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| Publications of Paul S. Manos :chronological alphabetical combined listing:
%% Papers Published
@article{fds366845,
Author = {Crowl, AA and Fritsch, PW and Tiley, GP and Lynch, NP and Ranney, TG and Ashrafi, H and Manos, PS},
Title = {A first complete phylogenomic hypothesis for diploid
blueberries (Vaccinium section Cyanococcus).},
Journal = {Am J Bot},
Volume = {109},
Number = {10},
Pages = {1596-1606},
Year = {2022},
Month = {October},
url = {http://dx.doi.org/10.1002/ajb2.16065},
Abstract = {<h4>Premise</h4>The true blueberries (Vaccinium sect.
Cyanococcus; Ericaceae), endemic to North America, have been
intensively studied for over a century. However, with
species estimates ranging from nine to 24 and much confusion
regarding species boundaries, this ecologically and
economically valuable group remains inadequately understood
at a basic evolutionary and taxonomic level. As a first step
toward understanding the evolutionary history and taxonomy
of this species complex, we present the first phylogenomic
hypothesis of the known diploid blueberries.<h4>Methods</h4>We
used flow cytometry to verify the ploidy of putative diploid
taxa and a target-enrichment approach to obtain a genomic
data set for phylogenetic analyses.<h4>Results</h4>Despite
evidence of gene flow, we found that a primary phylogenetic
signal is present. Monophyly for all morphospecies was
recovered, with two notable exceptions: one sample of V.
boreale was consistently nested in the V. myrtilloides clade
and V. caesariense was nested in the V. fuscatum clade. One
diploid taxon, Vaccinium pallidum, is implicated as having a
homoploid hybrid origin.<h4>Conclusions</h4>This
foundational study represents the first attempt to elucidate
evolutionary relationships of the true blueberries of North
America with a phylogenomic approach and sets the stage for
multiple avenues of future study such as a taxonomic
revision of the group, the verification of a homoploid
hybrid taxon, and the study of polyploid lineages within the
context of a diploid phylogeny.},
Doi = {10.1002/ajb2.16065},
Key = {fds366845}
}
@article{fds362500,
Author = {Zhou, B-F and Yuan, S and Crowl, AA and Liang, Y-Y and Shi, Y and Chen,
X-Y and An, Q-Q and Kang, M and Manos, PS and Wang, B},
Title = {Phylogenomic analyses highlight innovation and introgression
in the continental radiations of Fagaceae across the
Northern Hemisphere.},
Journal = {Nature Communications},
Volume = {13},
Number = {1},
Pages = {1320},
Year = {2022},
Month = {March},
url = {http://dx.doi.org/10.1038/s41467-022-28917-1},
Abstract = {Northern Hemisphere forests changed drastically in the early
Eocene with the diversification of the oak family
(Fagaceae). Cooling climates over the next 20 million years
fostered the spread of temperate biomes that became
increasingly dominated by oaks and their chestnut relatives.
Here we use phylogenomic analyses of nuclear and plastid
genomes to investigate the timing and pattern of major
macroevolutionary events and ancient genome-wide signatures
of hybridization across Fagaceae. Innovation related to seed
dispersal is implicated in triggering waves of continental
radiations beginning with the rapid diversification of major
lineages and resulting in unparalleled transformation of
forest dynamics within 15 million years following the K-Pg
extinction. We detect introgression at multiple time scales,
including ancient events predating the origination of
genus-level diversity. As oak lineages moved into newly
available temperate habitats in the early Miocene, secondary
contact between previously isolated species occurred. This
resulted in adaptive introgression, which may have further
amplified the diversification of white oaks across
Eurasia.},
Doi = {10.1038/s41467-022-28917-1},
Key = {fds362500}
}
@article{fds357527,
Author = {Manos, PS and Hipp, AL},
Title = {An updated infrageneric classification of the north american
oaks (Quercus subgenus quercus): Review of the contribution
of phylogenomic data to biogeography and species
diversity},
Journal = {Forests},
Volume = {12},
Number = {6},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.3390/f12060786},
Abstract = {The oak flora of North America north of Mexico is both
phylogenetically diverse and species-rich, including 92
species placed in five sections of subgenus Quercus, the oak
clade centered on the Americas. Despite phylogenetic and
taxonomic progress on the genus over the past 45 years,
classification of species at the subsectional level remains
unchanged since the early treatments by WL Trelease, AA
Camus, and CH Muller. In recent work, we used a RAD-seq
based phylogeny including 250 species sampled from
throughout the Americas and Eurasia to reconstruct the
timing and biogeography of the North American oak radiation.
This work demonstrates that the North American oak flora
comprises mostly regional species radiations with limited
phylogenetic affinities to Mexican clades, and two sister
group connections to Eurasia. Using this framework, we
describe the regional patterns of oak diversity within North
America and formally classify 62 species into nine major
North American subsections within sections Lobatae (the red
oaks) and Quercus (the white oaks), the two largest sections
of subgenus Quercus. We also distill emerging evolutionary
and biogeographic patterns based on the impact of
phylogenomic data on the systematics of multiple species
complexes and instances of hybridization.},
Doi = {10.3390/f12060786},
Key = {fds357527}
}
@article{fds343319,
Author = {Crowl, AA and Manos, PS and McVay, JD and Lemmon, AR and Lemmon, EM and Hipp, AL},
Title = {Uncovering the genomic signature of ancient introgression
between white oak lineages (Quercus).},
Journal = {The New Phytologist},
Volume = {226},
Number = {4},
Pages = {1158-1170},
Year = {2020},
Month = {May},
url = {http://dx.doi.org/10.1111/nph.15842},
Abstract = {Botanists have long recognised interspecific gene flow as a
common occurrence within white oaks (Quercus section
Quercus). Historical allele exchange, however, has not been
fully characterised and the complex genomic signals
resulting from the combination of vertical and horizontal
gene transmission may confound phylogenetic inference and
obscure our ability to accurately infer the deep
evolutionary history of oaks. Using anchored enrichment, we
obtained a phylogenomic dataset consisting of hundreds of
single-copy nuclear loci. Concatenation, species-tree and
network analyses were carried out in an attempt to uncover
the genomic signal of ancient introgression and infer the
divergent phylogenetic topology for the white oak clade.
Locus and site-level likelihood comparisons were then
conducted to further explore the introgressed signal within
our dataset. Historical, intersectional gene flow is
suggested to have occurred between an ancestor of the
Eurasian Roburoid lineage and Quercus pontica and North
American Dumosae and Prinoideae lineages. Despite extensive
time past, our approach proved successful in detecting the
genomic signature of ancient introgression. Our results,
however, highlight the importance of sampling and the use of
a plurality of analytical tools and methods to sufficiently
explore genomic datasets, uncover this signal, and
accurately infer evolutionary history.},
Doi = {10.1111/nph.15842},
Key = {fds343319}
}
@article{fds346837,
Author = {Hipp, AL and Manos, PS and Hahn, M and Avishai, M and Bodénès, C and Cavender-Bares, J and Crowl, AA and Deng, M and Denk, T and Fitz-Gibbon,
S and Gailing, O and González-Elizondo, MS and González-Rodríguez,
A and Grimm, GW and Jiang, X-L and Kremer, A and Lesur, I and McVay, JD and Plomion, C and Rodríguez-Correa, H and Schulze, E-D and Simeone, MC and Sork, VL and Valencia-Avalos, S},
Title = {Genomic landscape of the global oak phylogeny.},
Journal = {The New Phytologist},
Volume = {226},
Number = {4},
Pages = {1198-1212},
Year = {2020},
Month = {May},
url = {http://dx.doi.org/10.1111/nph.16162},
Abstract = {The tree of life is highly reticulate, with the history of
population divergence emerging from populations of gene
phylogenies that reflect histories of introgression, lineage
sorting and divergence. In this study, we investigate global
patterns of oak diversity and test the hypothesis that there
are regions of the oak genome that are broadly informative
about phylogeny. We utilize fossil data and restriction-site
associated DNA sequencing (RAD-seq) for 632 individuals
representing nearly 250 Quercus species to infer a
time-calibrated phylogeny of the world's oaks. We use a
reversible-jump Markov chain Monte Carlo method to
reconstruct shifts in lineage diversification rates,
accounting for among-clade sampling biases. We then map the
> 20 000 RAD-seq loci back to an annotated oak genome and
investigate genomic distribution of introgression and
phylogenetic support across the phylogeny. Oak lineages have
diversified among geographic regions, followed by ecological
divergence within regions, in the Americas and Eurasia.
Roughly 60% of oak diversity traces back to four clades that
experienced increases in net diversification, probably in
response to climatic transitions or ecological opportunity.
The strong support for the phylogeny contrasts with high
genomic heterogeneity in phylogenetic signal and
introgression. Oaks are phylogenomic mosaics, and their
diversity may in fact depend on the gene flow that shapes
the oak genome.},
Doi = {10.1111/nph.16162},
Key = {fds346837}
}
@article{fds366846,
Author = {Hipp, AL and Manos, PS and Cavender-Bares, J},
Title = {ASCENT OF THE OAKS},
Journal = {Scientific American},
Volume = {323},
Number = {2},
Pages = {42-49},
Year = {2020},
Key = {fds366846}
}
@article{fds347007,
Author = {Denk, T and Hill, RS and Simeone, MC and Cannon, C and Dettmann, ME and Manos, PS},
Title = {Comment on "Eocene Fagaceae from Patagonia and Gondwanan
legacy in Asian rainforests".},
Journal = {Science (New York, N.Y.)},
Volume = {366},
Number = {6467},
Pages = {eaaz2189},
Year = {2019},
Month = {November},
url = {http://dx.doi.org/10.1126/science.aaz2189},
Abstract = {Wilf et al (Research Articles, 7 June 2019, eaaw5139) claim
that Castanopsis evolved in the Southern Hemisphere from
where it spread to its modern distribution in Southeast
Asia. However, extensive paleobotanical records of
Antarctica and Australia lack evidence of any Fagaceae, and
molecular patterns indicate shared biogeographic histories
of Castanopsis, Castanea, Lithocarpus, and Quercus subgenus
Cerris, making the southern route unlikely.},
Doi = {10.1126/science.aaz2189},
Key = {fds347007}
}
@article{fds346836,
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 = {fds346836}
}
@article{fds346838,
Author = {Hipp, AL and Whittemore, AT and Garner, M and Hahn, M and Fitzek, E and Guichoux, E and Cavender-Bares, J and Gugger, PF and Manos, PS and Pearse, IS and Cannon, CH},
Title = {Genomic Identity of White Oak Species in an Eastern North
American Syngameon},
Journal = {Annals of the Missouri Botanical Garden},
Volume = {104},
Number = {3},
Pages = {455-477},
Year = {2019},
Month = {October},
url = {http://dx.doi.org/10.3417/2019434},
Abstract = {The eastern North American white oaks, a complex of
approximately 16 potentially interbreeding species, have
become a classic model for studying the genetic nature of
species in a syngameon. Genetic work over the past two
decades has demonstrated the reality of oak species, but
gene flow between sympatric oaks raises the question of
whether there are conserved regions of the genome that
define oak species. Does gene flow homogenize the entire
genome? Do the regions of the genome that distinguish a
species in one part of its range differ from the regions
that distinguish it in other parts of its range, where it
grows in sympatry with different species? Or are there
regions of the genome that are relatively conserved across
species ranges? In this study, we revisit seven species of
the eastern North American white oak syngameon using a set
of 80 single-nucleotide polymorphisms (SNPs) selected in a
previous study because they show differences among, and
consistency within, the species. We test the hypothesis that
there exist segments of the genome that do not become
homogenized by repeated introgression, but retain distinct
alleles characteristic of each species. We undertake a
range-wide sampling to investigate whether SNPs that
appeared to be fixed based on a relatively small sample in
our previous work are fixed or nearly fixed across the range
of the species. Each of the seven species remains
genetically distinct across its range, given our diagnostic
set of markers, with relatively few individuals exhibiting
admixture of multiple species. SNPs map back to all 12
Quercus linkage groups (chromosomes) and are separated from
each other by an average of 7.47 million bp (± 8.74 million
bp, SD), but are significantly clustered relative to a
random null distribution, suggesting that our SNP toolkit
reflects genome-wide patterns of divergence while
potentially being concentrated in regions of the genome that
reflect a higher-than-average history of among-species
divergence. This application of a DNA toolkit designed for
the simple problem of identifying species in the field has
two important implications. First, the eastern North
American white oak syngameon is composed of entities that
most taxonomists would consider "good species." Second, and
more fundamentally, species in the syngameon are genetically
coherent because characteristic portions of the genome
remain divergent despite a history of introgression.
Understanding the conditions under which some loci diverge
while others introgress is key to understanding the origins
and maintenance of global tree diversity.},
Doi = {10.3417/2019434},
Key = {fds346838}
}
@article{fds334498,
Author = {Cavender-Bares, J and Kothari, S and Meireles, JE and Kaproth, MA and Manos, PS and Hipp, AL},
Title = {The role of diversification in community assembly of the
oaks (Quercus L.) across the continental
U.S.},
Journal = {American Journal of Botany},
Volume = {105},
Number = {3},
Pages = {565-586},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1002/ajb2.1049},
Abstract = {PREMISE OF THE STUDY:Evolutionary and biogeographic history,
including past environmental change and diversification
processes, are likely to have influenced the expansion,
migration, and extinction of populations, creating
evolutionary legacy effects that influence regional species
pools and the composition of communities. We consider the
consequences of the diversification process in shaping trait
evolution and assembly of oak-dominated communities
throughout the continental United States (U.S.).
METHODS:Within the U.S. oaks, we tested for phylogenetic and
functional trait patterns at different spatial scales,
taking advantage of a dated phylogenomic analysis of
American oaks and the U.S. Forest Service (USFS) Forest
Inventory and Analysis (FIA). KEY RESULTS:We find (1)
phylogenetic overdispersion at small grain sizes throughout
the U.S. across all spatial extents and (2) a shift from
overdispersion to clustering with increasing grain sizes.
Leaf traits have evolved in a convergent manner, and these
traits are clustered in communities at all spatial scales,
except in the far west, where species with contrasting leaf
types co-occur. CONCLUSIONS:Our results support the
hypotheses that (1) interspecific interactions were
important in parallel adaptive radiation of the genus into a
range of habitats across the continent and (2) that the
diversification process is a critical driver of community
assembly. Functional convergence of complementary species
from distinct clades adapted to the same local habitats is a
likely mechanism that allows distantly related species to
coexist. Our findings contribute to an explanation of the
long-term maintenance of high oak diversity and the
dominance of the oak genus in North America.},
Doi = {10.1002/ajb2.1049},
Key = {fds334498}
}
@article{fds332970,
Author = {Meireles, JE and Manos, PS},
Title = {Pervasive migration across rainforest and sandy coastal
plain Aechmea nudicaulis (Bromeliaceae) populations despite
contrasting environmental conditions.},
Journal = {Molecular Ecology},
Volume = {27},
Number = {5},
Pages = {1261-1272},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1111/mec.14512},
Abstract = {Understanding the colonization of extreme marginal habitats
and the relative roles of space and environment in
maintaining peripheral populations remains challenging.
Here, we leverage a system of pairs of rainforest and sandy
coastal plain communities that allow us to decouple spatial
and environmental effects in the population structure and
migration rates of the bromeliad Aechmea nudicaulis.
