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

Human Biology

Volumn 77, Issue 1, 2005, Pages 93-114

  Karafet, Tatiana M ^a   Lansing, J S ^a,b   Redd, Alan J ^a   Reznikova, Svetlana ^a   Watkins, Joseph C ^c   Surata, S P K ^d   Arthawiguna, W A ^e   Mayer, Laura ^a   Bamshad, Michael ^f   Jorde, Lynn B ^f   Hammer, Michael F ^a  

^a UNIVERSITY OF ARIZONA   (United States)

^b SANTA FE INSTITUTE   (United States)

^c University of Arizona   (United States)

^d Maharaswati University   (Indonesia)

^e Balai Penelitian Dan Pengkajian Teknologi Pertanian   (Indonesia)

^f UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author 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

Indexed keywords

AGRICULTURAL WORKER; ANIMAL HUNTING; ARTICLE; AUSTRALIA; CHINA; FEMALE; GENE FLOW; GENE POOL; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; HUMAN; INDIAN; INDONESIA; MAJOR CLINICAL STUDY; MALE; PHYLOGEOGRAPHY; SHORT TANDEM REPEAT; SOUTHEAST ASIA; Y CHROMOSOME;

EID: 21744455456     PISSN: 00187143     EISSN: None     Source Type: Journal    
DOI: 10.1353/hub.2005.0030     Document Type: Article

References (53)

