Elucidating biogeographical patterns in Australian native canids using genome wide SNPs

Kylie M. Cairns, Laura M. Shannon, Janice Koler-Matznick, William J.O. Ballard, Adam R. Boyko

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

Dingoes play a strong role in Australia’s ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.

Original languageEnglish (US)
Article numbere0198754
JournalPloS one
Volume13
Issue number6
DOIs
StatePublished - Jun 2018

Bibliographical note

Funding Information:
This work was supported by a Hermon Slade Foundation Research grant (HSF11/6) to JWOB, Alan N Wilton and KMC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Embark Veterinary Inc. provides support in the form of salary for author ARB, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The role of specific authors is articulated in the ?author contributions? section. Acknowledgements should be directed to Dr Danielle Stephens (UWA) for sharing dingo samples used in this research. Dr Barbara Zangerl (UNSW) provided guidance concerning the analysis of SNP genotype data. Dr Carolina Correa (UNSW) provided constructive criticism and comments concerning the manuscript. Dr Alan Wilton (UNSW) provided the original idea and impetus to using SNP data in dingoes; sadly he did not get to see the end result. As well appreciation must go to the large number of conservation organisations, dingo trappers, land managers and government agencies for contributing dingo samples to genetic research projects on the dingo.

Publisher Copyright:
© 2018 Cairns et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Copyright:
Copyright 2018 Elsevier B.V., All rights reserved.

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