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

Abstract

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.

Taxonomic status of the Australian dingo: the case for Canis dingo Meyer, 1793

“…These two lineages have a geographically subdivided distribution, where one is almost restricted to southeastern Australia (southeastern) and the other to the remaining parts of Australia (central; north and west; northwestern). Although less distinctly, Y-chromosome data also show evidence of geographical structure (Ardalan et al 2012;Sacks et al 2013;Cairns et al 2017) and suggest that the dingo could have originated from at least two migrations, forming two basic populations that subsequently experienced sex-biased admixture, with males being more mobile than females. The ultimate geographic origin of the male and female lineages is yet to be fully resolved, but the fact that one each of the mitochondrial and Y-chromosomal lineages are shared with New Guinea singing dogs indicates that some of the migrations might have occurred via the land bridge between New Guinea and Australia (completely disconnected by around ~ 7 ka; Torgersen et al 1988) -with or without human intervention (Cairns & Wilton 2016;Cairns et al 2017).…”

“…The incidence of hybridisation has seemingly changed little over the past few decades (e.g., Newsome & Corbett 1985, using skull morphology); however, high proportions of dingoes with no dog ancestry were found in other parts of Australia, particularly in central Australia (only 13% showing evidence of dog ancestry), and in Western Australia (41% with dog ancestry). There are three reasons why the frequency of dingo-domestic dog hybrids might be overstated; (1) Current DNA testing methods (i.e., Stephens et al 2015or Wilton 2001 were designed without knowledge of the geographical, phenotypic, and genetic variation within dingoes (Cairns & Wilton 2016, Cairns et al 2017. Thus, when comparing dingoes in southeast Australia to those in the northwest, they might appear different, and so could be falsely labelled as having dog ancestry.…”

“…1 There is more morphological variation in cranial shape within the domestic dog than there is among all species within the whole Carnivora (Drake & Klingenberg 2010); 2 Dingoes and dingo-dog hybrids can be difficult to separate morphologically (Newsome & Corbett 1982;Jones 1990;Elledge et al 2008;Newsome et al 2013;Parr et al 2016); 3 Morphological and molecular separation of dingoes and domestic dogs are based on post-European contact animals, or those that were captive (Newsome et al 1980;Newsome & Corbett, 1982;Elledge et al 2006Elledge et al , 2008Wilton et al 1999;Wilton, 2001); hence, samples could have contained pedigrees showing introgression; 4 Some dog breeds, particularly the Australian cattle dog, show evidence of past dingo hybridisation (Arnstein et al 1964), potentially causing difficulties in providing clear and consistent diagnostic features that separate dingoes from dogs in the past (Newsome et al 1980); 5 Dingoes exhibit morphological variation through space and time, mostly in size (Corbett 2001a,b;Radford et al 2012;Claridge et al 2014;Colman 2015); 6 There is genetic evidence for at least two sub-populations of the dingo, possibly the result of multiple introductions into Australia (Cairns & Wilton 2016;Cairns et al 2017). These sub-populations also show some evidence of morphological separation (Colman 2015), thus further clouding possible diagnostic features between dingoes and dogs.…”

“…There is a range of genetic markers that can distinguish dingoes from domestic dogs, including mitochondrial and Y-chromosome markers (Savolainen et al 2004;vonHoldt et al 2010, Oskarsson et al 2011Ardalan et al 2012;Sacks et al 2013;Cairns & Wilton, 2016;Cairns et al 2017), as well as microsatellites and nuclear single nucleotide polymorphisms (SNPs). Since the 1990s, microsatellite-based DNA testing has been used to distinguish dingoes, dingoes with dog ancestry, and feral domestic dogs.…”

Genomic regions under selection in the feralization of the dingoes

“…The dingo (Canis dingo) is a wild canid native to Australia, and its apex predator 17 . It originates from domestic dogs but has, since it arrived at least 3500 years ago, developed into a phenotypically and genetically distinct population of feral dogs.…”