Early austronesians: Into and out of Taiwan

American Journal of Human Genetics

Volumn 94, Issue 3, 2014, Pages 426-436

  Ko, Albert Min Shan ^a   Chen, Chung Yu ^b   Fu, Qiaomei ^a   Delfin, Frederick ^a,c   Li, Mingkun ^a   Chiu, Hung Lin ^d   Stoneking, Mark ^a   Ko, Ying Chin ^e  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b INSTITUTE OF HISTORY AND PHILOLOGY   (Taiwan)

^c University of the Philippines Diliman   (Philippines)

^d NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^e CHINA MEDICAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ABORIGINE; ARTICLE; CHINA; DNA EXTRACTION; DNA LIBRARY; GENE FLOW; GENE SEQUENCE; GENETIC LINKAGE; GENETIC VARIABILITY; GENOME; HAPLOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; LANGUAGE; MADAGASCAR; MOLECULAR CLOCK; NEOLITHIC; PACIFIC ISLANDS; PHYLOGENY; PRIORITY JOURNAL; TAIWAN;

ANTHROPOLOGY, PHYSICAL; ASIAN CONTINENTAL ANCESTRY GROUP; BAYES THEOREM; CLUSTER ANALYSIS; DNA, MITOCHONDRIAL; EMIGRATION AND IMMIGRATION; ETHNIC GROUPS; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LANGUAGE; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SKELETON; TAIWAN;

EID: 84896789927     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2014.02.003     Document Type: Article

References (62)

