
orders: Sphagnales and Ambuchananiales, each with one
family. The Ambuchananiaceae is monotypic, with A.
leucobryoides of Tasmania. Nucleotide sequences from five
genomic regions, two from the nuclear genome (ITS and 26S
nuclear ribosomal DNA) and three from the chloroplast genome
(psbT, rpl16, trnL) were subjected to cladistic analyses in
order to assess 1) the relationship between Ambuchanania and
Sphagnum, 2) the polarity of evolutionary change in Sphagnum
(i.e., infer a root for the infrageneric phylogeny), 3)
monophyly of the four large sections of Sphagnum
(Acutifolia, Cuspidata, Sphagnum, and Subsecunda) and 4)
phylogenetic relationships of the smaller or monotypic
sections. Ambuchanania is resolved as the sister group to
Sphagnum and is not nested within the latter as a highly
derived species. Polarity of evolutionary change in Sphagnum
is ambiguous; alternative hypotheses suggested by molecular
data place either the sect. Subsecunda or the sect. Sphagnum
as sister to all other species. The four large sections of
Sphagnum are each monophyletic if circumscribed to include
species traditionally placed in monotypic sections. Sphagnum
macrophyllum (sect. Isocladus) is nested within the
Subsecunda. Sphagnum pylaesii (sect. Hemitheca) is nested
within the Cuspidata and is closely related to S. tenellum
(sect. Mollusca). Sphagnum wulfianum (sect. Polyclada) is
nested within the Acutifolia, closely related to S.
fimbriatum and S. girgensohnii. Sphagnum aongstroemii (sect.
Insulosa) is either nested within the Acutifolia, or is
sister to other species of Acutifolia. Molecular evidence
supports a sister group relationship between the sections
Rigida and Sphagnum, and between the sections Squarrosa and
Acutifolia. Molecular data suggest that phylogenetic
structure in Sphagnum can be accommodated by four large
sections without segregating morphologically distinctive
taxa into smaller sections, as is traditionally done. A
revised classification is proposed in which the genus is
divided into four sections: Acutifolia, Cuspidata, Sphagnum,
and Subsecunda.},
Doi = {10.1639/0007-2745(2000)103[0277:POTSBO]2.0.CO;2},
Key = {fds304314}
}
@article{fds304321,
Author = {Shaw, AJ},
Title = {Schizymenium shevockii (Bryaceae), a new species of moss
from California, based on morphological and molecular
evidence},
Journal = {Systematic Botany},
Volume = {25},
Number = {2},
Pages = {188-196},
Publisher = {JSTOR},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.2307/2666638},
Abstract = {A new moss species, Schizymenium shevockii, is described
from Fresno County, California. Schizylnenium shevockii is
distinguished from North American species of Mielichhoferia
by a single endostomial peristome, and from Mexican species
of Schizymenium by dioicous sexuality, poorly developed
endostome segments, and the complete absence of exostome
teeth. The new species can also be distinguished from S.
pontevedrensis (the only European species of that genus),
Mielichhoferia mielichhoferiana, and Mielichhoferia elongata
by the presence of 38 and 29 nucleotide (nt) deletions in
the ITS1 region of nuclear ribosomal DNA, and a nine nt
insertion in the ITS2 region. Four additional insertions
and/or deletions distinguish S. shevockii from M. elongata
and/or M. mielichhoferiana. Moreover, Mielichhoferia
elongata and M. mielichhoferiana share 34 nucleotide
substitutions that distinguish them (as a monophyletic
group) from S. shevockii and S. pontevedrensis. A survey of
California populations using primers designed to take
advantage of molecular differences between S. shevockii and
morphologically similar but sterile plants of Mielichhoferia
elongata revealed plants of S. shevockii at three sites. At
one such site, S. shevockii was sympatric with M. elongata.
All samples of S. shevockii had identical ITS
sequences.},
Doi = {10.2307/2666638},
Key = {fds304321}
}
@article{fds304322,
Author = {De Luna and E and Buck, WR and Akiyama, H and Arikawa, T and Tsubota, H and González, D and Newton, AE and Shaw, AJ},
Title = {Ordinal phylogeny within the hypnobryalean pleurocarpous
mosses inferred from cladistic analyses of three chloroplast
DNA sequence data sets: trnL-F, rps4, and
rbcL},
Journal = {Bryologist},
Volume = {103},
Number = {2},
Pages = {242-256},
Publisher = {American Bryological and Lichenological Society},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(2000)103[0242:OPWTHP]2.0.CO;2},
Abstract = {Classification of families of hypnobryalean mosses into the
Hypnales, Leucodontales, and Hoolceriales has been
taxonomically difficult. Several researchers have sequenced
different genes for independent phylogenetic studies of
these three pleurocarp groups. Our goal is to summarize
available molecular data and compile the largest data set to
infer phylogenetic relationships among families as basis for
classification at ordinal level. Sequences of rbcL, trnL-F,
and rps4 loci for 38 exemplars of most families of Hypnales,
Leucodontales, and Hookeriales were analyzed to evaluate
whether or not each of the three orders is monophyletic.
