Death by sex in an Australian icon: a continent‐wide survey reveals extensive hybridization between dingoes and domestic dogs

Hybridization between domesticated animals and their wild counterparts can disrupt adaptive gene combinations, reduce genetic diversity, extinguish wild populations and change ecosystem function. The dingo is a free‐ranging dog that is an iconic apex predator and distributed throughout most of mainland Australia. Dingoes readily hybridize with domestic dogs, and in many Australian jurisdictions, distinct management strategies are dictated by hybrid status. Yet, the magnitude and spatial extent of domestic dog–dingo hybridization is poorly characterized. To address this, we performed a continent‐wide analysis of hybridization throughout Australia based on 24 locus microsatellite DNA genotypes from 3637 free‐ranging dogs. Although 46% of all free‐ranging dogs were classified as pure dingoes, all regions exhibited some hybridization, and the magnitude varied substantially. The southeast of Australia was highly admixed, with 99% of animals being hybrids or feral domestic dogs, whereas only 13% of the animals from remote central Australia were hybrids. Almost all free‐ranging dogs had some dingo ancestry, indicating that domestic dogs could have poor survivorship in nonurban Australian environments. Overall, wild pure dingoes remain the dominant predator over most of Australia, but the speed and extent to which hybridization has occurred in the approximately 220 years since the first introduction of domestic dogs indicate that the process may soon threaten the persistence of pure dingoes.     

The Kintamani dog: genetic profile of an emerging breed from Bali, Indonesia

The Kintamani dog is an evolving breed indigenous to the Kintamani region of Bali. Kintamani dogs cohabitate with feral Bali street dogs, although folklore has the breed originating 600 years ago from a Chinese Chow Chow. The physical and personality characteristics of the Kintamani dog make it a popular pet for the Balinese, and efforts are currently under way to have the dog accepted by the Federation Cynologique Internationale as a recognized breed. To study the genetic background of the Kintamani dog, 31 highly polymorphic short tandem repeat markers were analyzed in Kintamani dogs, Bali street dogs, Australian dingoes, and nine American Kennel Club (AKC) recognized breeds of Asian or European origin. The Kintamani dog was identical to the Bali street dog at all but three loci. The Bali street dog and Kintamani dog were most closely aligned with the Australian dingo and distantly related to AKC recognized breeds of Asian but not European origin. Therefore, the Kintamani dog has evolved from Balinese feral dogs with little loss of genetic diversity.     

Cranial Shape and the Modularity of Hybridization in Dingoes and Dogs; Hybridization Does Not Spell the End for Native Morphology

Australia’s native wild dog, the dingo (Canis dingo), is threatened by hybridization with feral or domestic dogs. In this study we provide the first comprehensive three dimensional geometric morphometric evaluation of cranial shape for dingoes, dogs and their hybrids. We introduce a novel framework to assess whether modularity facilitates, or constrains, cranial shape change in hybridization. Our results show that hybrid and pure dingo morphology overlaps greatly, meaning that hybrids cannot be reliably distinguished from dingoes on the basis of cranial metrics. We find that dingo morphology is resistant, with observed hybrids exhibiting morphology closer to the dingo than to the parent group dog. We also find that that hybridization with dog breeds does not push the dingo cranial morphology towards the wolf phenotype. Disparity and integration analyses on the ten recovered modules provided empirical support for modularity facilitating shape change over short evolutionary time scales. However, our results show that this is may not be the case in hybridization events, which were not influenced by module integration or disparity levels. We conclude that although hybridization events may introduce breed dog DNA to the dingo population, the native cranial morphology, and therefore likely the feeding eco-niche, of the dingo population is resistant to change. Our results have implications for conservation and management of dingoes and, more broadly, for the influence of integration patterns over ecological time scales in relation to selection pressure.     

Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins

Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.     

Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry

The dingo (Canis lupus dingo) is an iconic animal in the native culture of Australia, but archaeological and molecular records indicate a relatively recent history on the continent. Studies of mitochondrial DNA (mtDNA) imply that the current dingo population was founded by a small population of already tamed dogs from Southeast Asia. However, the maternal genetic data might give a unilateral picture, and the gene pool has yet to be screened for paternal ancestry. We sequenced 14,437?bp of the Y-chromosome (Y-chr) from two dingoes and one New Guinea Singing Dog (NGSD). This positioned dingo and NGSD within the domestic dog Y-chr phylogeny, and produced one haplotype not detected before. With this data, we characterized 47 male dingoes in 30 Y-chr single-nucleotide polymorphism sites using protease-mediated allele-specific extension technology. Only two haplotypes, H3 and H60, were found among the dingoes, at frequencies of 68.1 and 31.9?%, respectively, compared to 27 haplotypes previously established in the domestic dog. While H3 is common among Southeast Asian dogs, H60 was specifically found in dingoes and the NGSD, but was related to Southeast Asian dog Y-chr haplotypes. H3 and H60 were observed exclusively in the western and eastern parts of Australia, respectively, but had a common range in Southeast. Thus, the Y-chr diversity was very low, similar to previous observations for d-loop mtDNA. Overall genetic evidence suggests a very restricted introduction of the first dingoes into Australia, possibly from New Guinea. This study further confirms the dingo as an isolated feral dog.     

Living with Wild Dogs: Personality Dimensions in Captive Dingoes (Canis dingo) and Implications for Ownership

Despite the commonly held belief that wild canines do not make “good” household companions, many people choose to live with them. The aim of the present study was to investigate owner-rated personality in a population of dingoes living as companion animals. Owners recruited from a registered dingo organization assessed the personality of 40 dingoes using the Monash Canine Personality Questionnaire- Revised (MCPQ-R). The dingoes (22 female; 18 male) ranged in age from 6 months to 11 years (M = 3.6 years, SD = 2.4); weighed an average of 19.07 kg (SD = 3.41); were mostly entire (i.e., not de-sexed or spayed or neutered; 62.5%) and lived in multiple dingo households (72.5%). Results show that dingoes were rated significantly higher than domestic dogs (n = 455; various breeds from a previous Australian study) for the dimension Motivation/Self-Assuredness (p < 0.001), and significantly lower than dogs for Training Focus (p < 0.001). Many of the personality traits of dingoes reside outside what is considered “ideal” characteristics important for a successful and rewarding dog–owner relationship. It is possible that dingo personality rests within the realms of what is “acceptable” pet canine behavior, at least for some owners, and that they may have adjusted their perception and attitudes to meet their expectations of the species. Motivations for dingo ownership and the applicability of using a domestic dog personality questionnaire on wild canids are discussed.     

Could a rabies incursion spread in the northern Australian dingo population? Development of a spatial stochastic simulation model

Australia, home to the iconic dingo, is currently free from canine rabies. However northern Australia, including Indigenous communities with large free-roaming domestic dog populations, is at increased risk of rabies incursion from nearby Indonesia. We developed a novel agent-based stochastic spatial rabies spread model to evaluate the potential spread of rabies within the dingo population of the Northern Peninsula Area (NPA) region of northern Australia. The model incorporated spatio-temporal features specific to this host-environment system, including landscape heterogeneity, demographic fluctuations, dispersal movements and dingo ecological parameters—such as home range size and density—derived from NPA field studies. Rabies spread between dingo packs in nearly 60% of simulations. In such situations rabies would affect a median of 22 dingoes (approximately 14% of the population; 2.5–97.5 percentiles: 2–101 dingoes) within the study area which covered 1,131 km², and spread 0.52 km/week for 191 days. Larger outbreaks occurred in scenarios in which an incursion was introduced during the dry season (vs. wet season), and close to communities (vs. areas with high risk of interaction between dingoes and hunting community dogs). Sensitivity analyses revealed that home range size and duration of infectious clinical period contributed most to the variance of outputs. Although conditions in the NPA would most likely not support a sustained propagation of the disease in the dingo population, due to the predicted number of infected dingoes following a rabies incursion and the proximity of Indigenous communities to dingo habitat, we conclude that the risk for human transmission could be substantial.     

