Data from: Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing

The field of phylogenetics is changing rapidly with the application of
high-throughput sequencing to non-model organisms. Cost-effective use of
this technology for phylogenetic studies, which often include a relatively
small portion of the genome but several taxa, requires strategies for
genome partitioning and sequencing multiple individuals in parallel. In
this study we estimated a multilocus phylogeny for the North American
chorus frog genus Pseudacris using anonymous nuclear loci that were
recently developed using a reduced representation library approach. We
sequenced 27 nuclear loci and three mitochondrial loci for 44 individuals
on 1/3 of an Illumina MiSeq run, obtaining 96.5% of the targeted amplicons
at less than 20% of the cost of traditional Sanger sequencing. We found
heterogeneity among gene trees, although four major clades (Trilling Frog,
Fat Frog, crucifer, and West Coast) were consistently supported, and we
resolved the relationships among these clades for the first time with
strong support. We also found discordance between the mitochondrial and
nuclear datasets that we attribute to mitochondrial introgression and a
possible selective sweep. Bayesian concordance analysis in BUCKy and
species tree analysis in *BEAST produced largely similar topologies,
although we identify taxa that require additional investigation in order
to clarify taxonomic and geographic range boundaries. Overall, we
demonstrate the utility of a reduced representation library approach for
marker development and parallel tagged sequencing on an Illumina MiSeq for
phylogenetic studies of non-model organisms.