1. R.D. Gray, A.J. Drummond, and S.J. Greenhill Language phylogenies reveal expansion pulses and pauses in Pacific settlement Science 323 2009 479 483
2. P. Soares, T. Rito, J. Trejaut, M. Mormina, C. Hill, E. Tinkler-Hundal, M. Braid, D.J. Clarke, J.H. Loo, and N. Thomson et al. Ancient voyaging and Polynesian origins Am. J. Hum. Genet. 88 2011 239 247
3. C. Hill, P. Soares, M. Mormina, V. Macaulay, D. Clarke, P.B. Blumbach, M. Vizuete-Forster, P. Forster, D. Bulbeck, S. Oppenheimer, and M. Richards A mitochondrial stratigraphy for island southeast Asia Am. J. Hum. Genet. 80 2007 29 43
4. S. Mirabal, A.M. Cadenas, R. Garcia-Bertrand, and R.J. Herrera Ascertaining the role of Taiwan as a source for the Austronesian expansion Am. J. Phys. Anthropol. 150 2013 551 564
5. H. Li, B. Wen, S.J. Chen, B. Su, P. Pramoonjago, Y. Liu, S. Pan, Z. Qin, W. Liu, and X. Cheng et al. Paternal genetic affinity between Western Austronesians and Daic populations BMC Evol. Biol. 8 2008 146
6. L. Sagart The expansion of Setaria farmers in East Asia: A linguistic and archaeological model A. Sanchez-Mazas, M. Ross, I. Peiros, M. Lin, Past Human Migrations in East Asia: Matching Archaeology, Linguistics and Genetics 2008 Routledge New York 133 167
7. R. Blust Selected papers from the Eighth International Conference on Austronesian Linguistics E. Zeitoun, P. Li, Symposium series of the Institute of Linguistics 1999 Academia Sinica Taipei, Taiwan 31 94
8. N. Rohland, H. Siedel, and M. Hofreiter A rapid column-based ancient DNA extraction method for increased sample throughput Mol. Ecol. Resour. 10 2010 677 683
9. M. Meyer, M. Kircher, M.T. Gansauge, H. Li, F. Racimo, S. Mallick, J.G. Schraiber, F. Jay, K. Prüfer, and C. de Filippo et al. A high-coverage genome sequence from an archaic Denisovan individual Science 338 2012 222 226
10. M. Meyer, and M. Kircher Illumina sequencing library preparation for highly multiplexed target capture and sequencing Cold Spring Harb Protoc 2010 2010 t5448
11. J. Dabney, and M. Meyer Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries Biotechniques 52 2012 87 94
12. M. Kircher, S. Sawyer, and M. Meyer Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform Nucleic Acids Res. 40 2012 e3
13. M. Margulies, M. Egholm, W.E. Altman, S. Attiya, J.S. Bader, L.A. Bemben, J. Berka, M.S. Braverman, Y.J. Chen, and Z. Chen et al. Genome sequencing in microfabricated high-density picolitre reactors Nature 437 2005 376 380
14. Q. Fu, M. Meyer, X. Gao, U. Stenzel, H.A. Burbano, J. Kelso, and S. Pääbo DNA analysis of an early modern human from Tianyuan Cave, China Proc. Natl. Acad. Sci. USA 110 2013 2223 2227
15. D. Reich, N. Patterson, M. Kircher, F. Delfin, M.R. Nandineni, I. Pugach, A.M. Ko, Y.C. Ko, T.A. Jinam, and M.E. Phipps et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania Am. J. Hum. Genet. 89 2011 516 528
16. R.M. Andrews, I. Kubacka, P.F. Chinnery, R.N. Lightowlers, D.M. Turnbull, and N. Howell Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA Nat. Genet. 23 1999 147
17. A.W. Briggs, J.M. Good, R.E. Green, J. Krause, T. Maricic, U. Stenzel, C. Lalueza-Fox, P. Rudan, D. Brajkovic, and Z. Kucan et al. Targeted retrieval and analysis of five Neandertal mtDNA genomes Science 325 2009 318 321
18. D. Reich, R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, B. Viola, A.W. Briggs, U. Stenzel, and P.L. Johnson et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia Nature 468 2010 1053 1060
19. R.E. Green, A.-S. Malaspinas, J. Krause, A.W. Briggs, P.L.F. Johnson, C. Uhler, M. Meyer, J.M. Good, T. Maricic, and U. Stenzel et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing Cell 134 2008 416 426
20. E.D. Gunnarsdóttir, M. Li, M. Bauchet, K. Finstermeier, and M. Stoneking High-throughput sequencing of complete human mtDNA genomes from the Philippines Genome Res. 21 2011 1 11
