Resolving the ancestry of Austronesian-speaking populations

Human Genetics

Volumn 135, Issue 3, 2016, Pages 309-326

  Soares, Pedro A ^a,b,c   Trejaut, Jean A ^d   Rito, Teresa ^a,b,e   Cavadas, Bruno ^b,f   Hill, Catherine ^c   Eng, Ken Khong ^c,g   Mormina, Maru ^c,h   Brandão, Andreia ^b,f,i   Fraser, Ross M ^j,k   Wang, Tse Yi ^d   Loo, Jun Hun ^d   Snell, Christopher ^c   Ko, Tsang Ming ^l   Amorim, António ^b,f   Pala, Maria ⁱ   Macaulay, Vincent ^m   Bulbeck, David ⁿ   Wilson, James F ^j,o   Gusmão, Leonor ^b,p   Pereira, Luísa ^b,f   Oppenheimer, Stephen ^q   Lin, Marie ^d   Richards, Martin B ^c,i   more..

^a UNIVERSITY OF MINHO   (Portugal)

^b UNIVERSITY OF PORTO   (Portugal)

^c UNIVERSITY OF LEEDS   (United Kingdom)

^d MACKAY MEMORIAL HOSPITAL   (Taiwan)

^e UNIVERSITY OF MINHO   (Portugal)

^f UNIVERSITY OF PORTO   (Portugal)

^g SCHOOL OF PHYSICS   (Malaysia)

^h UNIVERSITY OF WINCHESTER   (United Kingdom)

ⁱ UNIVERSITY OF HUDDERSFIELD   (United Kingdom)

^j UNIVERSITY OF EDINBURGH   (United Kingdom)

^k Synpromics Ltd   (United Kingdom)

^l NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^m UNIVERSITY OF GLASGOW   (United Kingdom)

ⁿ AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^o UNIVERSITY OF EDINBURGH   (United Kingdom)

^p STATE UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^q UNIVERSITY OF OXFORD   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ANCESTRY GROUP; ARTICLE; AUSTRONESIAN PEOPLE; CHINA; CULTURAL FACTOR; GENETIC VARIABILITY; GENOME; HAPLOGROUP; HUMAN; LANGUAGE; LATE HOLOCENE; MIGRATION; MITOCHONDRIAL GENOME; NEOLITHIC; PRIORITY JOURNAL; SOUTHEAST ASIA; TAIWAN; Y CHROMOSOME; ASIAN CONTINENTAL ANCESTRY GROUP; BIOLOGICAL MODEL; FEMALE; GENE LOCUS; GENETIC ASSOCIATION STUDY; GENETIC DATABASE; GENETICS; HUMAN GENOME; MALE; PHYLOGENY; PHYLOGEOGRAPHY; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ASIA, SOUTHEASTERN; ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOMES, HUMAN, Y; DATABASES, GENETIC; DNA, MITOCHONDRIAL; FEMALE; GENETIC ASSOCIATION STUDIES; GENETIC LOCI; GENOME, HUMAN; HUMANS; MALE; MODELS, GENETIC; PHYLOGENY; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 84958777413     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-015-1620-z     Document Type: Article

References (85)

1. Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A, Chen CH, Chen J, Chen YT, Chu J, Cutiongco-de La Paz EMC, De Ungria MCA, Delfin FC, Edo J, Fuchareon S, Ghang H, Gojobori T, Han J, Ho SF, Hoh BP, Huang W, Inoko H, Jha P, Jinam TA, Jin L, Jung J, Kangwanpong D, Kampuansai J, Kennedy GC, Khurana P, Kim HL, Kim K, Kim S, Kim WY, Kimm K, Kimura R, Koike T, Kulawonganunchai S, Kumar V, Lai PS, Lee JY, Lee S, Liu ET, Majumder PP, Mandapati KK, Marzuki S, Mitchell W, Mukerji M, Naritomi K, Ngamphiw C, Niikawa N, Nishida N, Oh B, Oh S, Ohashi J, Oka A, Ong R, Padilla CD, Palittapongarnpim P, Perdigon HB, Phipps ME, Png E, Sakaki Y, Salvador JM, Sandraling Y, Scaria V, Seielstad M, Sidek MR, Sinha A, Srikummool M, Sudoyo H, Sugano S, Suryadi H, Suzuki Y, Tabbada KA, Tan A, Tokunaga K, Tongsima S, Villamor LP, Wang E, Wang Y, Wang H, Wu JY, Xiao H, Xu S, Yang JO, Shugart YY, Yoo HS, Yuan W, Zhao G, Zilfalil BA (2009) Mapping human genetic diversity in Asia. Science 326:1541–1545
2. Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664
3. Anderson A (2005) Crossing the Luzon Strait: archaeological chronology in the Batanes Islands, Philippines and the regional sequence of Neolithic dispersal. J Austron Stud 1:25–44
4. Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, Van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, Von Wurmb-Schwark N, De Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M (2010) Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 87:341–353
5. Bandelt H-J, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human populations using median networks. Genetics 141:743–753
6. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48
7. Barker G, Richards MB (2013) Foraging-farming transitions in Island Southeast Asia. J Archaeol Method Theory 20:256–280
8. Bedford S, Spriggs M, Regenvanu R (2006) The Teouma Lapita site and the early human settlement of the Pacific Islands. Antiquity 80:812–828
9. Bellwood P (1997) Prehistory of the Indo-Malaysian archipelago. ANU E Press, Canberra
10. Bird MI, Austin WEN, Wurster CM, Fifield LK, Mojtahid M, Sargeant C (2010) Punctuated eustatic sea-level rise in the early mid-Holocene. Geology 38:803–806. doi:10.1130/g31066.1
11. Blanchon P, Shaw J (1995) Reef drowning during the last deglaciation: evidence for catastrophic sea-level rise and ice-sheet collapse. Geology 23:4–8
12. Blench R (2012) Almost everything you believed about the Austronesians isn’t true. Crossing Borders: Selected Papers from the 13th International Conference of the European Association of Southeast Asian Archaeologists 2012. National University of Singapore Press, pp 122–142
13. Blust R (1976) Austronesian culture history: some linguistic inferences and their relations to the archaeological record. World Archaeol 8:19–43
14. Blust R (1995) The prehistory of the Austronesian-speaking peoples: a view from language. J World Prehist 9:453–510
15. Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Sarkissian CD, Ganslmeier R, Friederich S, Dresely V, Van Oven M, Kenyon R, Van Der Hoek MB, Korlach J, Luong K, Ho SYW, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A, Adhikarla S, Ganesh Prasad AK, Pitchappan R, Varatharajan Santhakumari A, Balanovska E, Balanovsky O, Bertranpetit J, Comas D, Martínez-Cruz B, Melé M, Clarke AC, Matisoo-Smith EA, Dulik MC, Gaieski JB, Owings AC, Schurr TG, Vilar MG, Hobbs A, Soodyall H, Javed A, Parida L, Platt DE, Royyuru AK, Jin L, Li S, Kaplan ME, Merchant NC, John Mitchell R, Renfrew C, Lacerda DR, Santos FR, Soria Hernanz DF, Spencer Wells R, Swamikrishnan P, Tyler-Smith C, Paulo Vieira P, Ziegle JS (2013) Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 4:1764
16. Bulbeck D (2008) An integrated perspective on the Austronesian diaspora: the switch from cereal agriculture to maritime foraging in the colonisation of Island Southeast Asia. Aust Archaeol 67:31–52
17. Bulbeck D (2011) Biological and cultural evolution in the population and culture history of Homo sapiens in Malaya. In: Enfield N (ed) Dynamics of human diversity: the case of mainland Southeast Asia. Pacific Linguistics, Canberra, pp 207–255
