Geographic hot spots of dingo genetic ancestry in southeastern Australia despite hybridisation with domestic dogs

Ancient genomes reveal over two thousand years of dingo population structure

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

Population density and ranging behaviour of a generalist carnivore varies with human population

Canid species are highly adaptable, including to urban and peri-urban areas, where they can come into close contact with people. Understanding the mechanisms of wild canid population persistence in these areas is key to managing any negative impacts. The resource dispersion hypothesis predicts that animal density increases and home range size decreases as resource concentration increases, and may help to explain how canids are distributed in environments with an urban-natural gradient. In Australia, dingoes have adapted to human presence, sometimes living in close proximity to towns. Using a targeted camera trap survey and spatial capture-recapture models, we estimated spatial variation in the population density and detection rates of dingoes on Worimi Country in the Great Lakes region of the NSW coast. We tested whether dingo home range and population densities varied across a gradient of human population density, in a mixed-use landscape including, urban, peri-urban, and National Park environs. We found human population density to be a strong driver of dingo density (ranging from 0.025 to 0.433 dingoes/km2 across the natural-urban gradient), and to have a negative effect on dingo home range size. The spatial scale parameter changed depending on survey period, being smaller in the peak tourism period, when human population increases in the area, than in adjacent survey periods, potentially indicating reduced home range size when additional resources are available. Our study highlights the potential value of managing anthropogenic resource availability to manage carnivore densities and potential risk of human-carnivore interactions.

Genomic consequences of isolation and inbreeding in an island dingo population

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

An isolated population reveals greater genetic structuring of the Australian dingo

The Australian dingo is a recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed 34 microsatellite markers using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual level. The broader southern Australia sample (n = 1138) comprised mostly hybrid animals, with 30% considered pure dingoes. All western Victorian individuals (n = 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and low genetic diversity on all measures tested. Based upon our characterisation of this unusual mainland population, we advise against assuming homogeneity of dingoes across the continent.

Before Azaria: A Historical Perspective on Dingo Attacks

This paper investigates the origin of the once popular belief in Australian society that wild dingoes do not attack humans. To address this problem, a digital repository of archived newspaper articles and other published texts written between 1788 and 1979 were searched for references to dingoes attacking non-Indigenous people. A total of 52 accounts spanning the period between 1804 and 1928 was identified. A comparison of these historical accounts with the details of modern dingo attacks suggests that at least some of the former are credible. The paper also examined commonly held attitudes towards dingoes in past Australian society based on historical print media articles and other records. Early chroniclers of Australian rural life and culture maintained that dingoes occasionally killed and ate humans out of a predatory motivation. By the early decades of the 20th century, however, an opposing view of this species had emerged: namely, that dingoes were timid animals that continued to pose a danger to livestock, but never to people. This change in the cultural image of dingoes can possibly be linked to more than a century of lethal dingo control efforts greatly reducing the frequency of human–dingo interactions in the most populous parts of the country. This intensive culling may also have expunged the wild genetic pool of dingoes that exhibited bold behaviour around people and/or created a dingo population that was largely wary of humans.

The myth of wild dogs in Australia: are there any out there?

Hybridisation between wild and domestic canids is a global conservation and management issue. In Australia, dingoes are a distinct lineage of wild-living canid with a controversial domestication status. They are mainland Australia’s apex terrestrial predator. There is ongoing concern that the identity of dingoes has been threatened from breeding with domestic dogs, and that feral dogs have established populations in rural Australia. We collate the results of microsatellite DNA testing from 5039 wild canids to explore patterns of domestic dog ancestry in dingoes and observations of feral domestic dogs across the continent. Only 31 feral dogs were detected, challenging the perception that feral dogs are widespread in Australia. First generation dingo × dog hybrids were similarly rare, with only 27 individuals identified. Spatial patterns of genetic ancestry across Australia identified that dingo populations in northern, western and central Australia were largely free from domestic dog introgression. Our findings challenge the perception that dingoes are virtually extinct in the wild and that feral dogs are common. A shift in terminology from wild dog to dingo would better reflect the identity of these wild canids and allow more nuanced debate about the balance between conservation and management of dingoes in Australia.

Consequences of Hybridization in Mammals: A Systematic Review

Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.

Hybridisation between dingoes and domestic dogs in proximity to Indigenous communities in northern Australia

In northern Australia, wild dog populations potentially interact with domestic dogs from remote communities, which would create opportunities for disease transmission at the wild-domestic interface. An example is rabies, in the event of an incursion into northern Australia. However, the likelihood of such wild-domestic interactions is ambiguous. Hybridisation analyses based on 23 microsatellite DNA markers were performed on canine-origin scats collected in bushland areas around remote Indigenous communities in the Northern Peninsula Area, Queensland. Sufficient DNA was extracted from 6 of 41 scats to assess the percentage of dingo purity. These scats most likely originated from two 'pure' domestic dogs (0% dingo purity), one hybrid (20% dingo purity) and three 'pure' dingoes (92%-98% dingo purity). The two domestic dog samples were collected in the vicinity of communities. The location of two of the dingo-origin samples provides genetic evidence that dingoes are present in areas close to the communities. The availability of anthropogenic food resources likely creates opportunities for interactions with domestic dogs in the region. The hybrid sample demonstrates the occurrence of antecedent contacts between both populations by means of mating and supports the likelihood of a spatio-temporal overlap at the wild-domestic interface. This represents the first genetic survey involving a wild dog population of equatorial northern Queensland, with evidence of dingo purity. Our results have implications for potential disease transmission within a priority area for biosecurity in northern Australia.

