Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizardsReport as inadecuate




Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards - Download this document for free, or read online. Document in PDF available to download.

BMC Evolutionary Biology

, 15:62

First Online: 11 April 2015Received: 01 October 2014Accepted: 24 February 2015DOI: 10.1186-s12862-015-0318-0

Cite this article as: Brandley, M.C., Bragg, J.G., Singhal, S. et al. BMC Evol Biol 2015 15: 62. doi:10.1186-s12862-015-0318-0

Abstract

BackgroundHigh-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific-phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group Squamata: Scincidae. We sequenced 415 anchored hybrid enriched AHE loci for 43 individuals and mined 1650 exons 1648 loci from transcriptomes transcriptome mining from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration.

ResultsPhylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.

ConclusionsAnchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks.

KeywordsAnchored phylogenomics Coalescence Phylogeography Skink Transcriptome Ultraconserved elements Electronic supplementary materialThe online version of this article doi:10.1186-s12862-015-0318-0 contains supplementary material, which is available to authorized users.

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Author: Matthew C Brandley - Jason G Bragg - Sonal Singhal - David G Chapple - Charlotte K Jennings - Alan R Lemmon - Emily Mo

Source: https://link.springer.com/







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