Cladistic analyses of combined sequences, using five taxa in
the Bryales as outgroups, reveal a robust clade (decay > 5)
including all hypnobryalean pleurocarps. Within this group,
one clade (decay = 2) includes only taxa of the Hookeriales,
and is sister to a large monophyletic group (Hypnales sensu
lato) containing all other taxa (decay = 2) previously in
the Leucodontales and Hypnales. These relationships suggest
that the ordinal level taxonomy needs to be reconsidered
since major lineages detected do not correspond to the
traditional Leucodontales or Hypnales. These two orders are
not supported by any molecular evidence from rbcL, trnL-F,
or rps4, either analyzed singly or in different
combinations. Additionally, present results indicate the
need for changes to the current system of three suborders of
Hypnales and four of the Leucodontales. Phylogenetic
reconstructions based on molecular data emphasize the need
for a re-examination of the taxonomic relevance of
morphological characters and corroborate previous
interpretations of sporophytic morphological similarities as
multiple transitions to similar solutions to epiphytism
among the pleurocarps.},
Doi = {10.1639/0007-2745(2000)103[0242:OPWTHP]2.0.CO;2},
Key = {fds304322}
}
@article{fds230656,
Author = {Shaw, J},
Title = {Phylogeny of the Sphagnopsida based on nuclear and
chloroplast DNA sequences},
Journal = {Bryologist},
Volume = {103},
Number = {2},
Pages = {277-306},
Year = {2000},
Abstract = {Most reconstructions of basal land plant relationships
derived from morphological or molecular data suggest that
the Sphagnopsida form a critical clade at or near the base
of the mosses (Bryophyta s.s.). The Sphagnopsida include two
orders: Sphagnales and Ambuchananiales, each with one
family. The Ambuchananiaceae is monotypic, with A.
leucobryoides of Tasmania. Nucleotide sequences from five
genomic regions, two from the nuclear genome (ITS and 26S
nuclear ribosomal DNA) and three from the chloroplast genome
(psbT, rpl16, trnL) were subjected to cladistic analyses in
order to assess 1) the relationship between Ambuchanania and
Sphagnum, 2) the polarity of evolutionary change in Sphagnum
(i.e., infer a root for the infrageneric phylogeny), 3)
monophyly of the four large sections of Sphagnum
(Acutifolia, Cuspidata, Sphagnum, and Subsecunda) and 4)
phylogenetic relationships of the smaller or monotypic
sections. Ambuchanania is resolved as the sister group to
Sphagnum and is not nested within the latter as a highly
derived species. Polarity of evolutionary change in Sphagnum
is ambiguous; alternative hypotheses suggested by molecular
data place either the sect. Subsecunda or the sect. Sphagnum
as sister to all other species. The four large sections of
Sphagnum are each monophyletic if circumscribed to include
species traditionally placed in monotypic sections. Sphagnum
macrophyllum (sect. Isocladus) is nested within the
Subsecunda. Sphagnum pylaesii (sect. Hemitheca) is nested
within the Cuspidata and is closely related to S. tenellum
(sect. Mollusca). Sphagnum wulfianum (sect. Polyclada) is
nested within the Acutifolia, closely related to S.
fimbriatum and S. girgensohnii. Sphagnum aongstroemii (sect.
Insulosa) is either nested within the Acutifolia, or is
sister to other species of Acutifolia. Molecular evidence
supports a sister group relationship between the sections
Rigida and Sphagnum, and between the sections Squarrosa and
Acutifolia. Molecular data suggest that phylogenetic
structure in Sphagnum can be accommodated by four large
sections without segregating morphologically distinctive
taxa into smaller sections, as is traditionally done. A
revised classification is proposed in which the genus is
divided into four sections: Acutifolia, Cuspidata, Sphagnum,
and Subsecunda.},
Key = {fds230656}
}
@article{fds230658,
Author = {Shaw, J},
Title = {Schizymenuim shevockii, a new species based on morphological
and molecular evidence},
Journal = {Syst. Bot.},
Volume = {25},
Number = {2},
Pages = {188-196},
Year = {2000},
Abstract = {A new moss species, Schizymenium shevockii, is described
from Fresno County, California. Schizylnenium shevockii is
distinguished from North American species of Mielichhoferia
by a single endostomial peristome, and from Mexican species
of Schizymenium by dioicous sexuality, poorly developed
endostome segments, and the complete absence of exostome
teeth. The new species can also be distinguished from S.
pontevedrensis (the only European species of that genus),
Mielichhoferia mielichhoferiana, and Mielichhoferia elongata
by the presence of 38 and 29 nucleotide (nt) deletions in
the ITS1 region of nuclear ribosomal DNA, and a nine nt
insertion in the ITS2 region. Four additional insertions
and/or deletions distinguish S. shevockii from M. elongata
and/or M. mielichhoferiana. Moreover, Mielichhoferia
elongata and M. mielichhoferiana share 34 nucleotide
substitutions that distinguish them (as a monophyletic
group) from S. shevockii and S. pontevedrensis. A survey of
California populations using primers designed to take
advantage of molecular differences between S. shevockii and
morphologically similar but sterile plants of Mielichhoferia
elongata revealed plants of S. shevockii at three sites. At
one such site, S. shevockii was sympatric with M. elongata.
All samples of S. shevockii had identical ITS
sequences.},
Key = {fds230658}
}
@article{fds230662,
Author = {De Luna and E and Buck, WR and Akiyama, H and Arikawa, T and Tsubota, H and Gonzalez, D and Newton, AE and Shaw, AJ},
Title = {Phylogenetic patterns within the hypnobryalian pleurocarpous
mosses inferred from cladistic analyses of three sequence
data sets: trnL-trnF, rps4, and rbcL},
Journal = {Bryologist},
Volume = {103},
Number = {2},
Pages = {242-256},
Year = {2000},
Abstract = {Classification of families of hypnobryalean mosses into the
Hypnales, Leucodontales, and Hoolceriales has been
taxonomically difficult. Several researchers have sequenced
different genes for independent phylogenetic studies of
these three pleurocarp groups. Our goal is to summarize
available molecular data and compile the largest data set to
infer phylogenetic relationships among families as basis for
classification at ordinal level. Sequences of rbcL, trnL-F,
and rps4 loci for 38 exemplars of most families of Hypnales,
Leucodontales, and Hookeriales were analyzed to evaluate
whether or not each of the three orders is monophyletic.
