title: Deep Roots for Aboriginal Australian Y Chromosomes.
abstract: Australia was one of the earliest regions outside Africa to be colonized by fully modern humans, with archaeological evidence for human presence by 47,000 years ago (47 kya) widely accepted [1, 2]. However, the extent of subsequent human entry before the European colonial age is less clear. The dingo reached Australia about 4 kya, indirectly implying human contact, which some have linked to changes in language and stone tool technology to suggest substantial cultural changes at the same time [3]. Genetic data of two kinds have been proposed to support gene flow from the Indian subcontinent to Australia at this time, as well: first, signs of South Asian admixture in Aboriginal Australian genomes have been reported on the basis of genome-wide SNP data [4]; and second, a Y chromosome lineage designated haplogroup C(∗), present in both India and Australia, was estimated to have a most recent common ancestor around 5 kya and to have entered Australia from India [5]. Here, we sequence 13 Aboriginal Australian Y chromosomes to re-investigate their divergence times from Y chromosomes in other continents, including a comparison of Aboriginal Australian and South Asian haplogroup C chromosomes. We find divergence times dating back to ∼50 kya, thus excluding the Y chromosome as providing evidence for recent gene flow from India into Australia.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
authors.forename: Anders
authors.initials: A
authors.lastname: Bergström
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, VIC 3086, Australia.
authors.forename: Nano
authors.initials: N
authors.lastname: Nagle
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
authors.forename: Shane
authors.initials: S
authors.lastname: McCarthy
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Medicine, University of Cambridge, Cambridge CB2 2QQ, UK.
authors.forename: Martin O
authors.initials: MO
authors.lastname: Pollard
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
authors.forename: Qasim
authors.initials: Q
authors.lastname: Ayub
authors.affiliation: Australian Genome Research Facility, Melbourne, Victoria 3052, Australia; Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052 Australia.
authors.forename: Stephen
authors.initials: S
authors.lastname: Wilcox
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, VIC 3086, Australia.
authors.forename: Leah
authors.initials: L
authors.lastname: Wilcox
authors.affiliation: Office of the Chief Forensic Scientist, Victorian Police Forensic Services Department, Melbourne, VIC 3085, Australia.
authors.forename: Roland A H
authors.initials: RA
authors.lastname: van Oorschot
authors.affiliation: Griffith University, Brisbane, QLD 4222, Australia.
authors.forename: Peter
authors.initials: P
authors.lastname: McAllister
authors.affiliation: Community Elder and Cultural Advisor, Brisbane, QLD 4011, Australia.
authors.forename: Lesley
authors.initials: L
authors.lastname: Williams
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, VIC 3086, Australia. Electronic address: john.mitchell@latrobe.edu.au.
authors.forename: R John
authors.initials: RJ
authors.lastname: Mitchell
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. Electronic address: cts@sanger.ac.uk.
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
mesh_terms: D001315:Australia; D041322:Chromosomes, Human, Y / Q000235:genetics*; D051456:Gene Flow; D006239:Haplotypes; D006801:Humans; D007194:India; D008297:Male; D010219:Papua New Guinea / Q000208:ethnology; D010802:Phylogeny