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Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis

Cairns, Kylie M.1; Crowther, Mathew S.2; Parker, Heidi G.3; Ostrander, Elaine A.3; Letnic, Mike1

Published May 31, 2023 on Dryad. https://doi.org/10.5061/dryad.vq83bk3ww

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Abstract

Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to inter-specific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. There has been concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here we apply genome-wide single nucleotide polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes from across Australia and then carry out comparisons to domestic dogs, and perform ancestry modelling and biogeographic analyses to characterize population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes, challenging previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in southeastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policy makers to assess and inform dingo management policy and legislation moving forwards.