Cladistic analyses of combined sequences, using five taxa in
the Bryales as outgroups, reveal a robust clade (decay >
5) including all hypnobryalean pleurocarps. Within this
group, one clade (decay = 2) includes only taxa of the
Hookeriales, and is sister to a large monophyletic group
(Hypnales sensu lato) containing all other taxa (decay = 2)
previously in the Leucodontales and Hypnales. These
relationships suggest that the ordinal level taxonomy needs
to be reconsidered since major lineages detected do not
correspond to the traditional Leucodontales or Hypnales.
These two orders are not supported by any molecular evidence
from rbcL, trnL-F, or rps4, either analyzed singly or in
different combinations. Additionally, present results
indicate the need for changes to the current system of three
suborders of Hypnales and four of the Leucodontales.
Phylogenetic reconstructions based on molecular data
emphasize the need for a re-examination of the taxonomic
relevance of morphological characters and corroborate
previous interpretations of sporophytic morphological
similarities as multiple transitions to similar solutions to
epiphytism among the pleurocarps.},
Key = {fds230662}
}
@article{fds230529,
Author = {Shaw, J and Beer, SC},
Title = {Life history variation in gametophyte populations of the
moss Ceratodon purpureus (Ditrichaceae)},
Journal = {American Journal of Botany},
Volume = {86},
Number = {4},
Pages = {512-521},
Publisher = {WILEY},
Year = {1999},
Month = {January},
ISSN = {0002-9122},
url = {http://dx.doi.org/10.2307/2656812},
Abstract = {The life cycles of mosses and other bryophytes are unique
among land plants in that the haploid gametophyte stage is
free-living and the diploid sporophyte stage is ephemeral
and completes its development attached to the maternal
gametophyte. Despite predictions that populations of
haploids might contain low levels of genetic variation, moss
populations are characterized by substantial variation at
isozyme loci. The extent to which this is indicative of
ecologically important life history variation is, however,
largely unknown. Gametophyte plants from two populations of
the moss Ceratodon purpureus were grown from single-spore
isolates in order to assess variation in growth rates,
biomass accumulation, and reproductive output. The data were
analyzed using a nested analysis of variance, with haploid
sib families (gametophytes derived from the same sporophyte)
nested within populations. High levels of life history
variation were observed within both populations, and the
populations differed significantly in both growth and
reproductive characteristics. Overall gametophytic sex
ratios did not depart significantly from 1:1 within either
population, but there was significant variation among
families in both populations for progeny sex ratio. Some
families produced predominantly male gametophytes, while
others yielded predominantly females. Because C. purpureus
has a chromosomal mechanism of sex determination, these
observations suggest differential (but unpredictable)
germination of male and female spores. Life history
observations showed that male and female gametophytes are
dimorphic in size, maturation rates, and reproductive
output.},
Doi = {10.2307/2656812},
Key = {fds230529}
}
@article{fds230564,
Author = {Buck, WR and Harris, RC and Shaw, AJ and Piercey-Normore, MD and Tabaee,
A and Antonovics, J and Crone, EE},
Title = {Unusual lichens under electricity pylons on zinc-enriched
soil},
Journal = {Bryologist},
Volume = {102},
Number = {1},
Pages = {130-132},
Publisher = {JSTOR},
Year = {1999},
Month = {January},
url = {http://dx.doi.org/10.2307/3244476},
Abstract = {Two species of lichens, Vezdaea leprosa (P. James) Vezda and
Steinia geophana (Nyl.) B. Stein are here reported as new
for North America based on collections from Durham and
Orange Counties, North Carolina (U.S.A.). Both species occur
frequently in the area on zinc-contaminated soils below
galvanized electricity pylons. The species were not found in
areas between pylons, suggesting a central role for elevated
substrate zinc levels in determining the local distribution
of these species. This inference is consistent with the
ecology of these species in Britain and Europe.},
Doi = {10.2307/3244476},
Key = {fds230564}
}
@article{fds230565,
Author = {Shaw, AJ},
Title = {Genetic structure in relation to reproductive biology of 11
species of Pohlia Hedw. (Bryaceae)},
Journal = {Systematic Botany},
Volume = {24},
Number = {1},
Pages = {85-94},
Publisher = {JSTOR},
Year = {1999},
Month = {January},
url = {http://dx.doi.org/10.2307/2419388},
Abstract = {The moss genus Pohlia includes species with bisexual
gametophytes, unisexual gametophytes and no specialized
asexual propagules, and unisexual with specialized asexual
'gemmae.' A group of Northern Hemisphere species
characterized by having axillary gemmae are very similar in
other gametophytic characters, and virtually identical in
sporophyte morphology, in contrast to most other species of
Pohlia that differ in both gametophytic and sporophytic
features. This study tested the hypothesis that gemmiferous
taxa form a complex of 'microspecies' that are less distinct
genetically than are comparable sexual species. Fourteen
putative isozyme loci were screened in 50 populations
representing 11 species (7 gemmiferous and 4
nongemmiferous). The seven gemmiferous species are less
distinct from one another (mean I = 0.8999) than are the
four species that do not form gemmae (mean I = 0.7530).