18. Capelli C, Wilson JF, Richards M, Stumpf MPH, 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
19. Clark GR, Anderson A (2009) The early prehistory of Fiji. ANU E Press, Canberra
20. Delfin F, Myles S, Choi Y, Hughes D, Illek R, Van Oven M, Pakendorf B, Kayser M, Stoneking M (2012) Bridging Near and Remote Oceania: mtDNA and NRY variation in the Solomon Islands. Mol Biol Evol 29:545–564
21. Diamond J, Bellwood P (2003) Farmers and their languages: the first expansions. Science 300:597–603
22. Donohue M, Denham T (2010) Farming and language in Island Southeast Asia: reframing Austronesian history. Curr Anthropol 51:223–256
23. Donohue M, Denham T (2015) Becoming Austronesian: mechanisms of language dispersal across southern Island Southeast Asia. In: Gil D, McWhorter J (eds) Austronesian Undressed. Pacific Linguistics, Canberra (in press)
24. Drummond AJ, Rambaut A (2007) BEAST: bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
25. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185–1192
26. Duggan AT, Evans B, Friedlaender FR, Friedlaender JS, Koki G, Merriwether DA, Kayser M, Stoneking M (2014) Maternal history of oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion. Am J Hum Genet 94:721–733
27. Fitzpatrick SM, Callaghan RT (2013) Estimating trajectories of colonisation to the Mariana islands, western Pacific. Antiquity 87:840–853
28. Forster P, Harding R, Torroni A, Bandelt H-J (1996) Origin and evolution of native American mtDNA variation: a reappraisal. Am J Hum Genet 59:935–945
29. 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
30. Friedlaender JS, Friedlaender FR, Reed FA, Kidd KK, Kidd JR, Chambers GK, Lea RA, Loo JH, Koki G, Hodgson JA, Merriwether DA, Weber JL (2008) The genetic structure of Pacific Islanders. PLoS Genet 4:0173–0190
31. Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Pääbo S (2013a) DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci USA 110:2223–2227
32. Fu Q, Mittnik A, Johnson PLF, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, Krause J (2013b) A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol 23:553–559
33. Gusmão L, Sánchez-Diz P, Calafell F, Martín P, Alonso CA, Álvarez-Fernández F, Alves C, Borjas-Fajardo L, Bozzo WR, Bravo ML, Builes JJ, Capilla J, Carvalho M, Castillo C, Catanesi CI, Corach D, Di Lonardo AM, Espinheira R, Fagundes De Carvalho E, Farfán MJ, Figueiredo HP, Gomes I, Lojo MM, Marino M, Pinheiro MF, Pontes ML, Prieto V, Ramos-Luis E, Riancho JA, Souza Góes AC, Santapa OA, Sumita DR, Vallejo G, Vidal Rioja L, Vide MC, Vieira Da Silva CI, Whittle MR, Zabala W, Zarrabeitia MT, Alonso A, Carracedo A, Amorim A (2005) Mutation rates at Y chromosome specific microsatellites. Hum Mutat 26:520–528
34. Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S, Richards M (2007) A mitochondrial stratigraphy for Island Southeast Asia. Am J Hum Genet 80:29–43
35. Ho SYW, Kolokotronis SO, Allaby RG (2007) Elevated substitution rates estimated from ancient DNA sequences. Biol Lett 3:702–705
36. Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, Forster P (2007) Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci USA 104:8726–8730
37. Hung H-C, Carson MT, Bellwood P, Campos FZ, Piper PJ, Dizon E, Bolunia MJ, Oxenham M, Chi Z (2011) The first settlement of Remote Oceania: the Philippines to the Marianas: supplementary information on radiocarbon dating of the Nagsabaran site. Antiquity 85:909–926
38. Hunt CO, Gilbertson DD, Rushworth G (2007) Modern humans in Sarawak, Malaysian Borneo, during Oxygen Isotope Stage 3: palaeoenvironmental evidence from the Great Cave of Niah. J Archaeol Sci 34:1953–1969
39. Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS, Hammer MF (2010) Major east-west division underlies Y chromosome stratification across Indonesia. Mol Biol Evol 27:1833–1844
40. Kayser M, Brauer S, Weiss G, Underhill P, Roewer L, Schiefenhövel W, Stoneking M (2000) Melanesian origin of Polynesian Y chromosomes. Curr Biol 10:1237–1246
