Erratum: Genetic admixture history of Eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis (Molecular Biology and Evolution (2009) 26:8 (1865-1877) DOI: 10.1093/molbev/msp097);Genetic admixture history of eastern indonesia as revealed by Y-chromosome and mitochondrial DNA analysis

Molecular Biology and Evolution

Volumn 26, Issue 8, 2009, Pages 1865-1877

  Mona, Stefano ^a,b   Grunz, Katharina E ^c,i   Brauer, Silke ^a,d   Pakendorf, Brigitte ^c   Castr, Loredana ^e   Sudoyo, Herawati ^f   Marzuki, Sangkot ^f   Barnes, Robert H ^g   Schmidtke, Jörg ^h   Stoneking, Mark ^c   Kayser, Manfred ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF FERRARA   (Italy)

^c MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^d NETHERLANDS FORENSIC INSTITUTE   (Netherlands)

^e UNIVERSITY OF BOLOGNA   (Italy)

^f EIJKMAN INSTITUTE FOR MOLECULAR BIOLOGY   (Indonesia)

^g UNIVERSITY OF OXFORD   (United Kingdom)

^h HANNOVER MEDICAL SCHOOL   (Germany)

ⁱ MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

Admixture; Austronesian; Eastern Indonesia; MtDNA; Papuan; Y Chromosome

Indexed keywords

MITOCHONDRIAL DNA;

ABORIGINE; ARTICLE; AUSTRALIA; CHROMOSOME ANALYSIS; DNA DETERMINATION; GENE POOL; GENETIC VARIABILITY; HUMAN; INDONESIA; LINGUISTICS; MELANESIA; MOLECULAR PHYLOGENY; PALEOLITHIC; SOUTHEAST ASIA; Y CHROMOSOME;

GABAZA;

EID: 67749141990     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr122     Document Type: Erratum

References (78)

