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

Katie L Smith Date,Katja Boysen,Andrzej Kilian,Jane Melville,Margaret L Haines,Luke Hodkinson,Kirsten M Parris,Dominique A Potvin

doi:10.1098/rsos.161061

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.

Highlights

Population genetics and phylogeographic research have shown that many species consist of multiple, highly divergent genetic lineages, with evidence of hybridization and introgression between these lineages [1]
A fastSTRUCTURE analysis resolved the most likely number of clusters at K = 7, which equates to samples being assigned to C. ornatus, to each of the five putative subspecies within C. caudicinctus (C. c. caudicinctus, C. c. mensarum, C. c. infans, C. c. macropus/slateri and C. c. graafi), and to C. c. caudicinctus which is further divided into two clusters
One of these individuals (WAMR122612) had only a 6% genetic contribution from C. c. caudicinctus and as such was not included in the admixed individuals detailed above

Summary

Introduction

Population genetics and phylogeographic research have shown that many species consist of multiple, highly divergent genetic lineages, with evidence of hybridization and introgression between these lineages [1]. Genetic analyses have become a cornerstone of species delimitation and evolutionary biology [2]. Both theoretical and empirical work show that traditional genetic approaches may have a number of biases and shortfalls related to the stochasticity of evolutionary processes operating at the population scale, and that increased genetic sampling across the genome is fundamental for improved accuracy [3]. Examples include restriction site-associated DNA sequencing (RADseq), genotyping by sequencing (GBS) and others [6,7] Many of these NGS methods depend on restriction enzymes to produce a reduced representation of a genome, one such method is DArTseq (Diversity Array Technology sequencing)

Methods

Results

Discussion

Conclusion