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| Publications of Kathleen M. Pryer :chronological alphabetical combined listing:
%% Books
@book{fds16774,
Author = {Argus, G.W. and K.M. Pryer},
Title = {Rare vascular plants in Canada - our natural
heritage},
Pages = {277},
Publisher = {Canadian Museum of Nature},
Year = {1990},
Key = {fds16774}
}
@book{fds353312,
Author = {Argus, GW and Pryer, KM},
Title = {Rare vascular plants in Canada; our natural
heritage},
Publisher = {Ottawa, Ontario (Canada) Canadian Museum of Nature, Botany
Division},
Year = {1990},
url = {http://dx.doi.org/10.5962/bhl.title.132392},
Doi = {10.5962/bhl.title.132392},
Key = {fds353312}
}
@book{fds353570,
Author = {Argus, GW},
Title = {Atlas of the rare vascular plants of Ontario},
Publisher = {Botany Division, National Museum of Natural Sciences =
Division de la botanique, Musée national des sciences
naturelles},
Year = {1982},
ISBN = {0662504151},
url = {http://dx.doi.org/10.5962/bhl.title.51429},
Doi = {10.5962/bhl.title.51429},
Key = {fds353570}
}
%% Papers Published
@article{fds373350,
Author = {Hay, NM and Windham, MD and Mandáková, T and Lysak, MA and Hendriks,
KP and Mummenhoff, K and Lens, F and Pryer, KM and Bailey,
CD},
Title = {A Hyb-Seq phylogeny of Boechera and related genera using a
combination of Angiosperms353 and Brassicaceae-specific bait
sets.},
Journal = {American journal of botany},
Volume = {110},
Number = {10},
Pages = {e16226},
Year = {2023},
Month = {October},
url = {http://dx.doi.org/10.1002/ajb2.16226},
Abstract = {<h4>Premise</h4>Although Boechera (Boechereae, Brassicaceae)
has become a plant model system for both ecological genomics
and evolutionary biology, all previous phylogenetic studies
have had limited success in resolving species relationships
within the genus. The recent effective application of
sequence data from target enrichment approaches to resolve
the evolutionary relationships of several other challenging
plant groups prompted us to investigate their usefulness in
Boechera and Boechereae.<h4>Methods</h4>To resolve the
phylogeny of Boechera and closely related genera, we
utilized the Hybpiper pipeline to analyze two combined bait
sets: Angiosperms353, with broad applicability across
flowering plants; and a Brassicaceae-specific bait set
designed for use in the mustard family. Relationships for
101 samples representing 81 currently recognized species
were inferred from a total of 1114 low-copy nuclear genes
using both supermatrix and species coalescence
methods.<h4>Results</h4>Our analyses resulted in a
well-resolved and highly supported phylogeny of the tribe
Boechereae. Boechereae is divided into two major clades, one
comprising all western North American species of Boechera,
the other encompassing the eight other genera of the tribe.
Our understanding of relationships within Boechera is
enhanced by the recognition of three core clades that are
further subdivided into robust regional species
complexes.<h4>Conclusions</h4>This study presents the first
broadly sampled, well-resolved phylogeny for most known
sexual diploid Boechera. This effort provides the foundation
for a new phylogenetically informed taxonomy of Boechera
that is crucial for its continued use as a model
system.},
Doi = {10.1002/ajb2.16226},
Key = {fds373350}
}
@article{fds372242,
Author = {Hay, NM and Akinwuntan, JV and Cai, V and Windham, MD and Pryer,
KM},
Title = {Exploring Past and Future Distributions of the Rare
Appalachian Oak Fern Using MaxEnt Modeling},
Journal = {American Fern Journal},
Volume = {113},
Number = {2},
Pages = {109-125},
Year = {2023},
Month = {June},
url = {http://dx.doi.org/10.1640/0002-8444-113.2.109},
Abstract = {Abstract . Anthropogenic climate change is projected to have
an especially negative impact on the survival of plants that
are dependent on limited microclimatic refugia or that
already reside at their climatic extreme. Gymnocarpium
appalachianum is a narrowly endemic fern restricted to cold
mountaintops and algific vents in the central and southern
Appalachian region of eastern North America. It is the much
rarer of the two documented diploid parents of the
circumboreal allotetraploid G. dryopteris - one of the most
widespread fern species on the planet. Gymnocarpium
appalachianum is a good case study for forecasting how
evolutionarily significant, but rare, species might survive
on a warming planet. We utilize an ecological niche modeling
approach (MaxEnt) to explore the projected distribution of
G. appalachianum under past (Last Glacial Maximum) and
future climate models. All known verified herbarium records
of G. appalachianum were georeferenced, for a total of 70
occurrence points. Nineteen standard bioclimatic variables
extracted from WorldClim were used to model near-current
climate projections; representative concentration pathways
(RCPs 2.6 and 8.5) were used for future climate projections
(2070). The temperature annual range, mean temperature of
warmest quarter, precipitation of driest month,
precipitation of coldest quarter, and mean diurnal range
were identified as the key variables for shaping the
distribution of G. appalachianum. An unanticipated result
from our analyses is that G. appalachianum has past and
current projected habitat suitability in Alaska. Because
this overlaps with the current range of G. disjunctum, the
other diploid parent of G. dryopteris, it suggests a
possible region of origin for this circumboreal tetraploid
descendent of G. appalachianum - a research avenue to be
pursued in the future. Our study envisions a dire fate for
G. appalachianum; its survival will likely require an urgent
contingency plan that includes human-mediated population
relocation to cooler, northern locations. Understanding the
long-term sustainability of narrowly endemic plants such as
G. appalachianum is critical in decisions about their
management and conservation.},
Doi = {10.1640/0002-8444-113.2.109},
Key = {fds372242}
}
@article{fds369759,
Author = {Windham, MD and Picard, KT and Pryer, KM},
Title = {An in-depth investigation of cryptic taxonomic diversity in
the rare endemic mustard Draba maguirei.},
Journal = {American journal of botany},
Volume = {110},
Number = {3},
Pages = {1-22},
Year = {2023},
Month = {March},
url = {http://dx.doi.org/10.1002/ajb2.16138},
Abstract = {<h4>Premise</h4>Previously published evidence suggests that
Draba maguirei, a mustard endemic to a few localities in the
Bear River, Wellsville, and Wasatch Mountains of northern
Utah, may represent a cryptic species complex rather than a
single species. Conservation concerns prompted an in-depth
systematic study of this taxon and its putative
relatives.<h4>Methods</h4>Sampling most known populations of
D. maguirei s.l. (D. maguirei var. maguirei and D. maguirei
var. burkei), we integrate data from geography, ecology,
morphology, cytogenetics and pollen, enzyme electrophoresis,
and the phylogenetic analysis of nuclear internal
transcribed spacer sequences to explore potential taxonomic
diversity in the species complex.<h4>Results</h4>Draba
maguirei var. burkei is shown here to be a distinct species
(D. burkei) most closely related to D. globosa, rather than
to D. maguirei. Within D. maguirei s.s., the northern (high
elevation) and southern (low elevation) population clusters
are genetically isolated and morphologically
distinguishable, leading to the recognition here of the
southern taxon as D. maguirei subsp. stonei.<h4>Conclusions</h4>Our
study reveals that plants traditionally assigned to D.
maguirei comprise three genetically divergent lineages (D.
burkei and two newly recognized subspecies of D. maguirei),
each exhibiting a different chromosome number and occupying
a discrete portion of the geographic range. Although
previously overlooked and underappreciated taxonomically,
the three taxa are morphologically recognizable based on the
distribution and types of trichomes present on the leaves,
stems, and fruit. Our clarification of the diversity and
distribution of these taxa provides an improved framework
for conservation efforts.},
Doi = {10.1002/ajb2.16138},
Key = {fds369759}
}
@article{fds369760,
Author = {Windham, MD and Picard, KT and Pryer, KM},
Title = {Myriopteris grusziae: A New Species from Texas and Oklahoma
Segregated from the Chihuahuan Desert Taxon M. scabra
(Pteridaceae)},
Journal = {Systematic botany},
Volume = {47},
Number = {3},
Pages = {876-886},
Publisher = {American Society of Plant Taxonomists},
Year = {2022},
Month = {September},
url = {http://dx.doi.org/10.1600/036364422x16573022073590},
Abstract = {Myriopteris scabra (until recently called Cheilanthes
horridula) is a xeric-adapted fern species, endemic to the
southwestern United States and northern Mexico. It is one of
the most recognizable ferns in North America due to the
unusual nature of the indument present on its adaxial leaf
surfaces. This consists of rigid, multicellular trichomes
with glassy, needle-like apices and compact conical bodies
that are partially embedded in the leaf surface to form
swollen, pustulate bases. Despite the seemingly distinctive
nature of M. scabra, published chromosome counts indicate
that collections assigned to this taxon encompass both
diploids (n = 29) and tetraploids (n = 58). Here we
investigate this case of cryptic diversity by integrating
data from cytogenetic and spore analyses, observations of
sporophyte morphology, and geographic distributions.
Myriopteris scabra s.l. is shown to comprise two genetically
disparate, morphologically recognizable taxa that exhibit
little or no geographic overlap. The tetraploid taxon is
described as a new species, M. grusziae, which completely
supplants diploid M. scabra in the northeastern portion of
its range (central Texas and south-central Oklahoma). This
presumed allotetraploid is most like M. scabra but differs
in having ultimate segments with adaxial trichomes that are
longer, more flexible, mostly linear, and superficially
attached. In addition, tetraploid M. grusziae has larger,
more abundant scales that largely conceal the dark,
sclerified leaf rachises, and it produces consistently
larger spores than diploid M. scabra. We hypothesize that M.
grusziae is an allotetraploid hybrid that acquired half of
its chromosomes from M. scabra. However, the identity of the
other diploid parent has yet to be resolved.},
Doi = {10.1600/036364422x16573022073590},
Key = {fds369760}
}
@article{fds363346,
Author = {Windham, MD and Huiet, L and Metzgar, JS and Ranker, TA and Yatskievych,
G and Haufler, CH and Pryer, KM},
Title = {Once more unto the breach, dear friends: Resolving the
origins and relationships of the Pellaea wrightiana hybrid
complex.},
Journal = {American journal of botany},
Volume = {109},
Number = {5},
Pages = {821-850},
Year = {2022},
Month = {May},
url = {http://dx.doi.org/10.1002/ajb2.1850},
Abstract = {<h4>Premise</h4>The taxonomic status of Wright's cliff brake
fern, Pellaea wrightiana, has been in dispute ever since it
was first described by Hooker in 1858. Previously published
evidence suggested that this "taxon" may represent a
polyploid complex rather than a single discrete species, a
hypothesis tested here using a multifaceted analytical
approach.<h4>Methods</h4>Data derived from cytogenetics,
spore analyses, leaf morphometrics, enzyme electrophoresis,
and phylogenetic analyses of plastid and nuclear DNA
sequences are used to elucidate the origin, relationships,
and taxonomic circumscription of P. wrightiana.<h4>Results</h4>Plants
traditionally assigned to this taxon represent three
distinct polyploids. The most widespread, P. wrightiana, is
a fertile allotetraploid that arose through hybridization
between two divergent diploid species, P. truncata and P.
ternifolia. Sterile triploids commonly identified as P.
wrightiana, were found to be backcross hybrids between this
fertile tetraploid and diploid P. truncata. Relatively
common across Arizona and New Mexico, they are here assigned
to P. ×wagneri hyb. nov. In addition, occasional sterile
tetraploid plants assigned to P. wrightiana are shown here
to be hybrids between the fertile allotetraploid and the
tetraploid P. ternifolia subsp. arizonica. These tetraploid
hybrids originated independently in two regions of parental
sympatry (southern Arizona and west Texas) and are here
assigned to P. ×gooddingii hyb. nov.<h4>Conclusions</h4>Weaving
together data from a diversity of taxonomic approaches, we
show that plants identified as P. wrightiana represent three
morphologically distinguishable polyploids that have arisen
through repeated hybridization events involving the
divergent sexual taxa P. ternifolia and P.
truncata.},
Doi = {10.1002/ajb2.1850},
Key = {fds363346}
}
@article{fds365576,
Author = {Windham, MD and Pryer, KM},
Title = {FIRST REPORT OF UTAH FRAGILE FERN (CYSTOPTERIS:
CYSTOPTERIDACEAE) FROM NEW MEXICO, AND NEW NOMENCLATURAL
COMBINATIONS IN CYSTOPTERIS TENNESEENSIS},
Journal = {Journal of the Botanical Research Institute of
Texas},
Volume = {16},
Number = {1},
Year = {2022},
Month = {January},
url = {http://dx.doi.org/10.17348/jbrit.v16.i1.1215},
Abstract = {Two recently analyzed collections of Cystopteris from New
Mexico represent the first records of Utah fragile fern for
the state. Our morphological reexamination of this taxon
reveals a single character (the thickness of lateral cell
walls in rhizome and petiole base scales) that consistently
distinguishes it from tetraploid Cystopteris tennesseensis.
Therefore, we propose the new combination C. tennesseensis
subsp. utahensis to accommodate these disjunct, tetraploid
populations of the southwestern United States. A second new
combination, C. tennesseensis subsp. laurentiana, is
provided for morphologically similar hexaploids from the
northeastern U.S. and southern Canada.},
Doi = {10.17348/jbrit.v16.i1.1215},
Key = {fds365576}
}
@article{fds365577,
Author = {Windham, MD and Pryer, KM and Allphin, L},
Title = {AN OVERVIEW OF NEW MEXICAN BOECHERA (BRASSICACEAE) INCLUDING
THREE NEW SPECIES AND THIRTEEN NEW NOMENCLATURAL
COMBINATIONS},
Journal = {Journal of the Botanical Research Institute of
Texas},
Volume = {16},
Number = {1},
Pages = {9-24},
Year = {2022},
Month = {January},
url = {http://dx.doi.org/10.17348/jbrit.v16.i1.1216},
Abstract = {To provide a nomenclatural foundation for the treatment of
Boechera in the soon-to-be-published Flora of New Mexico, we
here discuss the current taxonomic situation in the genus,
name three new species (B. austromontana, B.
pseudoconsanguinea, and B. quadrangulensis), provide new
combinations for B. kelseyana, B. thompsonii, and B. villosa
as subspecies of B. crandallii, and propose subspecific
names under B. perennans for nine taxa currently treated as
species.},
Doi = {10.17348/jbrit.v16.i1.1216},
Key = {fds365577}
}
@article{fds359722,
Author = {Heron, K and Windham, MD and Farrar, DR and Pryer,
KM},
Title = {Looking Back on 130 Years of Fern and Lycophyte Research in
Glacier National Park, Montana: A Modern Taxonomic
Account},
Journal = {American fern journal.},
Volume = {111},
Number = {4},
Pages = {223-250},
Publisher = {American Fern Society},
Year = {2021},
Month = {November},
url = {http://dx.doi.org/10.1640/0002-8444-111.4.223},
Abstract = {Glacier National Park encompasses over one million acres in
the mountains of northwestern Montana, along the United
States–Canada border. Our survey of online databases
indicates that the earliest extant fern and lycophyte
collections from this area were taken by Robert S. Williams
in 1892. In the summer of 1919, Paul C. Standley, a botanist
with the United States National Museum, conducted a survey
of the flora of the newly created Park and recorded 39
species of ferns and lycophytes. In 2002, a revised flora
for the Park by Peter Lesica increased this number to 61.
Here we summarize 130 years of collections-based research on
the ferns and lycophytes of Glacier National Park,
documenting how our understanding of the flora has changed
through time. In the summer of 2019, the lead author
conducted a field survey to relocate as many ferns and
lycophytes as possible within park boundaries. In parallel,
we scoured herbarium online portals and databases for
high-resolution digitized specimen images to confirm or
refute historical vouchers of ferns and lycophytes collected
from the Park. In a few cases, specimen loans were requested
from herbaria to confirm our determinations. The results
from our combined field and online herbarium studies are
presented here. Of the 61 taxa recognized by Lesica in 2002,
we were able to confirm all but seven. In sum, we recognize
here a total of 71 fern and lycophyte taxa for the Park.
Most previously unreported taxa belong to Botrychium, a
genus that has seen a flurry of recent taxonomic work by
co-author Farrar and collaborators. These new data are
presented here together with updated nomenclature and
discussion to provide a current taxonomic account of the
fourteen fern and lycophyte families known to occur in
Glacier National Park. We anticipate this study will provide
a useful foundation for further investigations in the
Park.},
Doi = {10.1640/0002-8444-111.4.223},
Key = {fds359722}
}
@article{fds359082,
Author = {Sosa, K and Pryer, KM and Huiet, L and Yatskievych, G and Windham,
MD},
Title = {Cheilanthes ecuadorensis: A New Species of Cheilanthes s. s.
(Pteridaceae) from Northern South America},
Journal = {Systematic botany},
Volume = {46},
Number = {2},
Pages = {249-259},
Year = {2021},
Month = {August},
url = {http://dx.doi.org/10.1600/036364421x16231782047280},
Abstract = {Ongoing research on the taxonomically complex genus
Cheilanthes (Pteridaceae; Cheilanthoideae) has resulted in
the identification of a new species from Loja Province in
Ecuador, Cheilanthes ecuadorensis, described and illustrated
herein. Originally collected in 1988 and identified as C.
cf. rufopunctata, C. ecuadorensis is clearly distinct from
that species in having pubescent adaxial blade surfaces and
narrow, poorly-differentiated false indusia (rather than the
glabrous adaxial surfaces and wide false indusia of C.
rufopunctata). Among the South American species currently
included in Cheilanthes, C. ecuadorensis is superficially
most similar to C. pilosa. However, our molecular
phylogenetic analyses indicate that C. ecuadorensis is
sister to C. micropteris, the morphologically disparate
generitype of Cheilanthes. Here we examine the phylogenetic
relationships, morphology, cytogenetics, and geography of
these four South American Cheilanthes species in a study
that, once again, highlights the importance of herbaria in
the process of new species discovery.},
Doi = {10.1600/036364421x16231782047280},
Key = {fds359082}
}
@article{fds356426,
Author = {Fauskee, BD and Sigel, EM and Pryer, KM and Grusz,
AL},
Title = {Variation in frequency of plastid RNA editing within
Adiantum implies rapid evolution in fern
plastomes.},
Journal = {American journal of botany},
Volume = {108},
Number = {5},
Pages = {820-827},
Year = {2021},
Month = {May},
url = {http://dx.doi.org/10.1002/ajb2.1649},
Abstract = {<h4>Premise</h4>Recent studies of plant RNA editing have
demonstrated that the number of editing sites can vary
widely among large taxonomic groups (orders, families). Yet,
very little is known about intrageneric variation in
frequency of plant RNA editing, and no study has been
conducted in ferns.<h4>Methods</h4>We determined plastid
RNA-editing counts for two species of Adiantum
(Pteridaceae), A. shastense and A. aleuticum, by
implementing a pipeline that integrated read-mapping and
SNP-calling software to identify RNA-editing sites. We then
compared the edits found in A. aleuticum and A. shastense
with previously published edits from A. capillus-veneris by
generating alignments for each plastid gene.<h4>Results</h4>We
found direct evidence for 505 plastid RNA-editing sites in
A. aleuticum and 509 in A. shastense, compared with 350
sites in A. capillus-veneris. We observed striking variation
in the number and location of the RNA-editing sites among
the three species, with reverse (U-to-C) editing sites
showing a higher degree of conservation than forward
(C-to-U) sites. Additionally, sites involving start and stop
codons were highly conserved.<h4>Conclusions</h4>Variation
in the frequency of RNA editing within Adiantum implies that
RNA-editing sites can be rapidly gained or lost throughout
evolution. However, varying degrees of conservation between
both C-to-U and U-to-C sites and sites in start or stop
codons, versus other codons, hints at the likely independent
origin of both types of edits and a potential selective
advantage conferred by RNA editing.},
Doi = {10.1002/ajb2.1649},
Key = {fds356426}
}
@article{fds355319,
Author = {Grusz, AL and Windham, MD and Picard, KT and Pryer, KM and Schuettpelz,
E and Haufler, CH},
Title = {A drought-driven model for the evolution of obligate
apomixis in ferns: evidence from pellaeids
(Pteridaceae).},
Journal = {American journal of botany},
Volume = {108},
Number = {2},
Pages = {263-283},
Year = {2021},
Month = {February},
url = {http://dx.doi.org/10.1002/ajb2.1611},
Abstract = {<h4>Premise</h4>Xeric environments impose major constraints
on the fern life cycle, yet many lineages overcome these
limitations by evolving apomixis. Here, we synthesize
studies of apomixis in ferns and present an evidence-based
model for the evolution and establishment of this
reproductive strategy, focusing on genetic and environmental
factors associated with its two defining traits: the
production of "unreduced" spores (n = 2n) and the initiation
of sporophytes from gametophyte tissue (i.e., diplospory and
apogamy, respectively).<h4>Methods</h4>We evaluated existing
literature in light of the hypothesis that abiotic
characteristics of desert environments (e.g., extreme
diurnal temperature fluctuations, high light intensity, and
water limitation) drive the evolution of obligate apomixis.
Pellaeid ferns (Cheilanthoideae: Pteridaceae) were examined
in detail, as an illustrative example. We reconstructed a
plastid (rbcL, trnG-trnR, atpA) phylogeny for the clade and
mapped reproductive mode (sexual versus apomictic) and
ploidy across the resulting tree.<h4>Results</h4>Our
six-stage model for the evolution of obligate apomixis in
ferns emphasizes the role played by drought and associated
abiotic conditions in the establishment of this reproductive
approach. Furthermore, our updated phylogeny of pellaeid
ferns reveals repeated origins of obligate apomixis and
shows an increase in the frequency of apomixis, and rarity
of sexual reproduction, among taxa inhabiting increasingly
dry North American deserts.<h4>Conclusions</h4>Our findings
reinforce aspects of other evolutionary, physiological,
developmental, and omics-based studies, indicating a strong
association between abiotic factors and the establishment of
obligate apomixis in ferns. Water limitation, in particular,
appears critical to establishment of this reproductive
mode.},
Doi = {10.1002/ajb2.1611},
Key = {fds355319}
}
@article{fds349226,
Author = {Kao, T and Rothfels, CJ and Melgoza‐Castillo, A and Pryer, KM and Windham, MD},
Title = {Infraspecific diversification of the star cloak fern
(Notholaena standleyi) in the deserts of the United States
and Mexico},
Journal = {American Journal of Botany},
Volume = {107},
Number = {4},
Pages = {658-675},
Year = {2020},
url = {http://dx.doi.org/10.1002/ajb2.1461},
Abstract = {PREMISE:Not all ferns grow in moist and shaded habitats. One
well-known example is Notholaena standleyi, a species that
thrives in deserts of the southwestern United States and
Mexico. This species exhibits several "chemotypes" that
differ in farina (flavonoid exudates) color and chemistry.
By integrating data from molecular phylogenetics, cytology,
biochemistry, and biogeography, we circumscribed the major
evolutionary lineages within N. standleyi and reconstructed
their diversification histories. METHODS:Forty-eight samples
were selected from across the geographic distribution of N.
standleyi. Phylogenetic relationships were inferred using
four plastid and five nuclear markers. Ploidy levels were
inferred using spore sizes calibrated by chromosome counts,
and farina chemistry was compared using thin-layer
chromatography. RESULTS:Four clades are recognized, three of
which roughly correspond to previously recognized
chemotypes. The diploid clades G and Y are found in the
Sonoran and Chihuahuan deserts, respectively; they are
estimated to have diverged in the Pleistocene, congruent
with the postulated timing of climatological events
separating these two deserts. Clade P/YG is tetraploid and
partially overlaps the distribution of clade Y in the
eastern Chihuahuan Desert. It is apparently confined to
limestone, a geologic substrate rarely occupied by members
of the other clades. The cryptic (C) clade, a diploid group
known only from southern Mexico and highly disjunct from the
other three clades, is newly recognized here.
CONCLUSIONS:Our results reveal a complex intraspecific
diversification history of N. standleyi, traceable to a
variety of evolutionary drivers including classic allopatry,
parapatry with or without changes in geologic substrate, and
sympatric divergence through polyploidization.},
Doi = {10.1002/ajb2.1461},
Key = {fds349226}
}
@article{fds349481,
Author = {Windham, MD and Pryer, KM and Poindexter, DB and Li, F and Rothfels, CJ and Beck, JB},
Title = {A step‐by‐step protocol for meiotic chromosome counts in
flowering plants: A powerful and economical technique
revisited},
Journal = {Applications in Plant Sciences},
Volume = {8},
Number = {4},
Pages = {e11342},
Publisher = {John Wiley & Sons, Inc.},
Year = {2020},
url = {http://dx.doi.org/10.1002/aps3.11342},
Abstract = {<h4>Premise</h4>Counting chromosomes is a fundamental
botanical technique, yet it is often intimidating and
increasingly sidestepped. Once mastered, the basic protocol
can be applied to a broad range of taxa and research
questions. It also reveals an aspect of the plant genome
that is accessible with only the most basic of
resources-access to a microscope with 1000× magnification
is the most limiting factor.<h4>Methods and results</h4>Here
we provide a detailed protocol for choosing, staining, and
squashing angiosperm pollen mother cells. The protocol is
supplemented by figures and two demonstration
videos.<h4>Conclusions</h4>The protocol we provide will
hopefully demystify and reinvigorate a powerful and once
commonplace botanical technique that is available to
researchers regardless of their location and
resources.},
Doi = {10.1002/aps3.11342},
Key = {fds349481}
}
@article{fds350496,
Author = {Pryer, KM and Tomasi, C and Wang, X and Meineke, EK and Windham,
MD},
Title = {Using computer vision on herbarium specimen images to
discriminate among closely related horsetails
(Equisetum)},
Journal = {Applications in plant sciences},
Volume = {8},
Number = {6},
Pages = {e11372},
Year = {2020},
url = {http://dx.doi.org/10.1002/aps3.11372},
Abstract = {Premise:Equisetum is a distinctive vascular plant genus with
15 extant species worldwide. Species identification is
complicated by morphological plasticity and frequent
hybridization events, leading to a disproportionately high
number of misidentified specimens. These may be correctly
identified by applying appropriate computer vision tools.
Methods:We hypothesize that aerial stem nodes can provide
enough information to distinguish among Equisetum hyemale,
E. laevigatum, and E . ×ferrissii, the latter being a
hybrid between the other two. An object detector was trained
to find nodes on a given image and to distinguish E. hyemale
nodes from those of E. laevigatum. A classifier then took
statistics from the detection results and classified the
given image into one of the three taxa. Both detector and
classifier were trained and tested on expert manually
annotated images. Results:In our exploratory test set of 30
images, our detector/classifier combination identified all
10 E. laevigatum images correctly, as well as nine out of 10
E. hyemale images, and eight out of 10 E. ×ferrissii
images, for a 90% classification accuracy. Discussion:Our
results support the notion that computer vision may help
with the identification of herbarium specimens once enough
manual annotations become available.},
Doi = {10.1002/aps3.11372},
Key = {fds350496}
}
@article{fds350495,
Author = {Meineke, EK and Tomasi, C and Yuan, S and Pryer, KM},
Title = {Applying machine learning to investigate long‐term
insect–plant interactions preserved on digitized herbarium
specimens},
Journal = {Applications in plant sciences},
Volume = {8},
Number = {6},
Pages = {e11369},
Year = {2020},
url = {http://dx.doi.org/10.1002/aps3.11369},
Abstract = {<h4>Premise</h4>Despite the economic significance of insect
damage to plants (i.e., herbivory), long-term data
documenting changes in herbivory are limited. Millions of
pressed plant specimens are now available online and can be
used to collect big data on plant-insect interactions during
the Anthropocene.<h4>Methods</h4>We initiated development of
machine learning methods to automate extraction of herbivory
data from herbarium specimens by training an insect damage
detector and a damage type classifier on two distantly
related plant species (<i>Quercus bicolor</i> and <i>Onoclea
sensibilis</i>). We experimented with (1) classifying six
types of herbivory and two control categories of undamaged
leaf, and (2) detecting two of the damage categories for
which several hundred annotations were available.<h4>Results</h4>Damage
detection results were mixed, with a mean average precision
of 45% in the simultaneous detection and classification of
two types of damage. However, damage classification on
hand-drawn boxes identified the correct type of herbivory
81.5% of the time in eight categories. The damage classifier
was accurate for categories with 100 or more test
samples.<h4>Discussion</h4>These tools are a promising first
step for the automation of herbivory data collection. We
describe ongoing efforts to increase the accuracy of these
models, allowing researchers to extract similar data and
apply them to biological hypotheses.},
Doi = {10.1002/aps3.11369},
Key = {fds350495}
}
@article{fds343683,
Author = {Yang, EJ and Yoo, CY and Liu, J and Wang, H and Cao, J and Li, F and Pryer,
KM and Sun, T and Weigel, D and Zhou, P},
Title = {NCP activates chloroplast transcription by controlling
phytochrome-dependent dual nuclear and plastidial
switches},
Journal = {Nature communications},
Volume = {10},
Number = {1},
Pages = {1-13},
Publisher = {Nature Publishing Group},
Year = {2019},
url = {http://dx.doi.org/10.1038/s41467-019-10517-1},
Abstract = {Phytochromes initiate chloroplast biogenesis by activating
genes encoding the photosynthetic apparatus, including
photosynthesis-associated plastid-encoded genes (PhAPGs).