1. Adelaar KA, Himmelmann NP. 2005. The Austronesian languages of Asia and Madagascar. London: Routledge/Curzon. London.
2. Anderson DD. 1997. Cave archaeology in Southeast Asia. Geoarchaeology. 12:607-638.
3. Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37-48.
4. Barbujani G, Sokal RR. 1990. Zones of sharp genetic change in Europe are also linguistic boundaries. Proc Natl Acad Sci USA. 87:1816-1819.
5. Bellwood P. 1996. The northern Moluccas as a crossroad between Indonesia and the Pacific. International Conference on Linguistics and Culture Relations in East Indonesia, New Guinea and Australia. Gadjah Mada University, Yogyakarta.
6. Bellwood P. 1997. Prehistory of the Indo-Malayan archipelago. Honululu (HI): University of Hawai'i Press.(revised ed.)
7. Bellwood P. 2004. The origins and dispersals of agricultural communities in Southeast Asia. In: Glover I, Bellwood P, editors. Southeast Asia: from prehistory to history. London: RoutledgeCurzon. p. 21-40.
8. Bellwood P, Fox J, Tryon D. 1995. The Austronesians: historical and comparative perspectives. Canberra (Australia): Department of Anthropology (Australian National University).
9. Blust R. 1993. Central and Central-Eastern Malayo-Polynesian. Ocean Linguist. 32:241-293.
10. Blust R. 1999. Subgrouping, circularity and extinction: some issues in Austronesian comparative linguistics. Symp Ser Inst Linguist Acad Sinica. 1:31-94.
11. Capelli C, Wilson JF, Richards M, Stumpf MP, Gratrix F, Oppenheimer S, Underhill P, Pascali VL, Ko TM, Goldstein DB. 2001. A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania. Am J Hum Genet. 68:432-443.
12. Cavalli-Sforza LL, Piazza A, Menozzi P, Mountain J. 1988. Reconstruction of human evolution: bringing together genetic, archaeological, and linguistic data. Proc Natl Acad Sci USA. 85:6002-6006.
13. Cordaux R, Saha N, Bentley GR, Aunger R, Sirajuddin SM, Stoneking M. 2003. Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur J Hum Genet. 11:253-264.
14. Diamond J, Bellwood P. 2003. Farmers and their languages: the first expansions. Science. 300:597-603.
15. Donohue M. 2007. The Papuan language of Tambora. Ocean Linguist. 46:520-537.
16. Donohue M, Grimes CE. 2008. Yet more on the position of the languages of eastern Indonesia and East Timor. Ocean Linguist. 47:115-159.
17. Dunn M, Terrill A, Reesink G, Foley RA, Levinson SC. 2005. Structural phylogenetics and the reconstruction of ancient language history. Science. 309:2072-2075.
18. Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online. 1:47-50.
19. Foley WA. 1986. The Papuan languages of New Guinea. Cambridge: Cambridge University Press.
20. Foley WA. 2000. The language of New Guinea. Annu Rev Anthopol. 29:357-404.
21. Forster P, Harding R, Torroni A, Bandelt HJ. 1996. Origin and evolution of Native American mtDNA variation: a reappraisal. Am J Hum Genet. 59:935-945.
22. Forster P, Torroni A, Renfrew C, Rohl A. 2001. Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Mol Biol Evol. 18:1864-1881.
23. Friedlaender JS, Friedlaender FR, Hodgson JA, Stoltz M, Koki G, Horvat G, Zhadanov S, Schurr TG, Merriwether DA. 2007. Melanesian mtDNA Complexity. PLoS ONE. 2:e248.
24. Friedlaender JS, Friedlaender FR, Reed FA, et al. (11 coauthors). 2008. The genetic structure of Pacific Islanders. PLoS Genet. 4:e19.
25. Friedlaender J, Schurr T, Gentz F, et al. (12 co-authors). 2005. Expanding Southwest Pacific mitochondrial haplogroups P and Q. Mol Biol Evol. 22:1506-1517.
26. Gray RD, Drummond AJ, Greenhill SJ. 2009. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science. 323:479-483.
27. Gray RD, Jordan FM. 2000. Language trees support the express-train sequence of Austronesian expansion. Nature. 405:1052-1055.
28. Groube L, Chappell J, Muke J, Price D. 1986. A 40,000 year-old human occupation site at Huon Peninsula, Papua New Guinea. Nature. 324:453-455.
29. Hage P, Marck J. 2003. Matrilineality and the Melanesian origin of Polynesian Y chromosomes. Curr Anthropol. 44:121-127.
30. Handt O, Krings M, Ward RH, Paabo S. 1996. The retrieval of ancient human DNA sequences. Am J Hum Genet. 59:368-376.
