Balinese Y-chromosome perspective on the peopling of Indonesia: Genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders

Tatiana M. Karafet, J. S. Lansing, Alan J. Redd, Svetlana Reznikova, Joseph C. Watkins, S. P.K. Surata, W. A. Arthawiguna, Laura Mayer, Michael Bamshad, Lynn B. Jorde, Michael F. Hammer

Research output: Contribution to journalArticlepeer-review

67 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)93-114
Number of pages22
JournalHuman biology
Issue number1
StatePublished - Feb 2005


  • Austronesian expansion
  • Bali
  • Indian traders
  • Indians
  • Indonesia
  • Malaysians
  • Melanesia
  • Micronesia
  • Philippinos
  • Polynesia
  • Pre-neolithic hunter-gatherers
  • Saudi Arabians
  • Southern Chinese
  • Sri Lankans
  • Syrians
  • Taiwanese aboriginals
  • Vietnamese
  • Y chromosome

ASJC Scopus subject areas

  • General Medicine


Dive into the research topics of 'Balinese Y-chromosome perspective on the peopling of Indonesia: Genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders'. Together they form a unique fingerprint.

Cite this