Species lacking gemmae have higher total infraspecific gene
diversity (mean H(T) = 0.254) than gemmiferous species (mean
H(T) = 0.138).},
Doi = {10.2307/2419388},
Key = {fds230565}
}
@article{fds230566,
Author = {Goffinet, B and Shaw, J and Anderson, LE and Mishler,
BD},
Title = {Peristome development in mosses in relation to systematics
and evolution. V. Diplolepideae: Orthotrichaceae},
Journal = {Bryologist},
Volume = {102},
Number = {4},
Pages = {581-594},
Publisher = {JSTOR},
Year = {1999},
Month = {January},
url = {http://dx.doi.org/10.2307/3244248},
Abstract = {The classification of the Bryopsida is based to a large
extent on the architecture of the peristome teeth. Among
diplolepideous mosses, three peristome-types have been
recognized. The development of the amphithecium in taxa
characterized by an Orthotrichum-type peristome is described
here, thereby completing our survey of the ontogeny of all
three diplolepideous peristome types. Patterns of early
divisions leading to a three-layered amphithecium in
Schlotheimia rugifolia, Ulota crispa, and U. hutchinsiae are
identical to all other arthrodontous mosses that have been
studied. The subsequent anticlinal divisions occurring in
the eight celled Inner Peristomial Layer are clearly
asymmetric. Lack of alignment of adjacent anticlinal IPL and
Primary Peristomial Layer walls is further accentuated by
post-divisural lateral displacement of the IPL walls due to
swelling of the PPL cells. This development of the
amphithecial layers yielding a 4:2:4 pattern in the
Orthotrichaceae is identical to that described for the
Bryum-type peristome. The asymmetry of the critical late
stage division in the IPL is considered homologous between
these types. Based on recent phylogenetic hypotheses for the
Bryopsida, we propose to extend this homology assumption to
the Haplolepideae, the Diphysciales, and the Tetraphidales,
suggesting that the asymmetric division is likely
plesiomorphic within the Arthrodonteae. Whether the
peristome of the Orthotrichaceae represents a primitive
bryalean peristome, or whether it arose through reduction of
a bryoid-type remains to be addressed further.},
Doi = {10.2307/3244248},
Key = {fds230566}
}
@article{fds230527,
Author = {Shaw, AJ and Allen, B and Buck, WR},
Title = {New species of Bryaceae (Mielichhoferia, Brachymenium) from
Costa Rica and Reunion},
Journal = {Bryologist},
Volume = {101},
Number = {4},
Pages = {600-604},
Year = {1998},
Month = {January},
url = {http://dx.doi.org/10.2307/3244534},
Abstract = {Mielichhoferia paroica Shaw ang Allen is described from
Costa Rica. The plants are very small, paroicous, and have a
double peristome that consists of 16 long, papillose
exostome teeth and a rudimentary basal membrane that barely
reaches above the capsule rim. Mielichhoferia paroica is the
only known species of Mielichhoferia that is not dioicous.
Brachymenium gemmifarum Shaw and Buck is described from
Reunion. Plants of this species are extremely slender, and
have red capsules with a double peristome consisting of long
exostome teeth and a high endostomial membrane but no
well-defined segments. It differs from all other species of
Brachymenium in having axillary, obconic
gemmae.},
Doi = {10.2307/3244534},
Key = {fds230527}
}
@article{fds230528,
Author = {Patterson, E and Boles, SB and Shaw, AJ},
Title = {Nuclear ribosomal DNA variation in Leucobryum glaucum and L.
albidum (Leucobryaceae): A preliminary investigation},
Journal = {Bryologist},
Volume = {101},
Number = {2},
Pages = {272-277},
Publisher = {JSTOR},
Year = {1998},
Month = {January},
url = {http://dx.doi.org/10.1639/0007-2745(1998)101[272:nrdvil]2.0.co;2},
Abstract = {Leucobryum glaucum and L. albidum are generally
distinguished by quantitative differences in plant height,
leaf length, and transverse sectional leaf anatomy. Although
extremely small plants can be readily identified as L.
albidum, and large plants can be confidently assigned to L.
glaucum, intermediate forms are common and many
identifications are arbitrary. We amplified approximately
815 bp of the nuclear ribosomal DNA ITS from plants varying
in size, and cut the products with three restriction
endonucleases (Hhal, Hinfl, and Taql). Two DNA haplotypes
were detected in a sample of 23 plants growing at a forested
site in Durham, North Carolina. All plants with leaves 5.0
mm in length or shorter had one haplotype, and all plants
with leaves longer than 5.0 mm had the other haplotype. Our
results support the interpretation that L. albidum (small
plants) is genetically discontinuous with L. glaucum (large
plants), at least in the limited area from which we
sampled.},
Doi = {10.1639/0007-2745(1998)101[272:nrdvil]2.0.co;2},
Key = {fds230528}
}
@article{fds230526,
Author = {Shaw, AJ and Weir, BS and Shaw, FH},
Title = {THE OCCURRENCE AND SIGNIFICANCE OF EPISTATIC VARIANCE FOR
QUANTITATIVE CHARACTERS AND ITS MEASUREMENT IN
HAPLOIDS.},
Journal = {Evolution; international journal of organic
evolution},
Volume = {51},
Number = {2},
Pages = {348-353},
Year = {1997},
Month = {April},
url = {http://dx.doi.org/10.1111/j.1558-5646.1997.tb02421.x},
Abstract = {Epistatic genetic variance for quantitative traits may play
an important role in evolution, but detecting epistasis in
diploid organisms is difficult and requires complex breeding
programs and very large sample sizes. We develop a model for
detecting epistasis in organisms with a free-living haploid
stage in their life cycles. We show that epistasis is
indicated by greater variance among families of haploid
progeny derived from individual diploids than among clonally
replicated haploid sibs from the same sporophyte.