Structure and gene flow between populations were estimated
from Bayesian clustering and coalescent-based migration
models applied to chloroplast sequence and nuclear
microsatellite data. Contrary to our initial expectation,
the sharp environmental gradient between rainforest and
sandy plains does not seem to have affected the colonization
and migration dynamics in A. nudicaulis. Our analyses
uncover pervasive gene flow between neighbouring habitats in
both chloroplast and nuclear data despite the striking
differences in environmental conditions. This result is
consistent with a scenario of repeated colonization of the
sandy coastal plains from forest populations through seed
dispersal, as well as the maintenance of gene flow between
habitats through pollination. We also recovered a broad
north/south population structure that has been found in
other Atlantic rainforest groups and possibly reflects older
phylogeographic dynamics.},
Doi = {10.1111/mec.14512},
Key = {fds332970}
}
@article{fds332837,
Author = {Harnik, PG and Maherali, H and Miller, JH and Manos,
PS},
Title = {Geographic range velocity and its association with phylogeny
and life history traits in North American woody
plants.},
Journal = {Ecology and Evolution},
Volume = {8},
Number = {5},
Pages = {2632-2644},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1002/ece3.3880},
Abstract = {The geographic ranges of taxa change in response to
environmental conditions. Yet whether rates of range
movement (biotic velocities) are phylogenetically conserved
is not well known. Phylogenetic conservatism of biotic
velocities could reflect similarities among related lineages
in climatic tolerances and dispersal-associated traits. We
assess whether late Quaternary biotic velocities were
phylogenetically conserved and whether they correlate with
climatic tolerances and dispersal-associated traits. We used
phylogenetic regression and nonparametric correlation to
evaluate associations between biotic velocities,
dispersal-associated traits, and climatic tolerances for 28
woody plant genera and subgenera in North America. The
velocities with which woody plant taxa shifted their core
geographic range limits were positively correlated from time
step to time step between 16 and 7 ka. The strength of this
correlation weakened after 7 ka as the pace of climate
change slowed. Dispersal-associated traits and climatic
tolerances were not associated with biotic velocities.
Although the biotic velocities of some genera were
consistently fast and others consistently slow, biotic
velocities were not phylogenetically conserved. The rapid
late Quaternary range shifts of plants lacking traits that
facilitate frequent long-distance dispersal has long been
noted (i.e., Reid's Paradox). Our results are consistent
with this paradox and show that it remains robust when
phylogenetic information is taken into account. The lack of
association between biotic velocities, dispersal-associated
traits, and climatic tolerances may reflect several,
nonmutually exclusive processes, including rare
long-distance dispersal, biotic interactions, and cryptic
refugia. Because late Quaternary biotic velocities were
decoupled from dispersal-associated traits, trait data for
genera and subgenera cannot be used to predict longer-term
(millennial-scale) floristic responses to climate
change.},
Doi = {10.1002/ece3.3880},
Key = {fds332837}
}
@article{fds330891,
Author = {Deng, M and Jiang, X-L and Hipp, AL and Manos, PS and Hahn,
M},
Title = {Phylogeny and biogeography of East Asian evergreen oaks
(Quercus section Cyclobalanopsis; Fagaceae): Insights into
the Cenozoic history of evergreen broad-leaved forests in
subtropical Asia.},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {119},
Pages = {170-181},
Year = {2018},
Month = {February},
url = {http://dx.doi.org/10.1016/j.ympev.2017.11.003},
Abstract = {The evolutionary history of Quercus section Cyclobalanopsis,
a dominant lineage in East Asian evergreen broadleaved
forests (EBLFs), has not been comprehensively studied using
molecular tools. In this study, we reconstruct the first
comprehensive phylogeny of this lineage using a genomic
approach (restriction-site associated DNA sequencing,
RAD-seq), sampling 35 of the ca. 90 species currently
recognized, representing all main morphological groups of
section Cyclobalanopsis. In addition, 10 other species of
Quercus and two outgroups were also sampled. Divergence
times were estimated using a relaxed clock model and two
fossil calibrations. Ancestral areas and dispersal routes
were inferred using statistical dispersal-vicariance
analysis and the dispersal-extinction-cladogenesis (DEC)
model. The phylogeny of Quercus section Cyclobalanopsis
demonstrates the section to be monophyletic, comprising two
main lineages and six subclades that are well supported by
anatomical traits. Biogeographical reconstructions indicate
that the wide northern hemisphere distribution of Quercus
was disrupted in the Late Eocene, leading to the main extant
groups at about 33 Ma. The earliest divergences in section
Cyclobalanopsis correspond to the phased uplift of the
Himalayas and lateral extrusion of Indochina at the
transition of the Oligocene and Miocene, where the highest
rate of diversification occurred in the late Miocene.
Dispersal from Sino-Himalaya and the Palaeotropics to
Sino-Japan in the Miocene was facilitated by the increased
intensity of East Asian summer monsoons and by the Middle
Miocene Climatic Optimum. Our results highlight the
importance of climatic changes and Indo-Eurasian
collision-induced tectonic activities from the Neogene
onward to the spatial-temporal diversification patterns of
Asian EBLF lineages.},
Doi = {10.1016/j.ympev.2017.11.003},
Key = {fds330891}
}
@article{fds329084,
Author = {Hipp, AL and Manos, PS and González-Rodríguez, A and Hahn, M and Kaproth, M and McVay, JD and Avalos, SV and Cavender-Bares,
J},
Title = {Sympatric parallel diversification of major oak clades in
the Americas and the origins of Mexican species
diversity.},
Journal = {The New Phytologist},
Volume = {217},
Number = {1},
Pages = {439-452},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1111/nph.14773},
Abstract = {Oaks (Quercus, Fagaceae) are the dominant tree genus of
North America in species number and biomass, and Mexico is a
global center of oak diversity. Understanding the origins of
oak diversity is key to understanding biodiversity of
northern temperate forests. A phylogenetic study of
biogeography, niche evolution and diversification patterns
in Quercus was performed using 300 samples, 146 species.
Next-generation sequencing data were generated using the
restriction-site associated DNA (RAD-seq) method. A
time-calibrated maximum likelihood phylogeny was inferred
and analyzed with bioclimatic, soils, and leaf habit data to
reconstruct the biogeographic and evolutionary history of
the American oaks. Our highly resolved phylogeny
demonstrates sympatric parallel diversification in climatic
niche, leaf habit, and diversification rates. The two major
American oak clades arose in what is now the boreal zone and
radiated, in parallel, from eastern North America into
Mexico and Central America. Oaks adapted rapidly to niche
transitions. The Mexican oaks are particularly numerous, not
because Mexico is a center of origin, but because of high
rates of lineage diversification associated with high rates
of evolution along moisture gradients and between the
evergreen and deciduous leaf habits. Sympatric parallel
diversification in the oaks has shaped the diversity of
North American forests.},
Doi = {10.1111/nph.14773},
Key = {fds329084}
}
@article{fds330892,
Author = {Hauser, DA and Keuter, A and McVay, JD and Hipp, AL and Manos,
PS},
Title = {The evolution and diversification of the red oaks of the
California Floristic Province (Quercus section Lobatae,
series Agrifoliae).},
Journal = {American Journal of Botany},
Volume = {104},
Number = {10},
Pages = {1581-1595},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.3732/ajb.1700291},
Abstract = {<h4>Premise of the study</h4>The California Floristic
Province (CA-FP) is a unique and diverse region of floral
endemism, yet the timing and nature of divergence and
diversification of many lineages remain underexplored. We
seek to elucidate the evolutionary history of the red oaks
of the CA-FP, the Agrifoliae.<h4>Methods</h4>We collected
PstI-associated RAD-seq data as well as morphometrics from
individuals of the four species across their ranges,
including varieties and hybrids. Phylogeny and divergence
times were estimated. We analyzed morphological
differentiation in over 70 plants using PCA and assessed
species delimitation and admixture using genotype clustering
analysis in over 40 plants.<h4>Key results</h4>We find that
the Agrifoliae are monophyletic and sister to all other red
oak species. Within the Agrifoliae, all species are
supported, with Quercus kelloggii sister to a clade of
subevergreen taxa: (Quercus agrifolia - (Q. parvula + Q.
wislizeni)). Molecular and morphometric analyses are
equivocal for named varieties. Notably, Q. parvula var.
tamalpaisensis appears to be part of a hybrid swarm between
Q. parvula and Q. wislizeni. Dating estimates were
concordant with previous hypotheses and geological evidence,
with diversification occurring between 10 and 20 million
years ago.<h4>Conclusions</h4>The Agrifoliae represent a
geographically discrete, early-diverging red oak lineage
that diversified during the period of drying and warming
associated with Sierran uplift during the middle Miocene.
Molecular differentiation within the clade supports the
current taxonomy, including an east-west species level
pattern (Q. parvula and Q. wislizeni) and north-south
intraspecific patterns to some degree, although the latter
require additional study.},
Doi = {10.3732/ajb.1700291},
Key = {fds330892}
}
@article{fds325587,
Author = {Fitz-Gibbon, S and Hipp, AL and Pham, KK and Manos, PS and Sork,
VL},
Title = {Phylogenomic inferences from reference-mapped and de novo
assembled short-read sequence data using RADseq sequencing
of California white oaks (Quercus section
Quercus).},
Journal = {Genome},
Volume = {60},
Number = {9},
Pages = {743-755},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1139/gen-2016-0202},
Abstract = {The emergence of next generation sequencing has increased by
several orders of magnitude the amount of data available for
phylogenetics. Reduced representation approaches, such as
restriction-sited associated DNA sequencing (RADseq), have
proven useful for phylogenetic studies of non-model species
at a wide range of phylogenetic depths. However, analysis of
these datasets is not uniform and we know little about the
potential benefits and drawbacks of de novo assembly versus
assembly by mapping to a reference genome. Using RADseq data
for 83 oak samples representing 16 taxa, we identified
variants via three pipelines: mapping sequence reads to a
recently published draft genome of Quercus lobata, and de
novo assembly under two sets of locus filters. For each
pipeline, we inferred the maximum likelihood phylogeny. All
pipelines produced similar trees, with minor shifts in
relationships within well-supported clades, despite the fact
that they yielded different numbers of loci (68 000 -
111 000 loci) and different degrees of overlap with the
reference genome. We conclude that both the
reference-aligned and de novo assembly pipelines yield
reliable results, and that advantages and disadvantages of
these approaches pertain mainly to downstream uses of RADseq
data, not to phylogenetic inference per se.},
Doi = {10.1139/gen-2016-0202},
Key = {fds325587}
}
@article{fds326158,
Author = {Pham, KK and Hipp, AL and Manos, PS and Cronn, RC},
Title = {A time and a place for everything: phylogenetic history and
geography as joint predictors of oak plastome
phylogeny.},
Journal = {Genome},
Volume = {60},
Number = {9},
Pages = {720-732},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1139/gen-2016-0191},
Abstract = {Owing to high rates of introgressive hybridization, the
plastid genome is poorly suited to fine-scale DNA barcoding
and phylogenetic studies of the oak genus (Quercus,
Fagaceae). At the tips of the oak plastome phylogeny, recent
gene migration and reticulation generally cause topology to
reflect geographic structure, while deeper branches reflect
lineage divergence. In this study, we quantify the simple
and partial effects of geographic proximity and
nucleome-inferred phylogenetic history on oak plastome
phylogeny at different evolutionary scales. Our study
compares pairwise phylogenetic distances based on complete
plastome sequences, pairwise phylogenetic distances from
nuclear restriction site-associated DNA sequences (RADseq),
and pairwise geographic distances for 34 individuals of the
white oak clade representing 24 North American and Eurasian
species. Within the North American white oak clade alone,
phylogenetic history has essentially no effect on plastome
variation, while geography explains 11%-21% of plastome
phylogenetic variance. However, across multiple continents
and clades, phylogeny predicts 30%-41% of plastome
variation, geography 3%-41%. Tipwise attenuation of
phylogenetic informativeness in the plastome means that in
practical terms, plastome data has little use in solving
phylogenetic questions, but can still be a useful barcoding
or phylogenetic marker for resolving questions among major
clades.},
Doi = {10.1139/gen-2016-0191},
Key = {fds326158}
}
@article{fds328328,
Author = {McVay, JD and Hauser, D and Hipp, AL and Manos, PS},
Title = {Phylogenomics reveals a complex evolutionary history of
lobed-leaf white oaks in western North America.},
Journal = {Genome},
Volume = {60},
Number = {9},
Pages = {733-742},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1139/gen-2016-0206},
Abstract = {Species within the genus Quercus (oak) hybridize in complex
patterns that have yet to be fully explored with
phylogenomic data. Analyses to date have recovered
reasonable divergent patterns, suggesting that the impact of
introgression may not always be obvious in inferred oak
phylogenies. We explore this phenomenon using RADseq data
for 136 samples representing 54 oak species by conducting
phylogenetic analyses designed to distinguish signals of
lineage diversification and hybridization, focusing on the
lobed-leaf species Quercus gambelii, Q. lobata, and Q.
garryana in the context of a broad sampling of allied white
oaks (Quercus section Quercus), and particularly the
midwestern Q. macrocarpa. We demonstrate that historical
introgressive hybridization between once sympatric species
affects phylogeny estimation. Historical range expansion
during periods of favorable climate likely explains our
observations; analyses support genetic exchange between
ancestral populations of Q. gambelii and Q. macrocarpa. We
conclude that the genomic consequences of introgression
caused the attraction of distant lineages in phylogenetic
tree space, and that introgressive and divergent signals can
be disentangled to produce a robust estimate of the
phylogenetic history of the species.},
Doi = {10.1139/gen-2016-0206},
Key = {fds328328}
}
@article{fds326589,
Author = {McVay, JD and Hipp, AL and Manos, PS},
Title = {A genetic legacy of introgression confounds phylogeny and
biogeography in oaks.},
Journal = {Proceedings of the Royal Society B: Biological
Sciences},
Volume = {284},
Number = {1854},
Pages = {20170300},
Year = {2017},
Month = {May},
url = {http://dx.doi.org/10.1098/rspb.2017.0300},
Abstract = {Oaks (Quercus L.) have long been suspected to hybridize in
nature, and widespread genetic exchange between
morphologically defined species is well documented in two-
to six-species systems, but the phylogenetic consequences of
hybridization in oaks have never been demonstrated in a
phylogenetically diverse sample. Here, we present
phylogenomic analyses of a ca 30 Myr clade that strongly
support morphologically defined species and the resolution
of novel clades of white oaks; however, historical
hybridization across clade boundaries is detectable and,
undiagnosed, would obscure the imprint of biogeographic
history in the phylogeny. Phylogenetic estimation from
restriction-site-associated DNA sequencing data for 156
individuals representing 81 species supports two successive
intercontinental disjunctions of white oaks: an early
vicariance between the Eurasian and American white oaks, and
a second, independent radiation represented by two relictual
species. A suite of subsampled and partitioned analyses,
however, supports a more recent divergence of the Eurasian
white oaks from within the American white oaks and suggests
that historic introgression between the Eurasian white oaks
and a now-relictual lineage biases concatenated phylogenetic
estimates. We demonstrate how divergence and reticulation
both influence our understanding of the timing and nature of
diversification and global colonization in these
ecologically and economically important taxa.},
Doi = {10.1098/rspb.2017.0300},
Key = {fds326589}
}
@article{fds324884,
Author = {Yu, Y and Xiang, Q and Manos, PS and Soltis, DE and Soltis, PS and Song,
B-H and Cheng, S and Liu, X and Wong, G},
Title = {Whole-genome duplication and molecular evolution in Cornus
L. (Cornaceae) - Insights from transcriptome
sequences.},
Journal = {Plos One},
Volume = {12},
Number = {2},
Pages = {e0171361},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1371/journal.pone.0171361},
Abstract = {The pattern and rate of genome evolution have profound
consequences in organismal evolution. Whole-genome
duplication (WGD), or polyploidy, has been recognized as an
important evolutionary mechanism of plant diversification.