PhAPGs are transcribed by a bacterial-type RNA polymerase
(PEP), but how phytochromes in the nucleus activate
chloroplast gene expression remains enigmatic. We report
here a forward genetic screen in Arabidopsis that identified
NUCLEAR CONTROL OF PEP ACTIVITY (NCP) as a necessary
component of phytochrome signaling for PhAPG activation. NCP
is dual-targeted to plastids and the nucleus. While nuclear
NCP mediates the degradation of two repressors of
chloroplast biogenesis, PIF1 and PIF3, NCP in plastids
promotes the assembly of the PEP complex for PhAPG
transcription. NCP and its paralog RCB are non-catalytic
thioredoxin-like proteins that diverged in seed plants to
adopt nonredundant functions in phytochrome signaling. These
results support a model in which phytochromes control PhAPG
expression through light-dependent double nuclear and
plastidial switches that are linked by evolutionarily
conserved and dual-localized regulatory proteins.},
Doi = {10.1038/s41467-019-10517-1},
Key = {fds343683}
}
@article{fds341364,
Author = {Eily, AN and Pryer, KM and Li, F},
Title = {A first glimpse at genes important to the Azolla–Nostoc
symbiosis},
Journal = {Symbiosis},
Volume = {78},
Number = {2},
Pages = {149-162},
Publisher = {Springer Netherlands},
Year = {2019},
url = {http://dx.doi.org/10.1007/s13199-019-00599-2},
Abstract = {Azolla is a small genus of diminutive aquatic ferns with a
surprisingly vast potential to benefit the environment and
agriculture, as well as to provide insight into the
evolution of plant-cyanobacterial symbioses. This capability
is derived from the unique relationship Azolla spp. have
with their obligate, nitrogen-fixing cyanobacterial
symbiont, Nostoc azollae, that resides in their leaves.
Although previous work has specified the importance of the
exchange of ammonium and sucrose metabolites between these
two partners, we have yet to determine the underlying
molecular mechanisms that make this symbiosis so successful.
The newly sequenced and annotated reference genome of Azolla
filiculoides has allowed us to investigate gene expression
profiles of A. filiculoides—both with and without its
obligate cyanobiont, N. azollae—revealing genes
potentially essential to the Azolla-Nostoc symbiosis. We
observed the absence of differentially expressed glutamine
synthetase (GS) and glutamate synthase (GOGAT) genes,
leading to questions about how A. filiculoides regulates the
machinery it uses for nitrogen assimilation. Ushering A.
filiculoides into the era of transcriptomics sets the stage
to truly begin to understand the uniqueness of the
Azolla-Nostoc symbiosis.},
Doi = {10.1007/s13199-019-00599-2},
Key = {fds341364}
}
@article{fds343471,
Author = {Kao, T and Pryer, KM and Freund, FD and Windham, MD and Rothfels,
CJ},
Title = {Low-copy nuclear sequence data confirm complex patterns of
farina evolution in notholaenid ferns (Pteridaceae)},
Journal = {Molecular phylogenetics and evolution},
Volume = {138},
Pages = {139-155},
Publisher = {Academic Press},
Year = {2019},
url = {http://dx.doi.org/10.1016/j.ympev.2019.05.016},
Abstract = {Notholaenids are an unusual group of ferns that have adapted
to, and diversified within, the deserts of Mexico and the
southwestern United States. With approximately 40 species,
this group is noted for being desiccation-tolerant and
having "farina"-powdery exudates of lipophilic flavonoid
aglycones-that occur on both the gametophytic and
sporophytic phases of their life cycle. The most recent
circumscription of notholaenids based on plastid markers
surprisingly suggests that several morphological characters,
including the expression of farina, are homoplasious. In a
striking case of convergence, Notholaena standleyi appears
to be distantly related to core Notholaena, with several
taxa not before associated with Notholaena nested between
them. Such conflicts can be due to morphological homoplasy
resulting from adaptive convergence or, alternatively, the
plastid phylogeny itself might be misleading, diverging from
the true species tree due to incomplete lineage sorting,
hybridization, or other factors. In this study, we present a
species phylogeny for notholaenid ferns, using four low-copy
nuclear loci and concatenated data from three plastid loci.
A total of 61 individuals (49 notholaenids and 12 outgroup
taxa) were sampled, including 31 out of 37 recognized
notholaenid species. The homeologous/allelic nuclear
sequences were retrieved using PacBio sequencing and the
PURC bioinformatics pipeline. Each dataset was first
analyzed individually using maximum likelihood and Bayesian
inference, and the species phylogeny was inferred using
*BEAST. Although we observed several incongruences between
the nuclear and plastid phylogenies, our principal results
are broadly congruent with previous inferences based on
plastid data. By mapping the presence of farina and their
biochemical constitutions on our consensus phylogenetic
tree, we confirmed that the characters are indeed
homoplastic and have complex evolutionary histories.
Hybridization among recognized species of the notholaenid
clade appears to be relatively rare compared to that
observed in other well-studied fern genera.},
Doi = {10.1016/j.ympev.2019.05.016},
Key = {fds343471}
}
@article{fds346477,
Author = {George, LO and Pryer, KM and Kao, T and Huiet, L and Windham,
MD},
Title = {Baja: A New Monospecific Genus Segregated from Cheilanthes
sl (Pteridaceae)},
Journal = {Systematic Botany},
Volume = {44},
Number = {3},
Pages = {471-482},
Publisher = {American Society of Plant Taxonomists},
Year = {2019},
url = {http://dx.doi.org/10.1600/036364419x15620113920536},
Abstract = {The phylogenetic position of Cheilanthes brandegeei, a fern
endemic to the Baja California Peninsula of Mexico, was
investigated using three plastid markers (atpA, rbcL,
trnG-R) and comparative morphology. Here we present robust
evidence for the recognition of C. brandegeei as a member of
the bommeriids, the sister clade to all other cheilanthoid
ferns, and evidence that it is sister to all Bommeria
species within that clade. Because of its distinctive
morphology within the bommeriid clade (pinnate leaf
architecture, well-developed pseudoindusium, and narrow,
concolorous red-brown rhizome scales), here we propose the
new genus Baja to accommodate it. Our results place Baja
brandegeei together with other taxa that have a distribution
in the Baja California Peninsula and mainland Mexico, rather
than with hypothesized congeners in South America and
Africa. Morphological characters traditionally used to
classify this species as a Cheilanthes (patterns of
sporangial distribution, presence of a well-developed
pseudoindusium, and fractiferous petioles) are extensively
homoplasious across cheilanthoids. We identify three
characters that unite the newly expanded bommeriid clade:
leaf indument of acicular trichomes, reticulate-cristate
perispore morphology, and lateral initiation of the
gametophyte meristem.},
Doi = {10.1600/036364419x15620113920536},
Key = {fds346477}
}
@article{fds346456,
Author = {Sigel, EM and Der, JP and Windham, MD and Pryer, KM},
Title = {Expression Level Dominance and Homeolog Expression Bias in
Recurrent Origins of the Allopolyploid Fern Polypodium
hesperium},
Journal = {American Fern Journal},
Volume = {109},
Number = {3},
Pages = {224-247},
Publisher = {The American Fern Society},
Year = {2019},
url = {http://dx.doi.org/10.1640/0002-8444-109.3.224},
Abstract = {Allopolyploidization is a common mode of speciation in ferns
with many taxa having formed recurrently from distinct
hybridization events between the same parent species. Each
hybridization event marks the union of divergent parental
gene copies, or homeologs, and the formation of an
independently derived lineage. Little is known about the
effects of recurrent origins on the genomic composition and
phenotypic variation of allopolyploid fern taxa. To begin to
address this knowledge gap, we investigated gene expression
patterns in two naturally formed, independently derived
lineages of the allotetraploid fern Polypodium hesperium
relative to its diploid progenitor species, Polypodium
amorphum and Polypodium glycyrrhiza. Using RNA-sequencing to
survey total gene expression levels for 19194 genes and
homeolog-specific expression for 1073 genes, we found that,
in general, gene expression in both lineages of P. hesperium
was biased toward P. amorphum—both by mirroring expression
levels of P. amorphum and preferentially expressing
homeologs derived from P. amorphum. However, we recovered
substantial expression variation between the two lineages at
the level of individual genes and among individual
specimens. Our results align with similar transcriptome
profile studies of angiosperms, suggesting that expression
in many allopolyploid plants reflects the dominance of a
specific parental subgenome, but that recurrent origins
impart substantial expression, or phenotypic, variation to
allopolyploid taxa.},
Doi = {10.1640/0002-8444-109.3.224},
Key = {fds346456}
}
@article{fds330472,
Author = {Dijkhuizen, LW and Brouwer, P and Bolhuis, H and Reichart, G and Koppers, N and Huettel, B and Bolger, AM and Li, F and Cheng, S and Liu,
X},
Title = {Is there foul play in the leaf pocket? The metagenome of
floating fern Azolla reveals endophytes that do not fix N2
but may denitrify},
Journal = {New Phytologist},
Volume = {217},
Number = {1},
Pages = {453-466},
Year = {2018},
url = {http://dx.doi.org/10.1111/nph.14843},
Abstract = {Dinitrogen fixation by Nostoc azollae residing in
specialized leaf pockets supports prolific growth of the
floating fern Azolla filiculoides. To evaluate contributions
by further microorganisms, the A. filiculoides microbiome
and nitrogen metabolism in bacteria persistently associated
with Azolla ferns were characterized. A metagenomic approach
was taken complemented by detection of N2 O released and
nitrogen isotope determinations of fern biomass. Ribosomal
RNA genes in sequenced DNA of natural ferns, their enriched
leaf pockets and water filtrate from the surrounding ditch
established that bacteria of A. filiculoides differed
entirely from surrounding water and revealed species of the
order Rhizobiales. Analyses of seven cultivated Azolla
species confirmed persistent association with Rhizobiales.
Two distinct nearly full-length Rhizobiales genomes were
identified in leaf-pocket-enriched samples from ditch grown
A. filiculoides. Their annotation revealed genes for
denitrification but not N2 -fixation. 15 N2 incorporation
was active in ferns with N. azollae but not in ferns
without. N2 O was not detectably released from
surface-sterilized ferns with the Rhizobiales. N2 -fixing
N. azollae, we conclude, dominated the microbiome of Azolla
ferns. The persistent but less abundant heterotrophic
Rhizobiales bacteria possibly contributed to lowering O2
levels in leaf pockets but did not release detectable
amounts of the strong greenhouse gas N2 O.},
Doi = {10.1111/nph.14843},
Key = {fds330472}
}
@article{fds336265,
Author = {Li, F and Brouwer, P and Carretero-Paulet, L and Cheng, S and De Vries,
J and Delaux, P and Eily, A and Koppers, N and Kuo, L and Li,
Z},
Title = {Fern genomes elucidate land plant evolution and
cyanobacterial symbioses},
Journal = {Nature plants},
Volume = {4},
Number = {7},
Pages = {460-472},
Publisher = {Nature Publishing Group},
Year = {2018},
url = {http://dx.doi.org/10.1038/s41477-018-0188-8},
Abstract = {Ferns are the closest sister group to all seed plants, yet
little is known about their genomes other than that they are
generally colossal. Here, we report on the genomes of Azolla
filiculoides and Salvinia cucullata (Salviniales) and
present evidence for episodic whole-genome duplication in
ferns-one at the base of 'core leptosporangiates' and one
specific to Azolla. One fern-specific gene that we
identified, recently shown to confer high insect resistance,
seems to have been derived from bacteria through horizontal
gene transfer. Azolla coexists in a unique symbiosis with
N<sub>2</sub>-fixing cyanobacteria, and we demonstrate a
clear pattern of cospeciation between the two partners.
Furthermore, the Azolla genome lacks genes that are common
to arbuscular mycorrhizal and root nodule symbioses, and we
identify several putative transporter genes specific to
Azolla-cyanobacterial symbiosis. These genomic resources
will help in exploring the biotechnological potential of
Azolla and address fundamental questions in the evolution of
plant life.},
Doi = {10.1038/s41477-018-0188-8},
Key = {fds336265}
}
@article{fds336266,
Author = {Huiet, L and Li, F and Kao, T and Prado, J and Smith, AR and Schuettpelz,
E and Pryeri, KM},
Title = {A worldwide phylogeny of Adiantum (Pteridaceae) reveals
remarkable convergent evolution in leaf blade
architecture},
Journal = {Taxon},
Volume = {67},
Number = {3},
Pages = {488-502},
Publisher = {WILEY},
Year = {2018},
url = {http://dx.doi.org/10.12705/673.3},
Abstract = {Adiantum is among the most distinctive and easily recognized
leptosporangiate fern genera. Despite encompassing an
astonishing range of leaf complexity, all species of
Adiantum share a unique character state not observed in
other ferns: sporangia borne directly on the reflexed leaf
margin or “false indusium” (pseudoindusium). The over
200 species of Adiantum span six continents and are nearly
all terrestrial. Here, we present one of the most
comprehensive phylogenies for any large (200+ spp.)
monophyletic, subcosmopolitan genus of ferns to date. We
build upon previous datasets, providing new data from four
plastid markers (rbcL, atpA, rpoA, chlN) for 146 taxa. All
sampled taxa can be unequivocally assigned to one of nine
robustly supported clades. Although some of these unite to
form larger, well-supported lineages, the backbone of our
phylogeny has several short branches and generally weak
support, making it difficult to accurately assess deep
relationships. Our maximum likelihood-based ancestral
character state reconstructions of leaf blade architecture
reveal remarkable convergent evolution across multiple
clades for nearly all leaf forms. A single unique
synapomorphy—leaves once-pinnate, usually with prolonged
rooting tips—defines the philippense clade. Although a
rare occurrence in Adiantum, simple leaves occur in three
distinct clades (davidii, philippense, peruvianum). Most
taxa have leaves that are more than once-pinnate, and only a
few of these (in the formosum and pedatum clades) exhibit
the distinct pseudopedate form. Distributional ranges for
each of the terminal taxa show that most species (75%) are
restricted to only one of six major biogeographical regions.
Forty-eight of our sampled species (nearly one-third) are
endemic to South America.},
Doi = {10.12705/673.3},
Key = {fds336266}
}
@article{fds336267,
Author = {Schuettpelz, E and Rouhan, G and Pryer, KM and Rothfels, CJ and Prado,
J and Sundue, MA and Windham, MD and Moran, RC and Smith,
AR},
Title = {Are there too many fern genera?},
Journal = {Taxon},
Volume = {67},
Number = {3},
Pages = {473-480},
Publisher = {WILEY},
Year = {2018},
url = {http://dx.doi.org/10.12705/673.1},
Doi = {10.12705/673.1},
Key = {fds336267}
}
@article{fds332387,
Author = {Song, M and Kuo, L and Huiet, L and Pryer, KM and Rothfels, CJ and Li,
F},
Title = {A novel chloroplast gene reported for flagellate
plants},
Journal = {American journal of botany},
Volume = {105},
Number = {1},
Pages = {117-121},
Year = {2018},
url = {http://dx.doi.org/10.1002/ajb2.1010},
Abstract = {PREMISE OF THE STUDY:Gene space in plant plastid genomes is
well characterized and annotated, yet we discovered an
unrecognized open reading frame (ORF) in the fern lineage
that is conserved across flagellate plants. METHODS:We
initially detected a putative uncharacterized ORF by the
existence of a highly conserved region between rps16 and
matK in a series of matK alignments of leptosporangiate
ferns. We mined available plastid genomes for this ORF,
which we now refer to as ycf94, to infer evolutionary
selection pressures and assist in functional prediction. To
further examine the transcription of ycf94, we assembled the
plastid genome and sequenced the transcriptome of the
leptosporangiate fern Adiantum shastense Huiet & A.R. Sm.
KEY RESULTS:The ycf94 predicted protein has a distinct
transmembrane domain but with no sequence homology to other
proteins with known function. The nonsynonymous/synonymous
substitution rate ratio of ycf94 is on par with other fern
plastid protein-encoding genes, and additional homologs can
be found in a few lycophyte, moss, hornwort, and liverwort
plastid genomes. Homologs of ycf94 were not found in seed
plants. In addition, we report a high level of RNA editing
for ycf94 transcripts-a hallmark of protein-coding genes in
fern plastomes. CONCLUSIONS:The degree of sequence
conservation, together with the presence of a distinct
transmembrane domain and RNA-editing sites, suggests that
ycf94 is a protein-coding gene of functional significance in
ferns and, potentially, bryophytes and lycophytes. However,
the origin and exact function of this gene require further
investigation.},
Doi = {10.1002/ajb2.1010},
Key = {fds332387}
}
@article{fds339280,
Author = {Sigel, EM and Schuettpelz, E and Pryer, KM and Der,
JP},
Title = {Overlapping patterns of gene expression between gametophyte
and sporophyte phases in the fern Polypodium amorphum
(Polypodiales)},
Journal = {Frontiers in plant science},
Volume = {9},
Pages = {1450},
Publisher = {Frontiers},
Year = {2018},
url = {http://dx.doi.org/10.3389/fpls.2018.01450},
Abstract = {Ferns are unique among land plants in having sporophyte and
gametophyte phases that are both free living and fully
independent. Here, we examine patterns of sporophytic and
gametophytic gene expression in the fern <i>Polypodium
amorphum</i>, a member of the homosporous polypod lineage
that comprises 80% of extant fern diversity, to assess how
expression of a common genome is partitioned between two
morphologically, ecologically, and nutritionally independent
phases. Using RNA-sequencing, we generated transcriptome
profiles for three replicates of paired samples of
sporophyte leaf tissue and whole gametophytes to identify
genes with significant differences in expression between the
two phases. We found a nearly 90% overlap in the identity
and expression levels of the genes expressed in both
sporophytes and gametophytes, with less than 3% of genes
uniquely expressed in either phase. We compare our results
to those from similar studies to establish how
phase-specific gene expression varies among major land plant
lineages. Notably, despite having greater similarity in the
identity of gene families shared between <i>P. amorphum</i>
and angiosperms, <i>P. amorphum</i> has phase-specific gene
expression profiles that are more like bryophytes and
lycophytes than seed plants. Our findings suggest that
shared patterns of phase-specific gene expression among
seed-free plants likely reflect having relatively large,
photosynthetic gametophytes (compared to the gametophytes of
seed plants that are highly reduced). Phylogenetic analyses
were used to further investigate the evolution of
phase-specific expression for the phototropin, terpene
synthase, and MADS-box gene families.},
Doi = {10.3389/fpls.2018.01450},
Key = {fds339280}
}
@article{fds322311,
Author = {Rothfels, CJ and Pryer, KM and Li, F},
Title = {Next‐generation polyploid phylogenetics: Rapid resolution
of hybrid polyploid complexes using PacBio single‐molecule
sequencing},
Journal = {New Phytologist},
Volume = {213},
Number = {1},
Pages = {413-429},
Year = {2017},
url = {http://dx.doi.org/10.1111/nph.14111},
Abstract = {Difficulties in generating nuclear data for polyploids have
impeded phylogenetic study of these groups. We describe a
high-throughput protocol and an associated bioinformatics
pipeline (Pipeline for Untangling Reticulate Complexes
(Purc)) that is able to generate these data quickly and
conveniently, and demonstrate its efficacy on accessions
from the fern family Cystopteridaceae. We conclude with a
demonstration of the downstream utility of these data by
inferring a multi-labeled species tree for a subset of our
accessions. We amplified four c. 1-kb-long nuclear loci and
sequenced them in a parallel-tagged amplicon sequencing
approach using the PacBio platform. Purc infers the final
sequences from the raw reads via an iterative approach that
corrects PCR and sequencing errors and removes PCR-mediated
recombinant sequences (chimeras). We generated data for all
gene copies (homeologs, paralogs, and segregating alleles)
present in each of three sets of 50 mostly polyploid
accessions, for four loci, in three PacBio runs (one run per
set). From the raw sequencing reads, Purc was able to
accurately infer the underlying sequences. This approach
makes it easy and economical to study the phylogenetics of
polyploids, and, in conjunction with recent analytical
advances, facilitates investigation of broad patterns of
polyploid evolution.},
Doi = {10.1111/nph.14111},
Key = {fds322311}
}
@article{fds323623,
Author = {Hirai, RY and Schuettpelz, E and Huiet, L and Pryer, KM and Smith, AR and Prado, J},
Title = {Phylogeny and relationships of the neotropical Adiantum
raddianum group (Pteridaceae)},
Journal = {Taxon},
Volume = {65},
Number = {6},
Pages = {1225-1235},
Publisher = {WILEY},
Year = {2016},
url = {http://dx.doi.org/10.12705/656.1},
Abstract = {With more than 200 species, the maidenhair fern genus
Adiantum is among the top ten most diverse fern genera.
Adiantum is pantropical in distribution and, due to the
presence of a unique synapomorphy (sporangia borne on
indusia rather than laminae), perhaps the most easily
recognized fern genus. Many of its members, including
numerous cultivars derived from A. raddianum, are grown as
ornamentals. Because of its size, a comprehensive taxonomic
study of Adiantum is difficult and the genus is perhaps
better approached through a series of narrower studies.
Here, we focus specifically on A. raddianum and putative
allies. We find a newly defined A. raddianum group to be
strongly supported as monophyletic and segregated from other
maidenhair ferns on the basis of genetic as well as
morphological characteristics. Bayesian inference and
maximum likelihood analyses of plastid atpA, chlL, chlN,
rbcL, and rpoA sequences support the A raddianum clade as
sister to A poiretii and its allies. We identify
round-reniform indusia to be a characteristic of the
A.raddianum group (vs. lunate in the A.poiretii group).
Additionally, we find species in the Apoiretii group to
differ in having a unique 66 nucleotide deletion in our chlN
gene alignment. The neotropical Araddianum group comprises
at least 17 species (14 studied here), some widely
distributed; one was recently described (A.
alan-smithii).},
Doi = {10.12705/656.1},
Key = {fds323623}
}
@article{fds324241,
Author = {Haufler, CH and Pryer, KM and Schuettpelz, E and Sessa, EB and Farrar,
DR and Moran, R and Schneller, JJ and Watkins Jr and JE and Windham,
MD},
Title = {Sex and the single gametophyte: Revising the homosporous
vascular plant life cycle in light of contemporary
research},
Journal = {BioScience},
Volume = {66},
Number = {11},
Pages = {928-937},
Publisher = {Oxford University Press},
Year = {2016},
url = {http://dx.doi.org/10.1093/biosci/biw108},
Abstract = {Homosporous vascular plants are typically depicted as
extreme inbreeders, with bisexual gametophytes that produce
strictly homozygous sporophytes. This view is promulgated in
textbook life cycles despite ample evidence that natural
populations of most species regularly outcross. We review
research on a variety of mechanisms, including genetic load,
asynchronous production of eggs and sperm, and pheromonal
control of gamete production, that actively promote
heterozygosity in ferns and lycophytes. Evolution of the
land plants cannot be reconstructed without accurate
depictions of the unique life cycle that has helped make
ferns the second most diverse lineage of vascular plants on
Earth. With revised illustrations and definitions, we
provide scientists, educators, and students with a
contemporary understanding of fern and lycophyte
reproduction, revealing them as evolutionarily dynamic and
exploiting a wide range of mating systems.},
Doi = {10.1093/biosci/biw108},
Key = {fds324241}
}
@article{fds324242,
Author = {Li, F and Kuo, L and Pryer, KM and Rothfels, CJ},
Title = {Genes translocated into the plastid inverted repeat show
decelerated substitution rates and elevated GC
content},
Journal = {Genome Biology and Evolution},
Volume = {8},
Number = {8},
Pages = {2452-2458},
Publisher = {Oxford University Press},
Year = {2016},
url = {http://dx.doi.org/10.1093/gbe/evw167},
Abstract = {Plant chloroplast genomes (plastomes) are characterized by
an inverted repeat (IR) region and two larger single copy
(SC) regions. Patterns of molecular evolution in the IR and
SC regions differ, most notably by a reduced rate of
nucleotide substitution in the IR compared to the SC region.
In addition, the organization and structure of plastomes is
fluid, and rearrangements through time have repeatedly
shuffled genes into and out of the IR, providing recurrent
natural experiments on how chloroplast genome structure can
impact rates and patterns of molecular evolution. Here we
examine four loci (psbA, ycf2, rps7, and rps12 exon 2-3)
that were translocated from the SC into the IR during fern
evolution. We use a model-based method, within a
phylogenetic context, to test for substitution rate shifts.
All four loci show a significant, 2- to 3-fold deceleration
in their substitution rate following translocation into the
IR, a phenomenon not observed in any other, nontranslocated
plastid genes. Also, we show that after translocation, the
GC content of the third codon position and of the noncoding
regions is significantly increased, implying that gene
conversion within the IR is GC-biased. Taken together, our
results suggest that the IR region not only reduces
substitution rates, but also impacts nucleotide composition.
This finding highlights a potential vulnerability of
correlating substitution rate heterogeneity with organismal
life history traits without knowledge of the underlying
genome structure.},
Doi = {10.1093/gbe/evw167},
Key = {fds324242}
}
@article{fds322312,
Author = {Schuettpelz, E and Chen, C and Kessler, M and Pinson, JB and Johnson, G and Davila, A and Cochran, AT and Huiet, L and Pryer,
KM},
Title = {A revised generic classification of vittarioid ferns
(Pteridaceae) based on molecular, micromorphological, and
geographic data},
Journal = {Taxon},
Volume = {65},
Number = {4},
Pages = {708-722},
Publisher = {WILEY},
Year = {2016},
url = {http://dx.doi.org/10.12705/654.2},
Abstract = {Vittarioid ferns compose a well-supported clade of 100-130
species of highly simplified epiphytes in the family
Pteridaceae. Generic circumscriptions within the vittarioid
clade were among the first in ferns to be evaluated and
revised based on molecular phylogenetic data. Initial
analyses of rbcL sequences revealed strong geographic
structure and demonstrated that the two largest vittarioid
genera, as then defined, each had phylogenetically distinct
American and Old World components. The results of subsequent
studies that included as many as 36 individuals of 33
species, but still relied on a single gene, were generally
consistent with the early findings. Here, we build upon the
previous datasets, incorporating many more samples (138
individuals representing 72 species) and additional plastid
markers (atpA, chlN, rbcL, rpoA). Analysis of our larger
dataset serves to better characterize known lineages,
reveals new lineages, and ultimately uncovers an underlying
geographic signal that is even stronger than was previously
appreciated. In our revised generic classification, we
recognize a total of eleven vittarioid genera. Each genus,
including the new genus Antrophyopsis (Benedict) Schuettp.,
stat. nov., is readily diagnosable based on morphology, with
micromorphological characters related to soral paraphyses
and spores complementing more obvious features such as
venation and the distribution of sporangia. A key to the
currently recognized vittarioid genera, brief generic
descriptions, and five new species combinations are
provided.},
Doi = {10.12705/654.2},
Key = {fds322312}
}
@article{fds322313,
Author = {Pryer, KM and Huiet, L and Li, F and Rothfels, CJ and Schuettpelz,
E},
Title = {Maidenhair ferns, Adiantum, are indeed monophyletic and
sister to shoestring ferns, vittarioids (Pteridaceae)},
Journal = {Systematic Botany},
Volume = {41},
Number = {1},
Pages = {17-23},
Publisher = {American Society of Plant Taxonomists},
Year = {2016},
url = {http://dx.doi.org/10.1600/036364416x690660},
Abstract = {Across the tree of life, molecular phylogenetic studies
often reveal surprising relationships between taxa with
radically different morphologies that have long obscured
their close affiliations. A spectacular botanical example is
Rafflesia, a holoparasite that produces the largest flowers
in the world, but that evolved from tiny-flowered ancestors
within the Euphorbiaceae. Outside of parasitic lineages,
such abrupt transformations are rarely seen. One exception
involves the “maidenhair ferns” (Adiantum), which are
quintessential ferns: beautifully dissected, terrestrial,
and shade loving. The closely related “shoestring ferns”
(vittarioids), in contrast, have an extremely simplified
morphology, are canopy-dwelling epiphytes, and exhibit
greatly accelerated rates of molecular evolution. While
Adiantum and the vittarioids together have been shown to
form a robust monophyletic group (adiantoids), there remain
unanswered questions regarding the monophyly of Adiantum and
the evolutionary history of the vittarioids. Here we review
recent phylogenetic evidence suggesting support for the
monophyly of Adiantum, and analyze new plastid data to
confirm this result. We find that Adiantum is monophyletic
and sister to the vittarioids. With this robust phylogenetic
framework established for the broadest relationships in the
adiantoid clade, we can now focus on understanding the
evolutionary processes associated with the extreme
morphological, ecological, and genetic transitions that took
place within this lineage.},
Doi = {10.1600/036364416x690660},
Key = {fds322313}
}
@article{fds358011,
Author = {Wolf, PG and Sessa, EB and Marchant, DB and Li, F and Rothfels, CJ and Sigel, EM and Gitzendanner, MA and Visger, CJ and Banks, JA and Soltis,
DE},
Title = {An exploration into fern genome space},
Journal = {Genome Biology and Evolution},
Volume = {7},
Number = {9},
Pages = {2533-2544},
Publisher = {Oxford University Press},
Year = {2015},
Key = {fds358011}
}
@article{fds230052,
Author = {Schuettpelz, E and Pryer, KM and Windham, MD},
Title = {A unified approach to taxonomic delimitation in the fern
genus Pentagramma (Pteridaceae)},
Journal = {Systematic Botany},
Volume = {40},
Number = {3},
Pages = {629-644},
Publisher = {American Society of Plant Taxonomists},
Year = {2015},
ISSN = {0363-6445},
url = {http://hdl.handle.net/10161/10796 Duke open
access},
Abstract = {The native goldback and silverback ferns of western North
America, composing the genus Pentagramma, are
phylogenetically isolated within the xeric-adapted
cheilanthoid clade. Although species-poor compared to its
sister group, Pentagramma encompasses a diverse array of
morphotypes, cytotypes, and flavonoid chemotypes. Because
the differences are generally cryptic, however, the various
entities are usually recognized at an infraspecific level.
