Journal
MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 75, Issue -, Pages 78-90Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2014.02.007
Keywords
Anonymous nuclear locus; Reduced representation library; Targeted amplicon sequencing; High-throughput sequencing; Phylogenetics; Pseudacris
Funding
- NSF [DEB1120516]
- Florida State University
- NSF Graduate Research Fellowship Program [DGE-0952090]
- Direct For Biological Sciences
- Division Of Environmental Biology [1120516] Funding Source: National Science Foundation
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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 mitochondria] 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. (c) 2014 Elsevier Inc. All rights reserved.
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