Simulations show that the power to detect epistasis is
linearly related to the number of sporophytes and the number
of haploids per sporophyte in the dataset. We illustrate the
model with data from growth variation among gametophytes of
the moss, Ceratodon purpureus. The experiment failed to
detect epistatic variance for biomass production, although
there was evidence of additive variance.},
Doi = {10.1111/j.1558-5646.1997.tb02421.x},
Key = {fds230526}
}
@article{fds230563,
Author = {Shaw, AJ},
Title = {Genetic biogeography of the rate "copper moss", Scopelophila
cataractae (Pottiaceae)},
Journal = {Plant Systematics and Evolution},
Volume = {197},
Number = {1-4},
Pages = {43-58},
Publisher = {Springer Nature},
Year = {1995},
Month = {March},
ISSN = {0378-2697},
url = {http://dx.doi.org/10.1007/BF00984631},
Abstract = {Scopelophila cataractae, one of the so-called "copper
mosses", has a broad geographic distribution that includes
North, Central, and South America, Europe, and Asia, but is
rare throughout its range. A genetic analysis of 32
populations from the United States, Europe, and Asia based
on 15 putative allozyme loci indicates that levels of
genetic diversity vary among geographic regions. Six
European populations are fixed for the same alleles at all
15 loci, consistent with the hypothesis that S. cataractae
is a recent immigrant in that region. The species is more
diverse in the U.S., where it appears to be native. Five
populations collected on copper-enriched soils around
shrines and temples in Tokyo are genetically monomorphic,
but Asian populations from another Japanese site, India, and
Nepal are exceptionally diverse in terms of numbers of
alleles and multilocus haplotypes, total gene diversity
(HT), and in the degree of differentiation among populations
(measured as Nei's I and D). Long-distance dispersal has
probably played an important role in the geographic history
of S. cataractae, but the species appears to be native in
both the New and Old Worlds. Gene flow between plants
disjunct on different continents is insufficient to explain
the lack of geographically correlated morphological and
genetic differentiation in S. cataractae. © 1995
Springer-Verlag.},
Doi = {10.1007/BF00984631},
Key = {fds230563}
}
@article{fds230523,
Author = {Shaw, AJ and Srodon, M},
Title = {Clonal diversity in Sphagnum rubellum Wils.},
Journal = {Bryologist},
Volume = {98},
Number = {2},
Pages = {261-264},
Publisher = {JSTOR},
Year = {1995},
Month = {January},
url = {http://dx.doi.org/10.2307/3243313},
Doi = {10.2307/3243313},
Key = {fds230523}
}
@article{fds230524,
Author = {Shaw, AJ and Schneider, RE},
Title = {Genetic biogeography of the rare copper moss,″
Mielichhoferia elongata (Bryaceae)},
Journal = {American Journal of Botany},
Volume = {82},
Number = {1},
Pages = {8-17},
Publisher = {WILEY},
Year = {1995},
Month = {January},
url = {http://dx.doi.org/10.2307/2445780},
Doi = {10.2307/2445780},
Key = {fds230524}
}
@article{fds230562,
Author = {Shaw, AJ and Owens, H},
Title = {Ecological and experimental studies on the "copper mosses':
Mielichhoferia elongata (Bryaceae) and Scopelophila
cataractae (Pottiaceae)},
Journal = {Fragmenta Floristica et Geobotanica},
Volume = {40},
Number = {1},
Pages = {519-531},
Year = {1995},
Month = {January},
Abstract = {Substrate analyses of 41 samples for Mielichhoferia elongata
and three each for M. mielichhoferiana and M. macrocarpa
were conducted to determine if high copper concentrations
are a constant feature of their habitats. Soil analyses
showed that relatively few populations of M. elongata grew
on soil with significant copper enrichment. Many sites,
however, contained higher than normal levels of aluminium,
iron, or manganese, or various combinations of these metals.
M. elongata was neither tolerant of high copper supplied in
nutrient media, nor did it require excess copper for
vigorous growth. Scopelophila cataractae, in contrast, grew
best on media containing 9 ppm copper. -From
Authors},
Key = {fds230562}
}
@article{fds230525,
Author = {Heller, LI and Shaw, AJ and Jacobson, JS},
Title = {Exposure of red spruce seedlings to acid mist: Importance of
droplet composition just prior to drying
periods},
Journal = {New Phytologist},
Volume = {129},
Number = {1},
Pages = {55-61},
Year = {1995},
Key = {fds230525}
}
@article{fds230522,
Author = {Shaw, AJ},
Title = {Adaptation to metals in widespread and endemic
plants.},
Journal = {Environmental health perspectives},
Volume = {102 Suppl 12},
Number = {SUPPL. 12},
Pages = {105-108},
Year = {1994},
Month = {December},
url = {http://dx.doi.org/10.1289/ehp.94102s12105},
Abstract = {Bryophytes, including the mosses, liverworts, and hornworts,
occur in a variety of habitats with high concentrations of
metals and have other characteristics that are advantageous
for studies of metal tolerance. Mosses may evolve
genetically specialized, metal-tolerant races less
frequently than flowering plants. Some species of mosses
appear to have inherently high levels of metal tolerance
even in individuals that have not been subjected to natural
selection in contaminated environments. Scopelophila
cataractae, one of the so-called copper mosses, not only
tolerates extremely high concentrations of metals in its
substrates, but requires these substrates for optimum
growth. This species should be included in mechanistic
studies of tolerance at the cellular and molecular
levels.},
Doi = {10.1289/ehp.94102s12105},
Key = {fds230522}
}
@article{fds230557,
Author = {Shaw, AJ and Buck, WR},
Title = {Brachymenium deceptivum sp. nov. (Bryaceae) from
Ethiopia},
Journal = {Brittonia},
Volume = {46},
Number = {2},
Pages = {95-98},
Publisher = {Springer Nature},
Year = {1994},
Month = {April},
ISSN = {0007-196X},
url = {http://dx.doi.org/10.2307/2807150},
Abstract = {Brachymenium deceptivum, known only from the type specimen,
is described from Ethiopia. It is immediately distinguished
from all other species of the genus by its complete lack of
an exostome. © 1994 The New York Botanical
Garden.},
Doi = {10.2307/2807150},
Key = {fds230557}
}
@article{fds230556,
Author = {Shaw, AJ},
Title = {Systematics of Mielichhoferia (Bryaceae: Musci).
