publication . Other literature type . Article . 2012

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

Gabriela Parra-Olea; Joshua S. Williams; X. Aguilar-Miguel; H. Bradley Shaffer; Eric M. O'Neill; Rachel S. Schwartz; Rachel S. Schwartz; David W. Weisrock; C. Thomas Bullock;
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  • Published: 12 Oct 2012
  • Publisher: (:unav)
Abstract
Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome-wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next-generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander (Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this large data set (344 330 reads), we developed a pipeline that sorts PTS data by barcode and locus, identifies high-quality variable nucleotides and yields ...
Subjects
free text keywords: Genetics, Ecology, Evolution, Behavior and Systematics, DNA sequencing, Evolutionary biology, Tiger salamander, biology.organism_classification, biology, Coalescent theory, Locus (genetics), Amplicon, Population, education.field_of_study, education, Phylogenetic tree, Species complex
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