Major east-west division underlies y chromosome stratification across Indonesia

Tatiana Karafet, Brian Hallmark, Murray P. Cox, Herawati Sudoyo, Sean Downey, J. Stephen Lansing, Michael F Hammer

Research output: Contribution to journalArticle

90 Citations (Scopus)

Abstract

The early history of island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul ∼45 ka ago and the much later Neolithic expansion of Austronesian-speaking farmers ∼4 ka ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 single-nucleotide polymorphisms/indels and 12 short tandem repeats, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., ΦST = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M, and S subclades) and likely reflect the initial wave of colonization of the region, whereas the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201 and P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122 and O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion.

Original languageEnglish (US)
Pages (from-to)1833-1844
Number of pages12
JournalMolecular Biology and Evolution
Volume27
Issue number8
DOIs
StatePublished - 2010

Fingerprint

Indonesia
Y Chromosome
Y chromosome
chromosome
stratification
Chromosomes
chromosomes
Paleolithic
Gene Pool
colonization
Islands
Chromosomes, Human, Y
Southeastern Asia
hunter-gatherer
Genetic Markers
gene
Microsatellite Repeats
Single Nucleotide Polymorphism
Analysis of Variance
South East Asia

Keywords

  • Austronesian
  • colonization
  • Paleolithic
  • Wallace's line
  • Y chromosome

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Medicine(all)

Cite this

Major east-west division underlies y chromosome stratification across Indonesia. / Karafet, Tatiana; Hallmark, Brian; Cox, Murray P.; Sudoyo, Herawati; Downey, Sean; Lansing, J. Stephen; Hammer, Michael F.

In: Molecular Biology and Evolution, Vol. 27, No. 8, 2010, p. 1833-1844.

Research output: Contribution to journalArticle

Karafet, Tatiana ; Hallmark, Brian ; Cox, Murray P. ; Sudoyo, Herawati ; Downey, Sean ; Lansing, J. Stephen ; Hammer, Michael F. / Major east-west division underlies y chromosome stratification across Indonesia. In: Molecular Biology and Evolution. 2010 ; Vol. 27, No. 8. pp. 1833-1844.
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