III.Hybridization between M.elongata and
M.mielichhoferiana},
Journal = {American Journal of Botany},
Volume = {81},
Number = {6},
Pages = {782-790},
Publisher = {WILEY},
Year = {1994},
Month = {January},
url = {http://dx.doi.org/10.2307/2445659},
Doi = {10.2307/2445659},
Key = {fds230556}
}
@article{fds230558,
Author = {Shaw, AJ and Gutkin, MS and Bernstein, BR},
Title = {Systematics of tree mosses (Climacium: Musci): Genetic and
morphological evidence},
Journal = {Systematic Botany},
Volume = {19},
Number = {2},
Pages = {263-272},
Publisher = {JSTOR},
Year = {1994},
Month = {January},
url = {http://dx.doi.org/10.2307/2419601},
Doi = {10.2307/2419601},
Key = {fds230558}
}
@article{fds230559,
Author = {Shaw, AJ},
Title = {Systematics of Mielichhoferia (Bryaceae: Musci).
II.Morphological variation among disjunct populations of
M.elongata and M.mielichhoferiana},
Journal = {Bryologist},
Volume = {97},
Number = {1},
Pages = {47-55},
Publisher = {JSTOR},
Year = {1994},
Month = {January},
url = {http://dx.doi.org/10.2307/3243348},
Doi = {10.2307/3243348},
Key = {fds230559}
}
@article{fds230560,
Author = {Shaw, AJ and Rooks, PE},
Title = {Systematics of Mielichhoferia (Bryaceae: Musci)
I.Morphological and genetic analyses of M.elongata and
M.mielichhoferiana},
Journal = {Bryologist},
Volume = {97},
Number = {1},
Pages = {1-12},
Publisher = {JSTOR},
Year = {1994},
Month = {January},
url = {http://dx.doi.org/10.2307/3243342},
Doi = {10.2307/3243342},
Key = {fds230560}
}
@article{fds230561,
Author = {Jules, ES and Shaw, AJ},
Title = {Adaptation to metal-contaminated soils in populations of the
moss, Ceratodon purpureus: Vegetative growth and
reproductive expression},
Journal = {American Journal of Botany},
Volume = {81},
Number = {6},
Pages = {791-797},
Publisher = {WILEY},
Year = {1994},
Month = {January},
url = {http://dx.doi.org/10.2307/2445660},
Doi = {10.2307/2445660},
Key = {fds230561}
}
@article{fds230520,
Author = {Shaw, AJ},
Title = {Population biology of the rare copper moss, Scopelophila
cataractae},
Journal = {American Journal of Botany},
Volume = {80},
Number = {9},
Pages = {1034-1041},
Publisher = {WILEY},
Year = {1993},
Month = {January},
url = {http://dx.doi.org/10.2307/2445751},
Abstract = {In Scopelophila cataractae (Pottiaceae) only the haploid
gametophyte generation exists in the USA, although
sporophytes occur in tropical America and in Asia. Over 50%
of US plants in every population were devoid of gametangia,
and no population contained plants with both male and female
gametangia. Morphological differences between plants from
putative male and female populations suggested gametophytic
sexual dimorphism, but generalized sexual differences were
not maintained under common garden conditions. Growth on
soils with low, moderate, or high concentrations of metals
demonstrated extensive morphological variability, and thus
genetic polymorphism, among five asexual populations.
Morphological traits were also significnatly plastic in
response to differing soil types. All populations produced
higher cover area and individual plants formed larger leaves
on the most highly metal-contaminated soil. -from
Author},
Doi = {10.2307/2445751},
Key = {fds230520}
}
@article{fds230521,
Author = {Shaw, AJ and Gaughan, JF},
Title = {Control of sex ratios in haploid populations of the moss,
Ceratodon purpureus},
Journal = {American Journal of Botany},
Volume = {80},
Number = {5},
Pages = {584-591},
Publisher = {WILEY},
Year = {1993},
Month = {January},
url = {http://dx.doi.org/10.2307/2445376},
Abstract = {A survey of 11 populations of Ceratodon purpureus showed
that sex ratios are heterogeneous, but that female biases
occur in more than half the populations: 160 single spore
isolates representing 40 sporophytes from one population
demonstrated that female gametophytes outnumbered males by a
ratio of 3:2 at the time of germination. Female gametophytic
clones formed significantly more biomass than male clones,
and individudal female shoots were more robust. Male clones,
however, produced more numerous stems. These sexually
dimorphic traits may be related to life history differences
between male and female gametophytes since females must
provide nutritional support to the "parasitic' sporophyte
generation, a burden that males do not share. -from
Authors},
Doi = {10.2307/2445376},
Key = {fds230521}
}
@article{fds230555,
Author = {Shaw, AJ},
Title = {The evolutionary capacity of bryophytes and
lichens},
Journal = {Bryophytes and lichens in a changing environment},
Pages = {362-380},
Year = {1992},
Month = {January},
Abstract = {Evolutionary capacity can be thought of as the capacity for
speciation, or as the rate at which a population responds to
natural selection. The genetic structures of lichen and
bryophyte species are described in relation to such
evolutionary capacity. A pressing problem with lichens is
the question of what constitutes an individual, with a
better understanding required of the genetic and
evolutionary relationships between phycobiont and mycobiont.