However, in non-model plants the molecular signals of genome
duplications have remained largely unexplored.
High-throughput transcriptome data from next-generation
sequencing have set the stage for novel investigations of
genome evolution using new bioinformatic and methodological
tools in a phylogenetic framework. Here we compare ten de
novo-assembled transcriptomes representing the major
lineages of the angiosperm genus Cornus (dogwood) and
relevant outgroups using a customized pipeline for analyses.
Using three distinct approaches, molecular dating of
orthologous genes, analyses of the distribution of
synonymous substitutions between paralogous genes, and
examination of substitution rates through time, we detected
a shared WGD event in the late Cretaceous across all taxa
sampled. The inferred doubling event coincides temporally
with the paleoclimatic changes associated with the initial
divergence of the genus into three major lineages. Analyses
also showed an acceleration of rates of molecular evolution
after WGD. The highest rates of molecular evolution were
observed in the transcriptome of the herbaceous lineage, C.
canadensis, a species commonly found at higher latitudes,
including the Arctic. Our study demonstrates the value of
transcriptome data for understanding genome evolution in
closely related species. The results suggest dramatic
increase in sea surface temperature in the late Cretaceous
may have contributed to the evolution and diversification of
flowering plants.},
Doi = {10.1371/journal.pone.0171361},
Key = {fds324884}
}
@article{fds366847,
Author = {Denk, T and Grimm, GW and Manos, PS and Deng, M and Hipp,
AL},
Title = {An Updated Infrageneric Classification of the Oaks: Review
of Previous Taxonomic Schemes and Synthesis of Evolutionary
Patterns},
Pages = {13-38},
Booktitle = {Tree Physiology},
Publisher = {Springer International Publishing},
Year = {2017},
ISBN = {9783319690988},
url = {http://dx.doi.org/10.1007/978-3-319-69099-5_2},
Doi = {10.1007/978-3-319-69099-5_2},
Key = {fds366847}
}
@article{fds322301,
Author = {Johnson, MG and Lang, K and Manos, P and Golet, GH and Schierenbeck,
KA},
Title = {Evidence for genetic erosion of a California native tree,
Platanus racemosa, via recent, ongoing introgressive
hybridization with an introduced ornamental
species},
Journal = {Conservation Genetics},
Volume = {17},
Number = {3},
Pages = {593-602},
Publisher = {Springer Nature},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1007/s10592-015-0808-z},
Abstract = {When non-native, genetically diverse species are introduced,
hybridization with native congeners may erode the genetic
composition of local species, perhaps even resulting in
extinction. While such events may lead to adverse
consequences at the community and ecosystem level, few
studies exist on ecologically important tree species. In the
genus Platanus, introgressive hybridization is widespread,
and one common ornamental species, introduced to California
during the late 19th century, is itself a hybrid. Our
microsatellite analysis of more than 400 Platanus trees from
north-central California reveals a complex pattern of
invasion and hybridization in an age-structured population.
By using size as a proxy for age, we have demonstrated that
the Platanus population of north-central California has
recently gained genetic diversity and effective population
size. Principal coordinate analysis (PCoA) and genetic
admixture analysis (STRUCTURE) both reveal a strong
differentiation of genotypes into two main genetic clusters,
with a large number of admixed genotypes. One of the genetic
clusters identified is heavily biased towards younger trees,
including samples from locations with relatively recently
planted ornamental trees likely to be P. × hispanica
(formerly known as P. × acerifolia). We conclude that the
two genetic clusters correspond to the native P. racemosa
and the introduced invasive hybrid species
P. × hispanica. Additional hybridization between the
invasive ornamental and the native species has occurred in
California, and recent hybrid trees are more likely to be
younger than trees without admixture. Our findings suggest
that the observed increase in genetic diversity among
California Platanus is due to rampant ongoing introgression,
which may be threatening the continued genetic
distinctiveness of the native species. This is cause for
concern from a conservation standpoint, due to a direct loss
of genetic distinctiveness, and a potential reduction in
habitat value of associated species.},
Doi = {10.1007/s10592-015-0808-z},
Key = {fds322301}
}
@article{fds322302,
Author = {Cavender-Bares, J and González-Rodríguez, A and Eaton, DAR and Hipp, AAL and Beulke, A and Manos, PS},
Title = {Phylogeny and biogeography of the American live oaks
(Quercus subsection Virentes): a genomic and population
genetics approach.},
Journal = {Molecular Ecology},
Volume = {24},
Number = {14},
Pages = {3668-3687},
Year = {2015},
Month = {July},
url = {http://dx.doi.org/10.1111/mec.13269},
Abstract = {The nature and timing of evolution of niche differentiation
among closely related species remains an important question
in ecology and evolution. The American live oak clade,
Virentes, which spans the unglaciated temperate and tropical
regions of North America and Mesoamerica, provides an
instructive system in which to examine speciation and niche
evolution. We generated a fossil-calibrated phylogeny of
Virentes using RADseq data to estimate divergence times and
used nuclear microsatellites, chloroplast sequences and an
intron region of nitrate reductase (NIA-i3) to examine
genetic diversity within species, rates of gene flow among
species and ancestral population size of disjunct sister
species. Transitions in functional and morphological traits
associated with ecological and climatic niche axes were
examined across the phylogeny. We found the Virentes to be
monophyletic with three subclades, including a southwest
clade, a southeastern US clade and a Central American/Cuban
clade. Despite high leaf morphological variation within
species and transpecific chloroplast haplotypes, RADseq and
nuclear SSR data showed genetic coherence of species. We
estimated a crown date for Virentes of 11 Ma and implicated
the formation of the Sea of Cortés in a speciation event
~5 Ma. Tree height at maturity, associated with fire
tolerance, differs among the sympatric species, while
freezing tolerance appears to have diverged repeatedly
across the tropical-temperate divide. Sympatric species thus
show evidence of ecological niche differentiation but share
climatic niches, while allopatric and parapatric species
conserve ecological niches, but diverge in climatic niches.
The mode of speciation and/or degree of co-occurrence may
thus influence which niche axis plants diverge
along.},
Doi = {10.1111/mec.13269},
Key = {fds322302}
}
@article{fds226577,
Author = {Manos, PS and Meireles, JE},
Title = {Biogeographic analysis of the woody plants of the Southern
Appalachians: Implications for the origins of a regional
flora.},
Journal = {Am J Bot},
Volume = {102},
Number = {5},
Pages = {780-804},
Year = {2015},
Month = {May},
ISSN = {0002-9122},
url = {http://hdl.handle.net/10161/10229 Duke open
access},
Abstract = {<h4>Premise of the study</h4>We investigated the origins of
252 Southern Appalachian woody species representing 158
clades to analyze larger patterns of biogeographic
connectivity around the northern hemisphere. We tested
biogeographic hypotheses regarding the timing of species
disjunctions to eastern Asia and among areas of North
America.<h4>Methods</h4>We delimited species into
biogeographically informative clades, compiled sister-area
data, and generated graphic representations of area
connections across clades. We calculated taxon diversity
within clades and plotted divergence times.<h4>Key
results</h4>Of the total taxon diversity, 45% were
distributed among 25 North American endemic clades. Sister
taxa within eastern North America and eastern Asia were
proportionally equal in frequency, accounting for over 50%
of the sister-area connections. At increasing phylogenetic
depth, connections to the Old World dominated. Divergence
times for 65 clades with intercontinental disjunctions were
continuous, whereas 11 intracontinental disjunctions to
western North America and nine to eastern Mexico were
temporally congruent.<h4>Conclusions</h4>Over one third of
the clades have likely undergone speciation within the
region of eastern North America. The biogeographic pattern
for the region is asymmetric, consisting of mostly
mixed-aged, low-diversity clades connecting to the Old
World, and a minority of New World clades. Divergence time
data suggest that climate change in the Late Miocene to
Early Pliocene generated disjunct patterns within North
America. Continuous splitting times during the last 45
million years support the hypothesis that widespread
distributions formed repeatedly during favorable periods,
with serial cooling trends producing pseudocongruent area
disjunctions between eastern North America and eastern
Asia.},
Doi = {10.3732/ajb.1400530},
Key = {fds226577}
}
@article{fds226576,
Author = {Cavender-Bares, J. and D. Eaton and A. Gonzalez-Rodriguez and A.
Hipp, A. Beulke and P.S. Manos},
Title = {Phylogeny and biogeography of the American live oaks
(Quercus subsection Virentes): A genomic and population
genetic approach},
Journal = {Molecular Ecology},
Year = {2015},
Key = {fds226576}
}
@article{fds226578,
Author = {Hipp, AL and Eaton, DAR and Cavender-Bares, J and Fitzek, E and Nipper,
R and Manos, PS},
Title = {A framework phylogeny of the American oak clade based on
sequenced RAD data.},
Journal = {Plos One},
Volume = {9},
Number = {4},
Pages = {e93975},
Year = {2014},
Month = {January},
url = {http://dx.doi.org/10.1371/journal.pone.0093975},
Abstract = {Previous phylogenetic studies in oaks (Quercus, Fagaceae)
have failed to resolve the backbone topology of the genus
with strong support. Here, we utilize next-generation
sequencing of restriction-site associated DNA (RAD-Seq) to
resolve a framework phylogeny of a predominantly American
clade of oaks whose crown age is estimated at 23-33 million
years old. Using a recently developed analytical pipeline
for RAD-Seq phylogenetics, we created a concatenated matrix
of 1.40 E06 aligned nucleotides, constituting 27,727
sequence clusters. RAD-Seq data were readily combined across
runs, with no difference in phylogenetic placement between
technical replicates, which overlapped by only 43-64% in
locus coverage. 17% (4,715) of the loci we analyzed could be
mapped with high confidence to one or more expressed
sequence tags in NCBI Genbank. A concatenated matrix of the
loci that BLAST to at least one EST sequence provides
approximately half as many variable or parsimony-informative
characters as equal-sized datasets from the non-EST loci.
The EST-associated matrix is more complete (fewer missing
loci) and has slightly lower homoplasy than non-EST
subsampled matrices of the same size, but there is no
difference in phylogenetic support or relative attribution
of base substitutions to internal versus terminal branches
of the phylogeny. We introduce a partitioned RAD
visualization method (implemented in the R package RADami;
http://cran.r-project.org/web/packages/RADami) to
investigate the possibility that suboptimal topologies
supported by large numbers of loci--due, for example, to
reticulate evolution or lineage sorting--are masked by the
globally optimal tree. We find no evidence for
strongly-supported alternative topologies in our study,
suggesting that the phylogeny we recover is a robust
estimate of large-scale phylogenetic patterns in the
American oak clade. Our study is one of the first to
demonstrate the utility of RAD-Seq data for inferring
phylogeny in a 23-33 million year-old clade.},
Doi = {10.1371/journal.pone.0093975},
Key = {fds226578}
}
@article{fds226579,
Author = {Burge, DO and Hopkins, R and Tsai, Y-HE and Manos,
PS},
Title = {Limited hybridization across an edaphic disjunction between
the gabbro-endemic shrub Ceanothus roderickii (Rhamnaceae)
and the soil-generalist Ceanothus cuneatus.},
Journal = {Am J Bot},
Volume = {100},
Number = {9},
Pages = {1883-1895},
Year = {2013},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24018856},
Abstract = {<h4>Unlabelled</h4><h4>Premise of the study</h4>Hybridization
is thought to have played an important role in
diversification of the speciose shrub genus Ceanothus;
putative hybrid species have been described, and data
suggest that intrinsic barriers may not exist among closely
related species. However, the extent to which hybridization
occurs in the wild is not known, and little is understood
about how extrinsic factors such as soil chemistry may
influence the process. The present research focuses on the
gabbro-endemic C. roderickii and the closely related
soil-generalist C. cuneatus. Though the species occur
peripatrically, they remain distinct across an edaphic
disjunction. •<h4>Methods</h4>AFLP was used to quantify
hybridization and introgression. Biological data and
experiments were used to test for prezygotic isolation.
Growth trials were used to test for local adaptation and
selection against hybrids. •<h4>Key results</h4>Ceanothus
cuneatus and C. roderickii were strongly differentiated
morphologically and genetically, despite a lack of evidence
for prezygotic barriers. Hybrids and back-crosses were
present but infrequent. Finally, there was selection against
hybrids in nonnative soil. •<h4>Conclusions</h4>There is
little genetic exchange between the focal species across an
edaphic disjunction, despite the absence of prezygotic
barriers. This result implies that soil conditions, as well
as other extrinsic factors, should be considered as forces
that may restrict hybridization and gene flow in Ceanothus,
influencing local adaptation and speciation. Findings
presented here are significant because they imply that
exchange of genetic material between plants may be limited
directly by the abiotic environment, rather than by the
biology of the plants.},
Doi = {10.3732/ajb.1200604},
Key = {fds226579}
}
@article{fds226587,
Author = {Kremer, A and Abbott, AG and Carlson, JE and Manos, PS and Plomion, C and Sisco, P and Staton, ME and Ueno, S and Vendramin,
GG},
Title = {Genomics of Fagaceae},
Journal = {Tree Genetics & Genomes},
Volume = {8},
Number = {3},
Pages = {583-610},
Publisher = {Springer Nature},
Year = {2012},
Month = {June},
ISSN = {1614-2942},
url = {http://dx.doi.org/10.1007/s11295-012-0498-3},
Abstract = {An overview of recent achievements and development of
genomic resources in the Fagaceae is provided, with major
emphasis on the genera Castanea and Quercus. The Fagaceae is
a large plant family comprising more than 900 species
belonging to 8-10 genera. Using a wide range of molecular
markers, population genetics and gene diversity surveys were
the focus of many studies during the past 20 years. This
work set the stage for investigations in genomics beginning
in the early 1990s and facilitated the application of
genetic and quantitative trait loci mapping approaches.
Transferability of markers across species and comparative
mapping have indicated tight macrosynteny between Quercus
and Castanea. Omic technologies were more recently developed
and the corresponding resources are accessible via
electronic and physical repositories (expressed sequence tag
sequences, single-nucleotide polymorphisms, candidate genes,
cDNA clones, bacterial artificial chromosome (BAC)
libraries) that have been installed in North America and
Europe. BAC libraries and physical maps were also
constructed in Castanea and Quercus and provide the
necessary resources for full nuclear genome sequencing
projects that are currently under way in Castanea mollissima
(Chinese chestnut) and Quercus robur (pedunculate oak). ©
2012 The Author(s).},
Doi = {10.1007/s11295-012-0498-3},
Key = {fds226587}
}
@article{fds226589,
Author = {Burge, DO and Erwin, DM and Islam, MB and Kellermann, J and Kembel, SW and Wilken, DH and Manos, PS},
Title = {Diversification of Ceanothus (Rhamnaceae) in the California
Floristic province},
Journal = {International Journal of Plant Sciences},
Volume = {172},
Number = {9},
Pages = {1137-1164},
Publisher = {University of Chicago Press},
Year = {2011},
Month = {November},
ISSN = {1058-5893},
url = {http://dx.doi.org/10.1086/662028},
Abstract = {High diversity and endemism in the California Floristic
Province (CFP) are an alleged response to the late Cenozoic
advent of Mediterranean-type climate in this region.
Ceanothus comprises two divergent subgenera with centers of
diversity in the CFP. We reconstruct the evolution of
Ceanothus by using DNA sequence data from the nuclear gene
nitrate reductase. We find that the timing of
diversification events is related to geological and climatic
history. In both subgenera, diversification is characterized
by recent divergence of extant taxa and geographically
structured phylogenetic relationships. A strong north-south
divergence of subgenus Cerastes across the Transverse Ranges
indicates that phylogenetic relationships may be structured
by climatically divergent regions of the CFP.
