Genome-wide data substantiate Holocene gene flow from India to Australia

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 5, 2013, Pages 1803-1808

  Pugach, Irina ^a   Delfin, Frederick ^a,b   Gunnarsdóttir, Ellen ^a,c   Kayser, Manfred ^d   Stoneking, Mark ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b University of the Philippines Diliman   (Philippines)

^c DECODE GENETICS   (Iceland)

^d ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Admixture time; Human evolution; Population history

Indexed keywords

ABORIGINE; ARTICLE; AUSTRALIA; CORRELATION ANALYSIS; ETHNIC GROUP; GENE FLOW; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HOLOCENE; HUMAN; INDIA; MIGRATION; MOLECULAR PHYLOGENY; PAPUA NEW GUINEA; PHILIPPINES; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTHEAST ASIA; TIME;

AFRICA; ASIAN CONTINENTAL ANCESTRY GROUP; AUSTRALIA; GENE FLOW; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HUMAN MIGRATION; HUMANS; INDIA; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; NEW GUINEA; OCEANIC ANCESTRY GROUP; PHILIPPINES; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; TIME FACTORS;

EID: 84873204283     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1211927110     Document Type: Article

References (50)

1. Ramachandran S, et al. (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci USA 102(44):15942-15947. (Pubitemid 41552847)
2. Liu H, Prugnolle F, Manica A, Balloux F (2006) A geographically explicit genetic model of worldwide human-settlement history. Am J Hum Genet 79(2):230-237. (Pubitemid 44141822)
3. Green RE, et al. (2010) A draft sequence of the Neandertal genome. Science 328(5979):710-722.
4. Reich D, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327):1053-1060.
5. Reich D, et al. (2011) Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet 89(4):516-528.
6. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5(10):e1000695.
7. Rasmussen M, et al. (2011) An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334(6052):94-98.
8. O'Connell J, Allen J (2004) Dating the colonization of Sahul (Pleistocene Australia-New Guinea): A review of recent research. J Archaeol Sci 31(6):835-853.
9. Kayser M (2010) The human genetic history of Oceania: Near and remote views of dispersal. Curr Biol 20(4):R194-R201.
10. Summerhayes GR, et al. (2010) Human adaptation and plant use in highland New Guinea 49, 000 to 44, 000 years ago. Science 330(6000):78-81.
11. Hudjashov G, et al. (2007) Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci USA 104(21):8726-8730. (Pubitemid 47175379)
12. McEvoy BP, et al. (2010) Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry. Am J Hum Genet 87(2):297-305.
13. Redd AJ, Stoneking M (1999) Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations. Am J Hum Genet 65(3):808-828. (Pubitemid 30468727)
14. Redd AJ, et al. (2002) Gene flow from the Indian subcontinent to Australia: Evidence from the Y chromosome. Curr Biol 12(8):673-677. (Pubitemid 34315853)
15. Kumar S, et al. (2009) Reconstructing Indian-Australian phylogenetic link. BMC Evol Biol 9:173.
16. Wollstein A, et al. (2010) Demographic history of Oceania inferred from genomewide data. Curr Biol 20(22):1983-1992.
17. Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461(7263):489-494.
18. Cordaux R, et al. (2003) Mitochondrial DNA analysis reveals diverse histories of tribal populations from India. Eur J Hum Genet 11(3):253-264. (Pubitemid 36519095)
19. Altshuler DM, et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467(7311):52-58.
20. Pugach I, Matveyev R, Wollstein A, Kayser M, Stoneking M (2011) Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol 12(2):R19.
21. Stringer C (2002) Modern human origins: Progress and prospects. Philos Trans R Soc Lond B Biol Sci 357(1420):563-579. (Pubitemid 34489865)
22. Zhivotovsky LA, Rosenberg NA, Feldman MW (2003) Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet 72(5):1171-1186. (Pubitemid 36530005)
23. Delfin F, et al. (2011) The Y-chromosome landscape of the Philippines: Extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. Eur J Hum Genet 19(2):224-230.
24. Tenesa A, et al. (2007) Recent human effective population size estimated from linkage disequilibrium. Genome Res 17(4):520-526. (Pubitemid 46556456)
25. McEvoy BP, Powell JE, Goddard ME, Visscher PM (2011) Human population dispersal "Out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res 21(6):821-829.
26. Jakobsson M, et al. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451(7181):998-1003. (Pubitemid 351301742)
27. Frazer KA, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449(7164):851-861. (Pubitemid 47598626)
28. Hayes BJ, Visscher PM, McPartlan HC, Goddard ME (2003) Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 13(4):635-643. (Pubitemid 36511922)
29. Gunnarsdóttir ED, Li M, Bauchet M, Finstermeier K, Stoneking M (2011) Highthroughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res 21(1):1-11.
30. DeGiorgio M, Jakobsson M, Rosenberg NA (2009) Out of Africa: Modern human origins special feature: Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proc Natl Acad Sci USA 106(38):16057-16062.
31. Plagnol V, Wall JD (2006) Possible ancestral structure in human populations. PLoS Genet 2(7):e105.
32. Moorjani P, et al. (2011) The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet 7(4):e1001373.
33. Moodley Y, et al. (2009) The peopling of the Pacific from a bacterial perspective. Science 323(5913):527-530.
34. Ballantyne KN, et al. (2012) MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Sci Int Genet 6(4):425-436.
35. McVean G (2009) A genealogical interpretation of principal components analysis. PLoS Genet 5(10):e1000686.
36. Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19(9):1655-1664.
37. Bryc K, et al. (2010) Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci USA 107(2):786-791.
38. Tang H, Peng J, Wang P, Risch NJ (2005) Estimation of individual admixture: Analytical and study design considerations. Genet Epidemiol 28(4):289-301. (Pubitemid 40559542)
39. Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8(11):e1002967.
40. Kunsch HR (1989) The jackknife and the bootstrap for general stationary observations. Ann Stat 17(3):1217-1241.
41. Stoneking M, et al. (1997) Alu insertion polymorphisms and human evolution: Evidence for a larger population size in Africa. Genome Res 7(11):1061-1071. (Pubitemid 127491555)
42. Fenner JN (2005) Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am J Phys Anthropol 128(2):415-423. (Pubitemid 41407413)
43. Glover I, Presland G (1985) Microliths in Indonesian flaked stone industries. Recent Advances in Indo-Pacific Prehistory, eds Misra V, Bellwood P (Oxford & IBH, New Dehli, India).
44. Beaton J (1977) Dangerous harvest: Investigations in the late prehistoric occupation of upland south-east central Queensland. PhD thesis (Australian National University, Canberra, Australia).
45. Hiscock P (2008) Archaeology of Ancient Australia (Routledge, London).
46. Gollan K (1985) Prehistoric dogs in Australia: An Indian origin? Recent Advances in Indo-Pacific Prehistory, eds Misra V, Bellwood P (Oxford & IBH, New Dehli, India).
47. Savolainen P, Leitner T, Wilton AN, Matisoo-Smith E, Lundeberg J (2004) A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proc Natl Acad Sci USA 101(33):12387-12390. (Pubitemid 39145453)
48. Eriksson A, Manica A (2012) Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proc Natl Acad Sci USA 109(35):13956-13960.
49. Sankararaman S, Patterson N, Li H, Pääbo S, Reich D (2012) The date of interbreeding between Neandertals and modern humans. PLoS Genet 8(10):e1002947.
50. Purcell S, et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559-575. (Pubitemid 47330214)