In recent years, as many as five subspecies have been
ascribed to P. triangularis, and only P. pallida has been
considered sufficiently divergent to warrant recognition as
a distinct species. In this study, we take a unified
approach to taxonomic delimitation in Pentagramma. Combining
spore studies with phylogenetic analyses of plastid and
nuclear sequences, we identify six genetically and
morphologically distinct diploid lineages, each of which is
here treated as a species. A new species is described (P.
glanduloviscida) and three new combinations are made (P.
maxonii, P. rebmanii, and P. viscosa).},
Doi = {10.1600/036364415x689366},
Key = {fds230052}
}
@article{fds230053,
Author = {Li, F and Rothfels, CJ and Melkonian, M and Villarreal, JC and Stevenson, DW and Graham, SW and Wong, GK-S and Mathews, S and Pryer,
KM},
Title = {The origin and evolution of phototropins},
Journal = {Frontiers in plant science},
Volume = {6},
Pages = {637},
Publisher = {Frontiers},
Year = {2015},
url = {http://hdl.handle.net/10161/10800 Duke open
access},
Abstract = {Plant phototropism, the ability to bend toward or away from
light, is predominantly controlled by blue-light
photoreceptors, the phototropins. Although phototropins have
been well-characterized in Arabidopsis thaliana, their
evolutionary history is largely unknown. In this study, we
complete an in-depth survey of phototropin homologs across
land plants and algae using newly available transcriptomic
and genomic data. We show that phototropins originated in an
ancestor of Viridiplantae (land plants + green algae).
Phototropins repeatedly underwent independent duplications
in most major land-plant lineages (mosses, lycophytes,
ferns, and seed plants), but remained single-copy genes in
liverworts and hornworts-an evolutionary pattern shared with
another family of photoreceptors, the phytochromes.
Following each major duplication event, the phototropins
differentiated in parallel, resulting in two specialized,
yet partially overlapping, functional forms that primarily
mediate either low- or high-light responses. Our detailed
phylogeny enables us to not only uncover new phototropin
lineages, but also link our understanding of phototropin
function in Arabidopsis with what is known in Adiantum and
Physcomitrella (the major model organisms outside of
flowering plants). We propose that the convergent functional
divergences of phototropin paralogs likely contributed to
the success of plants through time in adapting to habitats
with diverse and heterogeneous light conditions.},
Doi = {10.3389/fpls.2015.00637},
Key = {fds230053}
}
@article{fds230055,
Author = {Huiet, L and Lenz, M and Nelson, JK and Pryer, KM and Smith,
AR},
Title = {Adiantum shastense, a new species of maidenhair fern from
California},
Journal = {PhytoKeys},
Number = {53},
Pages = {73},
Publisher = {Pensoft Publishers},
Year = {2015},
ISSN = {1314-2011},
url = {http://hdl.handle.net/10161/10799 Duke open
access},
Abstract = {A new species of Adiantum is described from California. This
species is endemic to northern California and is currently
known only from Shasta County. We describe its discovery
after first being collected over a century ago and
distinguish it from Adiantumjordanii and
Adiantumcapillus-veneris. It is evergreen and is sometimes,
but not always, associated with limestone. The range of
Adiantumshastense Huiet & A.R.Sm., sp. nov., is similar to
several other Shasta County endemics that occur in the mesic
forests of the Eastern Klamath Range, close to Shasta Lake,
on limestone and metasedimentary substrates.},
Doi = {10.3897/phytokeys.53.5151},
Key = {fds230055}
}
@article{fds230056,
Author = {Rothfels, CJ and Li, F and Sigel, EM and Huiet, L and Larsson, A and Burge,
DO and Ruhsam, M and Deyholos, M and Soltis, DE and Stewart Jr,
CN},
Title = {The evolutionary history of ferns inferred from 25
low‐copy nuclear genes},
Journal = {American Journal of Botany},
Volume = {102},
Number = {7},
Pages = {1089-1107},
Publisher = {Botanical Society of America},
Year = {2015},
ISSN = {0002-9122},
url = {http://hdl.handle.net/10161/10798 Duke open
access},
Abstract = {<h4>Unlabelled</h4>•<h4>Premise of the
study</h4>Understanding fern (monilophyte) phylogeny and its
evolutionary timescale is critical for broad investigations
of the evolution of land plants, and for providing the point
of comparison necessary for studying the evolution of the
fern sister group, seed plants. Molecular phylogenetic
investigations have revolutionized our understanding of fern
phylogeny, however, to date, these studies have relied
almost exclusively on plastid data.•<h4>Methods</h4>Here
we take a curated phylogenomics approach to infer the first
broad fern phylogeny from multiple nuclear loci, by
combining broad taxon sampling (73 ferns and 12 outgroup
species) with focused character sampling (25 loci comprising
35877 bp), along with rigorous alignment, orthology
inference and model selection.•<h4>Key results</h4>Our
phylogeny corroborates some earlier inferences and provides
novel insights; in particular, we find strong support for
Equisetales as sister to the rest of ferns, Marattiales as
sister to leptosporangiate ferns, and Dennstaedtiaceae as
sister to the eupolypods. Our divergence-time analyses
reveal that divergences among the extant fern orders all
occurred prior to ∼200 MYA. Finally, our species-tree
inferences are congruent with analyses of concatenated data,
but generally with lower support. Those cases where
species-tree support values are higher than expected involve
relationships that have been supported by smaller plastid
datasets, suggesting that deep coalescence may be reducing
support from the concatenated nuclear data.•<h4>Conclusions</h4>Our
study demonstrates the utility of a curated phylogenomics
approach to inferring fern phylogeny, and highlights the
need to consider underlying data characteristics, along with
data quantity, in phylogenetic studies.},
Doi = {10.3732/ajb.1500089},
Key = {fds230056}
}
@article{fds230057,
Author = {Melkonian, M and Pryer, KM and Rothfels, CJ and Graham, SW and Li, F and Villarreal, JC and Wong, GK and Stevenson, DW and Mathews,
S},
Title = {Phytochrome diversity in green plants and the origin of
canonical plant phytochromes},
Volume = {6},
Number = {1},
Pages = {1-12},
Publisher = {Nature Publishing Group},
Year = {2015},
url = {http://hdl.handle.net/10161/10330 Duke open
access},
Abstract = {Phytochromes are red/far-red photoreceptors that play
essential roles in diverse plant morphogenetic and
physiological responses to light. Despite their functional
significance, phytochrome diversity and evolution across
photosynthetic eukaryotes remain poorly understood. Using
newly available transcriptomic and genomic data we show that
canonical plant phytochromes originated in a common ancestor
of streptophytes (charophyte algae and land plants).
Phytochromes in charophyte algae are structurally diverse,
including canonical and non-canonical forms, whereas in land
plants, phytochrome structure is highly conserved.
Liverworts, hornworts and Selaginella apparently possess a
single phytochrome, whereas independent gene duplications
occurred within mosses, lycopods, ferns and seed plants,
leading to diverse phytochrome families in these clades.
Surprisingly, the phytochrome portions of algal and land
plant neochromes, a chimera of phytochrome and phototropin,
appear to share a common origin. Our results reveal novel
phytochrome clades and establish the basis for understanding
phytochrome functional evolution in land plants and their
algal relatives.},
Doi = {10.1038/ncomms8852},
Key = {fds230057}
}
@article{fds230060,
Author = {Rothfels, CJ and Johnson, AK and Hovenkamp, PH and Swofford, DL and Roskam, HC and Fraser-Jenkins, CR and Windham, MD and Pryer,
KM},
Title = {Natural hybridization between genera that diverged from each
other approximately 60 million years ago},
Journal = {The American Naturalist},
Volume = {185},
Number = {3},
Pages = {433-442},
Publisher = {University of Chicago Press Chicago, IL},
Year = {2015},
ISSN = {0003-0147},
url = {http://hdl.handle.net/10161/10248 Duke open
access},
Abstract = {A fern from the French Pyrenees-×Cystocarpium
roskamianum-is a recently formed intergeneric hybrid between
parental lineages that diverged from each other
approximately 60 million years ago (mya; 95% highest
posterior density: 40.2-76.2 mya). This is an
extraordinarily deep hybridization event, roughly akin to an
elephant hybridizing with a manatee or a human with a lemur.
In the context of other reported deep hybrids, this finding
suggests that populations of ferns, and other plants with
abiotically mediated fertilization, may evolve reproductive
incompatibilities more slowly, perhaps because they lack
many of the premating isolation mechanisms that characterize
most other groups of organisms. This conclusion implies that
major features of Earth's biodiversity-such as the
relatively small number of species of ferns compared to
those of angiosperms-may be, in part, an indirect by-product
of this slower "speciation clock" rather than a direct
consequence of adaptive innovations by the more diverse
lineages.},
Doi = {10.1086/679662},
Key = {fds230060}
}
@article{fds376514,
Author = {Li, F and Melkonian, M and Rothfels, CJ and Villarreal, JC and Stevenson, DW and Graham, SW and Wong, GK and Pryer, KM and Mathews,
S},
Title = {Phytochrome diversity in green plants and the origin of
canonical plant phytochromes},
Journal = {Nature communications},
Volume = {6},
Number = {1},
Pages = {1-12},
Publisher = {Nature Publishing Group},
Year = {2015},
Key = {fds376514}
}
@article{fds322315,
Author = {Kao, T and Pryer, KM and Turner, MD and White, RA and Korall,
P},
Title = {Origins of the endemic scaly tree ferns on the Galápagos
and Cocos Islands},
Journal = {International Journal of Plant Sciences},
Volume = {176},
Number = {9},
Pages = {869-879},
Publisher = {University of Chicago Press Chicago, IL},
Year = {2015},
url = {http://dx.doi.org/10.1086/683303},
Abstract = {Premise of research. Successful long-distance dispersal is
rarely observed in scaly tree ferns (Cyatheaceae).
Nevertheless, recent molecular evidence has suggested that
the four endemic scaly tree ferns on the Galápagos
Archipelago (Cyathea weatherbyana) and Cocos Island (Cyathea
alfonsiana, Cyathea nesiotica, and Cyathea notabilis), two
oceanic island groups west of Central and northern South
America, probably each originated from different mainland
America ancestors. However, the phylogenetic relationships
inferred among these endemics and their mainland relatives
have been unclear. This study is aimed at better resolving
the relationships and tracing the origins of these island
endemics. Methodology. Five plastid regions from 35 Cyathea
species were analyzed to reconstruct phylogenetic
relationships using parsimony, likelihood, and Bayesian
approaches. We also estimated divergence times of these
species, and our chronogram was used to reconstruct their
biogeographical range history. Pivotal results. Our
well-resolved phylogenetic tree of Cyathea, which is in
agreement with previous studies, shows that when the four
Galápagos and Cocos endemics are included, they each belong
to separate subclades. Our biogeographical study suggests
that the four endemics originated from independent
colonization events from mainland America and that there was
no dispersal of Cyathea between the island groups. We reveal
more detailed relationships among the endemics and their
respective close mainland relatives; some of these
relationships differ from previous studies. Our findings are
corroborated by new morphological data from ongoing stem
anatomy studies. Conclusions. The four scaly tree ferns
endemic to the Galápagos and Cocos Islands each did indeed
originate as independent colonization events from separate
sources in mainland America, and their closest relatives are
identified here.},
Doi = {10.1086/683303},
Key = {fds322315}
}
@article{fds322314,
Author = {Grusz, AL and Pryer, KM},
Title = {Development of microsatellite markers for the apomictic
triploid fern Myriopteris lindheimeri (Pteridaceae)},
Journal = {Applications in plant sciences},
Volume = {3},
Number = {11},
Pages = {1500061},
Publisher = {Botanical Society of America},
Year = {2015},
url = {http://dx.doi.org/10.3732/apps.1500061},
Abstract = {<h4>Premise of the study</h4>Microsatellite markers were
developed for investigating the population dynamics of
Myriopteris lindheimeri (Pteridaceae), an apomictic triploid
fern endemic to deserts of the southwestern United States
and Mexico.<h4>Methods and results</h4>Using 454 sequencing,
21 microsatellite markers were developed. Of these, 14 were
polymorphic with up to five alleles per locus and eight
markers amplified in one or more congeneric close relatives
(M. covillei, M. fendleri, M. aurea, and M. rufa). To
demonstrate marker utility, M. lindheimeri samples from
three Arizona populations were genotyped at nine loci. For
each population, diversity measures including percent
polymorphic loci, frequency of heterozygotes across all
loci, and genotypic diversity were calculated. Across the
three populations, on average, 63% of loci were polymorphic,
the average frequency of heterozygotes (across all loci) was
0.32, and average genotypic diversity was
0.34.<h4>Conclusions</h4>These markers provide a foundation
for future studies exploring polyploidy and apomixis in
myriopterid ferns.},
Doi = {10.3732/apps.1500061},
Key = {fds322314}
}
@article{fds353345,
Author = {Rothfels, CJ and Wong, GK and Stevenson, DW and Li, F and Mathews, S and Melkonian, M and Pryer, KM and Graham, SW and Villarreal,
JC},
Title = {The Origin and Evolution of Phototropins},
Year = {2015},
Key = {fds353345}
}
@article{fds230063,
Author = {Sessa, EB and Banks, JA and Barker, MS and Der, JP and Duffy, AM and Graham, SW and Hasebe, M and Langdale, J and Li, F-W and Marchant, DB and Pryer, KM and Rothfels, CJ and Roux, SJ and Salmi, ML and Sigel, EM and Soltis, DE and Soltis, PS and Stevenson, DW and Wolf,
PG},
Title = {Between two fern genomes},
Journal = {Gigascience},
Volume = {3},
Number = {1},
Pages = {15-15},
Publisher = {Oxford University Press},
Year = {2014},
Month = {September},
url = {http://hdl.handle.net/10161/10249 Duke open
access},
Abstract = {Ferns are the only major lineage of vascular plants not
represented by a sequenced nuclear genome. This lack of
genome sequence information significantly impedes our
ability to understand and reconstruct genome evolution not
only in ferns, but across all land plants. Azolla and
Ceratopteris are ideal and complementary candidates to be
the first ferns to have their nuclear genomes sequenced.
They differ dramatically in genome size, life history, and
habit, and thus represent the immense diversity of extant
ferns. Together, this pair of genomes will facilitate myriad
large-scale comparative analyses across ferns and all land
plants. Here we review the unique biological characteristics
of ferns and describe a number of outstanding questions in
plant biology that will benefit from the addition of ferns
to the set of taxa with sequenced nuclear genomes. We
explain why the fern clade is pivotal for understanding
genome evolution across land plants, and we provide a
rationale for how knowledge of fern genomes will enable
progress in research beyond the ferns themselves.},
Doi = {10.1186/2047-217x-3-15},
Key = {fds230063}
}
@article{fds230064,
Author = {Li, F-W and Pryer, KM},
Title = {Crowdfunding the Azolla fern genome project: a grassroots
approach.},
Journal = {GigaScience},
Volume = {3},
Number = {1},
Pages = {16},
Publisher = {Oxford University Press},
Year = {2014},
Month = {January},
url = {http://hdl.handle.net/10161/10250 Duke open
access},
Abstract = {Much of science progresses within the tight boundaries of
what is often seen as a "black box". Though familiar to
funding agencies, researchers and the academic journals they
publish in, it is an entity that outsiders rarely get to
peek into. Crowdfunding is a novel means that allows the
public to participate in, as well as to support and witness
advancements in science. Here we describe our recent
crowdfunding efforts to sequence the Azolla genome, a little
fern with massive green potential. Crowdfunding is a worthy
platform not only for obtaining seed money for exploratory
research, but also for engaging directly with the general
public as a rewarding form of outreach.},
Doi = {10.1186/2047-217x-3-16},
Key = {fds230064}
}
@article{fds230054,
Author = {Wolf, PG and Sessa, EB and Marchant, DB and Li, F and Rothfels, CJ and Sigel, EM and Gitzendanner, MA and Visger, CJ and Banks, JA and Soltis,
DE},
Title = {An Exploration of Fern Genome Space},
Volume = {7},
Number = {9},
Pages = {2533-2544},
Publisher = {Botanical Society of America},
Year = {2014},
url = {http://hdl.handle.net/10161/10797 Duke open
access},
Abstract = {Ferns are one of the few remaining major clades of land
plants for which a complete genome sequence is lacking.
Knowledge of genome space in ferns will enable broad-scale
comparative analyses of land plant genes and genomes,
provide insights into genome evolution across green plants,
and shed light on genetic and genomic features that
characterize ferns, such as their high chromosome numbers
and large genome sizes. As part of an initial exploration
into fern genome space, we used a whole genome shotgun
sequencing approach to obtain low-density coverage (∼0.4X
to 2X) for six fern species from the Polypodiales
(Ceratopteris, Pteridium, Polypodium, Cystopteris),
Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We
explore these data to characterize the proportion of the
nuclear genome represented by repetitive sequences
(including DNA transposons, retrotransposons, ribosomal DNA,
and simple repeats) and protein-coding genes, and to extract
chloroplast and mitochondrial genome sequences. Such initial
sweeps of fern genomes can provide information useful for
selecting a promising candidate fern species for whole
genome sequencing. We also describe variation of genomic
traits across our sample and highlight some differences and
similarities in repeat structure between ferns and seed
plants.},
Doi = {10.1093/gbe/evv163},
Key = {fds230054}
}
@article{fds230061,
Author = {Rothfels, CJ and Johnson, AK and Windham, MD and Pryer,
KM},
Title = {Low‐copy nuclear data confirm rampant allopolyploidy in
the Cystopteridaceae (Polypodiales)},
Journal = {Taxon},
Volume = {63},
Number = {5},
Pages = {1026-1036},
Publisher = {International Association for Plant Taxonomy},
Year = {2014},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.12705/635.32},
Abstract = {Here we present the first nuclear phylogeny for
Cystopteridaceae (Polypodiales), using the single-copy locus
gapCp “short”. This phylogeny corroborates broad results
from plastid data in demonstrating strong support for the
monophyly of the family’s three genera—Cystopteris,
Acystopteris, and Gymnocarpium—and of the major groups
within Cystopteris (C. montana, the sudetica and bulbifera
clades, and the C. fragilis complex). In addition, it
confirms the rampant hybridization (allopolyploidy) that has
long been suspected within both Cystopteris and
Gymnocarpium. In some cases, these data provide the first
DNA-sequence-based evidence for previous hypotheses of
polyploid species origins (such as the cosmopolitan G.
dryopteris being an allotetraploid derivative of the
diploids G. appalachianum and G. disjunctum). Most of the
allopolyploids, however, have no formal taxonomic names.
This pattern is particularly strong within the C. fragilis
complex, where our results imply that the eight included
accessions of “C. fragilis” represent at least six
distinct allopolyploid taxa.},
Doi = {10.12705/635.32},
Key = {fds230061}
}
@article{fds230062,
Author = {Sigel, EM and Windham, MD and Haufler, CH and Pryer,
KM},
Title = {Phylogeny, divergence time estimates, and phylogeography of
the diploid species of the Polypodium vulgare complex
(Polypodiaceae)},
Journal = {Systematic Botany},
Volume = {39},
Number = {4},
Pages = {1042-1055},
Publisher = {American Society of Plant Taxonomists},
Year = {2014},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364414x683921},
Abstract = {The Polypodium vulgare complex (Polypodiaceae) comprises a
well-studied group of fern taxa whose members are
cryptically differentiated morphologically and have
generated a confusing and highly reticulate species cluster.
Once considered a single species spanning much of northern
Eurasia and North America, P. vulgare has been segregated
into 17 diploid and polyploid taxa as a result of
cytotaxonomic work, hybridization experiments, and isozyme
studies conducted during the 20th century. Despite
considerable effort, however, the evolutionary relationships
among the diploid members of the P. vulgare complex remain
poorly resolved. Here we infer a diploids-only phylogeny of
the P. vulgare complex and related species to test previous
hypotheses concerning relationships within Polypodium sensu
stricto. Using sequence data from four plastid loci (atpA,
rbcL, matK, and trnG-trnR), we recovered a monophyletic P.
vulgare complex comprising four well-supported clades. The
P. vulgare complex is resolved as sister to the Neotropical
P. plesiosorum group and these, in turn, are sister to the
Asian endemic Pleurosoriopsis makinoi. Using divergence time
analyses incorporating previously derived age constraints
and fossil data, we estimate an early Miocene origin for the
P. vulgare complex and a late Miocene-Pliocene origin for
the four major diploid lineages of the complex, with the
majority of extant diploid species diversifying from the
late Miocene through the Pleistocene. Finally, we use our
node age estimates to reassess previous hypotheses, and to
propose new hypotheses, about the historical events that
shaped the diversity and current geographic distribution of
the diploid species of the P. vulgare complex.},
Doi = {10.1600/036364414x683921},
Key = {fds230062}
}
@article{fds230065,
Author = {Sigel, EM and Windham, MD and Pryer, KM},
Title = {Evidence for reciprocal origins in Polypodium hesperium
(Polypodiaceae): A fern model system for investigating how
multiple origins shape allopolyploid genomes},
Journal = {American Journal of Botany},
Volume = {101},
Number = {9},
Pages = {1476-1485},
Publisher = {Botanical Society of America},
Year = {2014},
ISSN = {0002-9122},
url = {http://dx.doi.org/10.3732/ajb.1400190},
Abstract = {<h4>Unlabelled</h4>•<h4>Premise of the study</h4>Many
polyploid species are composed of distinct lineages
originating from multiple, independent polyploidization
events. In the case of allopolyploids, reciprocal crosses
between the same progenitor species can yield lineages with
different uniparentally inherited plastid genomes. While
likely common, there are few well-documented examples of
such reciprocal origins. Here we examine a case of
reciprocal allopolyploid origins in the fern Polypodium
hesperium and present it as a natural model system for
investigating the evolutionary potential of duplicated
genomes.•<h4>Methods</h4>Using a combination of
uniparentally inherited plastid and biparentally inherited
nuclear sequence data, we investigated the distributions and
relative ages of reciprocally formed lineages in Polypodium
hesperium, an allotetraploid fern that is broadly
distributed in western North America.•<h4>Key
results</h4>The reciprocally derived plastid haplotypes of
Polypodium hesperium are allopatric, with populations north
and south of 42°N latitude having different plastid
genomes. Incorporating biogeographic information and
previously estimated ages for the diversification of its
diploid progenitors, we estimate middle to late Pleistocene
origins of P. hesperium.•<h4>Conclusions</h4>Several
features of Polypodium hesperium make it a particularly
promising system for investigating the evolutionary
consequences of allopolyploidy. These include reciprocally
derived lineages with disjunct geographic distributions,
recent time of origin, and extant diploid
progenitors.},
Doi = {10.3732/ajb.1400190},
Key = {fds230065}
}
@article{fds230067,
Author = {Grusz, AL and Windham, MD and Yatskievych, G and Huiet, L and Gastony,
GJ and Pryer, KM},
Title = {Patterns of diversification in the xeric-adapted fern genus
Myriopteris (Pteridaceae)},
Journal = {Systematic Botany},
Volume = {39},
Number = {3},
Pages = {698-714},
Publisher = {American Society of Plant Taxonomists},
Year = {2014},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364414x681518},
Abstract = {Strong selective pressures imposed by drought-prone habitats
have contributed to extensive morphological convergence
among the 400 + species of cheilanthoid ferns (Pteridaceae).
As a result, generic circumscriptions based exclusively on
macromorphology often prove to be non-monophyletic. Ongoing
molecular phylogenetic analyses are providing the foundation
for a revised classification of this challenging group and
have begun to clarify its complex evolutionary history. As
part of this effort, we generated and analyzed DNA sequence
data for three plastid loci (rbcL, atpA, and the intergenic
spacer trnG-trnR) for the myriopterid clade, one of the
largest monophyletic groups of cheilanthoid ferns. This
lineage encompasses 47 primarily North and Central American
taxa previously included in Cheilanthes but now placed in
the recircumscribed genus Myriopteris. Here, we infer a
phylogeny for the group and examine key morphological
characters across this phylogeny. We also include a brief
discussion of the three well-supported Myriopteris
subclades, along with a review of reproductive mode and
known ploidy levels for members of this early diverging
lineage of cheilanthoid ferns.},
Doi = {10.1600/036364414x681518},
Key = {fds230067}
}
@article{fds230068,
Author = {Li, F and Villarreal, JC and Kelly, S and Rothfels, CJ and Melkonian, M and Frangedakis, E and Ruhsam, M and Sigel, EM and Der, JP and Pittermann,
J},
Title = {Horizontal transfer of an adaptive chimeric photoreceptor
from bryophytes to ferns},
Journal = {Proceedings of the National Academy of Sciences},
Volume = {111},
Number = {18},
Pages = {6672-6677},
Publisher = {National Academy of Sciences},
Year = {2014},
ISSN = {0027-8424},
url = {http://dx.doi.org/10.1073/pnas.1319929111},
Abstract = {Ferns are well known for their shade-dwelling habits. Their
ability to thrive under low-light conditions has been linked
to the evolution of a novel chimeric photoreceptor--neochrome--that
fuses red-sensing phytochrome and blue-sensing phototropin
modules into a single gene, thereby optimizing phototropic
responses. Despite being implicated in facilitating the
diversification of modern ferns, the origin of neochrome has
remained a mystery. We present evidence for neochrome in
hornworts (a bryophyte lineage) and demonstrate that ferns
acquired neochrome from hornworts via horizontal gene
transfer (HGT). Fern neochromes are nested within hornwort
neochromes in our large-scale phylogenetic reconstructions
of phototropin and phytochrome gene families. Divergence
date estimates further support the HGT hypothesis, with fern
and hornwort neochromes diverging 179 Mya, long after the
split between the two plant lineages (at least 400 Mya). By
analyzing the draft genome of the hornwort Anthoceros
punctatus, we also discovered a previously unidentified
phototropin gene that likely represents the ancestral
lineage of the neochrome phototropin module. Thus, a
neochrome originating in hornworts was transferred
horizontally to ferns, where it may have played a
significant role in the diversification of modern
ferns.},
Doi = {10.1073/pnas.1319929111},
Key = {fds230068}
}
@article{fds230069,
Author = {Sigel, EM and Windham, MD and Smith, AR and Dyer, RJ and Pryer,
KM},
Title = {Rediscovery of Polypodium calirhiza (Polypodiaceae) in
Mexico},
Journal = {Brittonia},
Volume = {66},
Number = {3},
Pages = {278-286},
Publisher = {Springer US},
Year = {2014},
ISSN = {0007-196X},
url = {http://dx.doi.org/10.1007/s12228-014-9332-6},
Abstract = {This study addresses reported discrepancies regarding the
occurrence of Polypodium calirhiza in Mexico. The original
paper describing this taxon cited collections from Mexico,
but the species was omitted from the recent Pteridophytes of
Mexico. Originally treated as a tetraploid cytotype of P.
californicum, P. calirhiza now is hypothesized to have
arisen through hybridization between P. glycyrrhiza and P.
californicum. The tetraploid can be difficult to distinguish
from either of its putative parents, but especially so from
P. californicum. Our analyses show that a combination of
spore length and abaxial rachis scale morphology
consistently distinguishes P. calirhiza from P.
californicum, and we confirm that both species occur in
Mexico. Although occasionally found growing together in the
United States, the two species are strongly allopatric in
Mexico: P. californicum is restricted to coastal regions of
the Baja California peninsula and neighboring Pacific
islands, whereas P. calirhiza grows at high elevations in
central and southern Mexico. The occurrence of P. calirhiza
in Oaxaca, Mexico, marks the southernmost extent of the P.
vulgare complex in the Western Hemisphere. © 2014 The New
York Botanical Garden.},
Doi = {10.1007/s12228-014-9332-6},
Key = {fds230069}
}
@article{fds304306,
Author = {Korall, P and Pryer, KM},
Title = {Global biogeography of scaly tree ferns (Cyatheaceae):
evidence for Gondwanan vicariance and limited transoceanic
dispersal},
Journal = {Journal of biogeography},
Volume = {41},
Number = {2},
Pages = {402-413},
Year = {2014},
ISSN = {0305-0270},
url = {http://dx.doi.org/10.1111/jbi.12222},
Abstract = {Aim: Scaly tree ferns, Cyatheaceae, are a well-supported
group of mostly tree-forming ferns found throughout the
tropics, the subtropics and the south-temperate zone. Fossil
evidence shows that the lineage originated in the Late
Jurassic period. We reconstructed large-scale historical
biogeographical patterns of Cyatheaceae and tested the
hypothesis that some of the observed distribution patterns
are in fact compatible, in time and space, with a vicariance
scenario related to the break-up of Gondwana. Location:
Tropics, subtropics and south-temperate areas of the world.