Do wild dogs exclude foxes? Evidence for competition from dietary and spatial overlaps

Abstract The management of wild canids (wild dogs/dingoes and foxes) presents a conservation dilemma for land managers across Australia. These canids are predators of wildlife and domestic stock but dingoes are considered native and anecdotal reports suggest that they may suppress foxes such that dingo/dog conservation may have a net benefit to wildlife. This study examines dietary and spatial interactions between wild dogs and foxes in the Greater Blue Mountains region of NSW to address the possibility of suppression through competitive exclusion by dogs on foxes. Predator diets were compared using faecal analysis as well as an analysis of 19 dietary studies from similar forest habitats in eastern Australia. Spatial relationships were examined using data from an extensive canid control programme. Diets of wild dogs and foxes showed a high degree of overlap in species taken, indicating potential for competition. But there was also evidence of resource partitioning with the size and arboreality of mammalian prey differing between the two predators. Wild dogs and foxes responded to different landscape‐scale variation in the physical environment, but there was no clear evidence of large‐scale differences in their distribution. At the fine scale there was a negative association between these predators that indicated possible temporal avoidance or localized habitat shifts. Therefore, there is evidence for dietary competition and fine‐scale exclusion, but no support for landscape‐scale exclusion of foxes by wild dogs in the Blue Mountains.     

Linkage Disequilibrium and Demographic History of Wild and Domestic Canids

Assessing the extent of linkage disequilibrium (LD) in natural populations of a nonmodel species has been difficult due to the lack of available genomic markers. However, with advances in genotyping and genome sequencing, genomic characterization of natural populations has become feasible. Using sequence data and SNP genotypes, we measured LD and modeled the demographic history of wild canid populations and domestic dog breeds. In 11 gray wolf populations and one coyote population, we find that the extent of LD as measured by the distance at which r² = 0.2 extends <10 kb in outbred populations to >1.7 Mb in populations that have experienced significant founder events and bottlenecks. This large range in the extent of LD parallels that observed in 18 dog breeds where the r² value varies from ~20 kb to >5 Mb. Furthermore, in modeling demographic history under a composite-likelihood framework, we find that two of five wild canid populations exhibit evidence of a historical population contraction. Five domestic dog breeds display evidence for a minor population contraction during domestication and a more severe contraction during breed formation. Only a 5% reduction in nucleotide diversity was observed as a result of domestication, whereas the loss of nucleotide diversity with breed formation averaged 35%.     

Australian dingoes are definitive hosts of Neospora caninum

To provide objective data on the potential role of dingoes (Canis lupus dingo) in the life cycle of Neospora caninum in Australia, the production of N. caninum oocysts by experimentally infected canids was investigated. Three dingo pups raised in captivity and three domestic dogs were fed tissue from calves infected with an Australian isolate of N. caninum, Nc-Nowra. Oocysts of N. caninum, confirmed by species-specific PCR, were shed in low numbers by one dingo pup at 12-14 days p.i. The remaining animals did not shed oocysts. Furthermore, the blood from two out of three dingoes tested positive for DNA of N. caninum using PCR tests at 14 and 28 days p.i. Oocyst shedding from the intestinal tract of a dingo demonstrates that dingoes are definitive hosts of N. caninum and horizontal transmission of N. caninum from dingoes to farm animals and wildlife may occur in Australia.     

Not all predators are equal: a continent‐scale analysis of the effects of predator control on Australian mammals

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Conservation implications for dingoes from the maternal and paternal genome: Multiple populations,dog introgression,and demography

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.     

