Antiquity and Diversity of Aboriginal Australian Y-Chromosomes
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AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 00:00–00 (2015) Antiquity and Diversity of Aboriginal Australian Y-Chromosomes Nano Nagle,1 Kaye N. Ballantyne,2,3 Mannis van Oven,3 Chris Tyler-Smith,4 Yali Xue,4 Duncan Taylor,5,6 Stephen Wilcox,7 Leah Wilcox,1 Rust Turkalov,7 Roland A.H. van Oorschot,2 Peter McAllister,8 Lesley Williams,9 Manfred Kayser,3 Robert J. Mitchell,1* and The Genographic Consortium 1Department of Biochemistry and Genetics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, VIC, Australia 2Victorian Police Forensic Services Department, Office of the Chief Forensic Scientist, Melbourne, VIC, Australia 3Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Rotterdam, The Netherlands 4The Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, UK 5Forensic Science South Australia, 21 Divett Place, Adelaide, SA, 5000, Australia 6School of Biological Sciences, Flinders University, Adelaide, SA, 5001, Australia 7Australian Genome Research Facility, Melbourne, VIC, Australia 8Griffith University, Brisbane, QLD, Australia 9Department of Communities, Child Safety and Disability Services, Queensland Government, Brisbane, QLD, Australia KEY WORDS Y-chromosome; haplogroup; haplotype; Australia; Sahul; Aboriginals ABSTRACT Objective: Understanding the origins of Aboriginal Australians is crucial in reconstructing the evolution and spread of Homo sapiens as evidence suggests they represent the descendants of the earliest group to leave Africa. This study analyzed a large sample of Y-chromosomes to answer questions relating to the migration routes of their ancestors, the age of Y-haplogroups, date of colonization, as well as the extent of male-specific variation. Methods: Knowledge of Y-chromosome variation among Aboriginal Australians is extremely limited. This study examined Y-SNP and Y-STR variation among 657 self-declared Aboriginal males from locations across the continent. 17 Y-STR loci and 47 Y-SNPs spanning the Y-chromosome phylogeny were typed in total. Results: The proportion of non-indigenous Y-chromosomes of assumed Eurasian origin was high, at 56%. Y lineages of indigenous Sahul origin belonged to haplogroups C-M130*(xM8,M38,M217,M347) (1%), C-M347 (19%), K-M526*(xM147,P308,P79,P261,P256,M231,M175,M45,P202) (12%), S-P308 (12%), and M-M186 (0.9%). Haplogroups C-M347, K-M526*, and S-P308 are Aboriginal Australian-specific. Dating of C-M347, K-M526*, and S-P308 indicates that all are at least 40,000 years old, confirming their long-term presence in Australia. Haplogroup C-M347 comprised at least three sub-haplogroups: C-DYS390.1del, C-M210, and the unresolved paragroup C-M347*(xDYS390.1del,M210). Conclusions: There was some geographic structure to the Y-haplogroup variation, but most haplogroups were present throughout Australia. The age of the Australian-specific Y-haplogroups suggests New Guineans and Aborigi- nal Australians have been isolated for over 30,000 years, supporting findings based on mitochondrial DNA data. Our data support the hypothesis of more than one route (via New Guinea) for males entering Sahul some 50,000 years ago and give no support for colonization events during the Holocene, from either India or elsewhere. Am J Phys Anthropol 000:000–000, 2015. VC 2015 Wiley Periodicals, Inc. INTRODUCTION 1999), by anatomically and behaviorally modern humans. Genetic and archaeological evidence currently Under most scenarios of human prehistory Australia suggest that the ancestors of present-day Aboriginal is viewed as a continent that was settled very soon after Australians arrived at least 45 kya (O’Connell and the expansion “out of Africa,” some 60–100 thousand Allen, 2004; Summerhayes et al., 2010; Williams, 2013; years ago (kya) (Roberts and Jones, 1994; Thorne et al., O’Connell and Allen, 2015). This early settlement is Additional Supporting Information may be found in the online *Correspondence to: Robert J. Mitchell; Department of Biochemis- version of this article. try and Genetics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia. The authors declare no conflict of interest. E-mail: [email protected] Genographic Consortium members are listed in the Acknowledg- Received 1 April 2015; revised 1 October 2015; accepted 8 October ments section. 