Divergence-time estimation suggests that the age of extant
diversification in both subgenera is;6 Ma. This agrees with
the fossil record but predates the hypothesized Quaternary
(2-Ma) origin of Mediterranean-type climate in the region.
© 2011 by The University of Chicago. All rights
reserved.},
Doi = {10.1086/662028},
Key = {fds226589}
}
@article{fds226588,
Author = {Burge, DO and Manos, PS},
Title = {Edaphic ecology and genetics of the gabbro-endemic shrub
Ceanothus roderickii (Rhamnaceae).},
Journal = {Madroño},
Volume = {58},
Pages = {1-21},
Year = {2011},
Key = {fds226588}
}
@article{fds226590,
Author = {Tsai, Y-HE and Manos, PS},
Title = {Host density drives the postglacial migration of the tree
parasite, Epifagus virginiana.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {107},
Number = {39},
Pages = {17035-17040},
Year = {2010},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20841421},
Abstract = {To survive changes in climate, successful species shift
their geographic ranges to remain in suitable habitats. For
parasites and other highly specialized species,
distributional changes not only are dictated by climate but
can also be engineered by their hosts. The extent of host
control on parasite range expansion is revealed through
comparisons of host and parasite migration and demographic
histories. However, understanding the codistributional
history of entire forest communities is complicated by
challenges in synthesizing datasets from multiple
interacting species of differing datatypes. Here we
integrate genetic and fossil pollen datasets from a
host-parasite pair; specifically, the population structure
of the parasitic plant (Epifagus virginiana) was compared
with both its host (Fagus grandifolia) genetic patterns and
abundance data from the paleopollen record of the last
21,000 y. Through tests of phylogeographic structure and
spatial linear regression models we find, surprisingly, host
range changes had little effect on the parasite's range
expansion and instead host density is the main driver of
parasite spread. Unlike other symbionts that have been used
as proxies to track their host's movements, this parasite's
migration routes are incongruent with the host and instead
reflect the greater importance of host density in this
community's assembly. Furthermore, these results confirm
predictions of disease ecological models regarding the role
of host density in the spread of pathogens. Due to host
density constraints, highly specialized species may have low
migration capacities and long lag times before colonization
of new areas.},
Doi = {10.1073/pnas.1006225107},
Key = {fds226590}
}
@article{fds226591,
Author = {Stone, DE and Oh, S-H and Tripp, EA and G, LER and Manos,
PS},
Title = {Natural history, distribution, phylogenetic relationships,
and conservation of Central American black walnuts (Juglans
sect. Rhysocaryon)},
Journal = {Journal Torrey Botanical Society},
Volume = {136},
Number = {1},
Pages = {1-25},
Publisher = {Torrey Botanical Society},
Year = {2009},
Month = {February},
ISSN = {1095-5674},
url = {http://dx.doi.org/10.3159/08-RA-036R.1},
Abstract = {STONE, D. E., S.-H. OH, E.A. TRIPP (Department of Biology,
Duke University, Durham, NC 27708), L. E. RI´OS G. (Oficina
Te´cnica en Biodiversidad, Consejo Nacional de Areas
Protegidas, 5 av. 6-06, zona 1, Edificio del IPM, 7 mo.
nivel, Guatemala, Guatemala), and P. S. MANOS (Department of
Biology, Duke University, Durham, NC 27708). Natural
history, distribution, phylogenetic relationships, and
conservation of Central American black walnuts (Juglans
sect. Rhysocaryon). J. Torrey Bot. Soc. 136: 1–25.
2009.— The tree genus Juglans (nogal, walnut) is generally
thought of as a north temperate group, but most of the 16
species of black walnuts (Juglans sect. Rhysocaryon) occur
in subtropical areas of the New World, spanning Central
America, Andean South America, and the Greater Antilles. The
two species native to Central America (J. olanchana var.
olanchana and J. steyermarkii) and two closely related
Mexican taxa (J. olanchana var. standleyi and J. pyriformis)
have not been studied thoroughly from a comparative
systematic perspective, so here we provide a detailed
investigation of their morphology and natural history as a
first step towards a broad-based synthesis of J. sect.
Rhysocaryon. Fieldwork in Guatemala and Mexico provided the
material for germination studies, morphological analyses,
and phylogenetic reconstruction using DNA sequences. Juglans
steyermarkii was rediscovered in its type locality in
Guatemala, and new populations were located during the
course of fieldwork. SEM analysis of trichome diversity and
density, along with leaflet shape, provided characters to
differentiate among five taxa of Juglans in the accompanying
key. Staminate flowers and pollen examined for the first
time in J. steyermarkii showed close morphological
similarities to those of other species of black walnuts.
Variation in the pattern of nut-wall sculpture appears to be
a promising source of variation; however, adequate capture
and quantification of this variation will likely require
three-dimensional scanning techniques. There was high
variability in percent seed germination of the two Central
American species and no observed advantage to leaching,
scarification, or a prolonged stratification period. DNA
studies included in the exploration of three promising
sources of nuclear sequence variation: the ETS and ITS
(external and internal transcribed spacer of ribosomal DNA),
and the second intron of the LEAFY gene. Combined
phylogenetic analysis of these sequences provided a
moderately resolved topology containing two major groups of
black walnuts and a general correlation between phylogeny
and geography. The analyses supported a division between
taxa from northern Mexico and the USA, and those from
southern Mexico, Guatemala, the West Indies (Greater
Antilles), and South America. Observations on the geographic
range of Juglans in Mexico and Guatemala indicated a
frequent association with coffee plantations, suggesting
similar climatic requirements. Our studies of the dispersed
and most likely fragmented populations indicate that Juglans
may still be found in native plant communities as a canopy
tree, although it is much more common to observe populations
in cleared areas where the trees were retained as shade for
coffee. We are not aware of any major efforts to conserve
the native nogal in Central America, though they are
sometimes left and/or planted as shade trees in coffee
fincas. A study conducted in Mexico suggests that Juglans
might be useful in agroforestry efforts to rehabilitate
degraded sites. Key words: black walnuts, Central America,
conservation, DNA, Guatemala, Juglandaceae, Juglans, natural
history, nogal, Mexico, phylogeny.},
Doi = {10.3159/08-RA-036R.1},
Key = {fds226591}
}
@article{fds226592,
Author = {Gugger, PF and McLachlan, JS and Manos, PS and Clark,
JS},
Title = {Inferring long-distance dispersal and topographic barriers
during post-glacial colonization from the genetic structure
of red maple (Acer rubrum L.) in New England},
Journal = {Journal of Biogeography},
Volume = {35},
Number = {9},
Pages = {1665-1673},
Publisher = {WILEY},
Year = {2008},
Month = {September},
ISSN = {0305-0270},
url = {http://dx.doi.org/10.1111/j.1365-2699.2008.01915.x},
Abstract = {Aim: This study aims to assess the role of long-distance
seed dispersal and topographic barriers in the post-glacial
colonization of red maple (Acer rubrum L.) using chloroplast
DNA (cpDNA) variation, and to understand whether this
explains the relatively higher northern diversity found in
eastern North American tree species compared with that in
Europe. Location: North-eastern United States. Methods: The
distribution of intraspecific cpDNA variation in temperate
tree populations has been used to identify aspects of
post-glacial population spread, including topographic
barriers to population expansion and spread by long-distance
seed dispersal. We sequenced c. 370 cpDNA base pairs from
221 individuals in 100 populations throughout the
north-eastern United States, and analysed spatial patterns
of diversity and differentiation. Results: Red maple has
high genetic diversity near its northern range limit, but
this diversity is not partitioned by topographic barriers,
suggesting that the northern Appalachian Mountains were not
a barrier to the colonization of red maple. We also found no
evidence of the patchy genetic structure that has been
associated with spread by rare long-distance seed dispersal
in previous studies. Main conclusions: Constraints on
post-glacial colonization in eastern North America seem to
have been less stringent than those in northern Europe,
where bottlenecks arising from long-distance colonization
and topographic barriers appear to have strongly reduced
genetic diversity. In eastern North America, high northern
genetic diversity may have been maintained by a combination
of frequent long-distance dispersal, minor topographic
obstacles and diffuse northern refugia near the ice sheet.
© 2008 The Authors.},
Doi = {10.1111/j.1365-2699.2008.01915.x},
Key = {fds226592}
}
@article{fds226598,
Author = {Tripp, EA and Manos, PS},
Title = {Is floral specialization an evolutionary dead-end?
Pollination system transitions in Ruellia
(Acanthaceae).},
Journal = {Evolution},
Volume = {62},
Number = {7},
Pages = {1712-1737},
Year = {2008},
Month = {July},
ISSN = {0014-3820},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18410536},
Abstract = {Pollination systems frequently reflect adaptations to
particular groups of pollinators. Such systems are
indicative of evolutionary specialization and have been
important in angiosperm diversification. We studied the
evolution of pollination systems in the large genus Ruellia.
Phylogenetic analyses, morphological ordinations, ancestral
state reconstructions, and a character mapping simulation
were conducted to reveal key patterns in the direction and
lability of floral characters associated with pollination.
We found significant floral morphological differences among
species that were generally associated with different groups
of floral visitors. Floral evolution has been highly labile
and also directional. Some specialized systems such as
hawkmoth or bat pollination are likely evolutionary
dead-ends. In contrast, specialized pollination by
hummingbirds is clearly not a dead-end. We found evidence
for multiple reverse transitions from presumed ancestral
hummingbird pollination to more derived bee or insect
pollination. These repeated origins of insect pollination
from hummingbird-pollinated ancestors have not evolved
without historical baggage. Flowers of insect-pollinated
species derived from hummingbird-pollinated ancestors are
morphologically more similar to hummingbird flowers than
they are to other more distantly related insect-pollinated
flowers. Finally, some pollinator switches were concomitant
with changes in floral morphology that are associated with
those pollinators. These observations are consistent with
the hypothesis that some transitions have been adaptive in
the evolution of Ruellia.},
Doi = {10.1111/j.1558-5646.2008.00398.x},
Key = {fds226598}
}
@article{fds226596,
Author = {Willson, CJ and Manos, PS and Jackson, RB},
Title = {Hydraulic traits are influenced by phylogenetic history in
the drought-resistant, invasive genus Juniperus
(Cupressaceae).},
Journal = {American Journal of Botany},
Volume = {95},
Number = {3},
Pages = {299-314},
Year = {2008},
Month = {March},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21632355},
Abstract = {In the conifer genus Juniperus (Cupressaceae), many species
are increasing rapidly in distribution, abundance, and
dominance in arid and semiarid regions. To help understand
the success of junipers in drier habitats, we studied
hydraulic traits associated with their water stress
resistance, including vulnerability to xylem cavitation,
specific conductivity (K(S)), tracheid diameter, conduit
reinforcement, and wood density in stems and roots, as well
as specific leaf area (SLA) of 14 species from the United
States and the Caribbean. A new phylogeny based on DNA
sequences tested the relationships between vulnerability to
cavitation and other traits using both traditional
cross-species correlations and independent contrast
correlations. All species were moderately to highly
resistant to water-stress-induced cavitation in both roots
and shoots. We found strong phylogenetic support for two
clades previously based on leaf margin serration (serrate
and smooth). Species in the serrate clade were 34-39% more
resistant to xylem cavitation in stems and roots than were
species in the smooth clade and had ∼35% lower K(S) and
39% lower SLA. Root and stem resistance to cavitation and
SLA were all highly conserved traits. A high degree of
conservation within clades suggests that hydraulic traits of
Juniperus species strongly reflect phylogenetic history. The
high resistance to cavitation observed may help explain the
survival of junipers during recent extreme droughts in the
southwestern United States and their expansion into arid
habitats across the western and central United
States.},
Doi = {10.3732/ajb.95.3.299},
Key = {fds226596}
}
@article{fds226593,
Author = {Manos, PS and Cannon, CH and Oh, SH},
Title = {Phylogenetic relationships and taxonomic status of the
paleoendemic Fagaceae of western North America: recognition
of a new genus Notholithocarpus.},
Journal = {Madroño},
Volume = {55},
Pages = {181-190},
Year = {2008},
Key = {fds226593}
}
@article{fds226597,
Author = {Oh, SH and Manos, PS},
Title = {Molecular phylogenetics and cupule evolution in Fagaceae as
inferred from nuclear CRABS CLAW sequences},
Journal = {Taxon},
Volume = {57},
Number = {2},
Pages = {434-451},
Year = {2008},
ISSN = {0040-0262},
Abstract = {Fagaceae include nine genera and ca. 900 species, making it
one of the largest and economically important groups within
Fagales. Phylogenetic relationships remain unresolved
despite a long history of systematic study. We used CRABS
CLAW, a single-copy nuclear gene, to generate over 2,900
base pairs of new sequence data, and combined it with
previously collected molecular data to examine morphological
evolution in the Fagaceae. We clarified the relationships of
Chrysolepis, Lithocarpus and Quercus, and in this improved
phylogenetic context we inferred morphological
transformations of the cupule. Phylogenetic analyses
supported an origin for Quercus from a castaneoid ancestor
and a novel sister group relationship for Asian Lithocarpus
and Chrysolepis; however the monophyly of both Lithocarpus
and subfamily Castaneoideae was rejected. Our data suggest
that North American Lithocarpus densiflorus is distantly
related to Asian Lithocarpus and more closely related to
Quercus, supporting the hypothesis that the uniflorous
cupules of L. densiflorus and Quercus are derived from
dichasium cupules via loss of lateral flowers. The sister
group relationship of Asian Lithocarpus and Chrysolepis is
supported by the morphological synapomorphy that each fruit
is surrounded by a cupule. A new hypothesis is proposed to
explain the evolution of the unusual cupules of Asian
Lithocarpus and Chrysolepis. In this model, every flower
represents a reduced dichasium, and we interpret the cupules
of these taxa to be compound in nature, formed by multiple
single-flowered cupules.},
Key = {fds226597}
}
@article{fds303159,
Author = {Douglas, NA and Manos, PS},
Title = {Molecular phylogeny of Nyctaginaceae: taxonomy,
biogeography, and characters associated with a radiation of
xerophytic genera in North America.},
Journal = {Am J Bot},
Volume = {94},
Number = {5},
Pages = {856-872},
Year = {2007},
Month = {May},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21636455},
Abstract = {The four o'clock family (Nyctaginaceae) has a number of
genera with unusual morphological and ecological characters,
several of which appear to have a "tendency" to evolve
repeatedly in Nyctaginaceae. Despite this, the Nyctaginaceae
have attracted little attention from botanists. To produce a
phylogeny for the Nyctaginaceae, we sampled 51 species
representing 25 genera (of 28-31) for three chloroplast loci
(ndhF, rps16, rpl16, and nrITS) and included all genera from
North America. Parsimony, likelihood, and Bayesian methods
were used to reconstruct the phylogeny for the family. The
family is neotropical in origin. A radiation of woody taxa
unites Pisonia and Pisoniella with the difficult tropical
genera Neea and Guapira, which also form a clade, though
neither appears to be monophyletic. This group is sister to
a clade containing Bougainvillea, Belemia, and Phaeoptilum.
A dramatic radiation of genera occurred in the deserts of
North America. The tribe Nyctagineae and its subtribes are
paraphyletic, due to over-reliance on a few homoplasious
characters, i.e., pollen morphology and involucre presence.
