Elucidating biogeographical patterns in Australian native canids using genome wide SNPs

Cairns, Kylie M.; Shannon, Laura M.; Koler-Matznick, Janice; Ballard, J. William O.; Boyko, Adam R.

doi:10.1371/journal.pone.0198754

Cited by 28 publications

(46 citation statements)

References 102 publications

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“…We find an admixture of these four components with varying proportions among indigenous dogs from northern China, some dog breeds and the village dogs from India and New Guinea, consistent with the results of the PCA. Notably, two dingoes, D05 and D06, show a mixture indicating hybridization with European breed dogs, and D05 originate from the region in Australia with highest incident of dingo-dog hybridization (the Southeast) [26][27][28][29] . Therefore, we performed D-statistics analysis using qpDstat in the Admixtools software package 38 to test events of gene flow between the dingoes and European breeds in the form of D (Dhole, European breed; Pop1, Pop2), where Pop1 was all dog groups tested in turn and Pop2 was each individual dingo.…”

Section: Resultsmentioning

confidence: 99%

“…Secondly, the dingoes have been isolated from both their domestic and their wild ancestor during this feralization except the last 200 years, because of Australia's position outside the natural range of wolves and its isolation until the arrival of Europeans. Today, dingoes and European breeds hybridize, especially in the Southeast, but in most other regions hybridization is limited [26][27][28][29] . Therefore, unlike the feral chickens of Kauai island and weedy rice, the dingoes have not experienced hybridization with ancestral populations which may complicate the deciphering of the genomic mechanisms of feralization.…”

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confidence: 99%

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Genomic regions under selection in the feralization of the dingoes

Zhang

Wang

et al. 2020

Nat Commun

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Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Genomic regions under selection in the feralization of the dingoes

Zhang

Wang

et al. 2020

Nat Commun

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“…Combining new and publicly available data, we created a dataset of 1,346 dogs from 161 breeds as well as 9 nondog canids, 16 captive NGSD, and 25 wild dingoes (14,16,17). Phylogenetic inference of this genotypic dataset places HWD as a monophyletic clade with 100% bootstrap support (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…If the existing HWD does indeed represent the predecessor population of the famed NGSD, it is imperative that it be protected. Breeding programs should be established to infuse what is expected to be comparatively robust genetics of the free-breeding HWD into the genetically compromised captive NGSD population, for which inbreeding coefficients have been estimated at >0.50 (14). Finally, truly wild populations of dogs are rare, including the dingo and potentially the HWD, highlighting the need for rapid and well-organized conservation plans.…”

Section: Significancementioning

confidence: 99%

New Guinea highland wild dogs are the original New Guinea singing dogs

Surbakti

Parker

McIntyre³

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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New Guinea singing dogs (NGSD) are identifiable by their namesake vocalizations, which are unlike any other canid population. Their novel behaviors and potential singular origin during dog domestication make them an attractive, but elusive, subject for evolutionary and conservation study. Although once plentiful on the island of New Guinea (NG), they were presumed to currently exist only in captivity. This conclusion was based on the lack of sightings in the lowlands of the island and the concurrent expansion of European- and Asian-derived dogs. We have analyzed the first nuclear genomes from a canid population discovered during a recent expedition to the highlands of NG. The extreme altitude (>4,000 m) of the highland wild dogs’ (HWD) observed range and confirmed vocalizations indicate their potential to be a wild NGSD population. Comparison of single-nucleotide polymorphism genotypes shows strong similarity between HWD and the homogeneous captive NGSD, with the HWD showing significantly higher genetic diversity. Admixture analyses and estimation of shared haplotypes with phylogenetically diverse populations also indicates the HWD is a novel population within the distinct evolutionary lineage of Oceanic canids. Taken together, these data indicate the HWD possesses a distinct potential to aid in the conservation of NGSD both in the wild and under human care.

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“…Contrary to Smith et al 's (2019) claims, most sampling was done in areas of low human activity as in Western Australia where most of the samples came from or across the complete regional distribution of free-ranging dogs, as in Victoria (Fig 1 of Stephens et al 2015 andFig 2 in Cairns et al 2017). Cairns et al (2018). We filtered the data from the different studies to include only breeds of interest, and we kept shared SNPs using PLINK v1.90b5 (Chang et al 2015).…”

Section: Genetically Distinctmentioning

confidence: 99%

The Dogma of Dingoes—Taxonomic status of the dingo: A reply to Smith et al.

Jackson¹,

Fleming

Eldridge

et al. 2019

Zootaxa

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Adopting the name Canis dingo for the Dingo to explicitly denote a species-level taxon separate from other canids was suggested by Crowther et al. (2014) as a means to eliminate taxonomic instability and contention. However, Jackson et al. (2017), using standard taxonomic and nomenclatural approaches and principles, called instead for continued use of the nomen C. familiaris for all domestic dogs and their derivatives, including the Dingo. (This name, C. familiaris, is applied to all dogs that derive from the domesticated version of the Gray Wolf, Canis lupus, based on nomenclatural convention.) The primary reasons for this call by Jackson et al. (2017) were: (1) a lack of evidence to show that recognizing multiple species amongst the dog, including the Dingo and New Guinea Singing Dog, was necessary taxonomically, and (2) the principle of nomenclatural priority (the name familiaris Linnaeus, 1758, antedates dingo Meyer, 1793). Overwhelming current evidence from archaeology and genomics indicates that the Dingo is of recent origin in Australia and shares immediate ancestry with other domestic dogs as evidenced by patterns of genetic and morphological variation. Accordingly, for Smith et al. (2019) to recognise Canis dingo as a distinct species, the onus was on them to overturn current interpretations of available archaeological, genomic, and morphological datasets and instead show that Dingoes have a deeply divergent evolutionary history that distinguishes them from other named forms of Canis (including C. lupus and its domesticated version, C. familiaris). A recent paper by Koepfli et al. (2015) demonstrates exactly how this can be done in a compelling way within the genus Canis—by demonstrating deep evolutionary divergence between taxa, on the order of hundreds of thousands of years, using data from multiple genetic systems. Smith et al. (2019) have not done this; instead they have misrepresented the content and conclusions of Jackson et al. (2017), and contributed extraneous arguments that are not relevant to taxonomic decisions. Here we dissect Smith et al. (2019), identifying misrepresentations, to show that ecological, behavioural and morphological evidence is insufficient to recognise Dingoes as a separate species from other domestic dogs. We reiterate: the correct binomial name for the taxon derived from Gray Wolves (C. lupus) by passive and active domestication, including Dingoes and other domestic dogs, is Canis familiaris. We are strongly sympathetic to arguments about the historical, ecological, cultural, or other significance of the Dingo, but these are issues that will have to be considered outside of the more narrow scope of taxonomy and nomenclature.

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Elucidating biogeographical patterns in Australian native canids using genome wide SNPs

Cited by 28 publications

References 102 publications

Genomic regions under selection in the feralization of the dingoes

Genomic regions under selection in the feralization of the dingoes

New Guinea highland wild dogs are the original New Guinea singing dogs

The Dogma of Dingoes—Taxonomic status of the dingo: A reply to Smith et al.

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