2015 Grant sponsor: National Geographic Society, IBM, Waitt Family DOI: 10.1002/ajpa.22886 Foundation. Published online 00 Month 2015 in Wiley Online Library (wileyonlinelibrary.com). Ó 2015 WILEY PERIODICALS, INC. 2 NAGLE ET AL. supported by archaeological sites widely spread across the oldest continuous populations found outside Africa, the continent, such as Devil’s Lair in Western Australia with little evidence of genetic introgression from other (Turney et al., 2001a), Carpenter’s Gap in northern populations until historical times (Rasmussen et al., Western Australia (O’Connor, 1995), Lake Mungo in 2011; Reich et al., 2011). New South Wales (Bowler et al., 1970) and Lynch’s There are few studies that focus on Y-chromosome Crater in Queensland (Turney et al., 2001b), as well diversity in Aboriginal Australians (Vandenberg et al., as by DNA evidence (van Holst Pellekaan et al., 2006; 1999; Kayser et al., 2001; Underhill et al., 2001b; Redd Hudjashov et al., 2007; Rasmussen et al., 2011; Reich et al., 2002; Hudjashov et al., 2007; Taylor et al., 2012). et al., 2011). Their long-term in situ presence makes Apart from the Taylor et al. (2012) analysis of Aboriginal Aboriginal Australians central to the study of modern males from South Australia, all Y-chromosome studies human origins and early dispersals. have been restricted to the northern areas of Australia While there may exist some consensus about the date and, therefore, provided an inadequate coverage of the of the first arrival of modern humans in Sahul (the continent. Sample sizes were usually very small and/or ancient continent comprising the then connected islands sample locations were not reported. Some of these studies of New Guinea and Australia in the Pleistocene epoch), also had a risk of sampling relatives or resampling indi- there is still controversy over the route(s) taken and viduals who participated in preceding genetic studies (as their points of entry into Sahul (Birdsell, 1977; Dixon, discussed in White, 1997; van Holst Pellekaan, 2013). 1980; Redd et al., 2002; Hudjashov et al., 2007; Reich Earlier Y-chromosome studies were also greatly lim- et al., 2011; Pugach et al., 2013). There is also conflicting ited by the low numbers of markers used. Some studies evidence regarding whether or not the ancestors of reported Y-SNPs only (Underhill et al., 2001b; Hudja- present-day New Guineans and Aboriginal Australians shov et al., 2007; Karafet et al., 2014), others typed only entered as a single founder population into Sahul with Y-STRs (Forster et al., 1998; Vandenberg et al., 1999), subsequent dispersal within it, or if there were separate whilst others typed differing combinations of Y-SNPs founder populations for these two groups (Tsintsof et al., and Y-STRs (Kayser et al., 2001; Redd et al., 2002). Con- 1990; Roberts-Thomson et al., 1996; Evans, 2005; Hudja- sequently, there is great difficulty in comparing datasets. shov et al., 2007). Further, there is still ongoing debate In addition, European admixture in Aboriginal Austral- surrounding the number and source of any subsequent ians is considerable, especially in the paternal line (Tay- incursions into Australia that may have occurred prior lor et al., 2012), and has been so since first contact with to the well-documented European invasions of historical Europeans (Radcliffe-Brown, 1930; Williams, 2013), but times (Kayser et al., 2001; Redd et al., 2002; Hudjashov its extent is variable between regions (Walsh et al., et al., 2007; McEvoy et al., 2010; Rasmussen et al., 2011; 2007). Accordingly, small sample sizes, limited geograph- Pugach et al., 2013). ical coverage, the difficulty of comparing existing One factor contributing to the long-running contro- Y-chromosome datasets, plus the great, but unquanti- versy over Aboriginal origins and the extent of diversity fied, reduction in the frequencies of indigenous is that they are among the most poorly studied groups of Y-chromosomes through two centuries of European humans with respect to their genetic structure. This admixture, make attempts at reconstructing past pat- dearth of information reflects the experiences of Aborigi- terns of male mediated diversity at a tribal or group nal people participating in earlier anthropological/ level, as well as possible routes of migration, extremely genetic studies (Dodson, 2000; van Holst Pellekaan, difficult (van Holst Pellekaan, 2008). 2000a,b,2008; Kowal, 2012). To further our knowledge of Y-chromosome diversity Controversy over Aboriginal origins has a long history, among this poorly studied population, we assembled a extending back to Tindale and Birdsell’s trihybrid theory large sample of Y-chromosomes from individuals who in which three distinct migrant groups were identified, self-reported as Aboriginal Australian for analysis of each colonizing at different times, but all within the last both Y-SNP and Y-STR variation. Seventeen Y-STR loci 10 ky (Birdsell, 1977). No genetic or anthropometric evi- and 47 Y-SNPs were typed in total. This dataset was dence has substantiated this trihybrid hypothesis (Kirk drawn widely from across the continent, especially from et al., 1963, 1972; Gao and Serjeantson, 1991; White,