Two notable characters associated with the desert radiation
are cleistogamy and edaphic endemism on gypsum soils. We
discuss evolutionary trends in these traits in light of
available data about self-incompatibility and gypsum
tolerance in Nyctaginaceae.},
Doi = {10.3732/ajb.94.5.856},
Key = {fds303159}
}
@article{fds226594,
Author = {Manos Soltis and PS and Soltis, DE and Manchester, SR and Oh, SH and Bell,
CD and Dilcher, DL and Stone, DE},
Title = {Phylogeny of extant and extinct Juglandaceae inferred from
the integration of molecular and morphological data
sets},
Journal = {Systematic Biology},
Volume = {56},
Number = {3},
Pages = {412-430},
Year = {2007},
ISSN = {1063-5157},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17558964},
Abstract = {It is widely acknowledged that integrating fossils into data
sets of extant taxa is imperative for proper placement of
fossils, resolution of relationships, and a better
understanding of character evolution. The importance of this
process has been further magnified because of the crucial
role of fossils in dating divergence times. Outstanding
issues remain, including appropriate methods to place
fossils in phylogenetic trees, the importance of molecules
versus morphology in these analyses, as well as the impact
of potentially large amounts of missing data for fossil
taxa. In this study we used the angiosperm clade
Juglandaceae as a model for investigating methods of
integrating fossils into a phylogenetic framework of extant
taxa. The clade has a rich fossil record relative to low
extant diversity, as well as a robust molecular phylogeny
and morphological database for extant taxa. After combining
fossil organ genera into composite and terminal taxa, our
objectives were to (1) compare multiple methods for the
integration of the fossils and extant taxa (including total
evidence, molecular scaffolds, and molecular matrix
representation with parsimony [MRP]); (2) explore the impact
of missing data (incomplete taxa and characters) and the
evidence for placing fossils on the topology; (3) simulate
the phylogenetic effect of missing data by creating
"artificial fossils"; and (4) place fossils and compare the
impact of single and multiple fossil constraints in
estimating the age of clades. Despite large and variable
amounts of missing data, each of the methods provided
reasonable placement of both fossils and simulated
"artificial fossils" in the phylogeny previously inferred
only from extant taxa. Our results clearly show that the
amount of missing data in any given taxon is not by itself
an operational guideline for excluding fossils from
analysis. Three fossil taxa (Cruciptera simsonii,
Paleoplatycarya wingii, and Platycarya americana) were
placed within crown clades containing living taxa for which
relationships previously had been suggested based on
morphology, whereas Polyptera manningii, a mosaic taxon with
equivocal affinities, was placed firmly as sister to two
modern crown clades. The position of Paleooreomunnea
stoneana was ambiguous with total evidence but conclusive
with DNA scaffolds and MRP. There was less disturbance of
relationships among extant taxa using a total evidence
approach, and the DNA scaffold approach did not provide
improved resolution or internal support for clades compared
to total evidence, whereas weighted MRP retained comparable
levels of support but lost crown clade resolution. Multiple
internal minimum age constraints generally provided
reasonable age estimates, but the use of single constraints
provided by extinct genera tended to underestimate clade
ages.},
Doi = {10.1080/10635150701408523},
Key = {fds226594}
}
@article{fds226595,
Author = {Douglas, NA and Manos, PS},
Title = {Nyctaginaceae phylogeny, classification, and characters
associated with a radiation of xerophytic genera in North
America},
Journal = {American Journal of Botany},
Volume = {94},
Number = {5},
Pages = {856-872},
Year = {2007},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21636455},
Abstract = {The four o'clock family (Nyctaginaceae) has a number of
genera with unusual morphological and ecological characters,
several of which appear to have a "tendency" to evolve
repeatedly in Nyctaginaceae. Despite this, the Nyctaginaceae
have attracted little attention from botanists. To produce a
phylogeny for the Nyctaginaceae, we sampled 51 species
representing 25 genera (of 28-31) for three chloroplast loci
(ndhF, rps16, rpl16, and nrITS) and included all genera from
North America. Parsimony, likelihood, and Bayesian methods
were used to reconstruct the phylogeny for the family. The
family is neotropical in origin. A radiation of woody taxa
unites Pisonia and Pisoniella with the difficult tropical
genera Neea and Guapira, which also form a clade, though
neither appears to be monophyletic. This group is sister to
a clade containing Bougainvillea, Belemia, and Phaeoptilum.
A dramatic radiation of genera occurred in the deserts of
North America. The tribe Nyctagineae and its subtribes are
paraphyletic, due to over-reliance on a few homoplasious
characters, i.e., pollen morphology and involucre presence.
Two notable characters associated with the desert radiation
are cleistogamy and edaphic endemism on gypsum soils. We
discuss evolutionary trends in these traits in light of
available data about self-incompatibility and gypsum
tolerance in Nyctaginaceae.},
Doi = {10.3732/ajb.94.5.856},
Key = {fds226595}
}
@article{fds226599,
Author = {Soltis, DE and Morris, AB and McLachlan, JS and Manos, PS and Soltis,
PS},
Title = {Comparative phylogeography of unglaciated eastern North
America.},
Journal = {Molecular Ecology},
Volume = {15},
Number = {14},
Pages = {4261-4293},
Year = {2006},
Month = {December},
ISSN = {0962-1083},
url = {http://dx.doi.org/10.1111/j.1365-294x.2006.03061.x},
Abstract = {Regional phylogeographical studies involving co-distributed
animal and plant species have been conducted for several
areas, most notably for Europe and the Pacific Northwest of
North America. Until recently, phylogeographical studies in
unglaciated eastern North America have been largely limited
to animals. As more studies emerge for diverse lineages
(including plants), it seems timely to assess the
phylogeography across this region: (i) comparing and
contrasting the patterns seen in plants and animals; (ii)
assessing the extent of pseudocongruence; and (iii)
discussing the potential applications of regional
phylogeography to issues in ecology, such as response to
climatic change. Unglaciated eastern North America is a
large, geologically and topographically complex area with
the species examined having diverse distributions.
Nonetheless, some recurrent patterns emerge: (i) maritime -
Atlantic vs. Gulf Coast; (ii) Apalachicola River
discontinuity; (iii) Tombigbee River discontinuity; (iv) the
Appalachian Mountain discontinuity; (v) the Mississippi
River discontinuity; and (vi) the Apalachicola River and
Mississippi River discontinuities. Although initially
documented in animals, most of these patterns are also
apparent in plants, providing support for phylogeographical
generalizations. These patterns may generally be
attributable to isolation and differentiation during
Pleistocene glaciation, but in some cases may be older
(Pliocene). Molecular studies sometimes agree with
longstanding hypotheses of glacial refugia, but also suggest
additional possible refugia, such as the southern
Appalachian Mountains and areas close to the Laurentide Ice
Sheet. Many species exhibit distinct patterns that reflect
the unique, rather than the shared, aspects of species'
phylogeographical histories. Furthermore, similar modern
phylogeographical patterns can result from different
underlying causal factors operating at different times (i.e.
pseudocongruence). One underemphasized component of
pseudocongruence may result from the efforts of researchers
to categorize patterns visually - similar patterns may, in
fact, not fully coincide, and inferring agreement may
obscure the actual patterns and lead to erroneous
conclusions. Our modelling analyses indicate no clear
spatial patterning and support the hypothesis that
phylogeographical structure in diverse temperate taxa is
complex and was not shaped by just a few
barriers.},
Doi = {10.1111/j.1365-294x.2006.03061.x},
Key = {fds226599}
}
@article{fds226600,
Author = {Whitson, M and Manos, PS},
Title = {Untangling Physalis (Solanaceae) from the physaloids: A
two-gene phylogeny of the physalinae},
Journal = {Systematic Botany},
Volume = {30},
Number = {1},
Pages = {216-230},
Publisher = {American Society of Plant Taxonomists},
Year = {2005},
Month = {January},
url = {http://dx.doi.org/10.1600/0363644053661841},
Abstract = {Physalis (75+ species, Solanaceae) is most diverse in
Mexico, with only the type, P. alkekengi, native to the Old
World. Interspecific relationships are poorly known, and
despite the distinctive inflated fruiting calyces, generic
limits remain uncertain. Sequence data from part of the
nuclear gene waxy (622 bp) and the internal transcribed
spacer of the nrDNA (652 bp) were used to generate a
phylogeny of subtribe Physalinae. Thirty-five species of
Physalis and eight physaloid genera were sequenced. Data
analysis included Bayesian and maximum parsimony methods.
The Physalinae was monophyletic, but while the
morphologically typical Physalis species formed a strongly
supported clade, the morphologically atypical species made
the genus paraphyletic. A grade of physaloid genera
(Quincula, Oryctes, and Chamaesaracha) and Physalis subgenus
Physalodendron separate P. alkekengi, P. carpenteri, and P.
microphysa from other Physalis species. The Physalis clade
consists of Margaranthus and species with solitary yellow
flowers and highly inflated calyces. Most sections of
Physalis do not appear to be monophyletic. Leucophysalis
viscosa and the Central American physaloid genera
Brachistus, Tzeltalia, and Witheringia formed a clade at the
base of the Physalinae. © Copyright 2005 by the American
Society of Plant Taxonomists.},
Doi = {10.1600/0363644053661841},
Key = {fds226600}
}
@article{fds226601,
Author = {McLachlan, JS and Clark, JS and Manos, PS},
Title = {Molecular indicators of tree migration capacity under rapid
climate change},
Journal = {Ecology},
Volume = {86},
Number = {8},
Pages = {2088-2098},
Publisher = {WILEY},
Year = {2005},
Month = {January},
url = {http://dx.doi.org/10.1890/04-1036},
Abstract = {Recent models and analyses of paleoecological records
suggest that tree populations are capable of rapid migration
when climate warms. Fossil pollen is commonly interpreted as
suggesting that the range of many temperate tree species
expanded at rates of 100-1000 m/yr during the early
Holocene. We used chloroplast DNA surveys to show that the
geography of postglacial range expansion in two eastern
North American tree species differs from that expected from
pollen-based reconstructions and from patterns emerging from
European molecular studies. Molecular evidence suggests that
American beech (Fagus grandifolia) and red maple (Acer
rubrum) persisted during the late glaciation as low-density
populations, perhaps within 500 km of the Laurentide Ice
Sheet. Because populations were closer to modern range
limits than previously thought, postglacial migration rates
may have been slower than those inferred from fossil pollen.
Our estimated rates of <100 m/yr are consistent with model
predictions based on life history and dispersal data, and
suggest that past migration rates were substantially slower
than the rates that will be needed to track 21st-century
warming. © 2005 by the Ecological Society of
America.},
Doi = {10.1890/04-1036},
Key = {fds226601}
}
@article{fds226602,
Author = {Devos, N and Oh, SH and Raspé, O and Jacquemart, AL and Manos,
PS},
Title = {Nuclear ribosomal DNA sequence variation and evolution of
spotted marsh-orchids (Dactylorhiza maculata
group)},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {36},
Number = {3},
Pages = {568-580},
Year = {2005},
ISSN = {1055-7903},
url = {http://dx.doi.org/10.1016/j.ympev.2005.04.014},
Abstract = {Sequences of both internal and external transcribed spacers
of nuclear ribosomal DNA were sequenced for four species
belonging to the Dactylorhiza maculata group or "spotted
marsh-Orchids". These four species are D. fuchsii, D.
saccifera, D. foliosa, and D. maculata. Extensive nuclear
ribosomal DNA polymorphism was uncovered within the diploid
D. fuchsii and the putative autotetraploid D. maculata.
Within the phylogenetic trees reconstructed using parsimony
and Bayesian analyses, four main lineages (A, B, C, and D)
were well supported. While D. saccifera, D. maculata, and D.
foliosa were confined to clades B, C, and D, respectively,
D. fuchsii accessions were spread over three clades (A, B,
and C). Lineage C, which included accessions of the diploid
D. fuchsii and the tetraploid D. maculata, was closely
related to the lineage of D. foliosa (lineage D), an endemic
diploid species from Madeira. Moreover, intra-individual
polymorphism was found within accessions of D. maculata, D.
fuchsii, and D. saccifera. It is shown that in some
instances two lineages, contributed to the observed
intra-individual polymorphism (C and A in D. maculata, A and
B in D. fuchsii and D. saccifera). Evolutionary scenarios
leading to this extensive nuclear ribosomal DNA polymorphism
are discussed in the light of results from maternally
inherited chloroplast DNA markers and an autopolyploid
origin of D. maculata from a D. foliosa-like ancestor is
postulated.},
Doi = {10.1016/j.ympev.2005.04.014},
Key = {fds226602}
}
@article{fds226603,
Author = {Feng, Y and Oh, SH and Manos, PS},
Title = {Phylogeny and historical biogeography of the genus Platanus
as inferred from nuclear and chloroplast
DNA},
Journal = {Systematic Botany},
Volume = {30},
Number = {4},
Pages = {786-799},
Publisher = {American Society of Plant Taxonomists},
Year = {2005},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364405775097851},
Abstract = {Phylogenetic analyses of DNA sequences of six species of
Platanus were conducted to estimate species relationships
and analyze biogeographic history. On the basis of a broader
analysis of the third exon of the nuclear gene LEAFY, the
root node for the genus was confirmed to fall between subg.
Castaneophyllum (P. kerrii) and the species of subg.
Platanus. Separate phylogenetic analyses of the nuclear
ribosomal ITS region, the 3′ region of the second intron
of LEAFY, and the chloroplast region trnT-trnL intergenic
spacer provided various levels of resolution, and the
combined data yielded a fully resolved set of relationships
within subg. Platanus. Two major clades were identified: one
with species from Europe (EUR) and western North America
(WNA) (P. orientalis, P. racemosa s.l.), the other with
species from eastern North America (ENA; US and Canada) and
eastern Mexico (EMEX) (P. mexicana, P. occidentalis, and P.
rzedowskii). Within subg. Platanus, six subclades
corresponded to previously recognized taxa, and one
accession may be of hybrid origin. The historical
biogeography of Platanus was interpreted using phylogenetic
pattern, estimates of divergence times, the fossil record,
and climate reconstructions. The pattern of relationships
was consistent with a hypothesis of vicariance and the
oldest divergence between taxa within the set of area
relationships of ((WNA + EUR), (ENA + MEX)) suggested an
initial barrier affecting taxa that are now mostly confined
to North America. The second oldest divergence within subg.
Platanus involves the intercontinental disjunction of
semi-arid species from WNA + EUR, which diverged by at least
15 MYBP, consistent with the Madrean-Tethyan hypothesis.
Calibrated phylogenies were used to estimate divergence
times for five more recent intracontinental disjunctions.
