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Pryer Lab : Publications since January 2014

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Pryer, Kathleen M.   
   Author = {E Schuettpelz and KM Pryer and MD Windham},
   Title = {A Unified Approach to Taxonomic Delimitation in the Fern
             Genus Pentagramma (Pteridaceae)},
   Journal = {Systematic Botany},
   Volume = {40},
   Number = {3},
   Pages = {629-644},
   Year = {2015},
   Month = {October},
   ISSN = {0363-6445},
   url = {},
   Doi = {10.1600/036364415X689366},
   Key = {fds230052}

   Author = {PG Wolf and EB Sessa and DB Marchant and FW Li and CJ Rothfels and EM
             Sigel, MA Gitzendanner and CJ Visger and JA Banks and DE Soltis and PS
             Soltis, KM Pryer and JP Der},
   Title = {An Exploration into Fern Genome Space.},
   Journal = {Genome biology and evolution},
   Volume = {7},
   Number = {9},
   Pages = {2533-2544},
   Year = {2015},
   Month = {September},
   url = {},
   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
   Doi = {10.1093/gbe/evv163},
   Key = {fds230054}

   Author = {CJ Rothfels and FW Li and EM Sigel and L Huiet and A Larsson and DO Burge and M Ruhsam and M Deyholos and DE Soltis and CN Stewart and SW Shaw and L
             Pokorny, T Chen and C dePamphilis, L DeGironimo and L Chen and X Wei and X Sun and P Korall and DW Stevenson and SW Graham and GK Wong and KM
   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},
   Year = {2015},
   Month = {July},
   ISSN = {0002-9122},
   url = {},
   Abstract = {•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.•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.•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.•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
   Doi = {10.3732/ajb.1500089},
   Key = {fds230056}

   Author = {CJ Rothfels and AK Johnson and PH Hovenkamp and DL Swofford and HC
             Roskam, CR Fraser-Jenkins, MD Windham and 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},
   Year = {2015},
   Month = {March},
   ISSN = {0003-0147},
   url = {},
   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
   Doi = {10.1086/679662},
   Key = {fds230060}

   Author = {FW Li and CJ Rothfels and M Melkonian and JC Villarreal and DW
             Stevenson, SW Graham and GK Wong and S Mathews and KM
   Title = {The origin and evolution of phototropins.},
   Journal = {Frontiers in plant science},
   Volume = {6},
   Pages = {637},
   Year = {2015},
   Month = {January},
   url = {},
   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}

   Author = {L Huiet and M Lenz and JK Nelson and KM Pryer and AR
   Title = {Adiantumshastense, a new species of maidenhair fern from
   Journal = {PhytoKeys},
   Number = {53},
   Pages = {73-81},
   Year = {2015},
   Month = {January},
   ISSN = {1314-2011},
   url = {},
   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}

   Author = {FW Li and M Melkonian and CJ Rothfels and JC Villarreal and DW
             Stevenson, SW Graham and GK Wong and KM Pryer and S
   Title = {Phytochrome diversity in green plants and the origin of
             canonical plant phytochromes.},
   Journal = {Nature communications},
   Volume = {6},
   Pages = {7852},
   Year = {2015},
   Month = {January},
   url = {},
   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}

   Author = {CJ Rothfels and AK Johnson, MD Windham and KM
   Title = {Low-copy nuclear data confirm rampant allopolyploidy in the
             Cystopteridaceae (Polypodiales)},
   Journal = {Taxon},
   Volume = {63},
   Number = {5},
   Pages = {1026-1036},
   Year = {2014},
   Month = {October},
   ISSN = {0040-0262},
   url = {},
   Doi = {10.12705/635.32},
   Key = {fds230061}

   Author = {EM Sigel, MD Windham and CH Haufler and KM Pryer},
   Title = {Phylogeny, Divergence Time Estimates, and Phylogeography of
             the Diploid Species of the Polypodium vulgare Complex
   Journal = {Systematic Botany},
   Volume = {39},
   Number = {4},
   Pages = {1042-1055},
   Year = {2014},
   Month = {October},
   ISSN = {0363-6445},
   url = {},
   Doi = {10.1600/036364414X683921},
   Key = {fds230062}

   Author = {EM Sigel, MD Windham and KM Pryer},
   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},
   Year = {2014},
   Month = {September},
   ISSN = {0002-9122},
   url = {},
   Abstract = {•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.•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.•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.•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}

   Author = {Grusz, A.L. and M.D. Windham and G. Yatskievych and L. Huiet and G.J.
             Gastony and K.M. Pryer},
   Title = {Patterns of Diversification in the Xeric-adapted Fern Genus
             Myriopteris (Pteridaceae)},
   Journal = {Systematic Botany},
   Volume = {39},
   Number = {3},
   Pages = {698-714},
   Year = {2014},
   Month = {July},
   ISSN = {0363-6445},
   url = {},
   Doi = {10.1600/036364414X681518},
   Key = {fds230067}

   Author = {Li, F.W. ...(30 authors)... and K.M. Pryer},
   Title = {Horizontal transfer of an adaptive chimeric photoreceptor
             from bryophytes to ferns.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {111},
   Number = {18},
   Pages = {6672-6677},
   Year = {2014},
   Month = {May},
   ISSN = {0027-8424},
   url = {},
   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
   Doi = {10.1073/pnas.1319929111},
   Key = {fds230068}

   Author = {EB Sessa and JA Banks and MS Barker and JP Der and AM Duffy and SW Graham and M Hasebe and J Langdale and FW Li and DB Marchant and KM Pryer and CJ
             Rothfels, SJ Roux and ML Salmi and EM Sigel and DE Soltis and PS Soltis and DW Stevenson and PG Wolf},
   Title = {Between two fern genomes.},
   Journal = {GigaScience},
   Volume = {3},
   Pages = {15},
   Year = {2014},
   Month = {January},
   url = {},
   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}

   Author = {FW Li and KM Pryer},
   Title = {Crowdfunding the Azolla fern genome project: a grassroots
   Journal = {GigaScience},
   Volume = {3},
   Pages = {16},
   Year = {2014},
   Month = {January},
   url = {},
   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}

   Author = {Sigel, E.M. and M.D. Windham and A.R. Smith and R.J. Dyer and K.M.
   Title = {Rediscovery of Polypodium calirhiza (Polypodiaceae) in
   Journal = {Brittonia},
   Volume = {66},
   Number = {3},
   Pages = {278-286},
   Year = {2014},
   Month = {January},
   ISSN = {0007-196X},
   url = {},
   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}

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