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.

Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes

“…Comparison of median F het values between the dingo population clusters indicates that all dingoes have higher homozygosity levels than recent dingo backcrosses and dingo × dog hybrids (Figure 5), which is consistent with whole genome sequencing data that also reported higher levels of homozygosity in dingoes compared to domestic dogs (Kumar et al, 2023; Zhang et al, 2020). The Big Desert population has the highest median F het values, nearly 30% higher than the other dingo populations, indicating the population is extremely homozygous and likely inbred.…”

“…A recent microsatellite‐based study found the Big Desert dingo population to have genetic diversity levels up to 50% lower than other dingo populations (Stephens et al, 2022). While the absolute value of homozygosity measures calculated for dingoes in this study could be inflated due to ascertainment bias, whole genome data from a small number of captive and wild dingoes also reveal elevated homozygosity levels relative to domestic dogs (Field et al, 2022; Kumar et al, 2023; Zhang et al, 2020). Further research is needed to assess whether lethal management programmes have had an impact on homozygosity and genetic diversity levels in regional dingo populations, such as the Big Desert population (Hohenlohe et al, 2021; Quevedo et al, 2019; Weeks et al, 2016).…”

Genomic consequences of isolation and inbreeding in an island dingo population

“…SHAPEIT2.v904 (Delaneau et al 2014) was used with default parameters to phase the genotypes of all 41 canids, using the pedigree-based recombination map from Campbell, et al (Campbell et al 2016). The ancestral and derived states of each variant for the 18 dingo samples was taken from Kumar et al (Kumar et al 2023).…”

“…Sequencing data from 3 dingo samples from mainland Australia (2 from the Northwest, and 1 from the Southeast) were obtained from a recently published study (Kumar et al 2023). Ten dingo samples, comprising 1 from K'gari and 9 from mainland Australia (6 from the Northwest, and 3 from the Southeast), were obtained from a previous study (Zhang et al 2020).…”

Genomic insights into red squirrels in Scotland reveals loss of heterozygosity associated with extreme founder effects

“…Interventions of this type are becoming ever more common as wild populations become increasingly fragmented and disjunct. Founder effects, exacerbated by population fragmentation, have been observed across species (Adams and Edmands, 2023;Colpitts et al, 2022;Kumar et al, 2023;Wilder et al, 2022), and many genetically depauperate species are now successfully managed using a metapopulation strategy. For example, Kenyan populations of the eastern black rhinoceros Diceros bicornus micheali are now wholly managed as a country-wide metapopulation (Amin et al, 2017), and notable success has also been recorded…”