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

Tatiana 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 journalArticle

62 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)93-114
Number of pages22
JournalHuman Biology
Volume77
Issue number1
StatePublished - Feb 2005

Fingerprint

hunter-gatherer
Indonesia
Y Chromosome
Y chromosome
chromosome
Gene Pool
farmers
Islands
Southeastern Asia
polymorphism
Gene Flow
gene
Microsatellite Repeats
gene flow
Single Nucleotide Polymorphism
India
South East Asia
single nucleotide polymorphism
Melanesia
Oceania

Keywords

  • 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

  • Agricultural and Biological Sciences(all)
  • Genetics
  • Genetics(clinical)
  • Ecology, Evolution, Behavior and Systematics

Cite this

Balinese Y-chromosome perspective on the peopling of Indonesia : Genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders. / Karafet, Tatiana; Lansing, J. S.; Redd, Alan J.; Reznikova, Svetlana; Watkins, Joseph C; Surata, S. P K; Arthawiguna, W. A.; Mayer, Laura; Bamshad, Michael; Jorde, Lynn B.; Hammer, Michael F.

In: Human Biology, Vol. 77, No. 1, 02.2005, p. 93-114.

Research output: Contribution to journalArticle

Karafet, Tatiana ; Lansing, J. S. ; Redd, Alan J. ; Reznikova, Svetlana ; Watkins, Joseph C ; Surata, S. P K ; Arthawiguna, W. A. ; Mayer, Laura ; Bamshad, Michael ; Jorde, Lynn B. ; Hammer, Michael F. / Balinese Y-chromosome perspective on the peopling of Indonesia : Genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders. In: Human Biology. 2005 ; Vol. 77, No. 1. pp. 93-114.
@article{1427c7a51d1743eaaed69bef88782d11,
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.",
keywords = "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",
author = "Tatiana Karafet and Lansing, {J. S.} and Redd, {Alan J.} and Svetlana Reznikova and Watkins, {Joseph C} and Surata, {S. P K} and Arthawiguna, {W. A.} and Laura Mayer and Michael Bamshad and Jorde, {Lynn B.} and Hammer, {Michael F}",
year = "2005",
month = "2",
language = "English (US)",
volume = "77",
pages = "93--114",
journal = "Human Biology",
issn = "0018-7143",
publisher = "Wayne State University Press",
number = "1",

}

TY - JOUR

T1 - Balinese Y-chromosome perspective on the peopling of Indonesia

T2 - Genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders

AU - Karafet, Tatiana

AU - Lansing, J. S.

AU - Redd, Alan J.

AU - Reznikova, Svetlana

AU - Watkins, Joseph C

AU - Surata, S. P K

AU - Arthawiguna, W. A.

AU - Mayer, Laura

AU - Bamshad, Michael

AU - Jorde, Lynn B.

AU - Hammer, Michael F

PY - 2005/2

Y1 - 2005/2

N2 - 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.

AB - 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.

KW - Austronesian expansion

KW - Bali

KW - Indian traders

KW - Indians

KW - Indonesia

KW - Malaysians

KW - Melanesia

KW - Micronesia

KW - Philippinos

KW - Polynesia

KW - Pre-neolithic hunter-gatherers

KW - Saudi Arabians

KW - Southern Chinese

KW - Sri Lankans

KW - Syrians

KW - Taiwanese aboriginals

KW - Vietnamese

KW - Y chromosome

UR - http://www.scopus.com/inward/record.url?scp=21744455456&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=21744455456&partnerID=8YFLogxK

M3 - Article

C2 - 16114819

AN - SCOPUS:21744455456

VL - 77

SP - 93

EP - 114

JO - Human Biology

JF - Human Biology

SN - 0018-7143

IS - 1

ER -