31. Hastings WK. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 57:97-109.
32. Hill C, Soares P, Mormina M, et al. (10 co-authors). 2007. A mitochondrial stratigraphy for island southeast Asia. Am J Hum Genet. 80:29-43.
33. Hudjashov G, Kivisild T, Underhill PA, et al. (10 co-authors). 2007. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci USA. 104:8726-8730.
34. Hunley K, Dunn M, Lindstrom E, Reesink G, Terrill A, Healy ME, Koki G, Friedlaender FR, Friedlaender JS. 2008. Genetic and linguistic coevolution in Northern Island Melanesia. PLoS Genet. 4:e1000239.
35. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. 2008. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 18:830-838.
36. Kayser M, Brauer S, Cordaux R, Casto A, et al. (14 co-authors). 2006. Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific. Mol Biol Evol. 23:2234-2244.
37. Kayser M, Brauer S, Weiss G, Schiefenhovel W, Underhill P, Shen P, Oefner P, Tommaseo-Ponzetta M, Stoneking M. 2003. Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am J Hum Genet. 72:281-302.
38. Kayser M, Brauer S, Weiss G, Schiefenhovel W, Underhill PA, Stoneking M. 2001. Independent histories of human Y chromosomes from Melanesia and Australia. Am J Hum Genet. 68:173-190.
39. Kayser M, Brauer S, Weiss G, Underhill PA, Roewer L, Schiefenhovel W, Stoneking M. 2000. Melanesian origin of Polynesian Y chromosomes. Curr Biol. 10:1237-1246.
40. Kayser M, Choi Y, van Oven M, Mona S, Brauer S, Trent RJ, Suarkia D, Schiefenhovel W, Stoneking M. 2008. The impact of the Austronesian expansion: evidence from mtDNA and Y-chromosome diversity in the Admiralty Islands of Melanesia. Mol Biol Evol. 25:1362-1374.
41. Kayser M, Lao O, Stoneking M. 2008. Reply to Hedrick "East Asian and Melanesian Ancestry in Polynesians. Am J Hum Genet. 83:140-142.
42. Kirch PV. 1997. The Lapita peoples: ancestors of the oceanic world. Oxford: Blackwell.
43. Kivisild T, Tolk HV, Parik J, Wang Y, Papiha SS, Bandelt HJ, Villems R. 2002. The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol. 19:1737-1751.
44. Klamer M. 2002. Typical features of Austronesian languages in Central/Eastern Indonesia. Ocean Linguist. 41:363-383.
45. Klamer M, Reesink G, Van Staden M. 2008. East Nusantara as a linguistic area. In: Muysken P, editor. From linguistic areas to areal linguistics. Amsterdam (the Netherlands): John Benjamins. p. 95-149.
46. Lansing JS, Cox MP, Downey SS, et al. (11 co-authors). 2007. Coevolution of languages and genes on the island of Sumba, eastern Indonesia. Proc Natl Acad Sci USA. 104:16022-16026.
47. Lansing JS, Watkins JC, Hallmark B, Cox MP, Karafet TM, SudoyoH,Hammer MF. 2008.Male dominancerarelyskewsthe frequency distribution of Y chromosome haplotypes in human populations. Proc Natl Acad Sci USA. 105:11645-11650.
48. Lum JK, Cann RL. 1998. mtDNA and language support a common origin of Micronesians and Polynesians in Island Southeast Asia. Am J Phys Anthropol. 105:109-119.
49. Lum JK, Rickards O, Ching C, Cann RL. 1994. Polynesian mitochondrial DNAs reveal three deep maternal lineage clusters. Hum Biol. 66:567-590.
50. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. 1953. Equations of state calculations by fast computing machine. J Chem Phys. 21:1087-1091.
51. Mona S, Tommaseo-Ponzetta M, Brauer S, Sudoyo H, Marzuki S, Kayser M. 2007. Patterns of Y-chromosome diversity intersect with the Trans-New Guinea hypothesis. Mol Biol Evol. 24:2546-2555.
52. Moodley Y, Linz B, Yamaoka Y, et al. (15 co-authors). 2009. The peopling of the Pacific from a bacterial perspective. Science. 323:527-530.
53. Nasidze I, Quinque D, Rahmani M, Alemohamad SA, Stoneking M. 2006. Concomitant replacement of language and mtDNA in South Caspian populations of Iran. Curr Biol. 16:668-673.
54. O'Connor S, Spriggs M, Veth P. 2002. Excavations at Lene Hara Cave establishes occupation in East Timor at least 30,000 to 35,000 years ago. Antiquity. 76:45-50.
55. Ohta T, Kimura M. 1973. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res. 22:201-204.
56. Oppenheimer SJ, Richards M. 2001. Polynesian origins. Slow boat to Melanesia? Nature. 410:166-167.