1. Ardika, I. W., and P. Bellwood. 1991. Sembiran: The beginnings of Indian contact with Bali. Antiquity 65:221-232.
2. Bamshad, M., T. Kivisild, W. S. Watkins et al. 2001. Genetic evidence on the origins of Indian caste populations. Genome Res. 11:994-1,004.
3. Bandelt, H. J., P. Forster, and A. Rohl. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16:37-48.
4. Bellwood, P. 1997. Prehistory of the Indo-Malaysian Archipelago. Honolulu: University of Hawaii Press.
5. Bertorelle, G., and L. Excoffier. 1998. Inferring admixture proportions from molecular data. Mol. Biol. Evol. 15:1,298-1,311.
6. Bowler, J. M., H. Johnston, J. M. Olley et al. 2003. New ages for human occupation and climatic change at Lake Mungo, Australia. Nature 421:837-840.
7. Capelli, C., J. F. Wilson, M. Richards et al. 2001. A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania. Am. J. Hum. Genet. 68:432-443.
8. Chakraborty, R., M. I. Kamboh, M. Nwankwo et al. 1992. Caucasian genes in American blacks: New data. Am. J. Hum. Genet. 50:145-155.
9. de Knijff, P. 2000. Messages through bottlenecks: On the combined use of slow and fast evolving polymorphic markers on the human Y chromosome. Am. J. Hum. Genet. 67:1,055-1,061.
10. Diamond, J. 1988. Express train to Polynesia. Nature 336:307-308.
11. Dyen, I. 1962. A lexicostatistical classification of the Austronesian languages. Language 38:38-46.
12. Felsenstein, J. 1995. PHYLIP: Phylogeny Inference Package. Seattle: Department of Genetics, University of Washington.
13. Goldstein, D. B., A. Ruiz Linares, L. L. Cavalli-Sforza et al. 1995. An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463-471.
14. Hammer, M. F., F. Blackmer, D. Garrigan et al. 2003. Human population structure and its effects on sampling Y-chromosome sequence variation. Genetics 164:1,495-1,509.
15. Hammer, M. F., T. M. Karafet, A. J. Redd et al. 2001. Hierarchical patterns of global human Y-chromosome diversity. Mol. Biol. Evol. 18:1,189-1,203.
16. Hammer, M. F., and S. L. Zegura. 2002. The human Y-chromosome haplogroup tree: Nomenclature and phylogeography of its major divisions. Annu. Rev. Anthropol. 31:303-321.
17. Hurles, M. E., J. Nicholson, E. Bosch et al. 2002. Y chromosomal evidence for the origins of Oceanic-speaking peoples. Genetics 160:289-303.
18. Jobling, M. A., and C. Tyler-Smith. 2003. The human Y chromosome: An evolutionary marker comes of age. Nat. Rev. Genet. 4:598-612.
19. Karafet, T. M., L. P. Osipova, M. A. Gubina et al. 2002. High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life. Hum. Biol. 74:761-789.
20. Karafet, T., L. Xu, R. Du et al. 2001. Paternal population history of East Asia: Sources, patterns, and microevolutionary processes. Am. J. Hum. Genet. 69:615-628.
21. Kayser, M., S. Brauer, G. Weiss et al. 2000. Melanesian origin of Polynesian Y chromosomes. Curr. Biol. 10:1,237-1,246.
22. Kayser, M., S. Brauer, G. Weiss et al. 2001. Independent histories of human Y chromosomes from Melanesia and Australia. Am. J. Hum. Genet. 68:173-190.
23. Kayser, M., S. Brauer, G. Weiss et al. 2003. Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from west New Guinea. Am. J. Hum. Genet. 72:281-302.
24. Kayser, M., P. de Knijff, P. Dieltjes et al. 1997. Applications of microsatellite-based Y chromosome haplotyping. Electrophoresis 18:1,602-1,607.
25. Kayser, M., L. Roewer, M. Hedman et al. 2000. Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am. J. Hum. Genet. 66:1,580-1,588.
26. Kivisild, T., S. Rootsi, M. Metspalu et al. 2003. The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am. J. Hum. Genet. 72:313-332.
27. Lansing, J. S. 1983. The "Indianization" of Bali. J South Southeast Asian Stud. 14:409-421.
28. Lansing, J. S. 1995. The Balinese. Orlando: Harcourt Brace.
29. Lansing, J. S., A. J. Redd, T. M. Karafet et al. 2004. An Indian trader in Bali? Antiquity 78:287-293.
30. Majumdar, R. C. 1963. Ancient Indian Colonization in Southeast Asia. Calcutta: Baroda.
31. Melton, T., S. Clifford, J. Martinson et al. 1998. Genetic evidence for the proto-Austronesian home-land in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes. Am. J. Hum. Genet. 63:1,807-1,823.
32. Minch, E., A. Ruiz-Linares, D. B. Goldstein et al. 1997. Microsat 1.5: A Computer Program for Calculating Various Statistics on Microsatellite Allele Data. Palo Alto, CA: Department of Genetics, Stanford University.
33. Oppenheimer, S. 1998. Eden in East: The Drowned Continent of Southeast Asia. London: Weidenfield & Nicholson.
34. Pandya, A., T. E. King, F. R. Santos et al. 1998. A polymorphic human Y-chromosomal G to A transition found in India. Ind. J. Hum. Genet. 4:52-61.
35. Ramana, G. V., B. Su, L. Jin et al. 2001. Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India. Eur. J. Hum. Genet. 9:695-700.
36. Redd, A. J., A. B. Agellon, V. A. Kearney et al. 2002. Forensic value of 14 novel STRs on the human Y chromosome. Forensic Sci. Int. 130:97-111.
37. Redd, A. J., J. Roberts-Thomson, T. Karafet et al. 2002. Gene flow from the Indian subcontinent to Australia: Evidence from the Y chromosome. Curr. Biol. 12:673-677.
38. Redd, A. J., N. Takezaki, S. T. Sherry et al. 1995. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific. Mol. Biol. Evol. 12:604-615.
39. Richards, B., J. Skoletsky, A. P. Shuber et al. 1993. Multiplex PCR amplification from the CFTR gene using DNA prepared from buccal brushes/swabs. Hum. Mol. Genet. 2:159-163.
40. Richards, M., S. Oppenheimer, and B. Sykes. 1998. mtDNA suggests Polynesian origins in Eastern Indonesia. Am. J. Hum. Genet. 63:1,234-1,236.
41. Roberts, D. F., and R. W. Hiorns. 1965. Methods of analysis of the genetic composition of a hybrid population. Hum. Biol. 37:38-43.
42. Santos, F. R., A. Pandya, M. Kayser et al. 2000. A polymorphic L1 retroposon insertion in the centromere of the human Y chromosome. Hum. Mol. Genet. 9:421-430.
43. Semino, O., G. Passarino, P. J. Oefner et al. 2000. The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y-chromosome perspective. Science 290:1,155-1,159.
44. Stumpf, M. P., and D. B. Goldstein. 2001. Genealogical and evolutionary inference with the human Y chromosome. Science 291:1,738-1,742.
45. Su, B., L. Jin, P. Underhill et al. 2000. Polynesian origins: Insights from the Y chromosome. Proc. Natl. Acad. Sci. USA 97:8,225-8,228.
46. Su, B., C. Xiao, R. Deka et al. 2000. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Hum. Genet. 107:582-590.
47. Su, B., J. Xiao, P. Underhill et al. 1999. Y-chromosome evidence for a northward migration of modern humans into Eastern Asia during the last ice age. Am. J. Hum. Genet. 65:1,718-1,724.
48. Sykes, B., A. Leiboff, J. Low-Beer et al. 1995. The origins of the Polynesians: An interpretation from mitochondrial lineage analysis. Am. J. Hum. Genet. 57:1,463-1,475.
49. Thorne, A., R. Grun, G. Mortimer et al. 1999. Australia's oldest human remains: Age of the Lake Mungo 3 skeleton. J. Hum. Evol. 36:591-612.
50. Underhill, P. A., P. Shen, A. A. Lin et al. 2000. Y-chromosome sequence variation and the history of human populations. Nat. Genet. 26:358-361.
51. van Leur, J. C. 1955. Indonesian Trade and Society: Essays in Asian Social and Economic History. Nijhoff, Netherlands: Hague Banding.
52. Wells, R. S., N. Yuldasheva, R. Ruzibakiev et al. 2001. The Eurasian heartland: A continental perspective on Y-chromosome diversity. Proc. Natl. Acad. Sci. USA 98:10,244-10,249.
53. Y-Chromosome Consortium. 2002. A nomenclature system for the tree of Y-chromosomal binary haplogroups. Genome Res. 12:339-348.