41. Kayser M, Choi Y, Van Oven M, Mona S, Brauer S, Trent RJ, Suarkia D, Schiefenhövel W, Stoneking M (2008a) 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
42. Kayser M, Lao O, Saar K, Brauer S, Wang X, Nürnberg P, Trent R, Stoneking M (2008b) Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. Am J Hum Genet 82:194–198
43. Ko AMS, Chen CY, Fu Q, Delfin F, Li M, Chiu HL, Stoneking M, Ko YC (2014) Early Austronesians: into and out of Taiwan. Am J Hum Genet 94:426–436
44. Lipson M, Loh PR, Patterson N, Moorjani P, Ko YC, Stoneking M, Berger B, Reich D (2014) Reconstructing Austronesian population history in Island Southeast Asia. Nat Commun 5:4689
45. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F, Taha A, Shaari NK, Raja JM, Ismail P, Zainuddin Z, Goodwin W, Bulbeck D, Bandelt H-J, Oppenheimer S, Torroni A, Richards M (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034–1036
46. Manguin P-Y, Mani A, Wade G (2011) Early interactions between South and Southeast Asia. Institute of Southeast Asian Studies, Singapure
47. Mellars P, Gori KC, Carr M, Soares PA, Richards MB (2013) Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proc Natl Acad Sci USA 110:10699–10704
48. Melton T, Peterson R, Redd AJ, Saha N, Sofro ASM, Martinson J, Stoneking M (1995) Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am J Hum Genet 57:403–414
49. Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, Liu E, Tongsima S, Consortium HP-AS (2011) PanSNPdb: the Pan-Asian SNP genotyping database. PLoS One 6:e21451
50. Oppenheimer S (1998) Eden in the east: the drowned continent of Southeast Asia. Phoenix, London
51. Oppenheimer S (2004) The ‘Express Train from Taiwan to Polynesia’: on the congruence of proxy lines of evidence. World Archaeol 36:591–600
52. Oppenheimer S, Richards M (2001) Fast trains, slow boats, and the ancestry of the Polynesian islanders. Sci Prog 84:157–181
53. Paz V (2002) Island Southeast Asia: spread or friction zone. In: Bellwood P, Renfrew C (eds) Examining the farming/language dispersal hypothesis. MacDonald Institute for Archaeological Research, Cambridge, pp 275–285
54. Pelejero C, Kienast M, Wang L, Grimalt JO (1999) The flooding of Sundaland during the last deglaciation: imprints in hemipelagic sediments from the southern South China Sea. Earth Planet Sci Lett 171:661–671
55. Pereira L, Silva NM, Franco-Duarte R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares P, Behar DM, Richards MB, Macaulay V (2010) Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC Evol Biol 10:390
56. Pierron D, Razafindrazaka H, Pagani L, Ricaut FX, Antao T, Capredon M, Sambo C, Radimilahy C, Rakotoarisoa JA, Blench RM, Letellier T, Kivisild T (2014) Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar. Proc Natl Acad Sci USA 111:936–941
57. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, De Bakker PIW, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575
58. Redd AJ, Takezaki N, Sherry ST, McGarvey ST, Sofro ASM, Stoneking M (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
59. Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, Rengo C, Sellitto D, Cruciani F, Kivisild T, Villems R, Thomas M, Rychkov S, Rychkov O, Rychkov Y, Golge M, Dimitrov D, Hill E, Bradley D, Romano V, Cali F, Vona G, Demaine A, Papiha S, Triantaphyllidis C, Stefanescu G, Hatina J, Belledi M, Di Rienzo A, Novelletto A, Oppenheim A, Norby S, Al-Zaheri N, Santachiara-Benerecetti S, Scozzari R, Torroni A, Bandelt H-J (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67:1251–1276
60. Rieth TM, Hunt TL (2008) A radiocarbon chronology for Sāmoan prehistory. J Archaeol Sci 35:1901–1927
61. Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P (2013) The first modern human dispersals across Africa. PLoS One 8:e80031
62. Ross M (2005) The Batanic languages in relation to the early history of the Malayo-Polynesian subgroup of Austronesian. J Austron Stud 1:P1–P24
