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Pryer Lab : Publications since January 2016

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Pryer, Kathleen M.   
@article{fds322311,
   Author = {Rothfels, CJ and Pryer, KM and Li, F-W},
   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},
   Month = {January},
   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, R and Schuettpelz, E and Huiet, L and Pryer, K and Smith, A and Prado, J},
   Title = {Phylogeny and relationships of the neotropical Adiantum
             raddianum group (Pteridaceae)},
   Journal = {Taxon},
   Volume = {65},
   Number = {6},
   Pages = {1225-1235},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.12705/656.1},
   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, JE and Windham,
             MD},
   Title = {Sex and the Single Gametophyte: Revising the Homosporous
             Vascular Plant Life Cycle in Light of Contemporary
             Research},
   Journal = {BioScience (BioOne)},
   Volume = {66},
   Number = {11},
   Pages = {928-937},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1093/biosci/biw108},
   Doi = {10.1093/biosci/biw108},
   Key = {fds324241}
}

@article{fds322312,
   Author = {Schuettpelz, E and Chen, C-W 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},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.12705/654.2},
   Doi = {10.12705/654.2},
   Key = {fds322312}
}

@article{fds322313,
   Author = {Pryer, KM and Huiet, L and Li, F-W 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},
   Year = {2016},
   Month = {March},
   url = {http://dx.doi.org/10.1600/036364416X690660},
   Doi = {10.1600/036364416X690660},
   Key = {fds322313}
}

@article{fds324242,
   Author = {Li, F-W and Kuo, L-Y 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},
   Year = {2016},
   Month = {January},
   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}
}


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