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PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
  • D. Eaton
  • Biology, Computer Science
  • Bioinform.
  • 1 July 2014
PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets. Expand
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Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here weExpand
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ipyrad: Interactive assembly and analysis of RADseq datasets
SUMMARY ipyrad is a free and open source tool for assembling and analyzing restriction-site associated DNA sequence (RADseq) datasets using de novo and/or reference-based approaches. It is designedExpand
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Misconceptions on Missing Data in RAD‐seq Phylogenetics with a Deep‐scale Example from Flowering Plants
Abstract Restriction‐site associated DNA (RAD) sequencing and related methods rely on the conservation of enzyme recognition sites to isolate homologous DNA fragments for sequencing, with theExpand
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Floral diversity and community structure in Pedicularis (Orobanchaceae)
A pervasive hypothesis at the interface of ecology and evolution is that biotic interactions contribute to regional biodiversity by accelerating adaptation and speciation. We investigated thisExpand
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Historical introgression among the American live oaks and the comparative nature of tests for introgression
Introgressive hybridization challenges the concepts we use to define species and infer phylogenetic relationships. Methods for inferring historical introgression from the genomes of extant species,Expand
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Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach
The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spansExpand
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Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: a case study in Carex (Cyperaceae).
Determining phylogenetic relationships among very closely related species has remained a challenge for evolutionary biologists due to interlocus phylogenetic discordance and the difficulty ofExpand
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Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa.
Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remainsExpand
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Differences in flowering time maintain species boundaries in a continental radiation of Viburnum.
PREMISE We take an integrative approach in assessing how introgression and Pleistocene climate fluctuations have shaped the diversification of the core Lentago clade of Viburnum, a group of fiveExpand
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