21. M. van Oven, and M. Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation Hum. Mutat. 30 2009 E386 E394
22. J.Y. Wang Population change of Formosan aborigines Academia Sinica Monographs 1967 Institute of Ethnology Nankang, Taipei 36
23. J.A. Trejaut, T. Kivisild, J.H. Loo, C.L. Lee, C.L. He, C.J. Hsu, Z.Y. Lee, and M. Lin Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations PLoS Biol. 3 2005 e247
24. H.J. Bandelt, P. Forster, and A. Röhl Median-joining networks for inferring intraspecific phylogenies Mol. Biol. Evol. 16 1999 37 48
25. A.J. Drummond, M.A. Suchard, D. Xie, and A. Rambaut Bayesian phylogenetics with BEAUti and the BEAST 1.7 Mol. Biol. Evol. 29 2012 1969 1973
26. V.N. Minin, E.W. Bloomquist, and M.A. Suchard Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics Mol. Biol. Evol. 25 2008 1459 1471
27. D. Darriba, G.L. Taboada, R. Doallo, and D. Posada jModelTest 2: more models, new heuristics and parallel computing Nat. Methods 9 2012 772
28. P. Soares, L. Ermini, N. Thomson, M. Mormina, T. Rito, A. Röhl, A. Salas, S. Oppenheimer, V. Macaulay, and M.B. Richards Correcting for purifying selection: an improved human mitochondrial molecular clock Am. J. Hum. Genet. 84 2009 740 759
29. L. Excoffier, and M. Foll fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27 2011 1332 1334
30. M.A. Beaumont, W. Zhang, and D.J. Balding Approximate Bayesian computation in population genetics Genetics 162 2002 2025 2035
31. T. Jombart, S. Devillard, and F. Balloux Discriminant analysis of principal components: a new method for the analysis of genetically structured populations BMC Genet. 11 2010 94
32. F. Delfin, A. Min-Shan Ko, M. Li, E.D. Gunnarsdóttir, K.A. Tabbada, J.M. Salvador, G.C. Calacal, M.S. Sagum, F.A. Datar, and S.G. Padilla et al. Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region Eur. J. Hum. Genet. 22 2014 228 237
33. T.A. Jinam, L.C. Hong, M.E. Phipps, M. Stoneking, M. Ameen, J. Edo, N. Saitou HUGO Pan-Asian SNP Consortium Evolutionary history of continental southeast Asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data Mol. Biol. Evol. 29 2012 3513 3527
34. E.D. Gunnarsdóttir, M.R. Nandineni, M. Li, S. Myles, D. Gil, B. Pakendorf, and M. Stoneking Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra Nat Commun 2 2011 228
35. P. Soares, J.A. Trejaut, J.H. Loo, C. Hill, M. Mormina, C.L. Lee, Y.M. Chen, G. Hudjashov, P. Forster, and V. Macaulay et al. Climate change and postglacial human dispersals in southeast Asia Mol. Biol. Evol. 25 2008 1209 1218
36. J.S. Friedlaender, F.R. Friedlaender, J.A. Hodgson, M. Stoltz, G. Koki, G. Horvat, S. Zhadanov, T.G. Schurr, and D.A. Merriwether Melanesian mtDNA complexity PLoS ONE 2 2007 e248
37. M.S. Peng, M.G. Palanichamy, Y.G. Yao, B. Mitra, Y.T. Cheng, M. Zhao, J. Liu, H.W. Wang, H. Pan, and W.Z. Wang et al. Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b BMC Biol. 9 2011 2
38. B. Shapiro, S.Y. Ho, A.J. Drummond, M.A. Suchard, O.G. Pybus, and A. Rambaut A Bayesian phylogenetic method to estimate unknown sequence ages Mol. Biol. Evol. 28 2011 879 887
39. Q. Fu, A. Mittnik, P.L. Johnson, K. Bos, M. Lari, R. Bollongino, C. Sun, L. Giemsch, R. Schmitz, and J. Burger et al. A revised timescale for human evolution based on ancient mitochondrial genomes Curr. Biol. 23 2013 553 559
40. L. Excoffier Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model Mol. Ecol. 13 2004 853 864
41. Q.P. Kong, C. Sun, H.W. Wang, M. Zhao, W.Z. Wang, L. Zhong, X.D. Hao, H. Pan, S.Y. Wang, and Y.T. Cheng et al. Large-scale mtDNA screening reveals a surprising matrilineal complexity in east Asia and its implications to the peopling of the region Mol. Biol. Evol. 28 2011 513 522
42. M.G. Vilar, C.W. Chan, D.R. Santos, D. Lynch, R. Spathis, R.M. Garruto, and J.K. Lum The origins and genetic distinctiveness of the Chamorros of the Marianas Islands: an mtDNA perspective Am. J. Hum. Biol. 25 2013 116 122