-P.J.Jarvis},
Key = {fds230555}
}
@article{fds230516,
Author = {Shaw, AJ},
Title = {The genetic structure of sporophytic and gametophytic
populations of the moss, Funaria hygrometrica
Hedw.},
Journal = {Evolution},
Volume = {45},
Number = {5},
Pages = {1260-1274},
Publisher = {WILEY},
Year = {1991},
Month = {January},
url = {http://dx.doi.org/10.1111/j.1558-5646.1991.tb04391.x},
Abstract = {Patterns of phenotypic and genotypic variability in two
populations of Funaria hygrometrica were investigated using
measurements of gametophytic and sporophytic morphology,
sporophytic reproductive output, spore germination,
gametophytic growth rates and tolerances of Cu, Cd, and low
nutrient conditions, and electrophoretically detectable
enzyme variation. Somatic mutation and/or nongenetic effects
appear to contribute significantly to phenotypic variability
in natural populations. -from Author},
Doi = {10.1111/j.1558-5646.1991.tb04391.x},
Key = {fds230516}
}
@article{fds230518,
Author = {Shaw, J and Jules, ES and Beer, SC},
Title = {Effects of metals on growth, morphology, and reproduction of
Ceratodon purpureus},
Journal = {Bryologist},
Volume = {94},
Number = {3},
Pages = {270-277},
Publisher = {JSTOR},
Year = {1991},
Month = {January},
url = {http://dx.doi.org/10.2307/3243964},
Abstract = {Gametophytic plants from six populations were grown on
substrates with varied degrees of heavy-metal contamination
in order to assess the effects of metal pollution on growth,
leaf size, and formation of archegonia and antheridia.
Plants from several populations that originated in
uncontaminated habitats grew as well on mine soil as plants
from a mine-site populations, suggesting an absence of
ecotypic differentiation. -from Authors},
Doi = {10.2307/3243964},
Key = {fds230518}
}
@article{fds230519,
Author = {Shaw, AJ},
Title = {Ecological genetics of serpentine tolerance in the moss,
Funaria flavicans: variation within and among haploid sib
families},
Journal = {American Journal of Botany},
Volume = {78},
Number = {11},
Pages = {1487-1493},
Publisher = {WILEY},
Year = {1991},
Month = {January},
url = {http://dx.doi.org/10.2307/2444973},
Abstract = {Two populations of Funaria flavicans, were grown on nutrient
media varying in Ni and Cr concentration and in the ratio of
Mg and Ca. There was no evidence that serpentine plants were
more tolerant of Ni, Cr, Mg/Ca, or high Ni combined with
high Mg/Ca. Plants from the nonserpentine population
produced more protonemal growth than the serpentine plants
on every medium except the control, on which plants from the
two populations were indistinguishable. Large differences in
Ni tolerance among haploid sib families (families of meiotic
progeny derived from the same sporophyte) from the
nonserpentine site provided evidence of genetic polymorphism
in that population. -from Author},
Doi = {10.2307/2444973},
Key = {fds230519}
}
@article{fds341864,
Author = {Fife, AJ and Shaw, AJ},
Title = {Epipterygium (Musci: Bryaceae) new to Australasia, with the
description of E. opararense, sp. novo},
Journal = {New Zealand Journal of Botany},
Volume = {28},
Number = {4},
Pages = {375-379},
Year = {1990},
Month = {October},
url = {http://dx.doi.org/10.1080/0028825X.1990.10412325},
Abstract = {Epipterygium opararense Fife and Shaw, sp. nov. is described
and illustrated, based on material from the Oparara River
valley in the Nelson Land District of the South Island, New
Zealand. The genus Epipterygium is predominantly tropical in
distribution, with a centre of diversity in tropical
America, and has not previously been recorded in
Australasia. The new species is unusual within Epipterygium
for having ½ phyllotaxy, which we consider to be an
apomorphic condition in the genus. © 1990 Taylor & Francis
Group, LLC.},
Doi = {10.1080/0028825X.1990.10412325},
Key = {fds341864}
}
@article{fds230517,
Author = {Shaw, AJ},
Title = {Metal tolerances and cotolerances in the moss Funaria
hygrometrica},
Journal = {Canadian Journal of Botany},
Volume = {68},
Number = {10},
Pages = {2275-2282},
Publisher = {Canadian Science Publishing},
Year = {1990},
Month = {January},
url = {http://dx.doi.org/10.1139/b90-290},
Abstract = {Protonemal growth in populations collected from most
Cu-contaminated soils was inhibited by only 10-30% on media
with 10 μg g -1 Cu, whereas populations from other sites
were inhibited by >80%. Population differences in tolerance
of Zn, Cd and Ni were not clearly related to environmental
contamination by these metals. Variation among populations
in growth on the metal treatments (except Cu) was related to
generalized differences in growth rates rather than to metal
tolerance per se. Populations differed by up to 400% in the
propensity to form stems on control nutrient medium, and
stem formation was negatively correlated with protonemal
growth, suggesting trade-offs between these 2 stages of
gametophyte development. In comparison with flowering
plants, generalized vigor and cross-tolerance between metals
may play a more important part in the ability of F.
hygrometrica to colonize contaminated oils, and
metal-specific tolerant ecotypes may be less important.
-from Author},
Doi = {10.1139/b90-290},
Key = {fds230517}
}
@article{fds230514,
Author = {Shaw, J},
Title = {Genetic variation for tolerance to copper and zinc within
and among populations of the moss, Funaria hygrometrica
Hedw.},
Journal = {New Phytologist},
Volume = {109},
Number = {2},
Pages = {211-222},
Year = {1988},
Abstract = {Tolerances of 2 life history stages (protonemal growth and
stem production) showed significant variation among
populations, and among individuals within all populations.