Phenotypic variation and promiscuity in a wild population of pure dingoes (Canis dingo)

Phenotypic diversity occurs in natural populations as a result of the interaction between an individual's genotype and the environment. Nevertheless, individual variation in phenotypic traits such as coat colour and body size is routinely used to differentiate between “pure” dingoes Canis dingo and dingo‐dog hybrids. Extensive anthropogenic impacts and widespread hybridization with domestic dogs has hindered our ability to study intact dingo populations and, therefore, most of our basic understanding of dingo biology (e.g., phenotypic variation, mating systems, genetic diversity) stems from observational studies on perturbed populations. We sampled a relatively undisturbed population of dingoes, from arid Australia, to determine their purity and genetic diversity. We explored their mating strategy using a pedigree built from genetic data and examined how phenotypic variation was influenced by age, sex, heterozygosity, and relatedness. Coat colour was our measure of phenotype and our population displayed four types (sandy, black & tan, white, and sable). All dingoes (n = 83) possessed a high level of dingo ancestry (mean purity > 90%) and were closely related to each other; with all but one individual related as full‐sibling or parent–offspring. Our pedigree shows both monogamous and promiscuous mating strategies exist within an undisturbed population. Variation in coat colour or body size cannot be used to infer a dingo's level of purity because the phenotype of pure dingoes is intrinsically variable. The breeding system of dingoes was long thought to be monogamous, but we provide genetic evidence for numerous mating strategies including both long‐term monogamy and extreme promiscuity.     

Interspecific and Geographic Variation in the Diets of Sympatric Carnivores: Dingoes/Wild Dogs and Red Foxes in South-Eastern Australia

Dingoes/wild dogs (Canis dingo/familiaris) and red foxes (Vulpes vulpes) are widespread carnivores in southern Australia and are controlled to reduce predation on domestic livestock and native fauna. We used the occurrence of food items in 5875 dingo/wild dog scats and 11,569 fox scats to evaluate interspecific and geographic differences in the diets of these species within nine regions of Victoria, south-eastern Australia. The nine regions encompass a wide variety of ecosystems. Diet overlap between dingoes/wild dogs and foxes varied among regions, from low to near complete overlap. The diet of foxes was broader than dingoes/wild dogs in all but three regions, with the former usually containing more insects, reptiles and plant material. By contrast, dingoes/wild dogs more regularly consumed larger mammals, supporting the hypothesis that niche partitioning occurs on the basis of mammalian prey size. The key mammalian food items for dingoes/wild dogs across all regions were black wallaby (Wallabia bicolor), brushtail possum species (Trichosurus spp.), common wombat (Vombatus ursinus), sambar deer (Rusa unicolor), cattle (Bos taurus) and European rabbit (Oryctolagus cuniculus). The key mammalian food items for foxes across all regions were European rabbit, sheep (Ovis aries) and house mouse (Mus musculus). Foxes consumed 6.1 times the number of individuals of threatened Critical Weight Range native mammal species than did dingoes/wild dogs. The occurrence of intraguild predation was asymmetrical; dingoes/wild dogs consumed greater biomass of the smaller fox. The substantial geographic variation in diet indicates that dingoes/wild dogs and foxes alter their diet in accordance with changing food availability. We provide checklists of taxa recorded in the diets of dingoes/wild dogs and foxes as a resource for managers and researchers wishing to understand the potential impacts of policy and management decisions on dingoes/wild dogs, foxes and the food resources they interact with.     

Assessing the taxonomic status of dingoes Canis familiaris dingo for conservation