Pesticide use is linked to increased body size in a large mammalian carnivore

Pollution and pesticide use have been linked to evolution of chemical resistance and phenotypic shifts in invertebrates, but less so in vertebrates. Here we provide evidence that poisoning directed towards a mammalian carnivore, the dingo (Canis dingo), is linked to an increase in dingo body mass. We compared the skull length of dingoes, a proxy for size, from three regions where dingo populations were controlled by distributing poisoned meat baits and an unbaited region, before and after the introduction of the toxin sodium fluoroacetate (Compound 1080). Following 1080 introduction, dingo skull length increased in baited regions but not in the unbaited region. We estimate that after 1080 introduction, the skull length of female and male dingoes in baited regions increased by 4.49 and 3.6 mm, respectively. This equates to a 1.02- and 0.86-kg increase in mean body masses of female and male dingoes, respectively. We hypothesize that dingo body size has increased in baited regions due to 1080 selecting for animals with larger body size or because a reduction in dingo abundance in baited areas may have removed constraints on growth imposed by intraspecific competition and prey availability. Our study provides evidence that pesticide use can prompt phenotypic change in comparatively large and long-lived large vertebrates.

What Is a Dingo? The Phenotypic Classification of Dingoes by Aboriginal and Torres Strait Islander Residents in Northern Australia

Simple Summary

Dingoes are an Australian icon with cultural, as well as ecological, value, yet defining a dingo is complicated by hybridisation with domestic dogs. Northern Australia is a high-risk zone for the arrival of rabies, a disease which affects dogs (including dingoes) and people. In a rabies outbreak, Aboriginal and Torres Strait Islander peoples who live in this region would want dingoes protected. We visited the Northern Peninsula Area (NPA), Queensland, in 2018–2019 and surveyed Aboriginal and Torres Strait Islander residents about how they define dingoes, using pictures from camera traps previously placed and operated in the area. We found that dingo definition was based on characteristics traditionally associated with the iconic dingo (medium to large-framed dogs, with a long nose, pointed ears, narrow abdomen, bushy tail, smooth tan coats, and white feet and tail tip) but hybrid features, such as curled tail or a lack of white points, were also acceptable features. Local definitions are important when designing and implementing management plans so that actions are supported by local communities, and our findings are a useful guide for identifying dingoes in the NPA so that, in the event of a rabies outbreak, locally valued dingoes could be identified and protected.

Abstract

Dingo classification and management is complicated by hybridisation with domestic dogs. Northern Australia is a relatively high-risk zone for a rabies incursion, and in the event of an incursion, Aboriginal and Torres Strait Islander peoples who reside in this region would prioritise the protection of dingoes. Therefore, the classification of dingoes in this context is important. Twelve pictures of canids with features associated with both dingoes and domestic dogs from camera traps in the Northern Peninsula Area (NPA), northern Queensland, were shown to Aboriginal and Torres Strait Islander rangers (n = 3), biosecurity officers (n = 2), environmental health workers (n = 2), and residents (n = 39) in the NPA. Nearly all pictures (10/12) were classified as dingo or domestic dog (none as hybrid) and two were inconclusive (no overall agreement). Dingoes were consistently identified as medium to large-framed dogs, with a long nose, pointed ears, narrow abdomen, a bushy or feathered tail, and smooth coats of a single base colour. Some hybrid features were acceptable, including sable coats, lack of white tail tip or feet, and curled tail. These findings are a preliminary guide for identifying canids in the NPA region for whom management might be controversial. Building on this approach via further consultation with residents is needed to inform rabies response policy. Our approach using locally acquired camera trap pictures could also be extended to other regions in which dingoes have value but their management is controversial.

Relaxed predation theory: size, sex and brains matter

Australia's wildlife is being considerably impacted by introduced mammalian predators such as cats (Felis catus), dogs (Canis lupus familiaris), and foxes (Vulpes vulpes). This is often attributed to native wildlife being naïve to these introduced predators. A systematic review of the literature reveals that native metatherians (body mass range 0.02-25 kg) do not recognise, and show relaxed antipredator behaviours towards, native and some introduced mammalian predators. Native eutherians (all with body mass < 2 kg), however, do appear to recognise and exhibit antipredator behaviours towards both native and introduced predators. Based on our findings, we propose a novel theory, the 'Relaxed Predation Theory'. Our new theory is based on the absence of large mammalian predators leading to reduced predation pressure in Australia during the past 40000-50000 years, and on three key differences between Australian metatherians and eutherians: size, sex, and brains. In light of this Relaxed Predation Theory, we make a number of recommendations for the conservation of Australian wildlife: (i) predator avoidance training of suitable species; (ii) exclusion fencing to exclude some, but not all, predators to facilitate the development of antipredator behaviours; (iii) captive breeding programs to prevent the extinction of some species; and (iv) reintroduction of Australia's larger predators, potentially to compete with and displace introduced predators. A more detailed understanding of the responses of Australian mammals to predators will hopefully contribute to the improved conservation of susceptible species.