These times correlated with the timing of geological events
in southwestern North America and northern Latin America. ©
Copyright 2005 by the American Society of Plant
Taxonomists.},
Doi = {10.1600/036364405775097851},
Key = {fds226603}
}
@article{fds226605,
Author = {Miller, RE and McDonald, JA and Manos, PS},
Title = {Systematics of Ipomoea subgenus Quamoclit (Convolvulaceae)
based on ITS sequence data and a Bayesian phylogenetic
analysis.},
Journal = {Am J Bot},
Volume = {91},
Number = {8},
Pages = {1208-1218},
Year = {2004},
Month = {August},
ISSN = {0002-9122},
url = {http://dx.doi.org/10.3732/ajb.91.8.1208},
Abstract = {A Bayesian phylogenetic analysis of 36 Ipomoea species using
sequence data from the internal transcribed spacer region
was compared with classification schemes based on
traditional methods and a previously published cpDNA
restriction fragment length polymorphism (RFLP) study. These
molecular studies support a diversity of groups that were
circumscribed on the basis of phenetic principles and agree
generally with the results from cpDNA RFLP analyses. The
congruence between the phylogenetic hypotheses based on new
molecular data and the understanding of relationships
developed in earlier studies indicate that these
classifications may reflect evolutionary history. Two large
clades of species, with one including sections Tricolores,
Calonyction, and Pharbitis and the other including sections
Mina and Leptocallis, were identified. Furthermore,
morphologically distinct groups of Ipomoea species received
support from the DNA sequence data. Indices of convergence
for the Markov chain Monte Carlo (MCMC) in the Bayesian
phylogenetic analysis were evaluated. A limited range of
posterior probabilities for each node in the trees from a
set of five MCMC samples provides a useful index of
convergence. Bayesian node support values were generally
higher than bootstrap values from a maximum parsimony
analysis. This is consistent with the notion that these
measures of support estimate different qualities of the
data.},
Doi = {10.3732/ajb.91.8.1208},
Key = {fds226605}
}
@article{fds226606,
Author = {Jaramillo, MA and Manos, PS and Zimmer, EA},
Title = {Phylogenetic relationships of the perianthless Piperales:
Reconstructing the evolution of floral development},
Journal = {International Journal of Plant Sciences},
Volume = {165},
Number = {3},
Pages = {403-416},
Publisher = {University of Chicago Press},
Year = {2004},
Month = {January},
url = {http://dx.doi.org/10.1086/382803},
Abstract = {The perianthless members of the Piperales are unique among
the basal lineages of angiosperms because they are mainly
herbaceous plants with over 2000 species possessing highly
reduced flowers. There have been several attempts to address
the evolution of the flower morphology in the group, but no
previous study has included a DNA-based estimate of
phylogeny. Here we present a robust reconstruction of the
phylogenetic relationships of the genera in the perianthless
Piperales using DNA sequence data from three genes (rbcL,
atpB, and 18S) and two genomes (nuclear and chloroplast). We
estimated the likelihood values of ancestral character
states of mature floral structures. Developmental sequences
also were analyzed using step matrices under specific models
of character state change to examine the origin of meristic
differences of the androecium and gynoecium. Developmental
lability is the general theme in the evolution of floral
merosity in the perianthless Piperales, with different
developmental processes giving rise to morphologically
identical mature stages. Our findings confirm this notion
based on several distinct patterns: (1) nonidentical
ontogenies give rise to homoplasious, six-staminate
androecia of Saururaceae and some Piperaceae most likely
through terminal addition; (2) identical ontogenies produce
the homoplasious two-staminate flowers in Peperomia and
Piper umbellatum through deletion; and (3) nearly identical
ontogenies produce homplasious tricarpellate gynoecia of
Piper and Anemopsis + Houttuynia clade, and the apocarpous
gynoecium of Saururus may be secondarily derived, both end
products occurring through deletion. We note that changes in
organ number and the degree of carpel fusion have been
important during the evolutionary history of the
perianthless Piperales as well as the basal angiosperms in
general and should be studied more extensively. Overall we
emphasize the lability of developmental pathways, especially
in the flower, and endorse the methodological utility of
developmental sequences for directing future investigations
of floral evolution.},
Doi = {10.1086/382803},
Key = {fds226606}
}
@article{fds226607,
Author = {Li, RQ and Chen, ZD and Lu, AM and Soltis, DE and Soltis, PS and Manos,
PS},
Title = {Phylogenetic relationships in Fagales based on DNA sequences
from three genomes},
Journal = {International Journal of Plant Sciences},
Volume = {165},
Number = {2},
Pages = {311-324},
Publisher = {University of Chicago Press},
Year = {2004},
Month = {January},
url = {http://dx.doi.org/10.1086/381920},
Abstract = {Nucleotide sequences of six regions from three plant genomes
- trnL-F, matK, rbcL, atpB (plastid), matR (mtDNA), and 18S
rDNA (nuclear) - were used to analyze inter- and
infrafamilial relationships of Fagales. All 31 extant genera
representing eight families of the order were sampled.
Congruence among data sets was assessed using the partition
homogeneity test, and five different combined data sets were
analyzed using maximum parsimony and the Bayesian approach.
At the familial level, the same phylogenetic relationships
were inferred from five different analyses of these data.
Nothofagus, followed by Fagaceae, are subsequent sisters to
the rest of the order. Fagaceae are then sister to the core
"higher" hamamelids, which consist of two main subclades,
one being Myricaceae (Rhoipteleaceae (Juglandaceae)) and the
other Casuarinaceae (Ticodendraceae (Betulaceae)). The
combined data sets provide the best-supported estimate of
evolutionary relationships within Fagales. Our results
suggest that the combination of different sequences from
several species within the same genus representing a
terminal taxon has little influence on phylogenetic
accuracy. Inclusion of taxa with some missing data in
combined data sets also does not have a major impact on the
topology.},
Doi = {10.1086/381920},
Key = {fds226607}
}
@article{fds303158,
Author = {Williams, KJ and Kress, WJ and Manos, PS},
Title = {The phylogeny, evolution, and classification of the genus
Globba and tribe Globbeae (Zingiberaceae): appendages do
matter.},
Journal = {American Journal of Botany},
Volume = {91},
Number = {1},
Pages = {100-114},
Year = {2004},
Month = {January},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21653367},
Abstract = {The genus Globba (100 species) is one of the largest genera
in the primarily tropical Zingiberaceae. Globba along with
the small genera Gagnepainia, Hemiorchis, and Mantisia
comprise the Globbeae, one of the two tribes of subfamily
Zingiberoideae. Traditional infrageneric classification in
Globba has focused on the number of anther appendages: zero,
two, or four. Parsimony and Bayesian analyses were conducted
on nuclear internal transcribed spacer (ITS) and plastid
trnK-matK data from a broad sampling of Globba and related
genera. Results show Mantisia to be monophyletic but nested
within Globba, while Hemiorchis and Gagnepainia are
monophyletic genera that are sister to each other. Anther
appendage number and shape, along with inflorescence and
fruit morphology, are the most important characters for
understanding evolutionary relationships in Globba. A new
infrageneric classification system for Globba, recognizing
three subgenera and seven sections is presented. The four
species of Mantisia are formally transferred into Globba but
retained as a distinct section. Within Globba, a notable
biogeographic boundary is seen at the Isthmus of Kra in
southern Thailand.},
Doi = {10.3732/ajb.91.1.100},
Key = {fds303158}
}
@article{fds226604,
Author = {Williams, KJ and Kress, WJ and Manos, PS},
Title = {Appendages do matter: the phylogeny, evolution, and
classification of the genus Globba and tribe Globbeae
(Zingiberaceae)},
Journal = {American Journal of Botany},
Volume = {91},
Number = {1},
Pages = {100-114},
Year = {2004},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21653367},
Abstract = {The genus Globba (100 species) is one of the largest genera
in the primarily tropical Zingiberaceae. Globba along with
the small genera Gagnepainia, Hemiorchis, and Mantisia
comprise the Globbeae, one of the two tribes of subfamily
Zingiberoideae. Traditional infrageneric classification in
Globba has focused on the number of anther appendages: zero,
two, or four. Parsimony and Bayesian analyses were conducted
on nuclear internal transcribed spacer (ITS) and plastid
trnK-matK data from a broad sampling of Globba and related
genera. Results show Mantisia to be monophyletic but nested
within Globba, while Hemiorchis and Gagnepainia are
monophyletic genera that are sister to each other. Anther
appendage number and shape, along with inflorescence and
fruit morphology, are the most important characters for
understanding evolutionary relationships in Globba. A new
infrageneric classification system for Globba, recognizing
three subgenera and seven sections is presented. The four
species of Mantisia are formally transferred into Globba but
retained as a distinct section. Within Globba, a notable
biogeographic boundary is seen at the Isthmus of Kra in
southern Thailand.},
Doi = {10.3732/ajb.91.1.100},
Key = {fds226604}
}
@article{fds226619,
Author = {McDowell, T and Volovsek, M and Manos, P},
Title = {Biogeography of Exostema (Rubiaceae) in the Caribbean region
in light of molecular phylogenetic analyses},
Journal = {Systematic Botany},
Volume = {28},
Number = {2},
Pages = {431-441},
Year = {2003},
Month = {April},
Abstract = {Exostema (Rubiaceae) comprises 25 neotropical woody species,
ranging from western South America and Mesoamerica to the
West Indies, with 19 species occurring in Cuba and
Hispaniola. Biogeographical hypotheses based upon a
phylogenetic analysis of morphological data depict a South
American origin for the group, with species radiations in
the Greater Antilles. Molecular phylogenetic analyses were
conducted using ITS and rbcL sequence data for a sample of
14 species of Exostema and nine species from eight closely
related genera. Results indicate that Exostema is
paraphyletic with respect to Coutarea, Erithalis, and
Chiococca. Hypotheses invoking independent South American
origins for subclades of Exostema are not supported.
Coutarea and the South American Exostema species form a
clade sister to the Caribbean Exostema species with terminal
inflorescences. Relationships among axillary flowered
Exostema species are not well resolved. Distribution,
ecology, and seed traits indicate over-water dispersal is
important for wide-spread species (e.g., E. caribaeum).
Sister species relationships between the Cuban and
Hispaniolan endemics E. salicifolium and E. acuminatum are
strongly supported. Disjunctions between various regions of
Cuba and Hispaniola are consistent with geohistorical
connections between these composite islands. Biogeographical
patterns found in Exostema are similar to those reported for
other Caribbean plant groups, with vicariance detected in
certain cases, and dispersal often indicated by
distribution, ecology and phylogeny for many
taxa.},
Key = {fds226619}
}
@article{fds226620,
Author = {Cannon, CH and Manos, PS},
Title = {Phylogeography of the Southeast Asian stone oaks
(Lithocarpus)},
Journal = {Journal of Biogeography},
Volume = {30},
Number = {2},
Pages = {211-226},
Publisher = {WILEY},
Year = {2003},
Month = {February},
url = {http://dx.doi.org/10.1046/j.1365-2699.2003.00829.x},
Abstract = {Aim: To describe current geographical patterns of genetic
diversity and infer the historical population dynamics of
the stone oaks (Lithocarpus) in Southeast Asia. Location: We
sampled three populations in Indochina: (1) Yunnan province,
China; (2) Pyin Oo Lwin area, Myanmar and (3) north-western
Vietnam; two in western Borneo: (1) South-western Sarawak
and (2) West Kalimantan, Indonesia; two in central Borneo:
(1) north coastal Sarawak and (2) north-eastern Sarawak,
Malaysia; and two in northern Borneo: (1) Central Sabah and
(2) Northern Sabah, Malaysia. Methods: A phylogenetic
reconstruction of chloroplast DNA sequence variation from
numerous individuals of multiple species was used to
determine geographical distribution of genetic diversity. A
resampling scheme was used to determine the significance of
these patterns at different hierarchical levels of the
phylogeny. Results were compared with a previously published
set of nuclear DNA sequence data. Results: A high level of
chloroplast sequence variation was found, which was divided
equally between two major clades separated by four
non-homoplasious changes. One clade was confined to the
island of Borneo, while the other was widespread. Strong
geographical structure was observed in the chloroplast
sequence variation. The Indochinese populations were much
more closely related than expected, comparable with the
highly endemic and isolated population on the western coast
of Borneo. Conversely, individuals from the Kelabit
Highlands were found to be more distantly related than
expected. The highest levels of genetic endemism were
observed in western Borneo. More geographical structure was
observed in the Bornean clade than in the Widespread clade,
because of limited genetic diversity in the Widespread
clade. Relatively weak geographical structure was found in
the nuclear sequence variation: only populations in southern
China and central Sabah were significantly related.
Conclusions: The high levels of chloroplast genetic
diversity and the persistence of an ancestral haplotype that
is a single step away from a haplotype found in Castanopsis
indicates the continuous presence of tropical rain forest in
Southeast Asia throughout the evolutionary history of the
genus (c. 40 Myr). This conclusion is supported by the high
frequency of numerous endemic types observed in every
population and the relatively few number of 'missing'
haplotypes. This situation suggests both limited migration
and limited extinction. In contrast, the nuclear genetic
diversity contained less geographical structure, indicating
that our taxonomic sampling among populations was unbiased
and that gene flow mediated through pollen is less
geographically restricted and contains less geographical
structure than purely seed-mediated (chloroplast) gene flow.
The most likely scenario suggested by the evidence involves
four major patterns: (1) the widespread presence of an
ancestral haplotype; (2) the large degree of separation
(four non-homoplasious base pairs) between the types found
in the two major clades; (3) the concentration of derived
types from both major clades found in central and northern
Borneo; and (4) the molecular endemism found in each
location. These patterns suggest four primary things about
the population dynamics of Lithocarpus since the late
Eocene: (1) populations have either spanned the entire
region throughout much of the evolutionary history of the
genus or substantial populations have persisted in both
Indochina and Borneo with limited migration between them;
(2) significant fragmentation has occurred subsequently
between the Asian mainland and the Melasian island
archipelago, leading to independent genetic diversification
in both regions; (3) several locations possessing
significant independent histories, have experienced little
migration and have never gone completely extinct; and (4)
that the central highlands of Borneo have been re-invaded
from the north and the west. The timing of these events is
difficult to ascertain but probably predate the Quaternary
Period, suggesting that although the recent ice ages might
have affected the overall distribution of rain forest in
Southeast Asia, it managed to persist in most regions even
through the most dramatic drying events.},
Doi = {10.1046/j.1365-2699.2003.00829.x},
Key = {fds226620}
}
@article{fds304279,
Author = {Miller, RE and Buckley, TR and Manos, PS},
Title = {An examination of the monophyly of morning glory taxa using
Bayesian phylogenetic inference.},
Journal = {Systematic Biology},
Volume = {51},
Number = {5},
Pages = {740-753},
Year = {2002},
Month = {October},
ISSN = {1063-5157},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12396588},
Abstract = {The objective of this study was to obtain a quantitative
assessment of the monophyly of morning glory taxa,
specifically the genus Ipomoea and the tribe Argyreieae.
Previous systematic studies of morning glories intimated the
paraphyly of Ipomoea by suggesting that the genera within
the tribe Argyreieae are derived from within Ipomoea;
however, no quantitative estimates of statistical support
were developed to address these questions. We applied a
Bayesian analysis to provide quantitative estimates of
monophyly in an investigation of morning glory relationships
using DNA sequence data. We also explored various approaches
for examining convergence of the Markov chain Monte Carlo
(MCMC) simulation of the Bayesian analysis by running 18
separate analyses varying in length. We found convergence of
the important components of the phylogenetic model (the tree
with the maximum posterior probability, branch lengths, the
parameter values from the DNA substitution model, and the
posterior probabilities for clade support) for these data
after one million generations of the MCMC simulations. In
the process, we identified a run where the parameter values
obtained were often outside the range of values obtained
from the other runs, suggesting an aberrant result. In
addition, we compared the Bayesian method of phylogenetic
analysis to maximum likelihood and maximum parsimony. The
results from the Bayesian analysis and the maximum
likelihood analysis were similar for topology, branch
lengths, and parameters of the DNA substitution model.
Topologies also were similar in the comparison between the
Bayesian analysis and maximum parsimony, although the
posterior probabilities and the bootstrap proportions
exhibited some striking differences. In a Bayesian analysis
of three data sets (ITS sequences, waxy sequences, and ITS +
waxy sequences) no supoort for the monophyly of the genus
Ipomoea, or for the tribe Argyreieae, was observed, with the
estimate of the probability of the monophyly of these taxa
being less than 3.4 x 10(-7).},
Doi = {10.1080/10635150290102401},
Key = {fds304279}
}
@article{fds226618,
Author = {Miller, RE and Buckley, TR and Manos, PS},
Title = {Application of Baysian phylogenetic inference to the
systematics of morning glories},
Journal = {Systematic Biology},
Volume = {51},
Number = {5},
Pages = {740-753},
Year = {2002},
ISSN = {1063-5157},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12396588},
Abstract = {The objective of this study was to obtain a quantitative
assessment of the monophyly of morning glory taxa,
specifically the genus Ipomoea and the tribe Argyreieae.
