Karafet, T. M., Lansing, J. S., Redd, A. J., Reznikova, S., Watkins, J. C., Surata, S. P. K. et al. Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-Neolithic hunter-gatherers, Austronesian farmers, and Indian traders. Hum. Biol. 77, 93-114

Division of Biotechnology, Biosciences West, University of Arizona, Tucson, AZ 85721, USA.
Human Biology (Impact Factor: 0.85). 03/2005; 77(1):93-114. DOI: 10.1353/hub.2005.0030
Source: PubMed

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.

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    • "Comparative data with other populations of south China, ISEA and Oceania were taken from the literature and comprised Yueh/Daic-speaking populations [27,30,36-38], Malayo-Polynesians and Papua New Guineans [39], and Han Chinese [7,8,12,29,30,40,41]. These datasets are shown in Additional file 1: Table S1. "
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    ABSTRACT: Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.
    BMC Genetics 06/2014; 15(1):77. DOI:10.1186/1471-2156-15-77 · 2.40 Impact Factor
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    • "The data collected for the eight Sungi river subaks were reanalyzed to discover whether there are significant differences between the demographic histories of the upstream and downstream subaks (supplement A, section 1.2). The methods used for the genetic analysis are fully described in Karafet et al. 2005 "
    Current Anthropology 04/2014; 55(2):232-9. DOI:10.1086/675429 · 2.93 Impact Factor
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    • "In contrast with this conclusion, Shi et al. (2008, 2005) estimate an older northward expansion of Y chromosome haplogroup D-M174 (60,000 years ago) than the above-mentioned O-M122 haplogroup (25–30,000 years ago), after an origin in southern East Asia. An even younger estimate of 4,400 years before present (BP) was obtained for O-M122 in Balinese populations (Karafet et al. 2005). – As the Munda exhibit a high frequency and diversity of Y chromosome M95 (O2a) haplotypes (Karafet et al. 2001; Kumar et al. 2007; Reddy and Kumar 2008; Sengupta et al. 2006; Su et al. 2000, 1999), the origin of the Austroasiatic phylum has been claimed to occur in India around 65,000 years BP according to the age estimated for this haplogroup (Kumar et al. 2007), by contrast to the young age of 8,800 years previously given by Kayser et al. (2003). "
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    ABSTRACT: Population genetic studies may provide crucial information for our knowledge on human peopling history and have been extensively applied to reconstruct East Asian prehistory in the last 10 years. However, different genetic investigations are not always consistent with each other and some results are conflicting or misinterpreted. This represents a main obstacle for scholars of other disciplines like archaeologists and linguists who try to relate the genetic information on past human migrations to their own results on the spread of domesticated crops or animals or on the dispersal of the main language families. In this paper, we review the current genetic evidence related to the peopling history of East Asia with a critical view on some interpretations. In this way, we hope to provide a useful reference for further interdisciplinary studies on our past.
    Rice 12/2011; 4(3-4). DOI:10.1007/s12284-011-9066-y · 3.92 Impact Factor
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