57. Pawley A. 1998. The Trans New Guinea phylum hypothesis: a reassessment. In: Miedema J, Odé C, Dam RAC, editors. Perspectives on the bird's head of Irian Jaya, Indonesia. Amsterdam (the Netherlands): Editions Rodopi. p. 655-689.
58. Pawley A. 1999. Chaising rainbows: implications of the rapid dispersal of Austronesian languages for subgrouping and reconstruction. In: Zeitoun E, Li PJ-K, editors. Selected papers from the Eighth International Conference on Austronesian Linguistics. Taipei (Taiwan): Academia Sinica. p. 95-138.
59. Pawley A. 2005. The chequered career of the Trans New Guina hypothesis: recent research and its implications. In: Pawley A, Attenborough R, Golson J, Hide R, editors. Papuan pasts: cultural, linguistic and biological histories of Papuan-speaking peoples. Canberra (Australia): Pacific Linguistics, Research School of Pacific and Asian Studies, The Australian National University. p. 67-107.
60. Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, Penny D. 2006. Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Mol Biol Evol. 23:1966-1975.
61. Rambaut A, Drummond AJ. 2004. TRACER. Version 1.3. Available from: http://beast.bio.ed.ac.uk/Tracer.
62. Redd AJ, Roberts-Thomson J, Karafet T, Bamshad M, Jorde LB, Naidu JM, Walsh B, Hammer MF. 2002. Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome. Curr Biol. 12:673-677.
63. Redd AJ, Stoneking M. 1999. Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations. Am J Hum Genet. 65:808-828.
64. Redd AJ, Takezaki N, Sherry ST, McGarvey ST, Sofro AS, Stoneking M. 1995. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochon-drial DNAs from the Pacific. Mol Biol Evol. 12:604-615.
65. Richards M, Oppenheimer S, Sykes B. 1998. mtDNA suggests Polynesian origins in Eastern Indonesia. Am J Hum Genet. 63:1234-1236.
66. Roberts RG, Jones R, Smith MA. 1990. Thermoluminescence dating of a 50,000-year-old human occupation site in northern Australia. Nature. 345:153-156.
67. Ross M. 2005. Pronouns as a preliminary diagnostic of grouping Papuan languages. In: Pawley A, Attenborough R, Golson J, Hide R, editors. Papuan pasts: cultural, linguistic and biological histories of Papuan-speaking peoples. Canberra (Australia): Pacific Linguistics. p. 15-65.
68. Saillard J, Forster P, Lynnerup N, Bandelt HJ, Norby S. 2000. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am J Hum Genet. 67:718-726.
69. Specht J. 2005. Revisiting the Bismarcks: some alternative views. In: Pawley A, Attenborough R, Golson J, Hide R, editors. Papuan pasts: cultural, linguistic and biological histories of Papuan-speaking peoples. Canberra (Australia): Pacific Linguistics. p. 235-288.
70. Spriggs M. 2000. Out of Asia? The spread of Southeast Asian Pleistocene and Neolithic maritime cultures in Island Southeast Asia and the western Pacific. In: O'Connor S, Veth P, editors. East of Wallace's line: studies of past and present maritime cultures of the Indo-Pacific region. Rotterdam (the Netherlands): A.A. Balkema. p. 51-75.
71. Spriggs M. 2003. Chronology of the Neolithic transition in Southeast Asia and the Western Pacific: a view from 2003. Rev Archaeol. 24:57-80.
72. Tommaseo-Ponzetta M, Attimonelli M, De Robertis M, Tanzariello F, Saccone C. 2002. Mitochondrial DNA variability of West New Guinea populations. Am J Phys Anthropol. 117:49-67.
73. Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, Hsu CJ, Li ZY, Lin M. 2005. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol. 3:e247.
74. Underhill PA, Passarino G, Lin AA, Shen P, Mirazon Lahr M, Foley RA, Oefner PJ, Cavalli-Sforza LL. 2001. The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet. 65:43-62.
75. Wilson IJ, Balding DJ. 1998. Genealogical inference from microsatellite data. Genetics. 150:499-510.
76. Wilson IJ, Weale ME, Balding DJ. 2003. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. J R Stat Soc Ser A (Stat Soc). 166:155-188.
77. Wurm SA, Hattori S. 1981. Language Atlas of the Pacific Area. Canberra (Australia): Australian Academy of the Humanities in collaboration with the Japan Academy.
78. Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP. 2002. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet. 70:635-651.