63. Ross M (2009) Proto Austronesian verbal morphology: a reappraisal. In: Adelaar A, Pawley A (eds) Austronesian historical linguistics and culture history: a festschrift for Robert Blust. Pacific Linguistics, Canberra, pp 295–326
64. Saillard J, Forster P, Lynnerup N, Bandelt H-J, Norby S (2000) mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am J Hum Genet 67:718–726
65. Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, Chen YM, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB (2008) Climate change and postglacial human dispersals in Southeast Asia. Mol Biol Evol 25:1209–1218
66. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84:740–759
67. Soares P, Rito T, Trejaut J, Mormina M, Hill C, Tinkler-Hundal E, Braid M, Clarke DJ, Loo JH, Thomson N, Denham T, Donohue M, Macaulay V, Lin M, Oppenheimer S, Richards MB (2011) Ancient voyaging and Polynesian origins. Am J Hum Genet 88:239–247
68. Soares P, Alshamali F, Pereira JB, Fernandes V, Silva NM, Afonso C, Costa MD, Musilová E, Macaulay V, Richards MB, Černý V, Pereira L (2012) The expansion of mtDNA haplogroup L3 within and out of Africa. Mol Biol Evol 29:915–927
69. Solheim WG (2006) Archaeology and culture in Southeast Asia: unraveling the Nusantao. UP Press, Philippines
70. Spriggs M (2003) Chronology of the Neolithic transition in Island Southeast Asia and the Western Pacific: a view from 2003. Rev Archaeol 24:57–80
71. Spriggs M (2007) The Neolithic and Austronesian expansion within Island Southeast Asia and into the Pacific. In: Chiu S, Sand C (eds) From Southeast Asia to the Pacific: Archaeological perspectives on the Austronesian expansion and the Lapita cultural complex. Academica Sinica, Taipei, pp 104–125
72. Spriggs M (2011) Archaeology and the Austronesian expansion: where are we now? Antiquity 85:510–528
73. Summerhayes GR, Leavesley M, Fairbairn A, Mandui H, Field J, Ford A, Fullagar R (2010) Human adaptation and plant use in highland New Guinea 49,000 to 44,000 years ago. Science 330:78–81
74. Sykes B, Leiboff A, Low-Beer J, Tetzner S, Richards M (1995) The origins of the Polynesians: an interpretation from mitochondrial lineage analysis. Am J Hum Genet 57:1463–1475
75. Terrell JE, Welsch RL (1997) Lapita and the temporal geography of prehistory. Antiquity 71:548–572
76. Torrence R, Swadling P (2008) Social networks and the spread of Lapita. Antiquity 82:600–616
77. Torroni A, Rengo C, Guida V, Cruciani F, Sellitto D, Coppa A, Calderon FL, Simionati B, Valle G, Richards M, Macaulay V, Scozzari R (2001) Do the four clades of the mtDNA haplogroup L2 evolve at different rates? Am J Hum Genet 69:1348–1356
78. Trejaut JA, Kivisild T, Jun HL, Chien LL, Chun LH, Chia JH, Zheng YL, Lin M (2005) Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol 3:e376
79. Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, He CL, Lin M (2014) Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia. BMC Genetics 15:77
80. Tumonggor MK, Karafet TM, Hallmark B, Lansing JS, Sudoyo H, Hammer MF, Cox MP (2013) The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific. J Hum Genet 58:165–173
81. Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonné-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26:358–361
82. Verdu P, Pemberton TJ, Laurent R, Kemp BM, Gonzalez-Oliver A, Gorodezky C, Hughes CE, Shattuck MR, Petzelt B, Mitchell J, Harry H, William T, Worl R, Cybulski JS, Rosenberg NA, Malhi RS (2014) Patterns of admixture and population structure in native populations of Northwest North America. PLoS Genet 10:e1004530
83. Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P, Stoneking M, Kayser M (2010) Demographic history of Oceania inferred from genome-wide data. Curr Biol 20:1983–1992
84. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556
85. Zhivotovsky LA, Underhill PA, Cinnioǧlu C, Kayser M, Morar B, Kivisild T, Scozzari R, Cruciani F, Destro-Bisol G, Spedini G, Chambers GK, Herrera RJ, Yong KK, Gresham D, Tournev I, Feldman MW, Kalaydjieva L (2004) The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am J Hum Genet 74:50–61