43. F.X. Ricaut, H. Razafindrazaka, M.P. Cox, J.M. Dugoujon, E. Guitard, C. Sambo, M. Mormina, M. Mirazon-Lahr, B. Ludes, and E. Crubézy A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar BMC Genomics 10 2009 605
44. F. Delfin, S. Myles, Y. Choi, D. Hughes, R. Illek, M. van Oven, B. Pakendorf, M. Kayser, and M. Stoneking Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands Mol. Biol. Evol. 29 2012 545 564
45. K.A. Tabbada, J. Trejaut, J.H. Loo, Y.M. Chen, M. Lin, M. Mirazón-Lahr, T. Kivisild, and M.C. De Ungria Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia? Mol. Biol. Evol. 27 2010 21 31
46. M.S. Peng, H.H. Quang, K.P. Dang, A.V. Trieu, H.W. Wang, Y.G. Yao, Q.P. Kong, and Y.P. Zhang Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA Mol. Biol. Evol. 27 2010 2417 2430
47. P. Bellwood, G. Chambers, M. Ross, and H.-C. Hung Are 'cultures' inherited? Multidisciplinary perspectives on the origins and migrations of Austronesian-speaking peoples prior 1000 BC B. Roberts, M. Vander Linden, Investigating Archaeological Cultures: Material Culture, Variability, and Transmission 2011 Springer New York 321 353
48. X. Qi, C. Cui, Y. Peng, X. Zhang, Z. Yang, H. Zhong, H. Zhang, K. Xiang, X. Cao, and Y. Wang et al. Genetic evidence of paleolithic colonization and neolithic expansion of modern humans on the tibetan plateau Mol. Biol. Evol. 30 2013 1761 1778
49. P. Bellwood The checkered prehistory of rice movement southwards as a domesticated cereal - from the Yangzi to the equator Rice 4 2011 93 103
50. C.H. Tsang Recent discoveries at the Tapenkeng culture sites in Taiwan: Implications for the problem of Austronesian origins R. Blench, L. Sagart, A. Sanchez-Mazas, The Peopling of East Asia: Putting Together Archaeology, Linguistics and Genetics 2005 Routledge/Curzon London 63 73
51. X. Yang, Z. Wan, L. Perry, H. Lu, Q. Wang, C. Zhao, J. Li, F. Xie, J. Yu, and T. Cui et al. Early millet use in northern China Proc. Natl. Acad. Sci. USA 109 2012 3726 3730
52. J. Molina, M. Sikora, N. Garud, J.M. Flowers, S. Rubinstein, A. Reynolds, P. Huang, S. Jackson, B.A. Schaal, and C.D. Bustamante et al. Molecular evidence for a single evolutionary origin of domesticated rice Proc. Natl. Acad. Sci. USA 108 2011 8351 8356
53. J. Diamond, and P. Bellwood Farmers and their languages: the first expansions Science 300 2003 597 603
54. B.V. Rolett, Z. Zheng, and Y. Yue Holocene sea-level change and the emergence of Neolithic seafaring in the Fuzhou Basin (Fujian, China) Quat. Sci. Rev. 30 2011 788 797
55. P. Bellwood Man's Conquest of the Pacific: The Prehistory of Southeast Asia and Oceania 1978 Oxford Univ. Press New York
56. P. Bellwood Prehistory of the Indo-Malaysian Archipelago 1997 University of Hawai'i Press Honolulu
57. P.J.K. Li Time perspective of Formosan aborigines A. Sanchez-Mazas, M. Ross, I. Peiros, M. Lin, Past Human Migrations in East Asia: Matching Archaeology, Linguistics and Genetics 2008 Routledge New York 211 218
58. M. Ross Proto Austronesian verbal morphology: A reappraisal A. Adelaar, A. Pawley, Austronesian Historical Linguistics and Culture History: A Festschrift for Robert Blust 2009 Pacific Linguistics Canberra 295 326
59. R.N. Gutenkunst, R.D. Hernandez, S.H. Williamson, and C.D. Bustamante Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data PLoS Genet. 5 2009 e1000695
60. S. Neuenschwander, C.R. Largiadèr, N. Ray, M. Currat, P. Vonlanthen, and L. Excoffier Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): inference under a Bayesian spatially explicit framework Mol. Ecol. 17 2008 757 772
61. J. Felsenstein The number of evolutionary trees Syst. Zool. 27 1978 27 33
62. C.F. Lin, J.D. Wang, P.H. Chen, S.J. Chang, Y.H. Yang, and Y.C. Ko Predictors of betel quid chewing behavior and cessation patterns in Taiwan aborigines BMC Public Health 6 2006 271