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

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.