Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

Abstract

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.

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

“…We observed that the H1 and H3 haplotypes found in dingoes were largely unique (not shared with SEA dogs). Further investigation, however, suggests that H1‐1c, H1‐6t, H1‐n7, and H1‐6q were observed in European domestic dog breeds (Brown et al., 2011; Sacks et al., 2013). Three novel H1 haplotypes were observed (H1‐k1, H1‐k7, and H1‐k5) that were unique to dingoes.…”

“…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.…”

“…(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.…”

“…(2013), we use H1 to refer to H1*, H2*, and H1 haplotypes. Five dinucleotide repeat–single tandem repeats (STR) were also genotyped from the NRY region: 650‐79.2b , 650‐79.3b , 990‐35 , MS34CA , and MS41B as previously described (Brown et al., 2011; Sacks et al., 2013). …”

“…(2013). Briefly, STRs were weighted as: 650‐79.2b  = 5, 650‐79.3b  = 2, 990‐35  =   9, MS34CA  = 6, MS41B  = 1, and SNP loci = 90 (Brown et al., 2011; Sacks et al., 2013). Y networks were drawn using our collected data and an additional dataset including 112 Oceanic samples from Sacks et al.…”