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dc.contributor.authorMelville, J
dc.contributor.authorHaines, ML
dc.contributor.authorBoysen, K
dc.contributor.authorHodkinson, L
dc.contributor.authorKilian, A
dc.contributor.authorDate, KLS
dc.contributor.authorPotvin, DA
dc.contributor.authorParris, KM
dc.date.accessioned2020-12-21T01:45:40Z
dc.date.available2020-12-21T01:45:40Z
dc.date.issued2017-07-01
dc.identifierpii: rsos161061
dc.identifier.citationMelville, J., Haines, M. L., Boysen, K., Hodkinson, L., Kilian, A., Date, K. L. S., Potvin, D. A. & Parris, K. M. (2017). Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates. ROYAL SOCIETY OPEN SCIENCE, 4 (7), https://doi.org/10.1098/rsos.161061.
dc.identifier.issn2054-5703
dc.identifier.urihttp://hdl.handle.net/11343/256647
dc.description.abstractNext-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.
dc.languageEnglish
dc.publisherROYAL SOC
dc.titleIdentifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates
dc.typeJournal Article
dc.identifier.doi10.1098/rsos.161061
melbourne.affiliation.departmentSchool of Ecosystem and Forest Sciences
melbourne.source.titleRoyal Society Open Science
melbourne.source.volume4
melbourne.source.issue7
dc.rights.licenseCC BY
melbourne.elementsid1226465
melbourne.contributor.authorParris, Kirsten
dc.identifier.eissn2054-5703
melbourne.accessrightsOpen Access


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