Methods: The historical biogeography of Cyatheaceae was
analysed in a maximum likelihood framework using Lagrange.
The 78 ingroup taxa are representative of the geographical
distribution of the entire family. The phylogenies that
served as a basis for the analyses were obtained by Bayesian
inference analyses of mainly previously published DNA
sequence data using MrBayes. Lineage divergence dates were
estimated in a Bayesian Markov chain Monte Carlo framework
using beast. Results: Cyatheaceae originated in the Late
Jurassic in either South America or Australasia. Following a
range expansion, the ancestral distribution of the
marginate-scaled clade included both these areas, whereas
Sphaeropteris is reconstructed as having its origin only in
Australasia. Within the marginate-scaled clade,
reconstructions of early divergences are hampered by the
unresolved relationships among the Alsophila, Cyathea and
Gymnosphaera lineages. Nevertheless, it is clear that the
occurrence of the Cyathea and Sphaeropteris lineages in
South America may be related to vicariance, whereas
transoceanic dispersal needs to be inferred for the range
shifts seen in Alsophila and Gymnosphaera. Main conclusions:
The evolutionary history of Cyatheaceae involves both
Gondwanan vicariance scenarios as well as long-distance
dispersal events. The number of transoceanic dispersals
reconstructed for the family is rather few when compared
with other fern lineages. We suggest that a causal
relationship between reproductive mode (outcrossing) and
dispersal limitations is the most plausible explanation for
the pattern observed. © 2013 The Authors Journal of
Biogeography Published by John Wiley & Sons
Ltd.},
Doi = {10.1111/jbi.12222},
Key = {fds304306}
}
@article{fds353382,
Author = {Li, F and Pryer, KM},
Title = {Crowdfunding the Azolla fern genome project: a grassroots
approach},
Journal = {GigaScience},
Volume = {3},
Number = {1},
Pages = {2047-217X},
Publisher = {Oxford University Press},
Year = {2014},
Key = {fds353382}
}
@article{fds353383,
Author = {Sessa, EB and Banks, JA and Barker, MS and Der, JP and Duffy, AM and Graham, SW and Hasebe, M and Langdale, J and Li, F and Marchant,
DB},
Title = {Between two fern genomes},
Journal = {GigaScience},
Volume = {3},
Number = {1},
Pages = {2047-217X},
Publisher = {Oxford University Press},
Year = {2014},
Key = {fds353383}
}
@article{fds230071,
Author = {Rothfels, CJ and Larsson, A and Li, F and Sigel, EM and Huiet, L and Burge,
DO and Ruhsam, M and Graham, SW and Stevenson, DW and Wong,
GK},
Title = {Transcriptome-mining for single-copy nuclear markers in
ferns},
Journal = {PloS one},
Volume = {8},
Number = {10},
Pages = {e76957},
Publisher = {Public Library of Science},
Year = {2013},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24116189},
Abstract = {<h4>Background</h4>Molecular phylogenetic investigations
have revolutionized our understanding of the evolutionary
history of ferns-the second-most species-rich major group of
vascular plants, and the sister clade to seed plants. The
general absence of genomic resources available for this
important group of plants, however, has resulted in the
strong dependence of these studies on plastid data; nuclear
or mitochondrial data have been rarely used. In this study,
we utilize transcriptome data to design primers for nuclear
markers for use in studies of fern evolutionary biology, and
demonstrate the utility of these markers across the largest
order of ferns, the Polypodiales.<h4>Principal
findings</h4>We present 20 novel single-copy nuclear
regions, across 10 distinct protein-coding genes: ApPEFP_C,
cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC,
SQD1, TPLATE, and transducin. These loci, individually and
in combination, show strong resolving power across the
Polypodiales phylogeny, and are readily amplified and
sequenced from our genomic DNA test set (from 15 diploid
Polypodiales species). For each region, we also present
transcriptome alignments of the focal locus and related
paralogs-curated broadly across ferns-that will allow
researchers to develop their own primer sets for fern taxa
outside of the Polypodiales. Analyses of sequence data
generated from our genomic DNA test set reveal strong
effects of partitioning schemes on support levels and, to a
much lesser extent, on topology. A model partitioned by
codon position is strongly favored, and analyses of the
combined data yield a Polypodiales phylogeny that is
well-supported and consistent with earlier studies of this
group.<h4>Conclusions</h4>The 20 single-copy regions
presented here more than triple the single-copy nuclear
regions available for use in ferns. They provide a
much-needed opportunity to assess plastid-derived hypotheses
of relationships within the ferns, and increase our capacity
to explore aspects of fern evolution previously unavailable
to scientific investigation.},
Doi = {10.1371/journal.pone.0076957},
Key = {fds230071}
}
@article{fds230103,
Author = {Rothfels, CJ and Windham, MD and Pryer, KM},
Title = {A plastid phylogeny of the cosmopolitan fern family
Cystopteridaceae (Polypodiopsida)},
Journal = {Systematic Botany},
Volume = {38},
Number = {2},
Pages = {295-306},
Publisher = {American Society of Plant Taxonomists},
Year = {2013},
url = {http://dx.doi.org/10.1600/036364413x666787},
Abstract = {Among the novel results of recent molecular phylogenetic
analyses are the unexpectedly close evolutionary
relationships of the genera Acystopteris, Cystopteris, and
Gymnocarpium, and the phylogenetic isolation of these genera
from Woodsia. As a consequence, these three genera have been
removed from Woodsiaceae and placed into their own family,
the Cystopteridaceae. Despite the ubiquity of this family in
rocky habitats across the northern hemisphere, and its
cosmopolitan distribution (occurring on every continent
except Antarctica), sampling of the Cystopteridaceae in
phylogenetic studies to date has been sparse. Here we
assemble a three-locus plastid dataset (matK, rbcL, trnG-R)
that includes most recognized species in the family and
multiple accessions of widespread taxa from across their
geographic ranges. All three sampled genera are robustly
supported as monophyletic, Cystopteris is strongly supported
as sister to Acystopteris, and those two genera together are
sister to Gymnocarpium. The Gymnocarpium phylogeny is deeply
divided into three major clades, which we label the
disjunctum clade, the robertianum clade, and core
Gymnocarpium. The Cystopteris phylogeny, similarly, features
four deeply diverged clades: C. montana, the sudetica clade,
the bulbifera clade, and the fragilis complex. Acystopteris
includes only three species, each of which is supported as
monophyletic, with A. taiwaniana sister to the
japonica/tenuisecta clade. Our results yield the first
species-level phylogeny of the Cystopteridaceae and the
first molecular phylogenetic evidence for species
boundaries. These data provide an essential foundation for
further investigations of complex patterns of geographic
diversification, speciation, and reticulation in this
family.},
Doi = {10.1600/036364413x666787},
Key = {fds230103}
}
@article{fds230105,
Author = {León, B and Rothfels, CJ and Arakaki, M and Young, KR and Pryer,
KM},
Title = {Revealing a cryptic fern distribution through DNA
sequencing: Pityrogramma trifoliata in the Western Andes of
Peru},
Journal = {American Fern Journal},
Volume = {103},
Number = {1},
Pages = {40-48},
Publisher = {The American Fern Society},
Year = {2013},
url = {http://dx.doi.org/10.1640/0002-8444-103.1.40},
Abstract = {Fern identification usually requires the use of mature
sporophytes, since attempts to identify juveniles using
morphological traits often provides unsatisfactory results.
Here we examined young sporophytes found among boulders in a
river basin of a xeric valley in central Peru. Attempts to
identify these sporophytes first pointed to four different
genera, two in Pteridaceae (Anogramma and Pityrogramma), and
the others in Aspleniaceae (Asplenium) and Cystopteridaceae
(Cystopteris). Here, we resolved this puzzle combining
morphology and sequences of DNA (rbcL and trnG-R) that point
to Pityrogramma trifoliata of Pteridaceae.},
Doi = {10.1640/0002-8444-103.1.40},
Key = {fds230105}
}
@article{fds230109,
Author = {Grusz, AL and Pryer, KM and Yatskievych, G and Huiet, RL and Gastony,
GJ and Windham, MD},
Title = {Refining the phylogeny of cheilanthoid ferns: The
resurrection and recircumscription of Myriopteris
(Pteridaceae)},
Journal = {Systematic Botany},
Year = {2013},
Key = {fds230109}
}
@article{fds230110,
Author = {Korall, P and Pryer, KM},
Title = {Global biogeography of scaly tree ferns (Cyatheaceae):
evidence for Gondwanan vicariance and limited transoceanic
dispersal},
Journal = {Journal of Biogeography},
Volume = {40},
Number = {2},
Pages = {in press},
Year = {2013},
ISSN = {0305-0270},
url = {http://dx.doi.org/10.1111/jbi.12222},
Abstract = {<h4>Aim</h4>Scaly tree ferns, Cyatheaceae, are a
well-supported group of mostly tree-forming ferns found
throughout the tropics, the subtropics and the
south-temperate zone. Fossil evidence shows that the lineage
originated in the Late Jurassic period. We reconstructed
large-scale historical biogeographical patterns of
Cyatheaceae and tested the hypothesis that some of the
observed distribution patterns are in fact compatible, in
time and space, with a vicariance scenario related to the
break-up of Gondwana.<h4>Location</h4>Tropics, subtropics
and south-temperate areas of the world.<h4>Methods</h4>The
historical biogeography of Cyatheaceae was analysed in a
maximum likelihood framework using Lagrange. The 78 ingroup
taxa are representative of the geographical distribution of
the entire family. The phylogenies that served as a basis
for the analyses were obtained by Bayesian inference
analyses of mainly previously published DNA sequence data
using MrBayes. Lineage divergence dates were estimated in a
Bayesian Markov chain Monte Carlo framework using
beast.<h4>Results</h4>Cyatheaceae originated in the Late
Jurassic in either South America or Australasia. Following a
range expansion, the ancestral distribution of the
marginate-scaled clade included both these areas, whereas
<i>Sphaeropteris</i> is reconstructed as having its origin
only in Australasia. Within the marginate-scaled clade,
reconstructions of early divergences are hampered by the
unresolved relationships among the <i>Alsophila</i>,
<i>Cyathea</i> and <i>Gymnosphaera</i> lineages.
Nevertheless, it is clear that the occurrence of the
<i>Cyathea</i> and <i>Sphaeropteris</i> lineages in South
America may be related to vicariance, whereas transoceanic
dispersal needs to be inferred for the range shifts seen in
<i>Alsophila</i> and <i>Gymnosphaera</i>.<h4>Main
conclusions</h4>The evolutionary history of Cyatheaceae
involves both Gondwanan vicariance scenarios as well as
long-distance dispersal events. The number of transoceanic
dispersals reconstructed for the family is rather few when
compared with other fern lineages. We suggest that a causal
relationship between reproductive mode (outcrossing) and
dispersal limitations is the most plausible explanation for
the pattern observed.},
Doi = {10.1111/jbi.12222},
Key = {fds230110}
}
@article{fds230106,
Author = {Beck, JB and Allison, JR and Pryer, KM and Windham,
MD},
Title = {Identifying multiple origins of polyploid taxa: a multilocus
study of the hybrid cloak fern (Astrolepis integerrima;
Pteridaceae).},
Journal = {American journal of botany},
Volume = {99},
Number = {11},
Pages = {1857-1865},
Year = {2012},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23108464},
Abstract = {<h4>Premise of the study</h4>Molecular studies have shown
that multiple origins of polyploid taxa are the rule rather
than the exception. To understand the distribution and
ecology of polyploid species and the evolutionary
significance of polyploidy in general, it is important to
delineate these independently derived lineages as accurately
as possible. Although gene flow among polyploid lineages and
backcrossing to their diploid parents often confound this
process, such post origin gene flow is very infrequent in
asexual polyploids. In this study, we estimate the number of
independent origins of the apomictic allopolyploid fern
Astrolepis integerrima, a morphologically heterogeneous
species most common in the southwestern United States and
Mexico, with outlying populations in the southeastern United
States and the Caribbean.<h4>Methods</h4>Plastid DNA
sequence and AFLP data were obtained from 33 A. integerrima
individuals. Phylogenetic analysis of the sequence data and
multidimensional clustering of the AFLP data were used to
identify independently derived lineages.<h4>Key
results</h4>Analysis of the two datasets identified 10
genetic groups within the 33 analyzed samples. These groups
suggest a minimum of 10 origins of A. integerrima in the
northern portion of its range, with both putative parents
functioning as maternal donors, both supplying unreduced
gametes, and both contributing a significant portion of
their genetic diversity to the hybrids.<h4>Conclusions</h4>Our
results highlight the extreme cryptic genetic diversity and
systematic complexity that can underlie a single polyploid
taxon.},
Doi = {10.3732/ajb.1200199},
Key = {fds230106}
}
@article{fds230108,
Author = {Johnson, AK and Rothfels, CJ and Windham, MD and Pryer,
KM},
Title = {Unique expression of a sporophytic character on the
gametophytes of notholaenid ferns (Pteridaceae).},
Journal = {American journal of botany},
Volume = {99},
Number = {6},
Pages = {1118-1124},
Year = {2012},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22542903},
Abstract = {<h4>Premise of the study</h4>Not all ferns grow in moist,
shaded habitats; some lineages thrive in exposed, seasonally
dry environments. Notholaenids are a clade of xeric-adapted
ferns commonly characterized by the presence of a waxy
exudate, called farina, on the undersides of their leaves.
Although some other lineages of cheilanthoid ferns also have
farinose sporophytes, previous studies suggested that
notholaenids are unique in also producing farina on their
gametophytes. For this reason, consistent farina expression
across life cycle phases has been proposed as a potential
synapomorphy for the genus Notholaena. Recent phylogenetic
studies have shown two species with nonfarinose sporophytes
to be nested within Notholaena, with a third nonfarinose
species well supported as sister to all other notholaenids.
This finding raises the question: are the gametophytes of
these three species farinose like those of their close
relatives, or are they glabrous, consistent with their
sporophytes?<h4>Methods</h4>We sowed spores of a diversity
of cheilanthoid ferns onto culture media to observe and
document whether their gametophytes produced farina. To
place these species within a phylogenetic context, we
extracted genomic DNA, then amplified and sequenced three
plastid loci. The aligned data were analyzed using maximum
likelihood to generate a phylogenetic tree.<h4>Key
results</h4>Here we show that notholaenids lacking
sporophytic farina also lack farina in the gametophytic
phase, and notholaenids with sporophytic farina always
display gametophytic farina (with a single exception).
Outgroup taxa never displayed gametophytic farina,
regardless of whether they displayed farina on their
sporophytes.<h4>Conclusions</h4>Notholaenids are unique
among ferns in consistently expressing farina across both
phases of the life cycle.},
Doi = {10.3732/ajb.1200049},
Key = {fds230108}
}
@article{fds230112,
Author = {Rothfels, CJ and Larsson, A and Kuo, L-Y and Korall, P and Chiou, W-L and Pryer, KM},
Title = {Overcoming deep roots, fast rates, and short internodes to
resolve the ancient rapid radiation of eupolypod II
ferns.},
Journal = {Systematic biology},
Volume = {61},
Number = {3},
Pages = {490-509},
Year = {2012},
Month = {May},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22223449},
Abstract = {Backbone relationships within the large eupolypod II clade,
which includes nearly a third of extant fern species, have
resisted elucidation by both molecular and morphological
data. Earlier studies suggest that much of the phylogenetic
intractability of this group is due to three factors: (i) a
long root that reduces apparent levels of support in the
ingroup; (ii) long ingroup branches subtended by a series of
very short backbone internodes (the "ancient rapid
radiation" model); and (iii) significantly heterogeneous
lineage-specific rates of substitution. To resolve the
eupolypod II phylogeny, with a particular emphasis on the
backbone internodes, we assembled a data set of five plastid
loci (atpA, atpB, matK, rbcL, and trnG-R) from a sample of
81 accessions selected to capture the deepest divergences in
the clade. We then evaluated our phylogenetic hypothesis
against potential confounding factors, including those
induced by rooting, ancient rapid radiation, rate
heterogeneity, and the Bayesian star-tree paradox artifact.
While the strong support we inferred for the backbone
relationships proved robust to these potential problems,
their investigation revealed unexpected model-mediated
impacts of outgroup composition, divergent effects of
methods for countering the star-tree paradox artifact, and
gave no support to concerns about the applicability of the
unrooted model to data sets with heterogeneous
lineage-specific rates of substitution. This study is among
few to investigate these factors with empirical data, and
the first to compare the performance of the two primary
methods for overcoming the Bayesian star-tree paradox
artifact. Among the significant phylogenetic results is the
near-complete support along the eupolypod II backbone, the
demonstrated paraphyly of Woodsiaceae as currently
circumscribed, and the well-supported placement of the
enigmatic genera Homalosorus, Diplaziopsis, and
Woodsia.},
Doi = {10.1093/sysbio/sys001},
Key = {fds230112}
}
@article{fds230104,
Author = {Pryer, KM},
Title = {The Distinguished Legacy of DMB: Donald MacPhail Britton
(1923–2012)},
Journal = {American Fern Journal},
Volume = {102},
Number = {4},
Pages = {241-251},
Publisher = {The American Fern Society},
Year = {2012},
ISSN = {0002-8444},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000318196200001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.1640/0002-8444-102.4.241},
Key = {fds230104}
}
@article{fds230107,
Author = {Rothfels, CJ and Sundue, MA and Kato, M and Larsson, A and Kuo, LY and Schuettpelz, E and Pryer, KM},
Title = {A revised classification for eupolypod II ferns
(Polypodiales: Polypodiopsida)},
Journal = {Taxon},
Volume = {61},
Number = {3},
Pages = {515-533},
Year = {2012},
ISSN = {0040-0262},
Abstract = {We present a family-level classification for the eupolypod
II clade of leptosporangiate ferns, one of the two major
lineages within the Eupolypods, and one of the few parts of
the fern tree of life where family-level relationships were
not well understood at the time of publication of the 2006
fern classification by Smith & al. Comprising over 2500
species, the composition and particularly the relationships
among the major clades of this group have historically been
contentious and defied phylogenetic resolution until very
recently. Our classification reflects the most current
available data, largely derived from published molecular
phylogenetic studies. In comparison with the five-family
(Aspleniaceae, Blechnaceae, Onocleaceae, Thelypteridaceae,
Woodsiaceae) treatment of Smith & al., we recognize 10
families within the eupolypod II clade. Of these,
Aspleniaceae, Thelypteridaceae, Blechnaceae, and Onocleaceae
have the same composition as treated by Smith & al.
Woodsiaceae, which Smith & al. acknowledged as possibly
non-monophyletic in their treatment, is circumscribed here
to include only Woodsia and its segregates; the other
"woodsioid" taxa are divided among Athyriaceae,
Cystopteridaceae, Diplaziopsidaceae, Rhachidosoraceae, and
Hemidictyaceae. We provide circumscriptions for each family,
which summarize their morphological, geographical, and
ecological characters, as well as a dichotomous key to the
eupolypod II families. Three of these families-
Diplaziopsidaceae, Hemidictyaceae, and Rhachidosoraceae-were
described in the past year based on molecular phylogenetic
analyses; we provide here their first morphological
treatment.},
Key = {fds230107}
}
@article{fds230111,
Author = {Li, F and Pryer, KM and Windham, MD},
Title = {Gaga, a new fern genus segregated from Cheilanthes
(Pteridaceae)},
Journal = {Systematic Botany},
Volume = {37},
Number = {4},
Pages = {845-860},
Publisher = {American Society of Plant Taxonomists},
Year = {2012},
ISSN = {0363-6445},
url = {http://hdl.handle.net/10161/5988 Duke open
access},
Abstract = {Ongoing molecular phylogenetic studies of cheilanthoid ferns
confirm that the genus Cheilanthes (Pteridaceae) is
polyphyletic. A monophyletic group of species within the
hemionitid clade informally called the “C. marginata
group” is here shown to be distinct from its closest
relatives (the genus Aspidotis) and phylogenetically distant
from the type species of Cheilanthes. This group is here
segregated from Cheilanthes as the newly described genus,
Gaga . In this study, we use molecular data from four DNA
regions (plastid: matK, rbcL, trnG-R; and nuclear: gapCp)
together with spore data to circumscribe the morphological
and geographical boundaries of the new genus and investigate
reticulate evolution within the group. Gaga is distinguished
from Aspidotis by its rounded to attenuate (vs. mucronate)
segment apices, minutely bullate margins of mature leaves
(vs. smooth at 40 ×), and less prominently lustrous and
striate adaxial blade surfaces. The new genus is
distinguished from Cheilanthes s. s. by its strongly
differentiated, inframarginal pseudoindusia, the production
of 64 small or 32 large spores (vs. 32 small or 16 large)
per sporangium, and usually glabrous leaf blades. A total of
nineteen species are recognized within Gaga; seventeen new
combinations are made, and two new species, Gaga germanotta
and Gaga monstraparva , are described.},
Doi = {10.1600/036364412x656626},
Key = {fds230111}
}
@article{fds304307,
Author = {Rothfels, CJ and Sundue, MA and Kuo, L and Larsson, A and Kato, M and Schuettpelz, E and Pryer, KM},
Title = {A revised family–level classification for eupolypod II
ferns (Polypodiidae: Polypodiales)},
Journal = {Taxon},
Volume = {61},
Number = {3},
Pages = {515-533},
Year = {2012},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.1002/tax.613003},
Abstract = {We present a family-level classification for the eupolypod
II clade of leptosporangiate ferns, one of the two major
lineages within the Eupolypods, and one of the few parts of
the fern tree of life where family-level relationships were
not well understood at the time of publication of the 2006
fern classification by Smith & al. Comprising over 2500
species, the composition and particularly the relationships
among the major clades of this group have historically been
contentious and defied phylogenetic resolution until very
recently. Our classification reflects the most current
available data, largely derived from published molecular
phylogenetic studies. In comparison with the five-family
(Aspleniaceae, Blechnaceae, Onocleaceae, Thelypteridaceae,
Woodsiaceae) treatment of Smith & al., we recognize 10
families within the eupolypod II clade. Of these,
Aspleniaceae, Thelypteridaceae, Blechnaceae, and Onocleaceae
have the same composition as treated by Smith & al.
Woodsiaceae, which Smith & al. acknowledged as possibly
non-monophyletic in their treatment, is circumscribed here
to include only Woodsia and its segregates; the other
"woodsioid" taxa are divided among Athyriaceae,
Cystopteridaceae, Diplaziopsidaceae, Rhachidosoraceae, and
Hemidictyaceae. We provide circumscriptions for each family,
which summarize their morphological, geographical, and
ecological characters, as well as a dichotomous key to the
eupolypod II families. Three of these families-
Diplaziopsidaceae, Hemidictyaceae, and Rhachidosoraceae-were
described in the past year based on molecular phylogenetic
analyses; we provide here their first morphological
treatment.},
Doi = {10.1002/tax.613003},
Key = {fds304307}
}
@article{fds197465,
Author = {Beck, J.B. and M.D. Windham and K.M. Pryer},
Title = {Do asexual lineages lead short evolutionary lives? A
case-study from the fern genus Astrolepis},
Journal = {Evolution 65: 3217-3229.},
Year = {2011},
Key = {fds197465}
}
@article{fds230099,
Author = {Wolf, PG and Der, JP and Duffy, AM and Davidson, JB and Grusz, AL and Pryer, KM},
Title = {The evolution of chloroplast genes and genomes in
ferns},
Journal = {Plant molecular biology},
Volume = {76},
Number = {3-5},
Pages = {251-261},
Publisher = {Springer Netherlands},
Year = {2011},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20976559},
Abstract = {Most of the publicly available data on chloroplast (plastid)
genes and genomes come from seed plants, with relatively
little information from their sister group, the ferns. Here
we describe several broad evolutionary patterns and
processes in fern plastid genomes (plastomes), and we
include some new plastome sequence data. We review what we
know about the evolutionary history of plastome structure
across the fern phylogeny and we compare plastome
organization and patterns of evolution in ferns to those in
seed plants. A large clade of ferns is characterized by a
plastome that has been reorganized with respect to the
ancestral gene order (a similar order that is ancestral in
seed plants). We review the sequence of inversions that gave
rise to this organization. We also explore global nucleotide
substitution patterns in ferns versus those found in seed
plants across plastid genes, and we review the high levels
of RNA editing observed in fern plastomes.},
Doi = {10.1007/s11103-010-9706-4},
Key = {fds230099}
}
@article{fds230100,
Author = {Beck, JB and Windham, MD and Pryer, KM},
Title = {Do asexual polyploid lineages lead short evolutionary lives?
A case study from the fern genus Astrolepis},
Journal = {Evolution: International Journal of Organic
Evolution},
Volume = {65},
Number = {11},
Pages = {3217-3229},
Publisher = {Blackwell Publishing Inc Malden, USA},
Year = {2011},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22023587},
Abstract = {A life-history transition to asexuality is typically viewed
as leading to a heightened extinction risk, and a number of
studies have evaluated this claim by examining the relative
ages of asexual versus closely related sexual lineages.
