Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates

Abstract

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.

Morphological and molecular characterization of freshwater prawn of genus Macrobrachium in the coastal area of Cameroon

“…These low values of PIC deviate from those seen in other commercially important nonaquatic species (PIC values range between 0.30 and 0.44; Raman et al, ; Sánchez‐Sevilla et al, ; Wenzl et al, ). The use of DArT in characterization of animals (and particularly aquatic animals) has been limited (Melville et al, ). In this study, even though up to 50,000 SNP markers were available after genotyping, only 1,814 met the criterion for further analysis, which limits the extent of the genetic diversity that can be captured.…”

Fresh is best: Accurate SNP genotyping from koala scats

“…There are a number of reasons for this: Firstly, the DArTseq ™ protocol utilized in this study is a well‐documented methodology. It has been used effectively across a range of species and specifically recommended for vertebrate studies (Melville et al., ). In particular, the standardization of loci genotyped across samples, and the repeatable complexity reduction methods provide a reliable and widely applicable methodology.…”

“…There are a number of reasons for this: Firstly, the DArTseq ™ protocol utilized in this study is a well-documented methodology. It has been used effectively across a range of species and specifically recommended for vertebrate studies (Melville et al, 2017).…”

“…SNP genotyping was conducted by Diversity Arrays Technology, Canberra, using proprietary DArTseq ™ technology. DArTseq ™ technology has been tested and used successfully for a wide range of genomic studies across a variety of vertebrate species (Melville et al, 2017). Examples of this include Cunningham's skinks (Egernia cunninghami) (Ofori, Beaumont, & Stow, 2017), North American green frog (Rana clamitans) (Lambert, Skelly, & Ezaz, 2016), trout cod (Maccullochella macquariensis) and Murray cod (Maccullochella peelii) (Couch, Unmack, Dyer, & Lintermans, 2016), yellowfin tuna (Thunnus albacares) (Grewe et al, 2015), eastern yellow robin (Eopsaltria australis) (Morales et al, 2017), and southern fiddler rays (Trygonrrhina dumerilii) (Donnellan et al, 2015).…”

A genome‐wide search for local adaptation in a terrestrial‐breeding frog reveals vulnerability to climate change

“…DArTseq has three major advantages including a lower DNA input, greater tolerance to low quality DNA and a higher call rate (Sánchez-Sevilla et al, 2015). Only ligated fragments with both a Pstl and Sphl adapter were amplified by polymerase chain reaction (PCR) with an initial denaturation step at 94°C for 1 min, followed by 30 cycles with a temperature profile as follows: denaturation at 94°C for 20 s, annealing at 58°C for 30 s and extension at 72°C for 45 s, with an additional final extension (Melville et al, 2017). DNA samples were processed in digestion/ ligation reactions (Kilian et al, 2012).…”