• 1 The conservation status of the dingo Canis familiaris dingo is threatened by hybridization with the domestic dog C. familiaris familiaris. A practical method that can estimate the different levels of hybridization in the field is urgently required so that animals below a specific threshold of dingo ancestry (e.g. 1/4 or 1/2 dingoes) can reliably be identified and removed from dingo populations.
• 2 Skull morphology has been traditionally used to assess dingo purity, but this method does not discriminate between the different levels of dingo ancestry in hybrids. Furthermore, measurements can only be reliably taken from the skulls of dead animals.
• 3 Methods based on the analysis of variation in DNA are able to discriminate between the different levels of hybridization, but the validity of this method has been questioned because the materials currently used as a reference for dingoes are from captive animals of unproven genetic purity. The use of pre‐European materials would improve the accuracy of this method, but suitable material has not been found in sufficient quantity to develop a reliable reference population. Furthermore, current methods based on DNA are impractical for the field‐based discrimination of hybrids because samples require laboratory analysis.
• 4 Coat colour has also been used to estimate the extent of hybridization and is possibly the most practical method to apply in the field. However, this method may not be as powerful as genetic or morphological analyses because some hybrids (e.g. Australian cattle dog × dingo) are similar to dingoes in coat colour and body form. This problem may be alleviated by using additional visual characteristics such as the presence/absence of ticking and white markings.

     

CRANIAL MORPHOLOGY OF DOMESTIC AND WILD CANIDS: THE INFLUENCE OF DEVELOPMENT ON MORPHOLOGICAL CHANGE

The domestic dog varies remarkably in cranial morphology. In fact, the differences in size and proportion between some dog breeds are as great as those between many genera of wild canids. In this study, I compare patterns of intracranial allometry and morphologic diversity between the domestic dog and wild canid species. The results demonstrate that the domestic dog is morphologically distinct from all other canids except its close relatives, the wolf-like canids. Following this, I compare patterns of static and ontogenetic scaling. Data on growth of domestic dogs are presented and used to investigate the developmental mechanisms underlying breed evolution. Apparently, most small breeds are paedomorphic with respect to certain morphologic characters. In dogs and other domestic animals, morphologic diversity among adults seems to depend on that expressed during development.     

A Simple Genetic Architecture Underlies Morphological Variation in Dogs

Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.     

Do dingoes suppress the activity of feral cats in northern Australia?

Large predators can have profound impacts on community composition. Not only do they directly affect prey abundance, they also indirectly affect prey abundance through their direct effects on smaller predators. In Australia, dingoes fill the role of a large predator and, in southern Australia, have clear impacts on introduced foxes. Their effect on introduced cats, however, is less clear. Here we present data from multiple sites across northern Australia (where foxes are absent), which reveal a negative correlation between cat and dingo activity. This relationship could arise because cats avoid areas where dingoes are active, or because cats are less abundant in areas with high dingo densities, or a combination of both. At a subset of our study sites, we experimentally reduced dingo (but not cat) abundance by poison baiting. This resulted in a 55% drop in dingo activity within 4 weeks of baiting, but without a compensatory increase in cat activity. This suggests the negative correlation between cat and dingo activity is not a simple consequence of cats reactively avoiding areas with higher dingo traffic, but rather, that there are fewer cats in areas where dingoes are more active. This study is a rare demonstration of the potential for dingoes to affect the behaviour and potentially the population size of feral cats, and therefore reduce the impact of feral cats on vulnerable native prey species.     

Genetic marker investigation of the source and impact of predation on a highly endangered species

In September and October 2000, the remains of a number of apparently predated northern hairy-nosed wombats (Lasiorhinus krefftii) were discovered in Epping Forest National Park, the site of the only known population of this highly endangered species. Analysis of DNA recovered from six carcasses and a section of intestine found nearby was carried out using microsatellite and Y-specific primers. This identified seven individual wombats, the identity of three of which was inferred from a genotype database prepared from animals sampled during trapping programmes. Six victims were male and one female, suggesting that female-biased predation rates are unlikely to be the cause of the current male-biased population sex ratio. DNA isolated from four canid faeces found in the vicinity revealed three distinct canid microsatellite genotypes with very high probabilities of belonging to dingoes (Canis familiaris dingo). A wombat genotype matching that of one of the dead individuals was identified from scats of two of the dingoes. In addition, two macropod microsatellites were amplified from two dingo scats. These observations provided vital information regarding predation on northern hairy-nosed wombats, and prompted the permanent exclusion of dingoes from the park by the erection of a dingo-proof fence.