Surprisingly, a rigorous assessment of the age of an asexual
plant lineage has never been published, although asexuality
is extraordinarily common among plants. Here, we estimate
the ages of sexual diploids and asexual polyploids in the
fern genus Astrolepis using a well-supported plastid
phylogeny and a relaxed-clock dating approach. The 50
asexual polyploid samples we included were conservatively
estimated to comprise 19 distinct lineages, including a
variety of auto- and allopolyploid genomic combinations. All
were either the same age or younger than the crown group
comprising their maternal sexual-diploid parents based
simply on their phylogenetic position. Node ages estimated
with the relaxed-clock approach indicated that the average
maximum age of asexual lineages was 0.4 My, and individual
lineages were on average 7 to 47 times younger than the
crown- and total-ages of their sexual parents. Although the
confounding association between asexuality and polyploidy
precludes definite conclusions regarding the effect of
asexuality, our results suggest that asexuality limits
evolutionary potential in Astrolepis.},
Doi = {10.1111/j.1558-5646.2011.01362.x},
Key = {fds230100}
}
@article{fds230101,
Author = {Sigel, EM and Windham, MD and Huiet, L and Yatskievych, G and Pryer,
KM},
Title = {Species relationships and farina evolution in the
cheilanthoid fern genus Argyrochosma (Pteridaceae)},
Journal = {Systematic Botany},
Volume = {36},
Number = {3},
Pages = {554-564},
Publisher = {American Society of Plant Taxonomists},
Year = {2011},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364411x583547},
Abstract = {Convergent evolution driven by adaptation to arid habitats
has made it difficult to identify monophyletic taxa in the
cheilanthoid ferns. Dependence on distinctive, but
potentially homoplastic characters, to define major clades
has resulted in a taxonomic conundrum: all of the largest
cheilanthoid genera have been shown to be polyphyletic. Here
we reconstruct the first comprehensive phylogeny of the
strictly New World cheilanthoid genus Argyrochosma. We use
our reconstruction to examine the evolution of farina
(powdery leaf deposits), which has played a prominent role
in the circumscription of cheilanthoid genera. Our data
indicate that Argyrochosma comprises two major monophyletic
groups: one exclusively non-farinose and the other primarily
farinose. Within the latter group, there has been at least
one evolutionary reversal (loss) of farina and the
development of major chemical variants that characterize
specific clades. Our phylogenetic hypothesis, in combination
with spore data and chromosome counts, also provides a
critical context for addressing the prevalence of polyploidy
and apomixis within the genus. Evidence from these datasets
provides testable hypotheses regarding reticulate evolution
and suggests the presence of several previously undetected
taxa of Argyrochosma.},
Doi = {10.1600/036364411x583547},
Key = {fds230101}
}
@article{fds230113,
Author = {Li, F and Kuo, L and Rothfels, CJ and Ebihara, A and Chiou, W and Windham,
MD and Pryer, KM},
Title = {rbcL and matK earn two thumbs up as the core DNA barcode for
ferns},
Journal = {PLoS One},
Volume = {6},
Number = {10},
Pages = {e26597},
Publisher = {Public Library of Science},
Year = {2011},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22028918},
Abstract = {<h4>Background</h4>DNA barcoding will revolutionize our
understanding of fern ecology, most especially because the
accurate identification of the independent but cryptic
gametophyte phase of the fern's life history--an endeavor
previously impossible--will finally be feasible. In this
study, we assess the discriminatory power of the core plant
DNA barcode (rbcL and matK), as well as alternatively
proposed fern barcodes (trnH-psbA and trnL-F), across all
major fern lineages. We also present plastid barcode data
for two genera in the hyperdiverse polypod clade--Deparia
(Woodsiaceae) and the Cheilanthes marginata group (currently
being segregated as a new genus of Pteridaceae)--to further
evaluate the resolving power of these loci.<h4>Principal
findings</h4>Our results clearly demonstrate the value of
matK data, previously unavailable in ferns because of
difficulties in amplification due to a major rearrangement
of the plastid genome. With its high sequence variation,
matK complements rbcL to provide a two-locus barcode with
strong resolving power. With sequence variation comparable
to matK, trnL-F appears to be a suitable alternative barcode
region in ferns, and perhaps should be added to the core
barcode region if universal primer development for matK
fails. In contrast, trnH-psbA shows dramatically reduced
sequence variation for the majority of ferns. This is likely
due to the translocation of this segment of the plastid
genome into the inverted repeat regions, which are known to
have a highly constrained substitution rate.<h4>Conclusions</h4>Our
study provides the first endorsement of the two-locus
barcode (rbcL+matK) in ferns, and favors trnL-F over
trnH-psbA as a potential back-up locus. Future work should
focus on gathering more fern matK sequence data to
facilitate universal primer development.},
Doi = {10.1371/journal.pone.0026597},
Key = {fds230113}
}
@article{fds230114,
Author = {Pryer, KM and Schuettpelz, E and Huiet, L and Grusz, AL and Rothfels,
CJ and Avent, T and Schwartz, D and Windham, MD},
Title = {DNA barcoding exposes a case of mistaken identity in the
fern horticultural trade.},
Journal = {Molecular ecology resources},
Volume = {10},
Number = {6},
Pages = {979-985},
Year = {2010},
Month = {November},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21565107},
Abstract = {Using cheilanthoid ferns, we provide an example of how DNA
barcoding approaches can be useful to the horticultural
community for keeping plants in the trade accurately
identified. We use plastid rbcL, atpA, and trnG-R sequence
data to demonstrate that a fern marketed as Cheilanthes
wrightii (endemic to the southwestern USA and northern
Mexico) in the horticultural trade is, in fact, Cheilanthes
distans (endemic to Australia and adjacent islands). Public
and private (accessible with permission) databases contain a
wealth of DNA sequence data that are linked to vouchered
plant material. These data have uses beyond those for which
they were originally generated, and they provide an
important resource for fostering collaborations between the
academic and horticultural communities. We strongly advocate
the barcoding approach as a valuable new technology
available to the horticulture industry to help correct plant
identification errors in the international
trade.},
Doi = {10.1111/j.1755-0998.2010.02858.x},
Key = {fds230114}
}
@article{fds230115,
Author = {Korall, P and Schuettpelz, E and Pryer, KM},
Title = {Abrupt deceleration of molecular evolution linked to the
origin of arborescence in ferns.},
Journal = {Evolution; international journal of organic
evolution},
Volume = {64},
Number = {9},
Pages = {2786-2792},
Year = {2010},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20394660},
Abstract = {Molecular rate heterogeneity, whereby rates of molecular
evolution vary among groups of organisms, is a
well-documented phenomenon. Nonetheless, its causes are
poorly understood. For animals, generation time is
frequently cited because longer-lived species tend to have
slower rates of molecular evolution than their shorter-lived
counterparts. Although a similar pattern has been uncovered
in flowering plants, using proxies such as growth form, the
underlying process has remained elusive. Here, we find a
deceleration of molecular evolutionary rate to be coupled
with the origin of arborescence in ferns. Phylogenetic
branch lengths within the “tree fern” clade are
considerably shorter than those of closely related lineages,
and our analyses demonstrate that this is due to a
significant difference in molecular evolutionary rate.
Reconstructions reveal that an abrupt rate deceleration
coincided with the evolution of the long-lived tree-like
habit at the base of the tree fern clade. This suggests that
a generation time effect may well be ubiquitous across the
green tree of life, and that the search for a responsible
mechanism must focus on characteristics shared by all
vascular plants. Discriminating among the possibilities will
require contributions from various biological
disciplines,but will be necessary for a full appreciation of
molecular evolution.},
Doi = {10.1111/j.1558-5646.2010.01000.x},
Key = {fds230115}
}
@article{fds230116,
Author = {Beck, JB and Windham, MD and Yatskievych, G and Pryer,
KM},
Title = {A Diploids-First Approach to Species Delimitation and
Interpreting Polyploid Evolution in the Fern Genus
Astrolepis (Pteridaceae)},
Journal = {Systematic botany},
Volume = {35},
Number = {2},
Pages = {223-234},
Publisher = {American Society of Plant Taxonomists},
Year = {2010},
Month = {April},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364410791638388},
Abstract = {Polyploidy presents a challenge to those wishing to delimit
the species within a group and reconstruct the phylogenetic
relationships among these taxa. A clear understanding of the
tree-like relationships among the diploid species can
provide a framework upon which to reconstruct the reticulate
events that gave rise to the polyploid lineages. In this
study we apply this ““diploids-first”” strategy to
the fern genus Astrolepis (Pteridaceae). Diploids are
identified using the number of spores per sporangium and
spore size. Analyses of plastid and low-copy nuclear
sequence data provide well-supported estimates of
phylogenetic relationships, including strong evidence for
two morphologically distinctive diploid lineages not
recognized in recent treatments. One of these corresponds to
the type of Notholaena deltoidea, a species that has not
been recognized in any modern treatment of Astrolepis. This
species is resurrected here as the new combination
Astrolepis deltoidea . The second novel lineage is that of a
diploid initially hypothesized to exist by molecular and
morphological characteristics of several established
Astrolepis allopolyploids. This previously missing diploid
species is described here as Astrolepis obscura.},
Doi = {10.1600/036364410791638388},
Key = {fds230116}
}
@article{fds353353,
Author = {Larsson, A and Rothfels, CJ and Kuo, LY and Shuettpelz, E and Pryer, K and Korall, P},
Title = {Var hör hällebräken, ekbräken och svartbräknar
hemma?-Äntligen en fylogeni över Eupolypods
II},
Journal = {Systematikdagarna, Göteborg, 22-23 november,
2010},
Year = {2010},
Key = {fds353353}
}
@article{fds230074,
Author = {Windham, MD and Huiet, L and Schuettpelz, E and Grusz, AL and Rothfels,
C and Beck, J and Yatskievych, G and Pryer, KM},
Title = {Using Plastid and Nuclear DNA Sequences to Redraw Generic
Boundaries and Demystif Species Complexes in Cheilanthoid
Ferns.},
Journal = {AMERICAN FERN JOURNAL},
Volume = {99},
Number = {2},
Pages = {128-132},
Publisher = {AMER FERN SOC INC},
Year = {2009},
Month = {April},
ISSN = {0002-8444},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000269677200010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds230074}
}
@article{fds230095,
Author = {Pryer, KM and Hearn, DJ},
Title = {Evolution of leaf form in marsileaceous ferns: evidence for
heterochrony},
Journal = {Evolution: International Journal of Organic
Evolution},
Volume = {63},
Number = {2},
Pages = {498-513},
Publisher = {Blackwell Publishing Inc Malden, USA},
Year = {2009},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19154361},
Abstract = {Using an explicit phylogenetic framework, ontogenetic
patterns of leaf form are compared among the three genera of
marsileaceous ferns (Marsilea, Regnellidium, and Pilularia)
with the outgroup Asplenium to address the hypothesis that
heterochrony played a role in their evolution. We performed
a Fourier analysis on a developmental sequence of leaves
from individuals of these genera. Principal components
analysis of the harmonic coefficients was used to
characterize the ontogenetic trajectories of leaf form in a
smaller dimensional space. Results of this study suggest
that the "evolutionary juvenilization" observed in these
leaf sequences is best described using a mixed model of
heterochrony (accelerated growth rate and early termination
at a simplified leaf form). The later stages of the
ancestral, more complex, ontogenetic pattern were lost in
Marsileaceae, giving rise to the simplified adult leaves of
Marsilea, Regnellidium, and Pilularia. Life-history traits
such as ephemeral and uncertain habitats, high reproductive
rates, and accelerated maturation, which are typical for
marsileaceous ferns, suggest that they may be "r
strategists." The evidence for heterochrony presented here
illustrates that it has resulted in profound ecological and
morphological consequences for the entire life history of
Marsileaceae.},
Doi = {10.1111/j.1558-5646.2008.00562.x},
Key = {fds230095}
}
@article{fds230096,
Author = {Schneider, H and Smith, AR and Pryer, KM},
Title = {Is morphology really at odds with molecules in estimating
fern phylogeny?},
Journal = {Systematic Botany},
Volume = {34},
Number = {3},
Pages = {455-475},
Publisher = {American Society of Plant Taxonomists},
Year = {2009},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364409789271209},
Abstract = {Using a morphological dataset of 136 vegetative and
reproductive characters, we infer the tracheophyte phylogeny
with an emphasis on early divergences of ferns
(monilophytes). The dataset comprises morphological,
anatomical, biochemical, and some DNA structural characters
for a taxon sample of 35 species, including representatives
of all major lineages of vascular plants, especially ferns.
Phylogenetic relationships among vascular plants are
reconstructed using maximum parsimony and Bayesian
inference. Both approaches yield similar relationships and
provide evidence for three major lineages of extant vascular
plants: lycophytes, ferns, and seed plants. Lycophytes are
sister to the euphyllophyte clade, which comprises the fern
and seed plant lineages. The fern lineage consists of five
clades: horsetails, whisk ferns, ophioglossoids,
marattioids, and leptosporangiate ferns. This lineage is
supported by characters of the spore wall and has a
parsimony bootstrap value of 76%, although the Bayesian
posterior probability is only 0.53. Each of the five fern
clades is well supported, but the relationships among them
lack statistical support. Our independent phylogenetic
analyses of morphological evidence recover the same deep
phylogenetic relationships among tracheophytes as found in
previous studies utilizing DNA sequence data, but differ in
some ways within seed plants and within ferns. We discuss
the extensive independent evolution of the five extant fern
clades and the evidence for the placement of whisk ferns and
horsetails in our morphological analyses.},
Doi = {10.1600/036364409789271209},
Key = {fds230096}
}
@article{fds230097,
Author = {Grusz, AL and Windham, MD and Pryer, KM},
Title = {Deciphering the origins of apomictic polyploids in the
Cheilanthes yavapensis complex (Pteridaceae)},
Journal = {American Journal of Botany},
Volume = {96},
Number = {9},
Pages = {1636-1645},
Publisher = {Botanical Society of America},
Year = {2009},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21622350},
Abstract = {Deciphering species relationships and hybrid origins in
polyploid agamic species complexes is notoriously difficult.
In this study of cheilanthoid ferns, we demonstrate
increased resolving power for clarifying the origins of
polyploid lineages by integrating evidence from a diverse
selection of biosystematic methods. The prevalence of
polyploidy, hybridization, and apomixis in ferns suggests
that these processes play a significant role in their
evolution and diversification. Using a combination of
systematic approaches, we investigated the origins of
apomictic polyploids belonging to the Cheilanthes yavapensis
complex. Spore studies allowed us to assess ploidy levels;
plastid and nuclear DNA sequencing revealed evolutionary
relationships and confirmed the putative progenitors (both
maternal and paternal) of taxa of hybrid origin; enzyme
electrophoretic evidence provided information on genome
dosage in allopolyploids. We find here that the widespread
apomictic triploid, Cheilanthes lindheimeri, is an
autopolyploid derived from a rare, previously undetected
sexual diploid. The apomictic triploid Cheilanthes wootonii
is shown to be an interspecific hybrid between C. fendleri
and C. lindheimeri, whereas the apomictic tetraploid C.
yavapensis is comprised of two cryptic and geographically
distinct lineages. We show that earlier morphology-based
hypotheses of species relationships, while not altogether
incorrect, only partially explain the complicated
evolutionary history of these ferns.},
Doi = {10.3732/ajb.0900019},
Key = {fds230097}
}
@article{fds230098,
Author = {Schuettpelz, E and Pryer, KM},
Title = {Evidence for a Cenozoic radiation of ferns in an
angiosperm-dominated canopy},
Journal = {Proceedings of the National Academy of Sciences},
Volume = {106},
Number = {27},
Pages = {11200-11205},
Publisher = {National Academy of Sciences},
Year = {2009},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19567832},
Abstract = {In today's angiosperm-dominated terrestrial ecosystems,
leptosporangiate ferns are truly exceptional--accounting for
80% of the approximately 11,000 nonflowering vascular plant
species. Recent studies have shown that this remarkable
diversity is mostly the result of a major leptosporangiate
radiation beginning in the Cretaceous, following the rise of
angiosperms. This pattern is suggestive of an ecological
opportunistic response, with the proliferation of flowering
plants across the landscape resulting in the formation of
many new niches--both on forest floors and within forest
canopies--into which leptosporangiate ferns could diversify.
At present, one-third of leptosporangiate species grow as
epiphytes in the canopies of angiosperm-dominated tropical
rain forests. However, we know too little about the
evolutionary history of epiphytic ferns to assess whether or
not their diversification was in fact linked to the
establishment of these forests, as would be predicted by the
ecological opportunistic response hypothesis. Here we
provide new insight into leptosporangiate diversification
and the evolution of epiphytism by integrating a 400-taxon
molecular dataset with an expanded set of fossil age
constraints. We find evidence for a burst of fern
diversification in the Cenozoic, apparently driven by the
evolution of epiphytism. Whether this explosive radiation
was triggered simply by the establishment of modern
angiosperm-dominated tropical rain forest canopies, or
spurred on by some other large-scale extrinsic factor (e.g.,
climate change) remains to be determined. In either case, it
is clear that in both the Cretaceous and Cenozoic,
leptosporangiate ferns were adept at exploiting newly
created niches in angiosperm-dominated ecosystems.},
Doi = {10.1073/pnas.0811136106},
Key = {fds230098}
}
@article{fds230088,
Author = {Christenhusz, MJM and Tuomisto, H and Metzgar, JS and Pryer,
KM},
Title = {Evolutionary relationships within the Neotropical,
eusporangiate fern genus Danaea (Marattiaceae)},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {46},
Number = {1},
Pages = {34-48},
Publisher = {Academic Press},
Year = {2008},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18042403},
Abstract = {Genera within the eusporangiate fern family Marattiaceae
have long been neglected in taxonomic and systematic
studies. Here we present the first phylogenetic hypothesis
of relationships within the exclusively Neotropical genus
Danaea based on a sampling of 60 specimens representing 31
species from various Neotropical sites. We used DNA sequence
data from three plastid regions (atpB, rbcL, and trnL-F),
morphological characters from both herbarium specimens and
live plants observed in the field, and geographical and
ecological information to examine evolutionary patterns.
Eleven representatives of five other marattioid genera
(Angiopteris, Archangiopteris, Christensenia, Macroglossum,
and Marattia) were used to root the topology. We identified
three well-supported clades within Danaea that are
consistent with morphological characters: the "leprieurii"
clade (containing species traditionally associated with the
name D. elliptica), the "nodosa" clade (containing all
species traditionally associated with the name D. nodosa),
and the "alata" clade (containing all other species). All
three clades are geographically and ecologically widely
distributed, but subclades within them show various
distribution patterns. Our phylogenetic hypothesis provides
a robust framework within which broad questions related to
the morphology, taxonomy, biogeography, evolution, and
ecology of these ferns can be addressed.},
Doi = {10.1016/j.ympev.2007.09.015},
Key = {fds230088}
}
@article{fds230090,
Author = {Nagalingum, NS and Nowak, MD and Pryer, KM},
Title = {Assessing phylogenetic relationships in extant heterosporous
ferns (Salviniales), with a focus on Pilularia and
Salvinia},
Journal = {Botanical Journal of the Linnean Society},
Volume = {157},
Number = {4},
Pages = {673-685},
Publisher = {Oxford University Press},
Year = {2008},
ISSN = {0024-4074},
url = {http://dx.doi.org/10.1111/j.1095-8339.2008.00806.x},
Abstract = {Heterosporous ferns (Salviniales) are a group of
approximately 70 species that produce two types of spores
(megaspores and microspores). Earlier broad-scale
phylogenetic studies on the order typically focused on one
or, at most, two species per genus. In contrast, our study
samples numerous species for each genus, wherever possible,
accounting for almost half of the species diversity of the
order. Our analyses resolve Marsileaceae, Salviniaceae and
all of the component genera as monophyletic. Salviniaceae
incorporate Salvinia and Azolla; in Marsileaceae, Marsilea
is sister to the clade of Regnellidium and Pilularia- this
latter clade is consistently resolved, but not always
strongly supported. Our individual species-level
investigations for Pilularia and Salvinia, together with
previously published studies on Marsilea and Azolla
(Regnellidium is monotypic), provide phylogenies within all
genera of heterosporous ferns. The Pilularia phylogeny
reveals two groups: Group I includes the European taxa P.
globulifera and P. minuta; Group II consists of P.
americana, P. novae-hollandiae and P. novae-zelandiae from
North America, Australia and New Zealand, respectively, and
are morphologically difficult to distinguish. Based on their
identical molecular sequences and morphology, we regard P.
novae-hollandiae and P. novae-zelandiae to be conspecific;
the name P. novae-hollandiae has nomenclatural priority. The
status of P. americana requires further investigation as it
consists of two geographically and genetically distinct
North American groups and also shows a high degree of
sequence similarity to P. novae-hollandiae. Salvinia also
comprises biogeographically distinct units - a Eurasian
group (S. natans and S. cucullata) and an American clade
that includes the noxious weed S. molesta, as well as S.
oblongifolia and S. minima.},
Doi = {10.1111/j.1095-8339.2008.00806.x},
Key = {fds230090}
}
@article{fds230091,
Author = {Metzgar, JS and Skog, JE and Zimmer, EA and Pryer,
KM},
Title = {The paraphyly of Osmunda is confirmed by phylogenetic
analyses of seven plastid loci},
Journal = {Systematic Botany},
Volume = {33},
Number = {1},
Pages = {31-36},
Publisher = {American Society of Plant Taxonomists},
Year = {2008},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364408783887528},
Abstract = {To resolve phylogenetic relationships among all genera and
subgenera in Osmundaceae, we analyzed over 8,500 characters
of DNA sequence data from seven plastid loci (atpA, rbcL,
rbcL–accD, rbcL–atpB, rps4–trnS,
trnG–trnR, and trnL–trnF). Our results confirm
those from earlier anatomical and single-gene (rbcL) studies
that suggested Osmunda s.l. is paraphyletic. Osmunda
cinnamomea is sister to the remainder of Osmundaceae
(Leptopteris, Todea, and Osmunda s.s.). We support the
recognition of a monotypic fourth genus, Osmundastrum, to
reflect these results. We also resolve subgeneric
relationships within Osmunda s.s. and find that subg.
Claytosmunda is strongly supported as sister to the rest of
Osmunda. A stable, well-supported classification for extant
Osmundaceae is proposed, along with a key to all genera and
subgenera.},
Doi = {10.1600/036364408783887528},
Key = {fds230091}
}
@article{fds230092,
Author = {Rothfels, CJ and Windham, MD and Grusz, AL and Gastony, GJ and Pryer,
KM},
Title = {Toward a monophyletic Notholaena (Pteridaceae): Resolving
patterns of evolutionary convergence in xeric‐adapted
ferns},
Journal = {Taxon},
Volume = {57},
Number = {3},
Pages = {712-724},
Year = {2008},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.1002/tax.573005},
Abstract = {Cheilanthoid ferns (Pteridaceae) are a diverse and
ecologically important clade, unusual among ferns for their
ability to colonize and diversify within xeric habitats.
These extreme habitats are thought to drive the extensive
evolutionary convergence, and thus morphological homoplasy,
that has long thwarted a natural classification of
cheilanthoid ferns. Here we present the first multigene
phylogeny to focus on taxa traditionally assigned to the
large genus Notholaena. New World taxa (Notholaena sensu
Tryon) are only distantly related to species occurring in
the Old World (Notholaena sensu Pichi Sermolli). The
circumscription of Notholaena adopted in recent American
floras is shown to be paraphyletic, with species usually
assigned to Cheilanthes and Cheiloplecton nested within it.
The position of Cheiloplecton is particularly surprising -
given its well-developed false indusium and non-farinose
blade, it is morphologically anomalous within the
"notholaenoids". In addition to clarifying natural
relationships, the phylogenetic hypothesis presented here
helps to resolve outstanding nomenclatural issues and
provides a basis for examining character evolution within
this diverse, desert-adapted clade.},
Doi = {10.1002/tax.573005},
Key = {fds230092}
}
@article{fds230093,
Author = {Schuettpelz, E and Grusz, AL and Windham, MD and Pryer,
KM},
Title = {The utility of nuclear gapCp in resolving polyploid fern
origins},
Journal = {Systematic Botany},
Volume = {33},
Number = {4},
Pages = {621-629},
Publisher = {American Society of Plant Taxonomists},
Year = {2008},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364408786500127},
Abstract = {Although polyploidy is rampant in ferns and plays a major
role in shaping their diversity, the evolutionary history of
many polyploid species remains poorly understood. Nuclear
DNA sequences can provide valuable information for
identifying polyploid origins; however, remarkably few
nuclear markers have been developed specifically for ferns,
and previously published primer sets do not work well in
many fern lineages. In this study, we present new primer
sequences for the amplification of a portion of the nuclear
gapCp gene (encoding a glyceraldehyde-3-phosphate
dehydrogenase). Through a broad survey across ferns, we
demonstrate that these primers are nearly universal for this
clade. With a case study in cheilanthoids, we show that this
rapidly evolving marker is a powerful tool for
discriminating between autopolyploids and allopolyploids.
Our results indicate that gapCp holds considerable potential
for addressing species-level questions across the fern tree
of life.},
Doi = {10.1600/036364408786500127},
Key = {fds230093}
}
@article{fds230094,
Author = {Hennequin, S and Schuettpelz, E and Pryer, KM and Ebihara, A and Dubuisson, J},
Title = {Divergence times and the evolution of epiphytism in filmy
ferns (Hymenophyllaceae) revisited},
Journal = {International Journal of Plant Sciences},
Volume = {169},
Number = {9},
Pages = {1278-1287},
Publisher = {The University of Chicago Press},
Year = {2008},
ISSN = {1058-5893},
url = {http://dx.doi.org/10.1086/591983},
Abstract = {Although the phylogeny of the filmy fern family
(Hymenophyllaceae) is rapidly coming into focus, much
remains to be uncovered concerning the evolutionary history
of this clade. In this study, we use two data sets
(108-taxon rbcL+ rps4, 204-taxon rbcL) and fossil
constraints to examine the diversification of filmy ferns
and the evolution of their ecology within a temporal
context. Our penalized likelihood analyses (with both data
sets) indicate that the initial divergences within the
Hymenophyllaceae (resulting in extant lineages) and those
within one of the two major clades (trichomanoids) occurred
in the early to middle Mesozoic. There was a considerable
delay in the crown group diversification of the other major
clade (hymenophylloids), which began to diversify only in
the Cretaceous. Maximum likelihood and Bayesian character
state reconstructions across the broadly sampled single-gene
(rbcL) phylogeny do not allow us to unequivocally infer the
ancestral habit for the family or for its two major clades.
However, adding a second gene (rps4) with a more restricted
taxon sampling results in a hypothesis in which filmy ferns
were ancestrally terrestrial, with epiphytism having evolved
several times independently during the Cretaceous. © 2008
by The University of Chicago. All rights
reserved.},
Doi = {10.1086/591983},
Key = {fds230094}
}
@article{fds353355,
Author = {Schuettpelz, ERIC and Pryer, KATHLEENM},
Title = {Fern phylogeny},
Journal = {Biology and evolution of ferns and lycophytes},
Volume = {395},
Pages = {416},
Publisher = {Cambridge University Press Cambridge},
Year = {2008},
Key = {fds353355}
}
@article{fds230082,
Author = {Nagalingum, NS and Schneider, H and Pryer, KM},
Title = {Molecular phylogenetic relationships and morphological
evolution in the heterosporous fern genus
Marsilea},
Journal = {Systematic Botany},
Volume = {32},
Number = {1},
Pages = {16-25},
Publisher = {American Society of Plant Taxonomists},
Year = {2007},
ISSN = {0363-6445},
url = {http://dx.doi.org/10.1600/036364407780360256},
Abstract = {Using six plastid regions, we present a phylogeny for 26
species of the heterosporous fern genus Marsilea. Two
well-supported groups within Marsilea are identified. Group
I includes two subgroups, and is relatively species-poor.
Species assignable to this group have glabrous leaves
(although land leaves may have a few hairs), sporocarps
lacking both a raphe and teeth, and share a preference for
submerged conditions (i.e., they are intolerant of
desiccation). Group II is relatively diverse, and its
members have leaves that are pubescent, sporocarps that bear
a raphe and from zero to two teeth, and the plants are often
emergent at the edges of lakes and ponds. Within Group II,
five subgroups receive robust support: three are
predominantly African, one is New World, and one Old World.
Phylogenetic assessment of morphological evolution suggests
that the presence of an inferior sporocarp tooth and the
place of sporocarp maturation are homoplastic characters,
and are therefore of unreliable taxonomic use at an
infrageneric level. In contrast, the presence of a raphe and
superior sporocarp tooth are reliable synapomorphies for
classification within Marsilea.},
Doi = {10.1600/036364407780360256},
Key = {fds230082}
}
@article{fds230084,
Author = {Haugen, P and Bhattacharya, D and Palmer, JD and Turner, S and Lewis,
LA and Pryer, KM},
Title = {Cyanobacterial ribosomal RNA genes with multiple,
endonuclease-encoding group I introns},
Journal = {BMC evolutionary biology},
Volume = {7},
Number = {1},
Pages = {159},
Publisher = {BioMed Central},
Year = {2007},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17825109},
Abstract = {<h4>Background</h4>Group I introns are one of the four major
classes of introns as defined by their distinct splicing
mechanisms. Because they catalyze their own removal from
precursor transcripts, group I introns are referred to as
autocatalytic introns. Group I introns are common in fungal
and protist nuclear ribosomal RNA genes and in organellar
genomes. In contrast, they are rare in all other organisms
and genomes, including bacteria.<h4>Results</h4>Here we
report five group I introns, each containing a LAGLIDADG
homing endonuclease gene (HEG), in large subunit (LSU) rRNA
genes of cyanobacteria. Three of the introns are located in
the LSU gene of Synechococcus sp. C9, and the other two are
in the LSU gene of Synechococcus lividus strain C1.
Phylogenetic analyses show that these introns and their HEGs
are closely related to introns and HEGs located at
homologous insertion sites in organellar and bacterial rDNA
genes. We also present a compilation of group I introns with
homing endonuclease genes in bacteria.<h4>Conclusion</h4>We
have discovered multiple HEG-containing group I introns in a
single bacterial gene. To our knowledge, these are the first
cases of multiple group I introns in the same bacterial gene
(multiple group I introns have been reported in at least one
phage gene and one prophage gene). The HEGs each contain one
copy of the LAGLIDADG motif and presumably function as
homodimers. Phylogenetic analysis, in conjunction with their
patchy taxonomic distribution, suggests that these
intron-HEG elements have been transferred horizontally among
organelles and bacteria. However, the mode of transfer and
the nature of the biological connections among the
intron-containing organisms are unknown.},
Doi = {10.1186/1471-2148-7-159},
Key = {fds230084}
}
@article{fds230085,
Author = {Metzgar, JS and Schneider, H and Pryer, KM},
Title = {Phylogeny and divergence time estimates for the fern genus
Azolla (Salviniaceae)},
Journal = {International Journal of Plant Sciences},
Volume = {168},
Number = {7},
Pages = {1045-1053},
Publisher = {The University of Chicago Press},
Year = {2007},
ISSN = {1058-5893},
url = {http://dx.doi.org/10.1086/519007},
Abstract = {A phylogeny for all extant species of the heterosporous fern
genus Azolla is presented here based on more than 5000 base
pairs of DNA sequence data from six plastid loci (rbcL,
atpB, rps4, trnL-trnF, trnG-trnR, and rps4-trnS). Our
results are in agreement with other recent molecular
phylogenetic hypotheses that support the monophyly of
sections Azolla and Rhizosperma and the proposed
relationships within section Azolla. Divergence times are
estimated within Azolla using a penalized likelihood
approach, integrating data from fossils and DNA sequences.
