Genomic signatures of bottleneck and founder effects in dingoes

Abstract

Dingoes arrived in Australia during the mid-Holocene and are the native top-order terrestrial predator on the mainland and some offshore islands. Although dingoes subsequently spread across the continent, the initial founding population(s) could have been small. To investigate this hypothesis, we examined the potential signatures of bottlenecks and founder effects in dingoes by sequencing the whole genomes of three dingoes and also obtaining the genome data from nine additional dingoes and 56 canines, including wolves, village dogs and breed dogs, and examined the signatures of bottlenecks and founder effects. We found that the nucleotide diversity of dingoes was low, and 36% less than highly inbred breed dogs and 3.3 times lower than wolves. The number of runs of homozygosity (RoH) segments in dingoes was 1.6 to 4.7 times higher than in other canines. Whilst examining deleterious mutational load, we observed that dingoes carried elevated ratios of nonsynonymous-to-synonymous diversities, significantly higher numbers of homozygous deleterious Single Nucleotide Variants (SNVs), and increased numbers of loss of function SNVs, compared to breed dogs, village dogs, and wolves. These results suggest dingoes experienced a severe bottleneck, potentially caused by the limited number of founding individuals. While many studies observe less diversity and a higher number of deleterious mutations in domesticated populations compared to their wild relatives, we observed the opposite - .i.e. wild dingoes have lower diversity and a greater number of harmful mutations than domesticated dogs. Our findings can be explained by bottlenecks and founder effects during the establishment of dingoes on mainland Australia. These findings highlight the need for conservation-based management of dingoes and need for wildlife managers to be cognisant of these findings when considering the use of lethal control measures across the landscape.