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Pryer Lab : Publications since January 2015

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Pryer, Kathleen M.   
@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},
   Year = {2015},
   Month = {October},
   ISSN = {0363-6445},
   url = {http://hdl.handle.net/10161/10796 Duke open
             access},
   Doi = {10.1600/036364415X689366},
   Key = {fds230052}
}

@article{fds230054,
   Author = {Wolf, PG and Sessa, EB and Marchant, DB and Li, FW and Rothfels, CJ and Sigel, EM and Gitzendanner, MA and Visger, CJ and Banks, JA and Soltis,
             DE and Soltis, PS and Pryer, KM and Der, JP},
   Title = {An Exploration into Fern Genome Space.},
   Journal = {Genome Biology and Evolution},
   Volume = {7},
   Number = {9},
   Pages = {2533-2544},
   Year = {2015},
   Month = {September},
   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{fds230056,
   Author = {Rothfels, CJ and Li, FW and Sigel, EM and Huiet, L and Larsson, A and Burge, DO and Ruhsam, M and Deyholos, M and Soltis, DE and Stewart, CN and Shaw, SW and Pokorny, L and Chen, T and dePamphilis, C and DeGironimo,
             L and Chen, L and Wei, X and Sun, X and Korall, P and Stevenson, DW and Graham, SW and Wong, GK and Pryer, 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 = {http://hdl.handle.net/10161/10798 Duke open
             access},
   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
             studies.},
   Doi = {10.3732/ajb.1500089},
   Key = {fds230056}
}

@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 = {American Naturalist},
   Volume = {185},
   Number = {3},
   Pages = {433-442},
   Year = {2015},
   Month = {March},
   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{fds230053,
   Author = {Li, FW and Rothfels, CJ and Melkonian, M and Villarreal, JC and Stevenson, DW and Graham, SW and Wong, GK and Mathews, S and Pryer,
             KM},
   Title = {The origin and evolution of phototropins.},
   Journal = {Frontiers in Plant Science},
   Volume = {6},
   Pages = {637},
   Year = {2015},
   Month = {January},
   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 = {Adiantumshastense, a new species of maidenhair fern from
             California.},
   Journal = {PhytoKeys},
   Number = {53},
   Pages = {73-81},
   Year = {2015},
   Month = {January},
   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{fds230057,
   Author = {Li, FW 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},
   Pages = {7852},
   Year = {2015},
   Month = {January},
   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}
}


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