Runs of homozygosity reveal extensive inbreeding among K’gari Island dingoes
Authors: Ana V. Leon-Apodaca 1; Manoharan Kumar 2; Gabriel Conroy 2; Steven Ogbourne 2; Kylie M. Cairns 3; Sankar Subramanian 2; Zachary A. Szpiech 1
Affiliations: 1) Pennsylvania State University; 2) University of the Sunshine Coast; 3) University of New South Wales
Keywords: Ecological & conservation genetics
Dingoes (Canis dingo) are wild canids from an ancient canid lineage, now naturalized in Australia. Their evolutionary history remains contested, and it is thought that they arrived in Australia via South-East Asia at least 5,000 years BP, via one or more founder events. As Australia’s largest native terrestrial predator, they play an important ecological role. They are found across many different bioregions of Australia, including on multiple offshore islands. A protected population exists on K’gari (Fraser Island) that is relatively free from the risk of hybridisation with domestic or wild dogs. K’gari is the world’s largest sand island and a World Heritage listed national park. Over 600,000 people visit K’gari each year resulting in occasional negative human-dingo interactions. While many management strategies are in place to minimize this occurrence, lethal control has been utilized significantly in the past, and still occasionally occurs. Previous research on K’gari dingoes using microsatellites, genome-wide SNPs, and mtDNA sequencing demonstrated divergence from mainland dingoes and low genetic diversity. However, whole-genome data is lacking from this important population. In this study, we analyze 18 whole genome sequences of dingoes sampled from mainland Australia (n=12) and K’gari Island (n=6) to assess the influence of their demographic histories on patterns of genetic diversity. Preliminary results showed that mainland dingoes and K’gari Island dingoes have distinct patterns of genetic diversity. We identify runs of homozygosity (ROH), indicators of small population size and inbreeding, in each population finding elevated levels of long ROH (>1 Mb) in both. However, K’gari dingoes showed significantly higher levels of very long ROH (>5 Mb; mean nROH = 71.2 for K’gari and 27.0 for the mainland, p = 5.35E-6; and mean sROH = 607.2 Mb for K’gari and 279.2 Mb for the mainland, p = 4.39E-4), providing clear evidence for inbreeding, isolation, small population size, and a strong founder effect. In the case of the K’gari dingo population, it appears that bottlenecks and isolation have maintained low levels of genetic diversity, while mainland dingoes show slightly higher diversity. We hypothesize that these ROH patterns may affect the distribution of deleterious homozygotes between mainland and K'gari dingoes. This work helps to elucidate the genetic structure and evolution of K’gari dingoes to inform conservation efforts.