Penalized likelihood analyses estimate a divergence time of
50.7 Ma (Eocene) for the split between sections Azolla and
Rhizosperma, 32.5 Ma (Oligocene) for the divergence of
Azolla nilotica from A. pinnata within section Rhizosperma,
and 16.3 Ma (Miocene) for the divergence of the two lineages
within section Azolla (the A. rubra lineage from the A.
mexicana complex).},
Doi = {10.1086/519007},
Key = {fds230085}
}
@article{fds230086,
Author = {Korall, P and Conant, DS and Metzgar, JS and Schneider, H and Pryer,
KM},
Title = {A molecular phylogeny of scaly tree ferns
(Cyatheaceae)},
Journal = {American Journal of Botany},
Volume = {94},
Number = {5},
Pages = {873-886},
Publisher = {Botanical Society of America},
Year = {2007},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21636456},
Abstract = {Tree ferns recently were identified as the closest sister
group to the hyperdiverse clade of ferns, the polypods.
Although most of the 600 species of tree ferns are
arborescent, the group encompasses a wide range of
morphological variability, from diminutive members to the
giant scaly tree ferns, Cyatheaceae. This well-known family
comprises most of the tree fern diversity (∼500 species)
and is widespread in tropical, subtropical, and south
temperate regions of the world. Here we investigate the
phylogenetic relationships of scaly tree ferns based on DNA
sequence data from five plastid regions (rbcL, rbcL-accD
IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal
dichotomy resolves Sphaeropteris as sister to all other taxa
and scale features support these two clades: Sphaeropteris
has conform scales, whereas all other taxa have marginate
scales. The marginate-scaled clade consists of a basal
trichotomy, with the three groups here termed (1) Cyathea
(including Cnemidaria, Hymenophyllopsis, Trichipteris), (2)
Alsophila sensu stricto, and (3) Gymnosphaera (previously
recognized as a section within Alsophila) + A. capensis.
Scaly tree ferns display a wide range of indusial
structures, and although indusium shape is homoplastic it
does contain useful phylogenetic information that supports
some of the larger clades recognised.},
Doi = {10.3732/ajb.94.5.873},
Key = {fds230086}
}
@article{fds230087,
Author = {Schuettpelz, E and Schneider, H and Huiet, L and Windham, MD and Pryer,
KM},
Title = {A molecular phylogeny of the fern family Pteridaceae:
assessing overall relationships and the affinities of
previously unsampled genera},
Journal = {Molecular phylogenetics and evolution},
Volume = {44},
Number = {3},
Pages = {1172-1185},
Publisher = {Academic Press},
Year = {2007},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17570688},
Abstract = {The monophyletic Pteridaceae accounts for roughly 10% of
extant fern diversity and occupies an unusually broad range
of ecological niches, including terrestrial, epiphytic,
xeric-adapted rupestral, and even aquatic species. In this
study, we present the results of the first broad-scale and
multi-gene phylogenetic analyses of these ferns, and
determine the affinities of several previously unsampled
genera. Our analyses of two newly assembled data sets
(including 169 newly obtained sequences) resolve five major
clades within the Pteridaceae: cryptogrammoids,
ceratopteridoids, pteridoids, adiantoids, and cheilanthoids.
Although the composition of these clades is in general
agreement with earlier phylogenetic studies, it is very much
at odds with the most recent subfamilial classification. Of
the previously unsampled genera, two (Neurocallis and
Ochropteris) are nested within the genus Pteris; two others
(Monogramma and Rheopteris) are early diverging vittarioid
ferns, with Monogramma resolved as polyphyletic; the last
previously unsampled genus (Adiantopsis) occupies a rather
derived position among cheilanthoids. Interestingly, some
clades resolved within the Pteridaceae can be characterized
by their ecological preferences, suggesting that the initial
diversification in this family was tied to ecological
innovation and specialization. These processes may well be
the basis for the diversity and success of the Pteridaceae
today.},
Doi = {10.1016/j.ympev.2007.04.011},
Key = {fds230087}
}
@article{fds230089,
Author = {Schuettpelz, E and Pryer, KM},
Title = {Fern phylogeny inferred from 400 leptosporangiate species
and three plastid genes},
Journal = {Taxon},
Volume = {56},
Number = {4},
Pages = {1037-1050},
Publisher = {WILEY},
Year = {2007},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.2307/25065903},
Abstract = {In an effort to obtain a solid and balanced approximation of
global fern phylogeny to serve as a tool for addressing
large-scale evolutionary questions, we assembled and
analyzed the most inclusive molecular dataset for
leptosporangiate ferns to date. Three plastid genes (rbcL,
atpB, atpA), totaling more than 4,000 bp, were sequenced for
each of 400 leptosporangiate fern species (selected using a
proportional sampling approach) and five outgroups. Maximum
likelihood analysis of these data yielded an especially
robust phylogeny: 80% of the nodes were supported by a
maximum likelihood bootstrap percentage ≥ 70. The scope of
our analysis provides unprecedented insight into overall
fern relationships, not only delivering additional support
for the deepest leptosporangiate divergences, but also
uncovering the composition of more recently emerging clades
and their relationships to one another.},
Doi = {10.2307/25065903},
Key = {fds230089}
}
@article{fds230076,
Author = {Korall, P and Conant, DS and Schneider, H and Ueda, K and Nishida, H and Pryer, KM},
Title = {On the Phylogenetic Position of Cystodium It's Not a Tree
Fern–It's a Polypod!},
Journal = {American Fern Journal},
Volume = {96},
Number = {2},
Pages = {45-53},
Publisher = {The American Fern Society},
Year = {2006},
ISSN = {0002-8444},
url = {http://dx.doi.org/10.1640/0002-8444(2006)96[45:OTPPOC]2.0.CO;2},
Abstract = {The phylogenetic position of Cystodium J. Sm. is studied
here for the first time using DNA sequence data. Based on a
broad sampling of leptosporangiate ferns and two plastid
genes (rbcL and atpB), we show that Cystodium does not
belong to the tree fern family Dicksoniaceae, as previously
thought. Our results strongly support including Cystodium
within the large polypod clade, and suggest its close
relationship to the species-poor grade taxa at the base of
the polypod topology (Sphenomeris and Lonchitis, or
Saccoloma in this study). Further studies, with an expanded
taxon sampling within polypods, are needed to fully
understand the more precise phylogenetic relationships of
Cystodium.},
Doi = {10.1640/0002-8444(2006)96[45:OTPPOC]2.0.CO;2},
Key = {fds230076}
}
@article{fds230078,
Author = {Schuettpelz, E and Pryer, KM},
Title = {Reconciling extreme branch length differences: decoupling
time and rate through the evolutionary history of filmy
ferns},
Journal = {Systematic Biology},
Volume = {55},
Number = {3},
Pages = {485-502},
Publisher = {Society of Systematic Zoology},
Year = {2006},
ISSN = {1063-5157},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16861211},
Abstract = {The rate of molecular evolution is not constant across the
Tree of Life. Characterizing rate discrepancies and
evaluating the relative roles of time and rate along
branches through the past are both critical to a full
understanding of evolutionary history. In this study, we
explore the interactions of time and rate in filmy ferns
(Hymenophyllaceae), a lineage with extreme branch length
differences between the two major clades. We test for the
presence of significant rate discrepancies within and
between these clades, and we separate time and rate across
the filmy fern phylogeny to simultaneously yield an
evolutionary time scale of filmy fern diversification and
reconstructions of ancestral rates of molecular evolution.
Our results indicate that the branch length disparity
observed between the major lineages of filmy ferns is indeed
due to a significant difference in molecular evolutionary
rate. The estimation of divergence times reveals that the
timing of crown group diversification was not concurrent for
the two lineages, and the reconstruction of ancestral rates
of molecular evolution points to a substantial rate
deceleration in one of the clades. Further analysis suggests
that this may be due to a genome-wide deceleration in the
rate of nucleotide substitution.},
Doi = {10.1080/10635150600755438},
Key = {fds230078}
}
@article{fds230079,
Author = {Korall, P and Pryer, KM and Metzgar, JS and Schneider, H and Conant,
DS},
Title = {Tree ferns: monophyletic groups and their relationships as
revealed by four protein-coding plastid loci},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {39},
Number = {3},
Pages = {830-845},
Publisher = {Academic Press},
Year = {2006},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16481203},
Abstract = {Tree ferns are a well-established clade within
leptosporangiate ferns. Most of the 600 species (in seven
families and 13 genera) are arborescent, but considerable
morphological variability exists, spanning the giant scaly
tree ferns (Cyatheaceae), the low, erect plants
(Plagiogyriaceae), and the diminutive endemics of the
Guayana Highlands (Hymenophyllopsidaceae). In this study, we
investigate phylogenetic relationships within tree ferns
based on analyses of four protein-coding, plastid loci
(atpA, atpB, rbcL, and rps4). Our results reveal four
well-supported clades, with genera of Dicksoniaceae (sensu )
interspersed among them: (A) (Loxomataceae, (Culcita,
Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia,
Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with
Hymenophyllopsidaceae nested within. How these four groups
are related to one other, to Thyrsopteris, or to Metaxyaceae
is weakly supported. Our results show that Dicksoniaceae and
Cyatheaceae, as currently recognised, are not monophyletic
and new circumscriptions for these families are
needed.},
Doi = {10.1016/j.ympev.2006.01.001},
Key = {fds230079}
}
@article{fds230080,
Author = {Nagalingum, NS and Schneider, H and Pryer, KM},
Title = {Comparative morphology of reproductive structures in
heterosporous water ferns and a reevaluation of the
sporocarp},
Journal = {International Journal of Plant Sciences},
Volume = {167},
Number = {4},
Pages = {805-815},
Publisher = {The University of Chicago Press},
Year = {2006},
ISSN = {1058-5893},
url = {http://dx.doi.org/10.1086/503848},
Abstract = {Heterosporous water ferns (Marsileaceae and Salviniaceae)
are the only extant group of plants to have evolved
heterospory since the Paleozoic. These ferns possess unusual
reproductive structures traditionally termed
“sporocarps.” Using an evolutionary framework,
we critically examine the complex homology issues pertaining
to these structures. Comparative morphological study reveals
that all heterosporous ferns bear indusiate sori on a
branched, nonlaminate structure that we refer to as the
sorophore; this expanded definition highlights homology
previously obscured by the use of different terms. By using
a homology-based concept, we aim to discontinue the use of
historically and functionally based morphological
terminology. We recognize the sorophore envelope as a
structure that surrounds the sorophore and sori. The
sorophore envelope is present in Marsileaceae as a
sclerenchymatous sporocarp wall and in Azolla as a
parenchymatous layer, but it is absent in Salvinia. Both
homology assessments and phylogenetic character-state
reconstructions using the Cretaceous fossil Hydropteris are
consistent with a single origin of the sorophore envelope in
heterosporous ferns. Consequently, we restrict the term
“sporocarp” to a sorophore envelope and all it
contains. Traditional usage of “sporocarp” is
misleading because it implies homology for nonhomologous
structures, and structures historically called sporocarps in
Salviniaceae are more appropriately referred to as
sori.},
Doi = {10.1086/503848},
Key = {fds230080}
}
@article{fds230081,
Author = {Smith, AR and Pryer, KM and Schuettpelz, E and Korall, P and Schneider,
H and Wolf, PG},
Title = {A classification for extant ferns},
Journal = {Taxon},
Volume = {55},
Number = {3},
Pages = {705-731},
Publisher = {WILEY},
Year = {2006},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.2307/25065646},
Abstract = {We present a revised classification for extant ferns, with
emphasis on ordinal and familial ranks, and a synopsis of
included genera. Our classification reflects recently
published phylogenetic hypotheses based on both
morphological and molecular data. Within our new
classification, we recognize four monophyletic classes, 11
monophyletic orders, and 37 families, 32 of which are
strongly supported as monophyletic. One new family,
Cibotiaceae Korall, is described. The phylogenetic
affinities of a few genera in the order Polypodiales are
unclear and their familial placements are therefore
tentative. Alphabetical lists of accepted genera (including
common synonyms), families, orders, and taxa of higher rank
are provided.},
Doi = {10.2307/25065646},
Key = {fds230081}
}
@article{fds230083,
Author = {Schuettpelz, E and Korall, P and Pryer, KM},
Title = {Plastid atpA data provide improved support for deep
relationships among ferns},
Journal = {Taxon},
Volume = {55},
Number = {4},
Pages = {897-906},
Publisher = {WILEY},
Year = {2006},
ISSN = {0040-0262},
url = {http://dx.doi.org/10.2307/25065684},
Abstract = {DNA sequence data and phylogenetic approaches have
contributed greatly to our understanding of fern
relationships. Nonetheless, the datasets analyzed to date
have not been sufficient to definitively resolve all parts
of the global fern phylogeny; additional data and more
extensive sampling are necessary. Here, we explore the
phylogenetic utility of the plastid atpA gene. Using newly
designed primers, we obtained atpA sequences for 52 fern and
6 outgroup taxa, and then evaluated the capabilities of atpA
relative to four other molecular markers, as well as the
contributions of atpA in combined analyses. The five
single-gene datasets differed markedly in the number of
variable characters they possessed; and although the
relationships resolved in analyses of these datasets were
largely congruent, the robustness of the hypotheses varied
considerably. The atpA dataset had more variable characters
and resulted in a more robustly supported phylogeny than any
of the other single gene datasets examined, suggesting that
atpA will be exceptionally useful in more extensive studies
of fern phylogeny and perhaps also in studies of other plant
lineages. When the atpA data were analyzed in combination
with the other four markers, an especially robust hypothesis
of fern relationships emerged. With the addition of the atpA
data, support increased substantially at several nodes;
three nodes, which were not well-supported previously,
received both good posterior probability and good bootstrap
support in the combined 5-gene (> 6 kb) analyses.},
Doi = {10.2307/25065684},
Key = {fds230083}
}
@article{fds230077,
Author = {Wikström, N and Pryer, KM},
Title = {Incongruence between primary sequence data and the
distribution of a mitochondrial atp1 group II intron among
ferns and horsetails},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {36},
Number = {3},
Pages = {484-493},
Publisher = {Academic Press},
Year = {2005},
ISSN = {1055-7903},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15922630},
Abstract = {Using DNA sequence data from multiple genes (often from more
than one genome compartment) to reconstruct phylogenetic
relationships has become routine. Augmenting this approach
with genomic structural characters (e.g., intron gain and
loss, changes in gene order) as these data become available
from comparative studies already has provided critical
insight into some long-standing questions about the
evolution of land plants. Here we report on the presence of
a group II intron located in the mitochondrial atp1 gene of
leptosporangiate and marattioid ferns. Primary sequence data
for the atp1 gene are newly reported for 27 taxa, and
results are presented from maximum likelihood-based
phylogenetic analyses using Bayesian inference for 34 land
plants in three data sets: (1) single-gene mitochondrial
atp1 (exon+intron sequences); (2) five combined genes
(mitochondrial atp1 [exon only]; plastid rbcL, atpB, rps4;
nuclear SSU rDNA); and (3) same five combined genes plus
morphology. All our phylogenetic analyses corroborate
results from previous fern studies that used plastid and
nuclear sequence data: the monophyly of euphyllophytes, as
well as of monilophytes; whisk ferns (Psilotidae) sister to
ophioglossoid ferns (Ophioglossidae); horsetails
(Equisetopsida) sister to marattioid ferns (Marattiidae),
which together are sister to the monophyletic
leptosporangiate ferns. In contrast to the results from the
primary sequence data, the genomic structural data (atp1
intron distribution pattern) would seem to suggest that
leptosporangiate and marattioid ferns are monophyletic, and
together they are the sister group to horsetails--a topology
that is rarely reconstructed using primary sequence
data.},
Doi = {10.1016/j.ympev.2005.04.008},
Key = {fds230077}
}
@article{fds230118,
Author = {Pryer, KM and Schuettpelz, E and Wolf, PG and Schneider, H and Smith,
AR and Cranfill, R},
Title = {Phylogeny and evolution of ferns (monilophytes) with a focus
on the early leptosporangiate divergences.},
Journal = {American journal of botany},
Volume = {91},
Number = {10},
Pages = {1582-1598},
Year = {2004},
Month = {October},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21652310},
Abstract = {The phylogenetic structure of ferns (= monilophytes) is
explored here, with a special focus on the early divergences
among leptosporangiate lineages. Despite considerable
progress in our understanding of fern relationships, a
rigorous and comprehensive analysis of the early
leptosporangiate divergences was lacking. Therefore, a data
set was designed here to include critical taxa that were not
included in earlier studies. More than 5000 bp from the
plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA)
genomes were sequenced for 62 taxa. Phylogenetic analyses of
these data (1) confirm that Osmundaceae are sister to the
rest of the leptosporangiates, (2) resolve a diverse set of
ferns formerly thought to be a subsequent grade as possibly
monophyletic (((Dipteridaceae, Matoniaceae),
Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid
ferns as sister to a large clade of "core leptosporangiates"
that includes heterosporous ferns, tree ferns, and polypods.
Divergence time estimates for ferns are reported from
penalized likelihood analyses of our molecular data, with
constraints from a reassessment of the fossil
record.},
Doi = {10.3732/ajb.91.10.1582},
Key = {fds230118}
}
@article{fds230117,
Author = {Schneider, H and Schuettpelz, E and Pryer, KM and Cranfill, R and Magallón, S and Lupia, R},
Title = {Ferns diversified in the shadow of angiosperms.},
Journal = {Nature},
Volume = {428},
Number = {6982},
Pages = {553-557},
Year = {2004},
Month = {April},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15058303},
Abstract = {The rise of angiosperms during the Cretaceous period is
often portrayed as coincident with a dramatic drop in the
diversity and abundance of many seed-free vascular plant
lineages, including ferns. This has led to the widespread
belief that ferns, once a principal component of terrestrial
ecosystems, succumbed to the ecological predominance of
angiosperms and are mostly evolutionary holdovers from the
late Palaeozoic/early Mesozoic era. The first appearance of
many modern fern genera in the early Tertiary fossil record
implies another evolutionary scenario; that is, that the
majority of living ferns resulted from a more recent
diversification. But a full understanding of trends in fern
diversification and evolution using only palaeobotanical
evidence is hindered by the poor taxonomic resolution of the
fern fossil record in the Cretaceous. Here we report
divergence time estimates for ferns and angiosperms based on
molecular data, with constraints from a reassessment of the
fossil record. We show that polypod ferns (> 80% of living
fern species) diversified in the Cretaceous, after
angiosperms, suggesting perhaps an ecological opportunistic
response to the diversification of angiosperms, as
angiosperms came to dominate terrestrial
ecosystems.},
Doi = {10.1038/nature02361},
Key = {fds230117}
}
@article{fds353357,
Author = {LUPIA, R and NOWAK, M and SCHNEIDER, H and NAGALINGUM, N and PRYER,
K},
Title = {HETEROSPOROUS FERNS: PHYLOGENY, ORIGIN AND
RADIATION},
Journal = {2004 Denver Annual Meeting},
Year = {2004},
Key = {fds353357}
}
@article{fds230120,
Author = {Des Marais and DL and Smith, AR and Britton, DM and Pryer,
KM},
Title = {Phylogenetic relationships and evolution of extant
Horsetails, Equisetum, based on chloroplast DNA sequence
data (rbcL and trnL-F).},
Journal = {International journal of plant sciences},
Volume = {164},
Number = {5},
Pages = {737-751},
Publisher = {University of Chicago Press},
Year = {2003},
Month = {September},
url = {http://dx.doi.org/10.1086/376817},
Abstract = {Equisetum is a small and morphologically distinct genus with
a rich fossil record. Two subgenera have been recognized
based principally on stomatal position and stem branching:
subg. Equisetum (eight species; superficial stomates; stems
branched) and subg. Hippochaete (seven species; sunken
stomates; stems generally unbranched). Prior attempts at
understanding Equisetum systematics, phylogeny, and
character evolution have been hampered by the high degree of
morphological plasticity in the genus as well as by frequent
hybridization among members within each subgenus. We present
the first explicit phylogenetic study of Equisetum,
including all 15 species and two samples of one widespread
hybrid, Equisetum ×ferrissii, based on a combined
analysis of two chloroplast markers, rbcL and trnL-F. Our
robustly supported phylogeny identifies two monophyletic
clades corresponding to the two subgenera recognized by
earlier workers. The phylogenetic placement of Equisetum
bogotense, however, is ambiguous. In maximum likelihood
analyses, it allies with subg. Hippochaete as the most basal
member, while maximum parsimony places it as sister to the
rest of the genus. A consensus phylogeny from the two
analyses is presented as a basal trichotomy (E. bogotense,
subg. Hippochaete, subg. Equisetum), and morphological
character evolution is discussed. We detected rate
heterogeneity in the rbcL locus between the two subgenera
that can be attributed to an increased rate of nucleotide
substitution (transversions) in subg. Hippochaete. We
calculated molecular-based age estimates using the penalized
likelihood approach, which accounts for rate heterogeneity
and does not assume a molecular clock. The Equisetum crown
group appears to have diversified in the early Cenozoic,
whereas the Equisetaceae total group is estimated to have a
Paleozoic origin. These molecular-based age estimates are in
remarkable agreement with current interpretations of the
fossil record.},
Doi = {10.1086/376817},
Key = {fds230120}
}
@article{fds230121,
Author = {Dubuisson, JY and Hennequin, S and Douzery, EJP and Cranfill, RB and Smith, AR and Pryer, KM},
Title = {rbcL phylogeny of the fern genus Trichomanes
(Hymenophyllaceae), with special reference to neotropical
taxa.},
Journal = {International journal of plant sciences},
Volume = {164},
Number = {5},
Pages = {753-761},
Publisher = {University of Chicago Press},
Year = {2003},
Month = {September},
url = {http://dx.doi.org/10.1086/377059},
Abstract = {In order to estimate evolutionary relationships within the
filmy fern genus Trichomanes (Hymenophyllaceae), we
performed a phylogenetic analysis using rbcL nucleotide data
from 46 species of Trichomanes belonging to all four of C.
V. Morton's subgenera: Achomanes, Didymoglossum,
Pachychaetum, and Trichomanes. Outgroups included four
species of Hymenophyllum in three different subgenera, plus
the monotypic genus Cardiomanes, from New Zealand. We find
high resolution and robust support at most nodes, regardless
of the phylogenetic optimization criterion used (maximum
parsimony or maximum likelihood). Two species belonging to
Morton's Asiatic sections Callistopteris and Cephalomanes
are in unresolved basal positions within Trichomanes s.l.,
suggesting that rbcL data alone are inadequate for
estimating the earliest cladogenetic events. Out of the four
Morton trichomanoid subgenera, only subg. Didymoglossum
appears monophyletic. Other noteworthy results include the
following: (1) lianescent sect. Lacostea is more closely
related to sect. Davalliopsis (traditionally placed in subg.
Pachychaetum) than to other members of subg. Achomanes; (2)
sections Davalliopsis and Lacostea, together with species of
the morphologically different subg. Achomanes, make up a
strongly supported Neotropical clade; (3) all hemiepiphytes
(but not true lianas) and strictly epiphytic or epipetric
species (Morton's subgenera Trichomanes and Didymoglossum)
group together in an ecologically definable clade that also
includes the terrestrial sect. Nesopteris; and (4) sect.
Lacosteopsis (sensu Morton) is polyphyletic and comprises
two distantly related clades: large hemiepiphytic climbers
and small strictly epiphytic/epipetric taxa. Each of these
associations is somewhat unexpected but is supported by
cytological, geographical, and/or ecological evidence. We
conclude that many morphological characters traditionally
used for delimiting groups within Trichomanes are, in part,
plesiomorphic or homoplastic. Additionally, we discuss
probable multiple origins of Neotropical
Trichomanes.},
Doi = {10.1086/377059},
Key = {fds230121}
}
@article{fds353358,
Author = {Pryer, KM and Schuettpelz, E and Cranfill, RC and Wolf, PG and Smith,
AR and Schneider, H},
Title = {Phylogeny of Early-Diverging Leptosporangiate Ferns Based on
Morphology and Multiple Genes: rbcL, atpB, rps4, and
18S},
Year = {2003},
Key = {fds353358}
}
@article{fds230122,
Author = {Pryer, KM and Schneider, H and Zimmer, EA and Ann Banks,
J},
Title = {Deciding among green plants for whole genome
studies.},
Journal = {Trends in plant science},
Volume = {7},
Number = {12},
Pages = {550-554},
Year = {2002},
Month = {December},
ISSN = {1360-1385},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12475497},
Abstract = {Recent comparative DNA-sequencing studies of chloroplast,
mitochondrial and ribosomal genes have produced an
evolutionary tree relating the diversity of green-plant
lineages. By coupling this phylogenetic framework to the
explosion of information on genome content, plant-genomic
efforts can and should be extended beyond angiosperm crop
and model systems. Including plant species representative of
other crucial evolutionary nodes would produce the
comparative information necessary to understand fully the
organization, function and evolution of plant genomes. The
simultaneous development of genomic tools for green algae,
bryophytes, 'seed-free' vascular plants and gymnosperms
should provide insights into the bases of the complex
morphological, physiological, reproductive and biochemical
innovations that have characterized the successful
transition of green plants to land.},
Doi = {10.1016/s1360-1385(02)02375-0},
Key = {fds230122}
}
@article{fds230123,
Author = {Schneider, H and Pryer, KM},
Title = {Structure and function of spores in the aquatic
heterosporous fern family Marsileaceae.},
Journal = {International journal of plant sciences},
Volume = {163},
Number = {4},
Pages = {485-505},
Publisher = {University of Chicago Press},
Year = {2002},
Month = {July},
url = {http://dx.doi.org/10.1086/340736},
Abstract = {Spores of the aquatic heterosporous fern family Marsileaceae
differ markedly from spores of Salviniaceae, the only other
family of heterosporous ferns and sister group to
Marsileaceae, and from spores of all homosporous ferns. The
marsileaceous outer spore wall (perine) is modified above
the aperture into a structure, the acrolamella, and the
perine and acrolamella are further modified into a
remarkable gelatinous layer that envelops the spore.
Observations with light and scanning electron microscopy
indicate that the three living marsileaceous fern genera
(Marsilea, Pilularia, and Regnellidium) each have
distinctive spores, particularly with regard to the perine
and acrolamella. Several spore characters support a division
of Marsilea into two groups. Spore character evolution is
discussed in the context of developmental and possible
functional aspects. The gelatinous perine layer acts as a
flexible, floating organ that envelops the spores only for a
short time and appears to be an adaptation of marsileaceous
ferns to amphibious habitats. The gelatinous nature of the
perine layer is likely the result of acidic polysaccharide
components in the spore wall that have hydrogel (swelling
and shrinking) properties. Megaspores floating at the
water/air interface form a concave meniscus, at the center
of which is the gelatinous acrolamella that encloses a
“sperm lake.” This meniscus creates a
vortex-like effect that serves as a trap for free-swimming
sperm cells, propelling them into the sperm
lake.},
Doi = {10.1086/340736},
Key = {fds230123}
}
@article{fds230124,
Author = {Smith, AR and Tuomisto, H and Pryer, KM and Hunt, JS and Wolf,
PG},
Title = {Metaxya lanosa, a second species in the genus and fern
family Metaxyaceae},
Journal = {Systematic Botany},
Volume = {26},
Number = {3},
Pages = {480-486},
Year = {2001},
Month = {October},
ISSN = {0363-6445},
Abstract = {We describe and illustrate Metaxya lanosa, the second known
species in the genus and the fern family Metaxyaceae
(Pteridophyta). It is currently known from four different
watersheds in Amazonian Peru and Venezuela. It can be
distinguished readily from M. rostrata by the noticeably
woolly-hairy stipes and rachises (hairs red-brown or
orange-brown and easily abraded), broader, more elliptic
pinnae, cartilaginous and whitish pinna margins, more
distinct veins abaxially, and longer pinna stalks,
especially on the distal pinnae, rbcL data from a very
limited sampling are ambiguous but do not reject support for
the recognition of at least two species within
Metaxya.},
Key = {fds230124}
}
@article{fds230125,
Author = {Pryer, KM and Smith, AR and Hunt, JS and Dubuisson,
JY},
Title = {rbcL data reveal two monophyletic groups of filmy ferns
(Filicopsida: Hymenophyllaceae).},
Journal = {American journal of botany},
Volume = {88},
Number = {6},
Pages = {1118-1130},
Year = {2001},
Month = {June},
ISSN = {0002-9122},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11410477},
Abstract = {The "filmy fern" family, Hymenophyllaceae, is traditionally
partitioned into two principal genera, Trichomanes s.l.
