Identifying hybridization and admixture using SNPs: Application of the DArTseq platforminphylogeographic research on vertebrates

J Melville; M L Haines; K Boysen; L Hodkinson; A Kilian; K L Smith Date; Dominique A Potvin; K M Parris

doi:10.1098/rsos.161061

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Identifying hybridization and admixture using SNPs: Application of the DArTseq platforminphylogeographic research on vertebrates

Journal article

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Identifying hybridization and admixture using SNPs: Application of the DArTseq platforminphylogeographic research on vertebrates

J Melville, M L Haines, K Boysen, L Hodkinson, A Kilian, K L Smith Date, Dominique A Potvin and K M Parris

Royal Society Open Science, Vol.4(7), 161061

2017

DOI: https://doi.org/10.1098/rsos.161061

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Abstract

DArTseq

genomics

hybridization

phylogeography

population genetics SNPs

Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii-Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization. © 2017 The Authors.

Details

Title: Identifying hybridization and admixture using SNPs: Application of the DArTseq platforminphylogeographic research on vertebrates
Authors: J Melville (Author) - Museum Victoria
M L Haines (Author) - Museum Victoria
K Boysen (Author) - Museum Victoria
L Hodkinson (Author) - Museum Victoria
A Kilian (Author) - University of Canberra
K L Smith Date (Author) - Museum Victoria
Dominique A Potvin (Author) - Museum Victoria
K M Parris (Author) - University of Melbourne
Publication details: Royal Society Open Science, Vol.4(7), 161061
Publisher: Royal Society of Chemistry (R S C) Publications
Date published: 2017
DOI: 10.1098/rsos.161061
ISSN: 2054-5703
Copyright note: Copyright © 2017 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering
Language: English
Record Identifier: 99451045902621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Genetics & Heredity