Genomic signatures of bottleneck and founder effect in dingoes

Dingoes who arrived in Australia during the mid-Holocene are the native top-orderterrestrial predator on the mainland and some offshore islands. Although dingoessubsequently spread across the continent over the years, the initial founding populationcould have been small. To investigate this hypothesis, we sequenced the whole genomesof three dingoes and obtained the genome data from nine more dingoes and 56 canines,including wolves, village, and breed dogs, and examined the signatures of bottlenecks andfounder effects. We found that the nucleotide diversity of dingoes was low and 36% lessthan highly inbred dogs and 3.3 times lower than wolves. The number of runs ofhomozygosity 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 elevatedratios of nonsynonymous to synonymous diversities, significantly higher numbers ofhomozygous deleterious Single Nucleotide Variants SNVs, and increased numbers ofloss of function SNVs, compared to breed dogs, village dogs, and wolves. These resultssuggest dingoes experienced a severe bottleneck, potentially caused by the limited numberof founding individuals. While many studies observe less diversity and a higher numberof deleterious mutations in domesticated populations compared to their wild relatives, weobserved the opposite the wild dingoes have lower diversity and a greater number ofharmful mutations than their domesticated dogs. Our findings can be explained bybottlenecks and founder effects during the establishment of dingoes on mainlandAustralia. These findings are of importance in cognisance of the lethal control measuresthat are still imparted on dingoes and stress the need for a conservation-based mindsetfor these populations.