Previous systematic studies of morning glories intimated the
paraphyly of Ipomoea by suggesting that the genera within
the tribe Argyreieae are derived from within Ipomoea;
however, no quantitative estimates of statistical support
were developed to address these questions. We applied a
Bayesian analysis to provide quantitative estimates of
monophyly in an investigation of morning glory relationships
using DNA sequence data. We also explored various approaches
for examining convergence of the Markov chain Monte Carlo
(MCMC) simulation of the Bayesian analysis by running 18
separate analyses varying in length. We found convergence of
the important components of the phylogenetic model (the tree
with the maximum posterior probability, branch lengths, the
parameter values from the DNA substitution model, and the
posterior probabilities for clade support) for these data
after one million generations of the MCMC simulations. In
the process, we identified a run where the parameter values
obtained were often outside the range of values obtained
from the other runs, suggesting an aberrant result. In
addition, we compared the Bayesian method of phylogenetic
analysis to maximum likelihood and maximum parsimony. The
results from the Bayesian analysis and the maximum
likelihood analysis were similar for topology, branch
lengths, and parameters of the DNA substitution model.
Topologies also were similar in the comparison between the
Bayesian analysis and maximum parsimony, although the
posterior probabilities and the bootstrap proportions
exhibited some striking differences. In a Bayesian analysis
of three data sets (ITS sequences, waxy sequences, and ITS +
waxy sequences) no supoort for the monophyly of the genus
Ipomoea, or for the tribe Argyreieae, was observed, with the
estimate of the probability of the monophyly of these taxa
being less than 3.4 x 10(-7).},
Doi = {10.1080/10635150290102401},
Key = {fds226618}
}
@article{fds226613,
Author = {Manos, PS and Miller, RE and Wilkin, P},
Title = {Phylogenetic analysis of Ipomoea, Argyreia, Stictocardia,
and Turbina suggests a generalized model of morphological
evolution in morning glories},
Journal = {Systematic Botany},
Volume = {26},
Number = {3},
Pages = {585-602},
Year = {2001},
Month = {October},
ISSN = {0363-6445},
Abstract = {We tested the phylogenetic hypothesis that the
circumscription of the genus Ipomoea comprises all members
of Hallier's historical taxon, subfamily "Echinoconiae",
including Argyreia, Astripomoea, Lepistemon, Rivea,
Stictocardia, and Turbina. Support for the paraphyly of
Ipomoea was found based on phylogenetic analysis of 45 taxa
using DNA sequences (the ITS region and three exons and two
introns of the 3′ end of the nuclear gene waxy) in
combination with morphological data. Two major clades within
Ipomoea s. 1. were resolved in the strict consensus of 16
most parsimonious trees. One clade included most of the
smaller segregate genera interspersed with species of
Ipomoea, whereas the other was formed by Ipomoea s.s. and
Astripomoea. Our results also indicated the genus Turbina is
polyphyletic and Rivea is nested within Argyreia. Together,
these results suggest new phylogenetic interpretations and
point towards a revised view of the nature of morphological
evolution among these taxa. We used both our current
understanding of morning glory systematics and the
distribution of character state variation in seven
taxonomically important characters to demonstrate that: 1)
the common Ipomoea form is widely distributed, 2) the common
form has given rise to specialized forms exhibiting a
diversity of character state combinations, and 3) many of
the specialized forms have arisen repeatedly. On the basis
of these observations, we forward a general model of mosaic
evolution that emphasizes extreme evolutionary lability in
morphology among morning glory species.},
Key = {fds226613}
}
@article{fds226616,
Author = {Jaramillo, MA and Manos, PS},
Title = {Phylogeny and patterns of floral diversity in the genus
Piper (Piperaceae).},
Journal = {Am J Bot},
Volume = {88},
Number = {4},
Pages = {706-716},
Year = {2001},
Month = {April},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11302858},
Abstract = {With ∼1000 species distributed pantropically, the genus
Piper is one of the most diverse lineages among basal
angiosperms. To rigorously address the evolution of Piper we
use a phylogenetic analysis of sequences of the internal
transcribed spacers (ITS) of nuclear ribosomal DNA based on
a worldwide sample. Sequences from a total of 51 species of
Piper were aligned to yield 257 phylogenetically informative
sites. A single unrooted parsimony network suggested that
taxa representing major geographic areas could potentially
form three monophyletic groups: Asia, the South Pacific, and
the Neotropics. The position of Pothomorphe was well
supported among groups of New World taxa. Simultaneous
phylogenetic analysis of an expanded alignment including
outgroups suggested that taxa from the South Pacific and
Asia formed a monophyletic group, provisionally supporting a
single origin of dioecy. Within the Neotropical sister
clade, resolution was high and strong bootstrap support
confirmed the monophyly of several traditionally recognized
infrageneric groups (e.g., Enckea [including Arctottonia],
Ottonia, Radula, Macrostachys). In contrast, some of the
species representing the highly polytypic subgroup
Steffensia formed a clade corresponding to the previously
recognized taxon Schilleria, while others were strongly
associated with several of the more specialized groups of
taxa. The distribution of putatively derived inflorescence
and floral character states suggested that both umbellate
and solitary axillary inflorescences have multiple origins.
Reduction in anther number appears to be associated with
highly packaged inflorescences or with larger anther
primordia per flower, trends that are consistent with the
suppression of later stages of androecial
development.},
Doi = {10.2307/2657072},
Key = {fds226616}
}
@article{fds226611,
Author = {Manos, PS and Donoghue, MJ},
Title = {Progress in Northern Hemisphere phytogeography: An
introduction},
Journal = {International Journal of Plant Sciences},
Volume = {162},
Number = {6 SUPPL.},
Pages = {S1-S2},
Publisher = {University of Chicago Press},
Year = {2001},
Month = {January},
url = {http://dx.doi.org/10.1086/324421},
Doi = {10.1086/324421},
Key = {fds226611}
}
@article{fds226612,
Author = {Manos, PS and Zhou, ZK and Cannon, CH},
Title = {Systematics of Fagaceae: Phylogenetic tests of reproductive
trait evolution},
Journal = {International Journal of Plant Sciences},
Volume = {162},
Number = {6},
Pages = {1361-1379},
Publisher = {University of Chicago Press},
Year = {2001},
Month = {January},
url = {http://dx.doi.org/10.1086/322949},
Abstract = {The family Fagaceae includes nine currently recognized
genera and ca. 1000 species, making it one of the largest
and most economically important groups within the order
Fagales. In addition to wide variation in cupule and fruit
morphology, polymorphism in pollination syndrome (wind vs.
generalistic insect) also contributes to the uniqueness of
the family. Phylogenetic relationships were examined using
179 accessions spanning the taxonomic breadth of the family,
emphasizing tropical, subtropical, and relictual taxa.
Nuclear ribosomal DNA sequences encoding the 5.8S rRNA gene
and two flanking internal transcribed spacers (ITS) were
used to evaluate phylogenetic hypotheses based on previous
morphological cladistic analysis and intuitive schemes.
Parsimony analyses rooted with Fagus supported two clades
within the family, Trigonobalanus sensu lato and a large
clade comprising Quercus and the castaneoid genera
(Castanea+Castanopsis, Chrysolepis, Lithocarpus). Three DNA
sequence data sets, 179-taxon ITS, 60-taxon ITS, and a
14-taxon combined nuclear and chloroplast (matK), were used
to test a priori hypotheses of reproductive character state
evolution. We used Templeton's (1983) test to assess
alternative scenarios of single and multiple origins of
derived and seemingly irreversible traits such as wind
pollination, hypogeal cotyledons, and flower cupules. On the
basis of previous exemplar-based and current in-depth
analyses of Fagaceae, we suggest that wind pollination
evolved at least three times and hypogeal cotyledons once.
Although we could not reject the hypothesis that the acorn
fruit type of Quercus is derived from a dichasium cupule,
combined analysis provided some evidence for a relationship
of Quercus to Lithocarpus and Chrysolepis, taxa with
dichasially arranged pistillate flowers, where each flower
is surrounded by cupular tissue. This indicates that a more
broadly defined flower cupule, in which individual
pistillate flowers seated within a separate cupule, may have
a single origin.},
Doi = {10.1086/322949},
Key = {fds226612}
}
@article{fds226614,
Author = {Krellwltz, EC and Kowallik, KV and Manos, PS},
Title = {Molecular and morphological analyses of Bryopsis
(Bryopsidales, Chlorophyta) from the western North Atlantic
and Caribbean},
Journal = {Phycologia},
Volume = {40},
Number = {4},
Pages = {330-339},
Publisher = {International Phycological Society},
Year = {2001},
Month = {January},
url = {http://dx.doi.org/10.2216/i0031-8884-40-4-330.1},
Abstract = {Three species of Bryopsis have commonly been reported from
the western North Atlantic, but continuous morphological
variation has often confounded specimen identification. This
study evaluates the utility of the coding and non-coding
sequences of the psbB gene cluster of Bryopsis, compared to
morphological characters, as a means of distinguishing
Bryopsis species. The sequences examined include a group II
intron within the psbT gene, the 3′ exon of this gene, the
spacer separating psbT and psbH, as well as the 5′ part of
the latter gene. Sequences of 616 bp of Bryopsis from 28
collections from the study area were aligned with those for
eight collections from elsewhere in the Atlantic and
Pacific, in order to test the monophyly of Atlantic
Bryopsis. The phylogenies were rooted using Lambia as an
outgroup. Parsimony analysis resolved the sequences into
five clades, with strong bootstrap support. Three of the
clades had wide distributions, two including individuals
from both the western and eastern North Atlantic and the
Pacific and one including plants from the Caribbean and the
Pacific. The other two clades were more restricted: one
clade was found only in the warm temperate western North
Atlantic, and the other derived from the central California
coast. Three methods of cluster analysis were applied to the
morphological data but failed to find robust higher level
structure; they neither supported nor refuted the molecular
data. The four clades from the western North Atlantic and
Caribbean appear to be either seasonally or geographically
disjunct throughout this region. The molecular data support
the current recognition of multiple species of Bryopsis
along the western North Atlantic, some with worldwide
distributions, but the morphological data do not correlate
with this.},
Doi = {10.2216/i0031-8884-40-4-330.1},
Key = {fds226614}
}
@article{fds226615,
Author = {Manos, PS and Stone, DE},
Title = {Evolution, phylogeny, and systematics of the
Juglandaceae},
Journal = {Annals of the Missouri Botanical Garden},
Volume = {88},
Number = {2},
Pages = {231-269},
Publisher = {JSTOR},
Year = {2001},
Month = {January},
url = {http://dx.doi.org/10.2307/2666226},
Abstract = {A comprehensive systematic investigation was conducted on
the extant Juglandaceae based on 25 species representing a
broad sample of generic and infrageneric diversity. A total
of 206 phylogenetically informative characters derived from
morphological, chemical, chromosomal, and sequence-based
studies formed the basis for comparative studies.
Phylogenetic analysis was used to infer relationships and
examine patterns of convergence in key biochemical and
morphological traits associated with dispersal biology.
Separate and combined parsimony analyses of three previously
unpublished data sets (ITS, chloroplast DNA,
morphology/chemistry) supported two major clades,
Juglandoideae and Engelhardioideae, in agreement with a
recent subfamilial classification. Within Engelhardioideae,
the genus Engelhardia was found to be paraphyletic, as E.
roxburghiana of the monotypic section Psilocarpeae was
resolved as sister taxon to a New World subclade composed of
Oreomunnea + Alfaroa. Within Juglandoideae, two tribes are
recognized: Platycaryeae and Juglandeae. The monotypic genus
Platycarya formed the sister group to Juglandeae, which was
resolved fully (Carya-(Juglans-(Cyclocarya + Pterocarya))).
Two new subtribes, Juglandinae and Caryinae, are described
based on the cladistic pattern. Unique morphological
apomorphies were detected for all genera, including the
previously little-studied Cyclocarya, which was also
determined to possess a novel base chromosome number for the
family (N = 28). The nested position of Annamocarya sinensis
within Old World Carya, combined with its lack of unique
apomorphies suggested sectional recognition within Carya
might be more appropriate for this taxon. Phylogenetic
context was used to interpret patterns of morphological and
chemical variation associated with the evolution of seed
dispersal and the tropical versus temperate habitat.
Although the syndrome of wind dispersal appears to be
ancestral within the family, four novel origins of wing
tissue are represented by Engelhardia/Oreomunnea,
Platycarya, Pterocarya, and Cyclocarya. The convergence on
animal dispersal has been achieved through three different
developmental pathways in the production of a husk in
Alfaroa, Carya, and Juglans. In general, wind-dispersed
seeds have epigeal germination and those that are
animal-dispersed are hypogeous, but Oreomunnea and
Cyclocarya are exceptions in their respective clades by
having wind-dispersed seeds with hypogeal germination. The
seed-energy reserves are also revealing. With the exception
of Oreommunea, wind-dispersed seeds have relatively high
concentrations of the unsaturated linolenic (C) and linoleic
(B) fatty acids (CB pattern), whereas all animal-dispersed
fruits (viz., Alfaroa, Carya, and Juglans), and Oreomunnea,
have relatively high concentrations of the unsaturated oleic
(A) and linoleic (B) fatty acids (BA or AB pattern).
Tropical genera, whether wind- or animal-dispersed (viz.,
Oreomunnea, Alfaroa, Annamocarya), have relatively high
concentrations of the saturated palmitic fatty acid.
Conversely, wind- and animal-dispersed fruits of temperate
genera (viz., Carya, Juglans, Cyclocarya, Pterocarya, and
Platycarya) have relatively low percentages of palmitic
acid. The explanation here is based on the fact that seed
fats must be fluid at the temperature of the living plant,
thus selecting for saturated fats in warm tropical climates
and unsaturated lipids in cool temperate
climates.},
Doi = {10.2307/2666226},
Key = {fds226615}
}
@article{fds304278,
Author = {Manos, PS and Stanford, AM},
Title = {The historical biogeography of Fagaceae: Tracking the
tertiary history of temperate and subtropical forests of the
Northern Hemisphere},
Journal = {International Journal of Plant Sciences},
Volume = {162},
Number = {6 SUPPL.},
Pages = {S77-S93},
Publisher = {University of Chicago Press},
Year = {2001},
Month = {January},
url = {http://dx.doi.org/10.1086/323280},
Abstract = {The angiosperm family Fagaceae is a central element of
several distinct community types throughout the Northern
Hemisphere and a prime candidate for modern biogeographic
analysis. The rich fossil record for the family provides an
unparalleled source to compare with modern distributions and
evaluate hypotheses of origin, migration, and vicariance. We
conducted separate phylogenetic analyses on genera with
intercontinentally disjunct distributions using various
noncoding regions of chloroplast and nuclear ribosomal DNA
sequences. Analyses generally supported the (North America -
(Europe + Asia)) pattern of area relationships. Divergence
times between disjunct species were estimated to aid in the
development of a comparative synthesis of historical
biogeography across the family. Fully resolved phylogenies
were analyzed biogeographically using three distinct
approaches: dispersal-vicariance analysis (DIVA), strict
vicariance, and dispersal analysis using Fitch parsimony.