(sensu lato) and Hymenophyllum s.l., based upon sorus shape
characters. This basic split in the family has been widely
debated this past century and hence was evaluated here by
using rbcL nucleotide sequence data in a phylogenetic study
of 26 filmy ferns and nine outgroup taxa. Our results
confirm the monophyly of the family and provide robust
support for two monophyletic groups that correspond to the
two classical genera. In addition, we show that some taxa of
uncertain affinity, such as the monotypic genera Cardiomanes
and Serpyllopsis, and at least one species of
Microtrichomanes, are convincingly included within
Hymenophyllum s.l. The tubular- or conical-based sorus that
typifies Trichomanes s.l. and Cardiomanes, the most basal
member of Hymenophyllum s.l., is a plesiomorphic character
state for the family. Tubular-based sori occurring in other
members of Hymenophyllum s.l. are most likely derived
independently and more than one time. While rbcL data are
able to provide a well-supported phylogenetic estimate
within Trichomanes s.l., they are inadequate for resolving
relationships within Hymenophyllum s.l., which will require
data from additional sources. This disparity in resolution
reflects differential rates of evolution for rbcL within
Hymenophyllaceae.},
Doi = {10.2307/2657095},
Key = {fds230125}
}
@article{fds230126,
Author = {Pryer, KM and Schneider, H and Smith, AR and Cranfill, R and Wolf, PG and Hunt, JS and Sipes, SD},
Title = {Horsetails and ferns are a monophyletic group and the
closest living relatives to seed plants.},
Journal = {Nature},
Volume = {409},
Number = {6820},
Pages = {618-622},
Year = {2001},
Month = {February},
ISSN = {0028-0836},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11214320},
Abstract = {Most of the 470-million-year history of plants on land
belongs to bryophytes, pteridophytes and gymnosperms, which
eventually yielded to the ecological dominance by
angiosperms 90 Myr ago. Our knowledge of angiosperm
phylogeny, particularly the branching order of the earliest
lineages, has recently been increased by the concurrence of
multigene sequence analyses. However, reconstructing
relationships for all the main lineages of vascular plants
that diverged since the Devonian period has remained a
challenge. Here we report phylogenetic analyses of combined
data--from morphology and from four genes--for 35
representatives from all the main lineages of land plants.
We show that there are three monophyletic groups of extant
vascular plants: (1) lycophytes, (2) seed plants and (3) a
clade including equisetophytes (horsetails), psilotophytes
(whisk ferns) and all eusporangiate and leptosporangiate
ferns. Our maximum-likelihood analysis shows unambiguously
that horsetails and ferns together are the closest relatives
to seed plants. This refutes the prevailing view that
horsetails and ferns are transitional evolutionary grades
between bryophytes and seed plants, and has important
implications for our understanding of the development and
evolution of plants.},
Doi = {10.1038/35054555},
Key = {fds230126}
}
@article{fds353360,
Author = {Pryer, KM and Schneider, H and Smith, AR and Wolf,
PG},
Title = {The Closest Living Relative to Seed Plants: Insights from
Four Genes and Morphology},
Volume = {87 (Suppl)},
Pages = {151},
Year = {2001},
Key = {fds353360}
}
@article{fds230119,
Author = {Lupia, R and Schneider, H and Moeser, GM and Pryer, KM and Crane,
PR},
Title = {Marsileaceae sporocarps and spores from the late cretaceous
of Georgia, U.S.A.},
Journal = {International Journal of Plant Sciences},
Volume = {161},
Number = {6},
Pages = {975-988},
Publisher = {University of Chicago Press},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1086/317567},
Abstract = {A new species provisionally assigned to the extant genus
Regnellidium Lindm. (Regnellidium upatoiensis sp. nov.) is
established for isolated sporocarps assignable to the
heterosporous water fern family Marsileaceae. Three
sporocarps and hundreds of dispersed megaspores were
recovered from unconsolidated clays and silts of the Eutaw
Formation (Santonian, Late Cretaceous) along Upatoi Creek,
Georgia, U.S.A. The sporocarps are ellipsoidal and
flattened, contain both megasporangia and microsporangia,
and possess a two-layered wall - an outer sclerenchymatous
layer and an inner parenchymatous layer. In situ megaspores
are spheroidal, with two distinct wall layers - an exine,
differentiated into two layers, and an outer ornamented
perine also differentiated into two layers. The megaspores
also possess an acrolamella consisting of six (five to
seven) triangular lobes that are twisted. In situ
microspores are trilete and spheroidal, with a strongly
rugulate perine, and show modification of the perine over
the laesura to form an acrolamella. Comparison of the fossil
sporocarps with those of four extant species of Marsileaceae
reveal marked similarity with Regnellidium diphyllum Lindm.,
particularly in megaspore and microspore morphology. If
found dispersed, the in situ megaspores would be assigned to
Molaspora lobata (Dijkstra) Hall and the microspores to
Crybelosporites Dettmann based on their size, shape, and
ornamentation. Regnellidium upatoiensis sp. nov. extends the
stratigraphic range of the genus back to the Santonian,
nearly contemporaneous with the first evidence of Marsilea,
and implies that the diversification of the Marsileaceae
into its extant lineages occurred in the
mid-Cretaceous.},
Doi = {10.1086/317567},
Key = {fds230119}
}
@article{fds353361,
Author = {Schneider, H and Pryer, KM and Smith, AR and Wolf, PG and Cranfill,
RC},
Title = {Phylogeny of vascular plants and the evolution of their body
plans},
Year = {2000},
Key = {fds353361}
}
@article{fds230133,
Author = {Pryer, KM},
Title = {Phylogeny of Marsileaceous Ferns and Relationships of the
Fossil Hydropteris pinnata Reconsidered.},
Journal = {International journal of plant sciences},
Volume = {160},
Number = {5},
Pages = {931-954},
Year = {1999},
Month = {September},
ISSN = {1058-5893},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10506474},
Abstract = {Recent phylogenetic studies have provided compelling
evidence that confirms the once disputed hypothesis of
monophyly for heterosporous leptosporangiate ferns
(Marsileaceae and Salviniaceae). Hypotheses for
relationships among the three genera of Marsileaceae
(Marsilea, Regnellidium, and Pilularia), however, have
continued to be in conflict. The phylogeny of Marsileaceae
is investigated here using information from morphology and
rbcL sequence data. In addition, relationships among all
heterosporous ferns, including the whole-plant fossil
Hydropteris pinnata are reconsidered. Data sets of 71
morphological and 1239 rbcL characters for 23
leptosporangiate ferns, including eight heterosporous
ingroup taxa and 15 homosporous outgroup taxa, were
subjected to maximum parsimony analysis. Morphological
analyses were carried out both with and without the fossil
Hydropteris, and it was excluded from all analyses with rbcL
data. An annotated list of the 71 morphological characters
is provided in the appendix. For comparative purposes, the
Rothwell and Stockey (1994) data set was also reanalyzed
here. The best estimate of phylogenetic relationships for
Marsileaceae in all analyses is that Pilularia and
Regnellidium are sister taxa and Marsilea is sister to that
clade. Morphological synapomorphies for various nodes are
discussed. Analyses that included Hydropteris resulted in
two most-parsimonious trees that differ only in the
placement of the fossil. One topology is identical to the
relationship found by Rothwell and Stockey (1994), placing
the fossil sister to the Azolla plus Salvinia clade. The
alternative topology places Hydropteris as the most basal
member of the heterosporous fern clade. Equivocal
interpretations for character evolution in heterosporous
ferns are discussed in the context of these two
most-parsimonious trees. Because of the observed degree of
character ambiguity, the phylogenetic placement of
Hydropteris is best viewed as unresolved, and recognition of
the suborder Hydropteridineae, as circumscribed by Rothwell
and Stockey (1994), is regarded as premature. The two
competing hypotheses of relationships for heterosporous
ferns are also compared with the known temporal distribution
of relevant taxa. Stratigraphic fit of the phylogenetic
estimates is measured by using the Stratigraphic Consistency
Index and by comparison with minimum divergence
times.},
Doi = {10.1086/314177},
Key = {fds230133}
}
@article{fds230140,
Author = {Turner, S and Pryer, KM and Miao, VP and Palmer, JD},
Title = {Investigating deep phylogenetic relationships among
cyanobacteria and plastids by small subunit rRNA sequence
analysis.},
Journal = {The Journal of eukaryotic microbiology},
Volume = {46},
Number = {4},
Pages = {327-338},
Publisher = {Lawrence, Kan.: Society of Protozoologists,
c1993-},
Year = {1999},
Month = {July},
ISSN = {1066-5234},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10461381},
Abstract = {Small subunit rRNA sequence data were generated for 27
strains of cyanobacteria and incorporated into a
phylogenetic analysis of 1,377 aligned sequence positions
from a diverse sampling of 53 cyanobacteria and 10
photosynthetic plastids. Tree inference was carried out
using a maximum likelihood method with correction for
site-to-site variation in evolutionary rate. Confidence in
the inferred phylogenetic relationships was determined by
construction of a majority-rule consensus tree based on
alternative topologies not considered to be statistically
significantly different from the optimal tree. The results
are in agreement with earlier studies in the assignment of
individual taxa to specific sequence groups. Several
relationships not previously noted among sequence groups are
indicated, whereas other relationships previously supported
are contradicted. All plastids cluster as a strongly
supported monophyletic group arising near the root of the
cyanobacterial line of descent.},
Doi = {10.1111/j.1550-7408.1999.tb04612.x},
Key = {fds230140}
}
@article{fds230129,
Author = {Wolf, PG and Sipes, SD and White, MR and Martines, ML and Pryer, KM and Smith, AR and Ueda, K},
Title = {Phylogenetic relationships of the enigmatic fern families
Hymenophyllopsidaceae and Lophosoriaceae: Evidence from rbcL
nucleotide sequences},
Journal = {Plant Systematics and Evolution},
Volume = {219},
Number = {3-4},
Pages = {263-270},
Publisher = {Springer Nature},
Year = {1999},
Month = {January},
url = {http://dx.doi.org/10.1007/BF00985583},
Abstract = {Nucleotide sequences from rbcL were used to infer
relationships of Lophosoriaceae and Hymenophyllopsidaceae.
The phylogenetic positions of these two monotypic fern
families have been debated, and neither group had been
included in recent molecular systematic studies of ferns.
Maximum parsimony analysis of our data supported a sister
relationship between Lophosoria and Dicksonia, and also
between Hymenophyllopsis and Cyathea. Thus, both
newly-examined families appear to be part of a previously
characterized and well-supported clade of tree ferns. The
inferred relationships of Lophosoria are consistent with
most (but not all) recent treatments. However,
Hymenophyllopsis includes only small delicate plants
superficially similar to filmy ferns (Hymenophyllaceae),
very different from the large arborescent taxa.
Nevertheless, some synapomorphic characteristics are shared
with the tree fern clade. Further studies on gametophytes of
Hymenophyllopsis are needed to test these hypotheses of
relationship.},
Doi = {10.1007/BF00985583},
Key = {fds230129}
}
@article{fds16716,
Author = {Pryer, K.M. and S.J. Hackett},
Title = {Field’s Museum’s Pritzker Laboratory of Molecular
Systematics and Evolution},
Year = {1999},
url = {http://www.fmnh.org/research_collections/pritzker_lab/pritzker/index.html},
Key = {fds16716}
}
@article{fds16717,
Author = {Pryer, K.M.},
Title = {Phylogeny, character evolution, and diversification of
extant ferns},
Year = {1999},
url = {http://www.fmnh.org/research_collections/botany/botany_sites/ferns/index.html},
Key = {fds16717}
}
@article{fds353363,
Author = {Pryer, KM and Schneider, H and Hunt, JS and Wolf, PG and Smith,
AR},
Title = {Basal Tracheophytes and the Phylogeny of" Pteridophyte"
Lineages},
Year = {1999},
Key = {fds353363}
}
@article{fds353365,
Author = {Hunt, JS and Pryer, KM and Vaghani, A and Smith, AR and Wolf,
PG},
Title = {Fern DNA Database: Using Filemaker Pro to Coordinate
DNA-Availability, DNA-Sequence Data, Vaoucher and Source
Information for Large-Scale and Collaborative Phylogeny
Studies},
Year = {1999},
Key = {fds353365}
}
@article{fds353366,
Author = {Pryer, KM and Smith, AR},
Title = {Leptosporangiate ferns},
Year = {1998},
url = {http://phylogeny.arizona.edu/tree/eukaryotes/green_plants/},
Abstract = {The Tree of Life: A distributed Internet project containing
information about phylogeny and biodiversity.},
Key = {fds353366}
}
@article{fds16719,
Author = {Pryer, K.M. and A.R. Smith},
Title = {Filicopsida},
Journal = {Maddison, D.R. and W. P. Maddison},
Year = {1997},
url = {http://phylogeny.arizona.edu/tree/eukaryotes/green_plants/},
Abstract = {The Tree of Life: A distributed Internet project containing
information about phylogeny and biodiversity.},
Key = {fds16719}
}
@article{fds353367,
Author = {Pryer, KM},
Title = {Phylogenetic relationships of extant ferns, with a special
emphasis on the Marsileaceae.},
Year = {1997},
Key = {fds353367}
}
@article{fds230127,
Author = {Pryer, KM and Smith, AR and Skog, JE},
Title = {Phylogenetic Relationships of Extant Ferns Based on Evidence
from Morphology and rbcL Sequences},
Journal = {American Fern Journal},
Volume = {85},
Number = {4},
Pages = {205-205},
Publisher = {JSTOR},
Year = {1995},
Month = {October},
ISSN = {0002-8444},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1995TY07900007&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.2307/1547810},
Key = {fds230127}
}
@article{fds230128,
Author = {Hasebe, M and Wolf, PG and Pryer, KM and Ueda, K and Ito, M and Sano, R and Gastony, GJ and Yokoyama, J and Manhart, JR and Murakami, N and Crane,
EH and Haufler, CH and Hauk, WD},
Title = {Fern Phylogeny Based on rbcL Nucleotide Sequences},
Journal = {American Fern Journal},
Volume = {85},
Number = {4},
Pages = {134-134},
Publisher = {JSTOR},
Year = {1995},
Month = {October},
ISSN = {0002-8444},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1995TY07900004&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.2307/1547807},
Key = {fds230128}
}
@article{fds230130,
Author = {Pryer, KM and Haufler, CH},
Title = {Isozymic and chromosomal evidence for the allotetraploid
origin of Gymnocarpium dryopteris (Dryopteridaceae)},
Journal = {Systematic botany},
Volume = {18},
Number = {1},
Pages = {150-172},
Publisher = {JSTOR},
Year = {1993},
Month = {January},
ISSN = {0363-6445},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1993KH85000013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {A critical examination of isozyme, chromosomal, and
morphological characters in subspecies formerly included in
Gymnocarpium dryopteris demonstrated that three sexual taxa
can be distinguished. We recognize these taxa as distinct
species: the widespread, fertile allotetraploid G.
dryopteris, with one genome derived from the western diploid
G. disjunctum and the other from G. appalachianum sp. nov.,
a previously undetected eastern North American diploid,
which is described and illustrated here and for which we
report a chromosome number of 2n = 80. Population
comparisons of allele frequencies between C. disjunctum and
G. appalachianum yielded an average Nei's genetic identity
value (I) of 0.274. A wide-ranging assemblage of putatively
triploid plants with both sterile, malformed spores and
large, round spores capable of germination is believed to
represent the backcrosses G. disjunctum X dryopteris and G.
appalachianum X dryopteris. The name G. X brittonianum comb.
nov. is applied here to G. disjunctum X dryopteris. A key to
fertile species, species descriptions and illustrations,
distribution maps, and habitat notes are
included.},
Doi = {10.2307/2419795},
Key = {fds230130}
}
@article{fds16676,
Author = {Pryer, K.M.},
Title = {Gymnocarpium},
Series = {Volume 2},
Pages = {258-262},
Booktitle = {Flora of North America North of Mexico},
Publisher = {Oxford University Press},
Editor = {Flora of North America Editorial Committee},
Year = {1993},
Key = {fds16676}
}
@article{fds230131,
Author = {Pryer, KM},
Title = {The status of Gymnocarpium heterosporum and Gymnocarpium
robertianum in Pennsylvania.},
Journal = {American fern journal.},
Volume = {82},
Number = {1},
Pages = {34-39},
Publisher = {JSTOR},
Year = {1992},
Month = {March},
ISSN = {0002-8444},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1992HQ04200006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Doi = {10.2307/1547760},
Key = {fds230131}
}
@article{fds230132,
Author = {Pryer, KM},
Title = {The limestone oak fern: new to the flora of
Manitoba},
Journal = {Blue Jay},
Volume = {48},
Number = {4},
Pages = {192-195},
Publisher = {University of Alberta Libraries},
Year = {1990},
url = {http://dx.doi.org/10.29173/bluejay4791},
Doi = {10.29173/bluejay4791},
Key = {fds230132}
}
@article{fds353371,
Author = {Argus, GW and Pryer, KM},
Title = {Les plantes vasculaires rares du Canada(notre patrimoine
naturel)},
Publisher = {Musée canadien de la nature},
Year = {1990},
Key = {fds353371}
}
@article{fds353372,
Author = {Argus, GW and Pryer, KM},
Title = {Les plantes vasculaires rares du Canada},
Journal = {Musée canadien de la nature, Ottawa, Ont},
Year = {1990},
Key = {fds353372}
}
@article{fds230134,
Author = {Pryer, KM and Phillippe, LR},
Title = {A synopsis of the genus Sanicula (Apiaceae) in eastern
Canada},
Journal = {Canadian Journal of Botany},
Volume = {67},
Number = {3},
Pages = {694-707},
Publisher = {Canadian Science Publishing},
Year = {1989},
Month = {January},
ISSN = {0008-4026},
url = {http://dx.doi.org/10.1139/b89-093},
Abstract = {Four species and 2 varieties of these native woodland
umbellifers are recognized. A key to the taxa, comparative
descriptions of diagnostic characters, and notes on the
taxonomy, distribution, habitat, and rare status are
provided. Eastern Canadian dot maps and North American range
maps are included for each taxon. -from Authors},
Doi = {10.1139/b89-093},
Key = {fds230134}
}
@article{fds353373,
Author = {Pryer, KM and Windham, MD},
Title = {A re-examination of Gymnocarpium dryopteris (L.) Newman in
North America},
Journal = {Amer. J. Bot},
Volume = {75},
Pages = {142},
Year = {1988},
Key = {fds353373}
}
@article{fds353374,
Author = {PRYER, K and ARGUS, G and HABER, E},
Title = {THE CANADIAN RARE AND ENDANGERED PLANTS PROJECT-A BAKERS
DECADE LATER},
Journal = {AMERICAN JOURNAL OF BOTANY},
Volume = {73},
Number = {5},
Pages = {781-782},
Publisher = {BOTANICAL SOC AMER INC OHIO STATE UNIV-DEPT BOTANY 1735 NEIL
AVE, COLUMBUS …},
Year = {1986},
Key = {fds353374}
}
@article{fds230135,
Author = {McNeill, J and Pryer, KM},
Title = {THE STATUS AND TYPIFICATION OF PHEGOPTERIS AND
GYMNOCARPIUM},
Journal = {TAXON},
Volume = {34},
Number = {1},
Pages = {136-143},
Publisher = {Wiley},
Year = {1985},
Month = {February},
ISSN = {0040-0262},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1985ADK6300024&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {<jats:title>Summary</jats:title><jats:p>It is concluded that
<jats:italic>Phegopteris</jats:italic> Fée
(Thelypteridaceae) is an apparently nomenclaturally
superfluous name, because, when published, it included what
is now established to be the type of <jats:italic>Gymnocarpium</jats:italic>
Newman. Despite this, <jats:italic>Phegopteris</jats:italic>
is a legitimate name as it has a legitimate basionym; it
must, however, be cited as <jats:italic>Phegopteris</jats:italic>
(Presl) Fée. The protologue of the basionym of
<jats:italic>Gymnocarpium dryopteris</jats:italic> does not
point to any specimen that could serve as type of that name,
and hence of <jats:italic>Gymnocarpium</jats:italic> Newman
(Athyriaceae). Moreover, there is no eligible specimen in
the Linnaean collections in London, Stockholm or Paris.
There is, however, a Burser specimen at Uppsala with a
Bauhin name that is not cited in any Linnaean work. This
specimen was determined by Linnaeus in his catalogue of the
Burser herbarium as <jats:italic>Polypodium
dryopteris</jats:italic>, the basionym of <jats:italic>G.
dryopteris</jats:italic>, and this is designated as the
lectotype. This lectotypification preserves existing usage
of both the generic and specific names.</jats:p>},
Doi = {10.2307/1221578},
Key = {fds230135}
}
@article{fds230136,
Author = {Pryer, KM and Britton, DM and McNeill, J},
Title = {A numerical analysis of chromatographic profiles in North
American taxa of the fern genus Gymnocarpium},
Journal = {Canadian Journal of Botany},
Volume = {61},
Number = {10},
Pages = {2592-2602},
Publisher = {Canadian Science Publishing},
Year = {1983},
Month = {October},
ISSN = {0008-4026},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1983RR31700012&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {<jats:p> As part of a systematic investigation of the genus
Gymnocarpium in North America, a survey of chromatographic
profiles in species and hybrids of the genus was initiated.
It was established through cluster analysis and ordination
of the phenolic data that morphologically distinguishable
taxa of Gymnocarpium can be recognized by their
chromatographic profiles alone. These data provide
supportive evidence for the recognition of G. robertianum
and G. jessoense ssp. parvulum as distinct taxa and for the
hybrid status of G. × intermedium. They also suggest that,
as currently circumscribed, G. jessoense ssp. jessoense is a
heterogeneous taxon. </jats:p>},
Doi = {10.1139/b83-285},
Key = {fds230136}
}
@article{fds230137,
Author = {Pryer, KM and Britton, DM},
Title = {Spore studies in the genus Gymnocarpium},
Journal = {Canadian Journal of Botany},
Volume = {61},
Number = {2},
Pages = {377-388},
Publisher = {Canadian Science Publishing},
Year = {1983},
Month = {February},
ISSN = {0008-4026},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1983QF41300001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {<jats:p> Scanning electron microscopy was used to examine
the variation in perispore characters within and between six
currently recognized taxa of the genus Gymnocarpium Newm. in
North America. Representative scanning electron micrographs
are presented and depict the perispore features observed.
Spores of those taxa studied here do not each possess a
distinctive morphology providing practical species
discrimination, rather they all exhibit similar patterns of
variation. Spore size was also examined and shown to be
correlated to ploidy level, permitting positive
identification of the diploid taxon G. dryopteris ssp.
disjunctum from the tetraploid G. dryopteris ssp.
dryopteris. </jats:p>},
Doi = {10.1139/b83-045},
Key = {fds230137}
}
@article{fds353376,
Author = {Argus, GW and Pryer, KM and White, DJ and Keddy, CJ},
Title = {1987},
Journal = {Atlas of the rare vascular plants of Ontario},
Volume = {4},
Year = {1982},
Key = {fds353376}
}
@article{fds230138,
Author = {Sarvela, J and Britton, DM and Pryer, K},
Title = {Studies on the Gymnocarpium robertianum complex in North
America},
Journal = {Rhodora},
Volume = {83},
Number = {835},
Pages = {421-431},
Publisher = {New England Botanical Club},
Year = {1981},
Key = {fds230138}
}
@article{fds230139,
Author = {Chase, R and Pryer, K and Baker, R and Madison, D},
Title = {Responses to conspecific chemical stimuli in the treatment
snail Achatina fulica (Pulmonata: Sigmurethra).},
Journal = {Behavioral biology},
Volume = {22},
Number = {3},
Pages = {302-315},
Year = {1978},
Month = {March},
ISSN = {0091-6773},
url = {http://dx.doi.org/10.1016/s0091-6773(78)92366-0},
Abstract = {The giant African snail, Achatina fulica, followed trails
made with the mucus of A. fulica, but did not follow those
consisting of mucus from Otala vermiculata. In olfactometer
experiments, A. fulica and Helix aperta oriented
preferentially toward the odor of their own species when
both odors were presented simultaneously. Species
specificity was less pronounced when the odor of O.
vermiculata was paired with either of the other two snail
odors. Sexually mature A. fulica that had been housed
individually for 30 days prior to testing followed mucus
trails better than did similar snails housed collectively.
Immature A. fulica did not follow trails better after
isolation, but showed a facilitative effect of isolation on
conspecific orientation in the olfactometer. Three-week-old
snails, maintained in individual containers from the time of
hatching, also oriented preferentially toward conspecific
odors. © 1978 Academic Press, Inc.},
Doi = {10.1016/s0091-6773(78)92366-0},
Key = {fds230139}
}
%% Papers Submitted
@article{fds220952,
Author = {Sigel, E.M. and M.D. Windham and C.H. Haufler and K.M.
Pryer},
Title = {Phylogeny, divergence time estimates, and phylogeography for
the diploid species of the Polypodium vulgare
complex},
Journal = {Systematic Botany, in review},
Year = {2013},
Key = {fds220952}
}
@article{fds220954,
Author = {Rothfels, C.J. and A.K. Johnson and P.H. Hovenkamp and D.L. Swofford and H.C. Roskam and C.R. Fraser-Jenkins and M.D. Windham and K.M.
Pryer},
Title = {A natural intergeneric hybrid between parental lineages that
diverged from one another over 50 million years
ago},
Journal = {Evolution, in review},
Year = {2013},
Key = {fds220954}
}
%% Book Chapters
@misc{fds219919,
Author = {Wang, Z.R. and K.M. Pryer},
Title = {Gymnocarpium},
Pages = {257-259},
Booktitle = {Z.Y. Wu, P.H. Raven & D.Y. Hong, eds., Flora of China, Vol.
2–3 (Pteridophytes). Beijing: Science Press; St. Louis:
Missouri Botanical Garden Press},
Year = {2013},
Key = {fds219919}
}
@misc{fds219920,
Author = {Wang, Z.R. and C.H. Haufler and K.M. Pryer and M.
Kato},
Title = {Cystopteridaceae},
Pages = {257},
Booktitle = {Z.Y. Wu, P.H. Raven & D.Y. Hong, eds., Flora of China, Vol.
2–3 (Pteridophytes). Beijing: Science Press; St. Louis:
Missouri Botanical Garden Press},
Year = {2013},
Key = {fds219920}
}
@misc{fds71728,
Author = {Pryer, K.M. and E. Schuettpelz},
Title = {Ferns},
Pages = {153-156},
Booktitle = {The Timetree of Life, Chapter 14 in S.B. Hedges and S. Kumar
(eds.)},
Publisher = {Oxford University Press, New York},
Year = {2009},
Key = {fds71728}
}
@misc{fds230058,
Author = {Schuettpelz, E and Pryer, KM},
Title = {Fern phylogeny},
Pages = {395-416},
Booktitle = {Biology and Evolution of Ferns and Lycophytes},
Publisher = {Cambridge University Press},
Year = {2008},
Month = {January},
ISBN = {9780521874113},
url = {http://dx.doi.org/10.1017/CBO9780511541827.016},
Abstract = {Introduction As a consequence of employing DNA sequence data
and phylogenetic approaches, unprecedented progress has been
made in recent years toward a full understanding of the fern
tree of life. At the broadest level, molecular phylogenetic
analyses have helped to elucidate which of the so-called
“fern allies” are indeed ferns, and which are only
distantly related (Nickrent et al., 2000; Pryer et al.,
2001a; Wikström and Pryer, 2005; Qiu et al., 2006).
Slightly more focused analyses have revealed the composition
of, and relationships among, the major extant fern clades
(Hasebe et al., 1995; Wolf, 1997; Pryer et al., 2004b;
Schneider et al., 2004c; Schuettpelz et al., 2006;
Schuettpelz and Pryer, 2007). A plethora of analyses, at an
even finer scale, has uncovered some of the most detailed
associations (numerous references cited below). Together,
these studies have helped to answer many long-standing
questions in fern systematics. In this chapter, a brief
synopsis of vascular plant relationships - as currently
understood - is initially provided to place ferns within a
broader phylogenetic framework. This is followed by an
overview of fern phylogeny, with most attention devoted to
the leptosporangiate clade that accounts for the bulk of
extant fern diversity. Discussion of finer scale
relationships is generally avoided; instead, the reader is
directed to the relevant literature, where more detailed
information can be found.},
Doi = {10.1017/CBO9780511541827.016},
Key = {fds230058}
}
@misc{fds230059,
Author = {Smith, AR and Pryer, KATHLEENM and Schuettpelz, ERIC and Korall, P and Schneider, HARALD and Wolf, PG},
Title = {Fern classification},
Pages = {417-467},
Booktitle = {Biology and Evolution of Ferns and Lycophytes},
Publisher = {Cambridge University Press},
Editor = {Ranker, T.A. and C.H. Haufler (eds.).},
Year = {2008},
ISBN = {9780521874113},
url = {http://dx.doi.org/10.1017/CBO9780511541827.017},
Abstract = {Introduction and historical summary Over the past 70 years,
many fern classifications, nearly all based on morphology,
most explicitly or implicitly phylogenetic, have been
proposed. The most complete and commonly used
classifications, some intended primarily as herbarium
(filing) schemes, are summarized in Table 16.1, and include:
Christensen (1938), Copeland (1947), Holttum (1947, 1949),
Nayar (1970), Bierhorst (1971), Crabbe et al. (1975), Pichi
Sermolli (1977), Ching (1978), Tryon and Tryon (1982),
Kramer (in Kubitzki, 1990), Hennipman (1996), and Stevenson
and Loconte (1996). Other classifications or trees implying
relationships, some with a regional focus, include Bower
(1926), Ching (1940), Dickason (1946), Wagner (1969), Tagawa
and Iwatsuki (1972), Holttum (1973), and M.ckel (1974).
