title: Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders.
abstract: The island of Bali lies near the center of the southern chain of islands in the Indonesian archipelago, which served as a stepping-stone for early migrations of hunter-gatherers to Melanesia and Australia and for more recent migrations of Austronesian farmers from mainland Southeast Asia to the Pacific. Bali is the only Indonesian island with a population that currently practices the Hindu religion and preserves various other Indian cultural, linguistic, and artistic traditions (Lansing 1983). Here, we examine genetic variation on the Y chromosomes of 551 Balinese men to investigate the relative contributions of Austronesian farmers and pre-Neolithic hunter-gatherers to the contemporary Balinese paternal gene pool and to test the hypothesis of recent paternal gene flow from the Indian subcontinent. Seventy-one Y-chromosome binary polymorphisms (single nucleotide polymorphisms, SNPs) and 10 Y-chromosome-linked short tandem repeats (STRs) were genotyped on a sample of 1,989 Y chromosomes from 20 populations representing Indonesia (including Bali), southern China, Southeast Asia, South Asia, the Near East, and Oceania. SNP genotyping revealed 22 Balinese lineages, 3 of which (O-M95, O-M119, and O-M122) account for nearly 83.7% of Balinese Y chromosomes. Phylogeographic analyses suggest that all three major Y-chromosome haplogroups migrated to Bali with the arrival of Austronesian speakers; however, STR diversity patterns associated with these haplogroups are complex and may be explained by multiple waves of Austronesian expansion to Indonesia by different routes. Approximately 2.2% of contemporary Balinese Y chromosomes (i.e., K-M9*, K-M230, and M lineages) may represent the pre-Neolithic component of the Indonesian paternal gene pool. In contrast, eight other haplogroups (e.g., within H, J, L, and R), making up approximately 12% of the Balinese paternal gene pool, appear to have migrated to Bali from India. These results indicate that the Austronesian expansion had a profound effect on the composition of the Balinese paternal gene pool and that cultural transmission from India to Bali was accompanied by substantial levels of gene flow.
authors.affiliation: Division of Biotechnology, Biosciences West, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Tatiana M
authors.initials: TM
authors.lastname: Karafet
authors.forename: J S
authors.initials: JS
authors.lastname: Lansing
authors.forename: Alan J
authors.initials: AJ
authors.lastname: Redd
authors.forename: Svetlana
authors.initials: S
authors.lastname: Reznikova
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Watkins
authors.forename: S P K
authors.initials: SP
authors.lastname: Surata
authors.forename: W A
authors.initials: WA
authors.lastname: Arthawiguna
authors.forename: Laura
authors.initials: L
authors.lastname: Mayer
authors.forename: Michael
authors.initials: M
authors.lastname: Bamshad
authors.forename: Lynn B
authors.initials: LB
authors.lastname: Jorde
authors.forename: Michael F
authors.initials: MF
authors.lastname: Hammer
mesh_terms: D001210:Asia, Southeastern; D041322:Chromosomes, Human, Y / Q000235:genetics*; D003627:Data Interpretation, Statistical; D005787:Gene Frequency; D005789:Genealogy and Heraldry; D005819:Genetic Markers; D005828:Genetics, Population / Q000706:statistics & numerical data*; D005838:Genotype; D005843:Geography; D006239:Haplotypes; D006801:Humans; D007214:Indonesia; D008297:Male; D010139:Pacific Islands
chemical_list: D005819:Genetic Markers