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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1007/s10709-012-9658-5) contains supplementary material, which is available to authorized users.

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

“…Mitochondrial and Y chromosome data corroborate the presence of at least two discrete populations of dingo, NW (H60/H3), and SE (H3/H1) (Ardalan et al., 2012; Cairns & Wilton, 2016; Sacks et al., 2013). A lack of intermediate haplotypes despite broad geographical sampling suggests that the observed pattern of population structure is due to historical events.…”

“…Notably, the Y haplogroups H3 and H60, which are both observed in dingoes, are not immediately related (Figure 10; Natanaelsson et al., 2006; Brown et al., 2011; Ardalan et al., 2012; Sacks et al., 2013). The H3 Y chromosome haplogroup is also observed in Southeast Asia.…”

“…However, seven of the eight haplotypes observed in dingoes were endemic to Australia, indicating shared ancestry with a history of isolation between dingoes and Southeast Asian dogs (Figure 10; Brown et al., 2011; Sacks et al., 2013). On the other hand, the H60 haplogroup is unique to dingoes and NGSD and most closely related to H5, a haplogroup found in Taiwan (Figure 10; Brown et al., 2011; Ardalan et al., 2012; Sacks et al., 2013). The distribution of Y chromosome haplotypes between the two mitochondrial lineages is nonrandom, corroborating the presence of strong geographic subdivision in dingoes (Ardalan et al., 2012; Cairns & Wilton, 2016).…”

“…(2013). These 29 SNPs form a panel of markers enabling differentiation between most observed dog Y chromosome haplogroups (Ardalan et al., 2012; Brown et al., 2011; Ding et al., 2011; Natanaelsson et al., 2006; Sacks et al., 2013). As in Sacks et al.…”

“…Early studies using mitochondrial DNA were unable to elucidate continent‐wide biogeographic patterns, as they restricted genetic sampling to the mitochondrial control region (Oskarsson et al., 2011; Savolainen et al., 2004). Y chromosome studies either had samples from mostly Western Australia or mostly eastern Australia, and differences in genetic marker sampling made it difficult to compare datasets (Ardalan et al., 2012; Sacks et al., 2013). …”