The Australian dingo is a relatively recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed genetic data using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual levels. Upon finding low genetic diversity in western Victoria, we tested for a recent genetic bottleneck. The broader southern Australia sample (n=1,138) comprised mostly hybrid animals, with ~30% dingoes. All western Victorian individuals (n= 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and no recent bottleneck. Based upon our characterisation of this unusual mainland population, we sound caution for future studies assuming homogeneity of dingoes across the continent.

Tissue specimens were collected opportunistically from deceased dogs by individuals involved in wildlife management and research in Victoria, New South Wales, and South Australia and submitted to ongoing research projects by PJSF and DS from 2007 to the present. Dog ear tissue specimens were stored in ~3 mL Longmire buffer until DNA extraction. Extractions were performed using Qiagen DNeasy blood and tissue kit (Qiagen Inc. CA, USA) with the recommended protocol. Extracts were amplified at 34 microsatellite markers in seven multiplexed PCRs.