Ancestral area reconstructions based on DIVA were preferred
because event-based inferences generally were consistent
with fossil evidence for migration and estimates of
divergence times. Reconstructions suggested an Asian origin
for the genus Fagus with bidirectional migration to Europe
and North America, consistent with a paraphyletic assemblage
of Asian species and intercontinental exchange via the
Bering Land Bridge (BLB). Reconstructions within Quercus
generally were more ambiguous in determining a center of
origin; however, one optimization pathway was consistent
with the vicariance of an ancestrally widespread
distribution and the initial divergence between largely
North American and Asian clades. Within the North American
clade, dispersal to Eurasia is inferred for section Quercus
(white oaks). Bidirectional floristic exchange via the BLB
is supported for these temperate taxa, followed by
intercontinental disjunction by the mid-Miocene. In
contrast, disjunctions based on living and fossil
distributions within evergreen Fagaceae (e.g., Castanopsis,
Lithocarpus, Trigonobalanus) suggest older, temporally
distinct biogeographic histories involving both the North
Atlantic and Bering Land Bridges.},
Doi = {10.1086/323280},
Key = {fds304278}
}
@article{fds226584,
Author = {Cannon, CH and Manos, PS},
Title = {Combining and comparing morphometric shape descriptors with
a molecular phylogeny: the case of fruit type evolution in
Bornean Lithocarpus (Fagaceae)},
Journal = {Systematic Biology},
Volume = {50},
Number = {6},
Pages = {1-21},
Year = {2001},
url = {http://dx.doi.org/10.1080/106351501753462849},
Abstract = {Fruit type in the genus Lithocarpus (Fagaceae) includes both
classic oak acorns and novel modifications. Bornean taxa
with modified fruits can be separated into two sections
(Synaedrys and Lithocarpus) based on subtle shape
differences. By following strict criteria for homology and
representation, this variation in shape can be captured and
the sections distinguished by using elliptic Fourier or
eigenshape analysis. Phenograms of fruit shape, constructed
by using restricted maximum likelihood techniques and these
morphometric descriptors, were incorporated into combined
and comparative analyses with molecular sequence data from
the internal transcribed spacer (ITS) region of the nuclear
rDNA, using branch-weighted matrix representation. The
combined analysis strongly suggested independent derivation
of the novel fruit type in the two sections from different
acornlike ancestors, while the comparative analysis
indicated frequent decoupling between the molecular and
morphological changes as inferred at well-supported nodes.
The acorn fruit type has undergone little modification
between ingroup and outgroup, despite large molecular
distance. Greater morphological than molecular change was
inferred at critical transitions between acorn and novel
fruit types, particularly for section Lithocarpus. The
combination of these two different types of data improved
our understanding of the macroevolution of fruit type in
this difficult group, and the comparative analysis
highlighted the significant incongruities in evolutionary
pattern between the two datasets.},
Doi = {10.1080/106351501753462849},
Key = {fds226584}
}
@article{fds226610,
Author = {Manos, PS and Stanford, AM},
Title = {The biogeography of Fagaceae: tracking the Tertiary history
of temperate and subtropical forests of the Northern
Hemisphere},
Journal = {International Journal of Plant Sciences},
Volume = {162},
Number = {6 SUPPL.},
Pages = {S77-S93},
Year = {2001},
Abstract = {The angiosperm family Fagaceae is a central element of
several distinct community types throughout the Northern
Hemisphere and a prime candidate for modern biogeographic
analysis. The rich fossil record for the family provides an
unparalleled source to compare with modern distributions and
evaluate hypotheses of origin, migration, and vicariance. We
conducted separate phylogenetic analyses on genera with
intercontinentally disjunct distributions using various
noncoding regions of chloroplast and nuclear ribosomal DNA
sequences. Analyses generally supported the (North America -
(Europe + Asia)) pattern of area relationships. Divergence
times between disjunct species were estimated to aid in the
development of a comparative synthesis of historical
biogeography across the family. Fully resolved phylogenies
were analyzed biogeographically using three distinct
approaches: dispersal-vicariance analysis (DIVA), strict
vicariance, and dispersal analysis using Fitch parsimony.
Ancestral area reconstructions based on DIVA were preferred
because event-based inferences generally were consistent
with fossil evidence for migration and estimates of
divergence times. Reconstructions suggested an Asian origin
for the genus Fagus with bidirectional migration to Europe
and North America, consistent with a paraphyletic assemblage
of Asian species and intercontinental exchange via the
Bering Land Bridge (BLB). Reconstructions within Quercus
generally were more ambiguous in determining a center of
origin; however, one optimization pathway was consistent
with the vicariance of an ancestrally widespread
distribution and the initial divergence between largely
North American and Asian clades. Within the North American
clade, dispersal to Eurasia is inferred for section Quercus
(white oaks). Bidirectional floristic exchange via the BLB
is supported for these temperate taxa, followed by
intercontinental disjunction by the mid-Miocene. In
contrast, disjunctions based on living and fossil
distributions within evergreen Fagaceae (e.g., Castanopsis,
Lithocarpus, Trigonobalanus) suggest older, temporally
distinct biogeographic histories involving both the North
Atlantic and Bering Land Bridges.},
Key = {fds226610}
}
@article{fds226617,
Author = {Cannon, CH and Manos, PS},
Title = {The Bornean Lithocarpus Bl. section Synaedrys (Lindl.)
Barnett (Fagaceae): Its circumscription and description of a
new species},
Journal = {Botanical Journal of the Linnean Society},
Volume = {133},
Number = {3},
Pages = {343-357},
Publisher = {Oxford University Press (OUP)},
Year = {2000},
Month = {January},
ISSN = {0024-4074},
url = {http://dx.doi.org/10.1006/bojl.1999.0325},
Abstract = {The Bornean species of Lithocarpus Bl. section Synaedrys
(Lindl.) Barnett (Fagaceae) are discussed in terms of their
unifying characteristics, and keys to the species are
provided. A novel morphological feature present in the
genus, where the seed in the mature fruit is enclosed by a
lignified and thickened receptacle, is illustrated. A new
species, L. palungensis Cannon and Manos, is described. It
can be distinguished from L. pulcher (King) Markgr. by its
submontane distribution, prominent reflexed cupular spines,
present at all stages, and broadly oblong leaves with
scattered open fasciculate trichomes on the abaxial surface.
Foliar trichome types present within the section are also
described. Distinctiveness of fruit wall and receptacle
shape, as described by two-dimensional elliptic Fourier
transformation, is demonstrated by principal components
analysis. (C) 2000 The Linnean Society of
London.},
Doi = {10.1006/bojl.1999.0325},
Key = {fds226617}
}
@article{fds226609,
Author = {Manos, PS and Doyle, JJ and Nixon, KC},
Title = {Phylogeny, biogeography, and processes of molecular
differentiation in Quercus subgenus Quercus
(Fagaceae).},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {12},
Number = {3},
Pages = {333-349},
Year = {1999},
Month = {August},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10413627},
Abstract = {Quercus is one of the most abundant and economically
important genera of woody plants in the Northern Hemisphere.
To infer phylogenetic relationships within Quercus subgenus
Quercus, chloroplast DNA (cpDNA) restriction sites and
nucleotide sequences of the internal transcribed spacers
(ITS) and the 5.8S coding region of the nuclear ribosomal
DNA repeat were obtained for 44 individuals, including 25
species, intraspecific samples, and three outgroups.
Separate parsimony analyses of each data set showed that
individual gene trees were congruent and often complementary
in supporting clades that generally corresponded to
previously recognized taxonomic groups. Only one instance of
strongly supported gene tree incongruence was detected and
this anomalous pattern was explained best by ancient
introgression of cpDNA across sectional boundaries.
Simultaneous parsimony analysis of the pruned data sets
supported the recognition of the strictly Eurasian section
Cerris and resolved a novel hypothesis for the major
infrageneric groups (Cerris- (Lobatae- (Protobalanus +
Quercus sensu stricto))). The biogeographic hypothesis that
all major oak lineages evolved locally at middle latitudes
within the general distribution of their fossil ancestors
was fully supported. This set of relationships also
suggested a New World origin for the widespread white oaks
of the Northern Hemisphere (section Quercus s. s.). For both
data sets, inter- and intraspecific sampling within section
Protobalanus showed little correspondence to morphological
species. Greater cladistic structure among the samples was
obtained by cpDNA restriction sites and two well-delimited
plastomes types comprising a total of 15 distinct haplotypes
were resolved. Haplotypes of 2 of the peripheral species in
this species complex occupy terminal portions of one of the
plastome clades, suggesting a more recent origin relative to
those of more widespread species. The phylogeography of the
two divergent plastome types suggested a north-south
pattern, consistent with a Late Tertiary disjunction in the
ancestral distribution of section Protobalanus.},
Doi = {10.1006/mpev.1999.0614},
Key = {fds226609}
}
@article{fds226608,
Author = {Miller, RE and Rausher, MD and Manos, PS},
Title = {Phylogenetic systematics of Ipomoea (Convolvulaceae) based
on ITS and Waxy sequences},
Journal = {Systematic Botany},
Volume = {24},
Number = {2},
Pages = {209-227},
Publisher = {JSTOR},
Year = {1999},
Month = {January},
url = {http://dx.doi.org/10.2307/2419549},
Abstract = {Ipomoea is a large and complex genus containing over 600
species of vines and shrubs widely distributed throughout
the tropics and subtropics. The phylogeny of 40 species
representing the three currently recognized subgenera and
nine sections within the genus was analyzed using sequences
of the internal transcribed spacer (ITS) region of nuclear
ribosomal DNA and sequences for three exons and two introns
of the 3' end of the nuclear gene waxy. Nucleotide data from
each gene or region were analyzed singly and in combination
using parsimony. Exon and intron sequences from the
relatively unexplored waxy gene provided appreciable levels
of site mutations, and intron sequences revealed several
phylogenetically informative deletions. ITS provided greater
resolution and was largely congruent with waxy. Combined
analyses using Merremia and Operculina as outgroups showed
strong support for two major clades, including a novel
assemblage of four Old World species and a larger clade
composed of the remaining sample. Within the larger clade
were numerous well-supported subclades, several of which
corresponded to previously recognized taxonomic groups.
Higher level hierarchical relationships within the two
clades and the among the subclades did not support the most
recent classification scheme, which divides Ipomoea into
three subgenera, Ipomoea, Quamoclit, and Eriospermum. A
striking result from this study was identifying a close
relationship between species of section Pharbitis (subgenus
Ipomoea) and species of subgenus Quamoclit. This clade is
comprised of taxa with a broad range of morphological
diversity, implying both floral and vegetative morphology
may have been evolutionarily labile within the genus. The
composition of three clades consisting largely of species of
subg. Eriospermum suggests a novel set of relationships
between New World and Australian species. Several clades
identified in this study are prime candidates for future
studies of character evolution, including several putative
cases of independent pigment transformations of red and
white flowers from purple flowers.},
Doi = {10.2307/2419549},
Key = {fds226608}
}
@article{fds226581,
Author = {Manos, P and Steele, K},
Title = {Phylogenetic analyses of "higher" Hamamelididae based on
plastid sequence data.},
Journal = {Am J Bot},
Volume = {84},
Number = {10},
Pages = {1407},
Year = {1997},
Month = {October},
url = {http://dx.doi.org/10.2307/2446139},
Abstract = {Phylogenetic relationships were examined within the "higher"
Hamamelididae using 21 species representing eight families
and related outgroups. Chloroplast DNA sequences encoding
the matK gene (/1 kilobase) provided 258 informative
nucleotide sites. Phylogenetic analysis of this variation
produced one most parsimonious tree supporting three
monophyletic groups. In this tree, Nothofagus was basal to a
well supported clade of remaining "higher" hamamelids, in
which Fagaceae, including Fagus, were sister to a clade of
core "higher" hamamelids that share wind-pollination,
bicarpellate flowers, granular pollen walls, and reduced
pollen apertures. Within the core "higher" hamamelids three
subclades were resolved, Myricaceae, (Casuarina-(Ticodendron-(Betulaceae))),
and (Rhoiptelea-Juglandaceae). Each subclade was well
supported but relationships among them were not. The basal
position of Nothofagus within the matK tree is consistent
with the fossil record of "higher" hamamelids in which
Nothofagus pollen appears earlier than microfossils with
affinities to other modern "higher" hamamelids. This
placement supports the exclusion of Nothofagus from Fagaceae
and suggests two hypotheses for the origin of the cupule.
The cupule may be ancestral within "higher" hamamelids and
subsequently lost in core members of the clade or there may
have been two independent origins. It is suggested that the
three clades (1) Nothofagaceae, (2) Fagaceae, and (3)
Juglandaceae, Rhoiptelea, Myricaceae, Casuarina,
Ticodendron, and Betulaceae be considered at the ordinal
level and that traditional orders, such as Fagales sensu
Cronquist (Fagaceae, Nothofagaceae, and Betulaceae) be
abandoned. Comparative analyses of matK sequences with
previously published rbcL sequences demonstrate that for the
taxa considered here matK sequences produced trees with
greater phylogenetic resolution and a higher consistency
index.},
Doi = {10.2307/2446139},
Key = {fds226581}
}
@article{fds226580,
Author = {Manos, P},
Title = {Systematics of Nothofagus (Nothofagaceae) based on rDNA
spacer sequences (ITS): taxonomic congruence with morphology
and plastid sequences.},
Journal = {Am J Bot},
Volume = {84},
Number = {8},
Pages = {1137},
Year = {1997},
Month = {August},
url = {http://dx.doi.org/10.2307/2446156},
Abstract = {Phylogenetic relationships were examined within the southern
beech family Nothofagaceae using 22 species representing the
four currently recognized subgenera and related outgroups.
Nuclear ribosomal DNA sequences encoding the 5.8s rRNA and
two flanking internal transcribed spacers (ITS) provided 95
phylogenetically informative nucleotide sites from a single
alignment of ~588 bases per species. Parsimony analysis of
this variation produced two equally parsimonious trees
supporting four monophyletic groups, which correspond to
groups designated by pollen type. These topologies were
compared to trees from reanalyses of previously reported
rbcL sequences and a modified morphological data set.
Results from parsimony analysis of the three data sets were
highly congruent, with topological differences restricted to
the placement of a few terminal taxa. Combined analysis of
molecular and morphological data produced six equally
parsimonious trees. The consensus of these trees suggests
two basal clades within Nothofagus. Within the larger of the
two clades, tropical Nothofagus (subgenus Brassospora) of
New Guinea and New Caledonia are strongly supported as
sister to cool-temperate species of South America (subgenus
Nothofagus). Most of the morphological apomorphies of the
cupule, fruit, and pollen of Nothofagus are distributed
within this larger clade. An area cladogram based on the
consensus of combined data supports three trans-Antarctic
relationships, two within pollen groups and one between
pollen groups. Fossil data support continuous ancestral
distributions for all four pollen groups prior to
continental drift; therefore, vicariance adequately explains
two of these disjunctions. Extinction of trans-Antarctic
sister taxa within formerly widespread pollen groups
explains the third disjunction; this results in a
biogeographic pattern indicative of phylogenetic
relationship not vicariance. For the biogeographically
informative vicariant clades, area relationships based on
total evidence support the recently advanced hypothesis that
New Zealand and Australia share a unique common ancestry.
Contrary to previous thought, the distribution of extant
Nothofagus is informative on the area relationships of the
Southern Hemisphere, once precise phylogenetic relationships
are placed in the context of fossil data.},
Doi = {10.2307/2446156},
Key = {fds226580}
}
%% Other
@misc{fds1745,
Author = {P.S. Manos},
Title = {Fagales},
Booktitle = {Encyclopedia of Life Sciences},
Publisher = {Macmillan Reference Ltd.},
Year = {2001},
Key = {fds1745}
}
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