Tryon (1952) and Pichi Sermolli (1973) reviewed and
reproduced many of these and still earlier classifications,
and Pichi Sermolli (1970, 1981, 1982, 1986) also summarized
information on family names of ferns. Smith (1996) provided
a summary and discussion of recent classifications. With the
advent of cladistic methods and molecular sequencing
techniques, there has been an increased interest in
classifications reflecting evolutionary relationships.
Phylogenetic studies robustly support a basal dichotomy
within vascular plants, separating the lycophytes (less than
1% of extant vascular plants) from the euphyllophytes
(Figure 16.1; Raubeson and Jansen, 1992, Kenrick and Crane,
1997; Pryer et al., 2001a, 2004a, 2004b; Qiu et al., 2006).
Living euphyllophytes, in turn, comprise two major clades:
spermatophytes (seed plants), which are in excess of 260000
species (Thorne, 2002; Scotland and Wortley, 2003), and
ferns (sensu Pryer et al. 2004b), with about 9000 species,
including horsetails, whisk ferns, and all eusporangiate and
leptosporangiate ferns.},
Doi = {10.1017/CBO9780511541827.017},
Key = {fds230059}
}
@misc{fds230075,
Author = {Pryer, KM and Schneider, H and Magallón, S},
Title = {The radiation of vascular plants},
Pages = {138-153},
Booktitle = {Assembling the Tree of Life},
Publisher = {Oxford University Press New York},
Editor = {Cracraft, J and Donoghue, MJ},
Year = {2004},
ISBN = {0-19-517234-5},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000225766900011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Key = {fds230075}
}
@misc{fds353359,
Author = {Schneider, H and Pryer, KM and Cranfill, R and Smith, AR and Wolf,
PG},
Title = {Evolution of vascular plant body plans: a phylogenetic
perspective},
Pages = {330-364},
Booktitle = {Developmental Genetics and Plant Evolution},
Publisher = {Taylor and Francis London},
Editor = {Q.C.B. Cronk and R.M. Bateman and J.A. Harris},
Year = {2002},
Key = {fds353359}
}
@misc{fds353311,
Author = {Wolf, PG and Pryer, KM and Smith, AR and Hasebe, M},
Title = {Phylogenetic studies of extant pteridophytes},
Pages = {541-556},
Booktitle = {Molecular systematics of plants II},
Publisher = {Springer, Boston, MA},
Editor = {D.E. Soltis and P.S. Soltis and J. J. Doyle},
Year = {1998},
ISBN = {9780412111310},
url = {http://dx.doi.org/10.1007/978-1-4615-5419-6_19},
Doi = {10.1007/978-1-4615-5419-6_19},
Key = {fds353311}
}
%% Published Abstracts
@misc{fds219932,
Author = {Li, F.-W. and C.J. Rothfels and A. Larsson and E.M. Sigel and L. Huiet and P. Korall and M. Ruhsam and D. Stevenson and S. Graham and G.K.-S. Wong and K.M. Pryer},
Title = {Mining fern transcriptome data for low-copy nuclear
markers},
Year = {2013},
Abstract = {http://2013.botanyconference.org/engine/search/index.php?func=detail&aid=626},
Key = {fds219932}
}
@misc{fds219933,
Author = {Johnson, A.K. and A.L. Grusz and J.B. Beck and K.M. Pryer and M.D.
Windham},
Title = {So, if they are evolutionary dead-ends, why are apomictic
cheilanthoid ferns more widely distributed than their sexual
diploid progenitors?},
Year = {2013},
Abstract = {http://2013.botanyconference.org/engine/search/index.php?func=detail&aid=803},
Key = {fds219933}
}
@misc{fds219934,
Author = {Sigel, E.M. and J. Der and C.W. De Pamphilis and K.M.
Pryer},
Title = {Time after time: Comparing homeolog expression patterns
between two independent origins of the allotetraploid fern
Polypodium hesperium.},
Year = {2013},
Abstract = {http://2013.botanyconference.org/engine/search/index.php?func=detail&aid=651},
Key = {fds219934}
}
@misc{fds212621,
Author = {Grusz, A.L. and M.D. Windham and K.M. Pryer},
Title = {Using next-generation sequencing to develop microsatellite
markers in ferns},
Year = {2012},
Abstract = {http://www.botanyconference.org/engine/search/index.php?func=detail&aid=946},
Key = {fds212621}
}
@misc{fds212623,
Author = {Beck, J. and J. Allison and K.M. Pryer and M.D.
Windham},
Title = {Identifying multiple origins of polyploid taxa: a multilocus
study of the hybrid cloak fern (Astrolepis integerrima;
Pteridaceae).},
Year = {2012},
Abstract = {http://www.botanyconference.org/engine/search/index.php?func=detail&aid=293},
Key = {fds212623}
}
@misc{fds212624,
Author = {Sigel, E.M. and M.D. Windham and C.H. Haufler and K.M.
Pryer},
Title = {Reassessing phylogenetic relationships in the Polypodium
vulgare complex (Polypodiaceae) using nuclear gapCp sequence
data},
Year = {2012},
Abstract = {http://www.botanyconference.org/engine/search/index.php?func=detail&aid=890},
Key = {fds212624}
}
@misc{fds212625,
Author = {Huiet, R.L. and K.M. Pryer and C.H. Haufler and M.D.
Windham},
Title = {Simplifying the complex: an integrative analysis using
cytogenetics, morphology, and DNA sequence data to resolve
relationships within the Pellaea wrightiana complex
(Pteridaceae).},
Year = {2012},
Abstract = {http://www.botanyconference.org/engine/search/index.php?func=detail&aid=651},
Key = {fds212625}
}
@misc{fds197476,
Author = {Li, F.-W. and L.-Y. Kuo and C.J. Rothfels and A. Ebihara and W.-L.
Chiou, M.D. Windham and K.M. Pryer},
Title = {The global two-locus plant barcode: a first evaluation of
its utility across ferns.},
Year = {2011},
url = {http://www.ibc2011.com/downloads/IBC2011_Abstract_Book.pdf},
Key = {fds197476}
}
@misc{fds197468,
Author = {Johnson, A.K.* and C.J. Rothfels and A.L. Grusz and E.M. Sigel and M.D.
Windham and K.M. Pryer},
Title = {Sporophytes and gametophytes of notholaenid ferns
(Pteridaceae) show correlated presence/absence of
farina.},
Year = {2011},
url = {http://2011.botanyconference.org/engine/search/index.php?func=detail&aid=536},
Key = {fds197468}
}
@misc{fds197469,
Author = {Hooper, E. and G. Yatskievych and L. Huiet and M.D. Windham and K.M.
Pryer},
Title = {Into or out of Africa? What do molecular data reveal about
the identity and biogeographic origin of Aleuritopteris
farinosa (Forssk.) Fee (Pteridaceae)?},
Year = {2011},
url = {http://2011.botanyconference.org/engine/search/index.php?func=detail&aid=723},
Key = {fds197469}
}
@misc{fds197470,
Author = {Li, F.-W. and L.-Y. Kuo and C.J. Rothfels and A. Ebihara and W.-L.
Chiou, M.D. Windham and K.M. Pryer},
Title = {rbcL and matK earn a thumbs up as the core DNA barcode for
ferns},
Year = {2011},
url = {http://2011.botanyconference.org/engine/search/index.php?func=detail&aid=669},
Key = {fds197470}
}
@misc{fds184015,
Author = {Grusz, AL, MD Windham and KM Pryer},
Title = {Examining the role of apomixis in the evolution of
desert-adapted ferns. Invited symposium presentation.},
Year = {2010},
Abstract = {http://2010.botanyconference.org/engine/search/index.php?func=detail&aid=717},
Key = {fds184015}
}
@misc{fds184017,
Author = {Nagalingum, N and R Lupia and KM Pryer},
Title = {The importance of paleobotanical and herbarium collections
in understanding the evolution of heterosporous ferns.
Invited symposium presentation.},
Year = {2010},
Abstract = {http://2010.botanyconference.org/engine/search/index.php?func=detail&aid=564},
Key = {fds184017}
}
@misc{fds184018,
Author = {Sigel, EM, MD Windham and KM Pryer},
Title = {Using spore data to infer ploidy and reproductive mode in
land plants. Invited symposium presentation.},
Year = {2010},
Abstract = {http://2010.botanyconference.org/engine/search/683.html},
Key = {fds184018}
}
@misc{fds184019,
Author = {Rothfels, CJ and E Schuettpelz and KM Pryer},
Title = {An accelerated rate of molecular evolution spans all three
genomes in vittarioid ferns.},
Year = {2010},
Abstract = {http://2010.evolutionmeeting.org/search/index.php?func=detail&aid=771},
Key = {fds184019}
}
@misc{fds184020,
Author = {Schuettpelz, E, MD Windham and KM Pryer},
Title = {Estimating divergence times and ancestral centers of
diversity for a xeric-adapted fern clade.},
Year = {2010},
Abstract = {http://2010.evolutionmeeting.org/search/index.php?func=detail&aid=652},
Key = {fds184020}
}
@misc{fds168402,
Author = {Grusz, A. L. and M.D. Windham and K.M. Pryer},
Title = {A Cheilanthes by any other name: Evolutionary complexity in
the New World myriopterid clade (Pteridaceae).},
Year = {2009},
Abstract = {http://2009.botanyconference.org/engine/search/index.php?func=detail&aid=892},
Key = {fds168402}
}
@misc{fds168403,
Author = {Sigel, E. M. and M.D. Windham and K.M. Pryer},
Title = {To have or have not: Using farina to delineate major clades
within the false cloak ferns (Argyrochosma).},
Year = {2009},
Abstract = {http://2009.botanyconference.org/engine/search/index.php?func=detail&aid=712},
Key = {fds168403}
}
@misc{fds168404,
Author = {Rothfels, C.J. and M.D. Windham and K.M. Pryer},
Title = {New insights into the relationships of Cystopteris,
Acystopteris, and Gymnocarpium.},
Year = {2009},
Abstract = {http://2009.botanyconference.org/engine/search/index.php?func=detail&aid=625},
Key = {fds168404}
}
@misc{fds168405,
Author = {Schuettpelz, E. and K.M. Pryer and M.D. Windham},
Title = {A phylogenetic approach to species delimitation in the fern
genus Pentagramma (Pteridaceae).},
Year = {2009},
Abstract = {http://2009.botanyconference.org/engine/search/index.php?func=detail&aid=511},
Key = {fds168405}
}
@misc{fds168406,
Author = {Beck, J. and M.D. Windham and K.M. Pryer},
Title = {Tempo and mode of evolution in the star-scaled cloak ferns
(Astrolepis).},
Year = {2009},
Abstract = {http://2009.botanyconference.org/engine/search/index.php?func=detail&aid=166},
Key = {fds168406}
}
@misc{fds152862,
Author = {Beck, J. and M.D. Windham and K.M. Pryer},
Title = {Investigating the early stages of polyploid evolution in the
star-scaled cloak ferns (Astrolepis)},
Year = {2008},
Abstract = {http://www.botanyconference.org/engine/search/index.php?func=detail&aid=105},
Key = {fds152862}
}
@misc{fds152863,
Author = {Windham, M.D. and J. Beck and A.L. Grusz and L. Huiet and C. Rothfels and E. Schuettpelz and G. Yatskievych and K.M.
Pryer},
Title = {Using plastid and nuclear DNA sequences to redraw generic
boundaries and demystify species complexes in cheilanthoid
ferns},
Year = {2008},
Abstract = {http://www.botanyconference.org/engine/search/index.php?func=detail&aid=686},
Key = {fds152863}
}
@misc{fds152864,
Author = {Pryer, K.M. and E.Y. Butler and D.R. Farrar and R. Moran and J.J.
Schneller, E. Schuettpelz and J.E. Watkins, Jr. and M.D.
Windham},
Title = {On the importance of portraying the plant life cycle
accurately: ferns as a case study},
Year = {2008},
Abstract = {http://www.botanyconference.org/engine/search/index.php?func=detail&aid=848},
Key = {fds152864}
}
@misc{fds152848,
Author = {Schuettpelz E. and H. Schneider and L. Huiet and M.D. Windham and K.M.
Pryer.},
Title = {A molecular phylogeny of pteroid ferns: rampant paraphyly
and polyphyly revealed.},
Year = {2007},
Abstract = {http://www.2007.botanyconference.org/engine/search/index.php?func=detail&aid=1604},
Key = {fds152848}
}
@misc{fds152847,
Author = {Rothfels, C.J. and M.D. Windham and K.M. Pryer and J.S. Metzgar and A.L. Grusz.},
Title = {Making Fronds in the Desert: Phylogenetics of Farinose Ferns
(Notholaena: Pteridaceae).},
Year = {2007},
Abstract = {http://www.2007.botanyconference.org/engine/search/index.php?func=detail&aid=1922},
Key = {fds152847}
}
@misc{fds152846,
Author = {Pryer, K.M. and E. Schuettpelz},
Title = {Ancient Origins and recent radiations in the evolutionary
history of ferns. Invited symposium presentation: Deep Time:
Integrating Paleobotany and Phylogenetics.},
Year = {2007},
Abstract = {http://www.2007.botanyconference.org/engine/search/index.php?func=detail&aid=2184},
Key = {fds152846}
}
@misc{fds152849,
Author = {Kleist, A.C. and C.L. Nelson and J.M.O. Geiger and P. Korall and T.A.
Ranker and K.M. Pryer},
Title = {Alternate pathways of fern dispersal to the Hawaiian
Islands, Part 3: Cibotium},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=579},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=579},
Key = {fds152849}
}
@misc{fds152850,
Author = {Schneider, H. and K.M. Pryer and A.R. Smith.},
Title = {Green spore evolution in ferns},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=141},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=141},
Key = {fds152850}
}
@misc{fds152851,
Author = {Metzgar, J.S. and J.E. Skog and E. Zimmer and K.M.
Pryer},
Title = {Is Osmunda paraphyletic?},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=501},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=501},
Key = {fds152851}
}
@misc{fds152852,
Author = {Lupia, R. and H. Schneider and N.S. Nagalingum and K.M.
Pryer},
Title = {Jurassic origin for the Salviniaceae: the last word or just
the first?},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=535},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=535},
Key = {fds152852}
}
@misc{fds152853,
Author = {Korall, P. and J.S. Metzgar and D.S. Conant and H. Schneider and K.M.
Pryer},
Title = {Phylogeny of scaly tree ferns (Cyatheaceae)},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=289},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=289},
Key = {fds152853}
}
@misc{fds152854,
Author = {Grusz, A.L. and M.D. Windham and J.S. Metzgar and K.M.
Pryer},
Title = {Polyploids and reticulate voids: the Cheilanthes fendleri
complex revisited},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=384},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=384},
Key = {fds152854}
}
@misc{fds152855,
Author = {Nagalingum, N.S. and K.M. Pryer and H. Schneider and D.
Hearn},
Title = {The age of heterosporous ferns as estimated by molecular
divergence dating and the fossil record},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=520},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=520},
Key = {fds152855}
}
@misc{fds152856,
Author = {K.M. Pryer and Schuettpelz, E.},
Title = {Toward a comprehensive phylogeny of extant
ferns},
Year = {2006},
url = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=469},
Abstract = {http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=469},
Key = {fds152856}
}
@misc{fds152857,
Author = {N. Nagalingum and K.M. Pryer and H. Schneider and M.D. Nowak and D.
Hearn, R. Lupia},
Title = {Dating the Marsileaceae: evolutionary and biogeographical
implications. Symposium 12.7.2 on DATING DIVERGENCE OF
ANGOIOSPERM RADIATIONS: PROGRESS AND PROSPECTS.},
Year = {2005},
Month = {Summer},
url = {http://www.ibc2005.ac.at/program/final_program_IBC2005.pdf},
Key = {fds152857}
}
@misc{fds152858,
Author = {Pryer, K.M. and E. Schuettpelz},
Title = {Evolutionary history of ferns: ancient origins and recent
radiations. Symposium 9.5.5 on EARLY EVOLUTION: MOLECULAR
PHYLOGENETICS AND ORGANELLAR GENOMICS.},
Year = {2005},
Month = {Summer},
url = {http://www.ibc2005.ac.at/program/final_program_IBC2005.pdf},
Key = {fds152858}
}
@misc{fds152859,
Author = {Hennequin, S. and E. Schuettpelz and K.M. Pryer and J.-Y.
Dubuisson},
Title = {Fast and slow filmy ferns: molecular rate heterogeneity a
chloroplast-wide phenomenon in the Hymenophyllaceae.
Symposium 6.9.3 on DIVERSIFICATION OF SEED-FREE VASCULAR
PLANTS IN THE SHADOW OF ANGIOSPERMS},
Year = {2005},
Month = {Summer},
url = {http://www.ibc2005.ac.at/program/final_program_IBC2005.pdf},
Key = {fds152859}
}
@misc{fds152860,
Author = {Nagalingum, N.S. and H. Schneider and K.M.
Pryer},
Title = {Comparative morphology of reproductive structures in
heterosporous water ferns: the homology of the sporocarp
reexamined},
Year = {2004},
Abstract = {http://www.botanyconference.org/engine/search/
index.php?func=detail&aid=634},
Key = {fds152860}
}
@misc{fds152861,
Author = {Schuettpelz, E. and H. Schneider and K.M. Pryer},
Title = {An evolutionary time-scale for ferns: ancient origins and
recent radiations},
Year = {2004},
Abstract = {http://www.botanyconference.org/engine/search/
index.php?func=detail&aid=249},
Key = {fds152861}
}
%% Other
@misc{fds212622,
Author = {Chai, N. and T. Shao and R.L. Huiet and M. Kim and C.J. Rothfels and J.
Golan and K.M. Pryer},
Title = {DUKE Vascular Type Specimens - Digital Images &
Protologues},
Year = {2012},
url = {http://herbarium.duke.edu/collections/vasculars/typespecimens},
Key = {fds212622}
}
@misc{fds44577,
Author = {Pryer, K.M.},
Title = {Fern DNA Database – an online database of vouchered DNA
sequence data for ferns},
Year = {2010},
url = {http://www.biology.duke.edu/pryerlab/ferndb/},
Key = {fds44577}
}
@misc{fds184615,
Author = {Nagalingum, N. and E. Schuettpelz and K.M.
Pryer},
Title = {Toward a comprehensive fern tree of life: exploration and
training in the forests of Malaysia},
Year = {2009},
Abstract = {http://malaysianferns.pryerlab.net/},
Key = {fds184615}
}
@misc{fds170472,
Author = {Pryer, K.M. and A.R. Smith and C.J. Rothfels},
Title = {Polypodiopsida Cronquist, Takht. & Zimmerm. 1966. Ferns. In
Maddison, D.R. and W. P. Maddison. The Tree of Life: A
distributed Internet project containing information about
phylogeny and biodiversity.},
Year = {2009},
url = {http://tolweb.org/Polypodiidae/21666},
Abstract = {http://tolweb.org/tree?group=Polypodiopsida&contgroup=Embryophytes},
Key = {fds170472}
}
@misc{fds36198,
Author = {K.M. Pryer},
Title = {Fern Image Database},
Year = {2007},
url = {http://www.pryerlab.net/img_dbase/index.shtml},
Key = {fds36198}
}
@misc{fds44573,
Author = {Windham, M.D. and D. Hearn and J. Metzgar and E. Schuettpelz and K.M.
Pryer},
Title = {Ferns of Arizona (an online flora)},
Year = {2005},
Month = {Summer},
url = {http://AZferns.org},
Key = {fds44573}
}
@misc{fds16763,
Author = {Schneider, H. and K.M. Pryer},
Title = {Convergent evolution in vegetative and reproductive
characters of aquatic vascular plants},
Year = {2003},
Key = {fds16763}
}
@misc{fds16765,
Author = {Schneider, H. and R. Cranfill and E.J. Schuettpelz and S. Magallón and K.M. Pryer},
Title = {Derived ferns diversified in the shadow of angiosperms:
evidence from the fossil record, phylogenetic patterns, and
divergence time estimates},
Year = {2003},
Key = {fds16765}
}
@misc{fds16767,
Author = {Chikarmane, S. and T. Rehse and K.M. Pryer},
Title = {Tracing the cultural and botanical origins of turmeric
(Curcuma longa L.)},
Year = {2003},
Key = {fds16767}
}
@misc{fds16768,
Author = {Schuettpelz, E.J. and K.M. Pryer},
Title = {Characterizing molecular rate heterogeneity between two
major lineages of filmy ferns (Hymenophyllaceae)},
Year = {2003},
Key = {fds16768}
}
@misc{fds44578,
Author = {K.M. Pryer},
Title = {Fern Image Database},
Year = {2003},
url = {http://www.pryerlab.net/img_dbase/index.shtml},
Key = {fds44578}
}
@misc{fds16775,
Title = {Atlas of the rare vascular plants of Ontario. Part
4.},
Editor = {Pryer, K.M. and G.W. Argus},
Year = {2003},
Key = {fds16775}
}
@misc{fds16761,
Author = {Pryer, K.M. and H. Schneider},
Title = {A phylogeny for extant heterosporous ferns},
Year = {2002},
Key = {fds16761}
}
@misc{fds16762,
Author = {Schuettpelz, E. and H. Schneider and K. M.
Pryer},
Title = {The phylogenetic history of Pterozonium (Pteridaceae)
revisited: from groundplan divergence to maximum
parsimony},
Year = {2002},
Key = {fds16762}
}
@misc{fds16759,
Author = {Schneider, H. and K. M. Pryer and R. Lupia},
Title = {A comparative analysis of structure and function of spores
in extant heterosporous ferns (Salviniales)},
Year = {2001},
Key = {fds16759}
}
@misc{fds16760,
Author = {Des Marais and D.L., K.M. Pryer and A.R. Smith},
Title = {Phylogeny, character evolution, and biogeography of extant
horsetails (Equisetum)},
Year = {2001},
Key = {fds16760}
}
@misc{fds16758,
Author = {Schneider, H. and K.M. Pryer},
Title = {Spore morphology of heterosporous ferns and its possible
implications for understanding the evolution of the seed
habit},
Journal = {American Journal of Botany},
Volume = {87 (Suppl)},
Pages = {31-32},
Year = {2000},
Key = {fds16758}
}
@misc{fds16748,
Author = {Pryer, K.M. and J.-Y. DuBuisson},
Title = {Symposium: Fern phylogeny with an emphasis on relationships
of basal lineages},
Journal = {XVI International Botanical Congress Abstracts},
Pages = {91},
Year = {1999},
Key = {fds16748}
}
@misc{fds16749,
Author = {DuBuisson, J.-Y. and J.S. Hunt and K.M. Pryer and A.R.
Smith},
Title = {Phylogeny of filmy ferns (Hymenophyllaceae)},
Journal = {XVI International Botanical Congress Abstracts},
Pages = {91},
Year = {1999},
Key = {fds16749}
}
@misc{fds16752,
Author = {Hunt, J.S. and K.M. Pryer and A. Vaghani and A.R. Smith and P.G.
Wolf},
Title = {"Fern DNA Database": using FileMaker Pro to coordinate
DNA-availability, DNA-sequence data, and voucher and source
information for large-scale and collaborative phylogenetic
studies},
Journal = {XVI International Botanical Congress Abstracts},
Pages = {720},
Year = {1999},
Key = {fds16752}
}
@misc{fds16753,
Author = {Moeser, G.M. and R. Lupia and H. Schneider and K.M.
Pryer},
Title = {Marsileaceae sporocarps and spores from the Late
Cretaceous},
Journal = {XVI International Botanical Congress Abstracts},
Pages = {338},
Year = {1999},
Key = {fds16753}
}
@misc{fds16755,
Author = {Schneider, H. and K.M.Pryer, J.S. Hunt and L. Sappelsa and P.G. Wolf and S. D. Sipes and A.R. Smith},
Title = {Basal tracheophytes and the phylogeny of “pteridophyte”
lineages – inferred from four large data sets: morphology,
18S nrDNA, rbcL, and atpB},
Journal = {14th Symposium for Biodiversität und Evolutionsbiologie,
Jena, Germany},
Pages = {163},
Year = {1999},
Key = {fds16755}
}
@misc{fds16756,
Author = {Schneider, H. and K.M. Pryer and J.S. Hunt and L. Sappelsa and P.G. Wolf and S. D. Sipes and A.R. Smith},
Title = {Basal tracheophytes and the phylogeny of “pteridophyte”
lineages – inferred from four large data sets: morphology,
18S nrDNA, rbcL, and atpB, Göttingen, Germany},
Journal = {XVIIIth meeting of the Willi Hennig Society},
Pages = {46},
Year = {1999},
Key = {fds16756}
}
@misc{fds16747,
Author = {Palmer, J.D. and S. Turner and K.M. Pryer},
Title = {Cyanobacterial origin of chloroplasts: once or more than
once?},
Journal = {Journal of Eukaryotic Microbiology},
Volume = {46},
Pages = {2A},
Year = {1998},
Key = {fds16747}
}
@misc{fds16744,
Author = {Pryer, K.M. and A.R. Smith and G. Rothwell and P.
Kenrick},
Title = {Symposium: Relationships and fossil history of
ferns},
Journal = {American Journal of Botany},
Volume = {84 (Suppl)},
Pages = {157-158},
Year = {1997},
Key = {fds16744}
}
@misc{fds16746,
Author = {Pryer, K.M. and A.R. Smith},
Title = {Character evolution and fern phylogeny},
Journal = {American Journal of Botany},
Volume = {84 (Suppl)},
Pages = {159},
Year = {1997},
Key = {fds16746}
}
@misc{fds16743,
Author = {Pryer, K.M.},
Title = {Ontogeny and phylogeny of marsileaceous ferns: evidence for
heterochronic evolution},
Journal = {American Journal of Botany},
Volume = {83 (Suppl)},
Pages = {130},
Year = {1996},
Key = {fds16743}
}
@misc{fds16738,
Author = {Hasebe, M. and P.G. Wolf and W. Hauk and J.R. Manhart and C.H. Haufler and R. Sano and G.J. Gastony and N. Crane and K.M. Pryer and N. Murakami and J.
Yokoyama and M. Ito},
Title = {A global analysis of fern phylogeny based on rbcL nucleotide
sequences},
Journal = {American Journal of Botany},
Volume = {81 (Suppl)},
Pages = {120-121},
Year = {1994},
Key = {fds16738}
}
@misc{fds16741,
Author = {Pryer, K.M. and F.M. Lutzoni and A.R. Smith},
Title = {Towards a fern phylogeny: integrating morphology and
molecules},
Journal = {American Journal of Botany},
Volume = {81 (Suppl)},
Pages = {122},
Year = {1994},
Key = {fds16741}
}
@misc{fds16737,
Author = {Pryer, K.M},
Title = {Ontogeny and phylogeny in the aquatic fern family
Marsileaceae: cladistic analysis of morphological and
molecular data},
Journal = {American Journal of Botany},
Volume = {80 (Suppl)},
Pages = {172},
Year = {1993},
Key = {fds16737}
}
@misc{fds16736,
Author = {Pryer, K.M. and M.D. Windham},
Title = {A re-examination of Gymnocarpium dryopteris
(L.)},
Journal = {Newman in North America. American Journal of
Botany},
Volume = {75 (Suppl)},
Pages = {142},
Year = {1988},
Key = {fds16736}
}
@misc{fds16735,
Author = {Pryer, K.M. and G.W. Argus and E. Haber},
Title = {The Canadian Rare and Endangered Plant's
Project},
Journal = {Botany '86 - Program of the 22nd Annual Meeting of the
Canadian Botanical Association},
Pages = {34},
Year = {1986},
Key = {fds16735}
}
@misc{fds16731,
Author = {Pryer, K.M. and D.M. Britton and J. McNeill},
Title = {Hybridization in the fern genus Gymnocarpium Newman in North
America},
Journal = {American Journal of Botany},
Volume = {71(Suppl)},
Pages = {142},
Year = {1984},
Key = {fds16731}
}
@misc{fds16727,
Author = {Pryer, K.M. and D.M. Britton and J. McNeill},
Title = {Systematic studies in the genus Gymnocarpium Newman in North
America},
Journal = {American Journal of Botany},
Volume = {70 (Suppl)},
Pages = {60},
Year = {1983},
Key = {fds16727}
}
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