Heritabilities for tolerance were high within 3 populations,
but were close to zero within a population that originated
on a copper mine. -from Author},
Key = {fds230514}
}
@article{fds230512,
Author = {Shaw, J},
Title = {Evolution of heavy metal tolerance in bryophytes II. An
ecological and experimental investigation of the "copper
moss', Scopelophila cataractae (Pottiaceae)},
Journal = {American Journal of Botany},
Volume = {74},
Number = {6},
Pages = {813-821},
Publisher = {WILEY},
Year = {1987},
Month = {January},
url = {http://dx.doi.org/10.2307/2443862},
Abstract = {Scopelophila cataractae is known from several sites in S
Arizona and occurs at 6 localities in the E USA. Chemical
analyses of substrates from the E US localities showed that
all but 1 population grew on Cu-enriched soil. The one
substrate sample low in Cu was very high in Fe. Plants from
5 of the 6 localities were grown experimentally on 4 soil
types ranging from highly to not contaminated, and all grew
best on the soil contaminated with Cu, Pb and Zn. There was
no significant variation in growth between populations on
the four soil treatments. This lack of population
differentiation may be related to the absence of sexual
reproduction in S. cataractae in North America. from
Author},
Doi = {10.2307/2443862},
Key = {fds230512}
}
@article{fds230513,
Author = {Shaw, J},
Title = {Effect of environmental pretreatment on tolerance to copper
and zinc in the moss Funaria hygrometrica},
Journal = {AM. J. BOT.},
Volume = {74},
Number = {10},
Pages = {1466-1475},
Publisher = {WILEY},
Year = {1987},
Month = {January},
url = {http://dx.doi.org/10.2307/2444041},
Abstract = {The effect of pretreatment on zinc- and copper-enriched
media on subsequent tolerance of F. hygrometrica to these
metals was tested in three individuals each from a tolerant
and a nontolerant population. Some individuals showed a
significant response to pretreatment and some did not, and
those that did varied in both intensity and direction. In
general, pretreatment affected protonemal growth more than
stem production. Although pretreatment effects were
demonstrated, genetic differences between individuals and
populations were more important determinants of the level of
tolerance.},
Doi = {10.2307/2444041},
Key = {fds230513}
}
@article{fds230515,
Author = {Shaw, J and Antonovics, J and Anderson, LE},
Title = {Inter- and intraspecific variation of mosses in tolerance to
copper and zinc},
Journal = {Evolution},
Volume = {41},
Number = {6},
Pages = {1312-1325},
Publisher = {WILEY},
Year = {1987},
Month = {January},
url = {http://dx.doi.org/10.1111/j.1558-5646.1987.tb02469.x},
Abstract = {Tolerance of Funaria hygrometrica to Cu and Zn was greater
in populations that originated on soil with high
concentrations of these metals. Protonemal growth was more
inhibited by the metals than was germination; Cu was more
toxic than Zn. The pattern of population differentiation for
heavy metal tolerance in this species is much like that of
flowering plants. Five populations of Physcomitrium
pyriforme, which does not occur on metal-contaminated soil,
were all highly tolerant of Zn but extremely intolerant of
Cu. Significant variation in tolerance to Cu and Zn occurred
among populations, but tolerance did not correlate with
metal contents in native substrates. This pattern differs
from that of flowering plants. from Authors},
Doi = {10.1111/j.1558-5646.1987.tb02469.x},
Key = {fds230515}
}
@article{fds339390,
Author = {SHAW, AJ},
Title = {HEAVY-METAL TOLERANCE IN SCOPELOPHILA-CATARACTAE (MITT)
BROTH},
Journal = {AMERICAN JOURNAL OF BOTANY},
Volume = {73},
Number = {5},
Pages = {611-611},
Publisher = {BOTANICAL SOC AMER INC},
Year = {1986},
Month = {May},
Key = {fds339390}
}
@article{fds230510,
Author = {Shaw, J},
Title = {The relevance of ecology to species concepts in
bryophytes.},
Journal = {Bryologist},
Volume = {88},
Number = {3},
Pages = {199-206},
Publisher = {JSTOR},
Year = {1985},
Month = {January},
url = {http://dx.doi.org/10.2307/3243029},
Abstract = {Relationships between the ecological niche and species
concepts are discussed by developing concepts of the niche
and of character and species hypervolumes. Ecological data
are best used to evaluate the biological/evolutionary
significance of species defined by other criteria.
Differences in patterns of ecological variation are as
important for delineating species as are differences in the
average or typical habitat. A classification of nine
gemmiferous Pohlia species summarizes more ecological than
morphological information, although the classification was
based on morphology. Combining P. annotina and P.
camptotrachela results in a loss of ecological information.
-from Author},
Doi = {10.2307/3243029},
Key = {fds230510}
}
@article{fds230511,
Author = {Shaw, J},
Title = {Character analysis, phylogeny, and classification of the
moss genus Pohlia.},
Journal = {Canadian Journal of Botany},
Volume = {62},
Number = {2},
Pages = {219-229},
Publisher = {Canadian Science Publishing},
Year = {1984},
Month = {January},
url = {http://dx.doi.org/10.1139/b84-036},
Abstract = {Forty-one Pohlia taxa coded for their expression of 36
qualitative morphological characters are analyzed using
cladistic and phenetic methods. Four major lineages within
the genus differ primarily in sporophyte characters, with
specific differences based largely on gametophytic features.
An infrageneric classification is proposed with diagnostic
descriptions and nomenclature provided. -from
Author},
Doi = {10.1139/b84-036},
Key = {fds230511}
}
%% Papers Accepted
@article{fds374503,
Author = {Wieczynski, D. and Yoshimura, K. and Denison, E. and Geisen, S. and DeBruyn, J. and Shaw, A. J. and Weston, D. and Pelletier, D. and Wilhelm, S. and J-P., Gibert},
Title = {Viral infections likely mediate microbial controls on
ecosystem responses to global warming},
Journal = {FEMS Microbiology Ecology},
Year = {2023},
Key = {fds374503}
}
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