Population genetic structure in indian austroasiatic speakers: The role of landscape barriers and sex-specific admixture

Molecular Biology and Evolution

Volumn 28, Issue 2, 2011, Pages 1013-1024

  Chaubey, Gyaneshwer ^a   Metspalu, Mait ^a   Choi, Ying ^b   Mägi, Reedik ^a,c   Romero, Irene Gallego ^d   Soares, Pedro ^e   Van Oven, Mannis ^b   Behar, Doron M ^a,f   Rootsi, Siiri ^a   Hudjashov, Georgi ^a   Mallick, Chandana Basu ^a   Karmin, Monika ^a   Nelis, Mari ^a,j   Parik, Jüri ^a   Reddy, Alla Goverdhana ^g   Metspalu, Ene ^a   Van Driem, George ^h   Xue, Yali ⁱ   Tyler Smith, Chris ⁱ   Thangaraj, Kumarasamy ^g   Singh, Lalji ^g   Remm, Maido ^a   Richards, Martin B ^e   Lahr, Marta Mirazon ^d   Kayser, Manfred ^b   Villems, Richard ^a   Kivisild, Toomas ^a,d   more..

^a UNIVERSITY OF TARTU   (Estonia)

^b ERASMUS MEDICAL CENTER   (Netherlands)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e UNIVERSITY OF LEEDS   (United Kingdom)

^f Molecular Medicine Laboratory   (Israel)

^g CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

^h UNIVERSITY OF BERN   (Switzerland)

ⁱ WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^j UNIVERSITY OF TARTU   (Estonia)

more..

Author keywords

admixture; Austroasiatic; autosomes; mtDNA; Y chromosome

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; GENETIC VARIABILITY; GENOME; HAPLOTYPE; HUMAN; INDIA; LANDSCAPE; POPULATION; POPULATION GENETIC STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTHEAST ASIA; SPEECH; Y CHROMOSOMAL INHERITANCE;

ASIA, SOUTHEASTERN; CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; EMIGRATION AND IMMIGRATION; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; INDIA; LANGUAGE;

EID: 78751529248     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq288     Document Type: Article

References (53)

1. Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19:1655-1664.
2. Allaby RG, Fuller DQ, Brown TA. 2008. The genetic expectations of a protracted model for the origins of domesticated crops. Proc Natl Acad Sci USA. 105:13982-13986.
3. Ammerman AJ, Cavalli-Sforza LL. 1984. The Neolithic transition and the genetics of populations in Europe. Princeton (NJ): Princeton University Press.
4. Anderson GDS. 2007. The Munda verb: typological perspectives. Berlin: Mouton De Gruyter.
5. Basu A, Mukherjee N, Roy S, et al. (11 co-authors). 2003. Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res. 13:2277-2290.
6. Behar DM, Yunusbayev B, Metspalu M, et al. (21 co-authors). 2010. The genome-wide structure of the Jewish people. Nature 466:238-242.
7. Bellwood PS, editor. 2005. First farmers. London: Wiley-Blackwell.
8. Chakravarti A. 2009. Human genetics: tracing India's invisible threads. Nature 461:487-488.
9. Chandrasekar A, Kumar S, Sreenath J, et al. (20 co-authors). 2009. Updating phylogeny of mitochondrial DNA macrohaplogroup m in India: dispersal of modern human in South Asian corridor. PloS One. 4:e7447.
10. Chaubey G, Karmin M, Metspalu E, et al. (31 co-authors). 2008. Phylogeography of mtDNA haplogroup R7 in the Indian peninsula. BMC Evol Biol. 8:227.
11. Chaubey G, Metspalu M, Karmin M, et al. (14 co-authors). 2008. Language shift by indigenous population: a model genetic study in South Asia. Intern J Hum Genet. 8:41.
12. Chaubey G, Metspalu M, Kivisild T, Villems R. 2007. Peopling of South Asia: investigating the caste-tribe continuum in India. Bioessays 29:91-100.
13. Cockerham CC, Weir BS. 1984. Covariances of relatives stemming from a population undergoing mixed self and random mating. Biometrics 40:157-164.
14. Cordaux R, Weiss G, Saha N, Stoneking M. 2004. The northeast Indian passageway: a barrier or corridor for human migrations? Mol Biol Evol. 21:1525-1533.
15. Diamond J, Bellwood P. 2003. Farmers and their languages: the first expansions. Science 300:597-603.
16. Diffloth, G. 2001. "Tentative calibration of time depths in Austroasiatic branches." Paper presented at the Colloque Perspective sur la Phylogenie des Langues d'Asoe Orientales at Perigueux, 30 August 2001.
17. Diffloth G. 2009. More on Dvaravati Old Mon. Paper presented at the Fourth International Conference on Austroasiatic Linguistics. Mahidol University: Salaya (India).
18. Ehret C, Keita SOY, Newman P. 2004. The origins of Afroasiatic. Science 306:1680; author reply 1680.
19. Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online. 1:47-50.
20. Fujimoto A, Kimura R, Ohashi J, et al. (14 co-authors). 2008. A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. Hum Mol Genet. 17:835-843.
21. Fuller D. 2003. An agricultural perspective on Dravidian historical linguistics: archaeological crop packages, livestock and Dravidian crop vocabulary. In: Bellwood P, Renfrew C, editors. Examining the farming/language dispersal hypothesis. Cambridge: The McDonald Institute for Archaeological Research. p. 191-214.
22. Fuller D. 2007. Non-Human Genetics, Agricultural Origins and Historical Linguistics in South Asia. In: Petraglia M, Allchin B, editors. Vertebrate Paleobiology and Paleoanthropology. The Netherlands: Springer. p. 393-443.
23. Fuller DQ, Qin L, Zheng Y, Zhao Z, Chen X, Hosoya LA, Sun GP. 2009. The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze. Science 323:1607-1610.
24. Handley LJL, Manica A, Goudet J, Balloux F. 2007. Going the distance: human population genetics in a clinal world. Trends Genet. 23:432-439.
25. Higham C. 2003. Languages and farming dispersals: austroasiatic languages and rice cultivation. In: Bellwood P, Renfrew C, editors. Examining the farming/language dispersal hypothesis. Cambridge: The McDonald Institute for Archaeological Research. p. 223-233.
26. Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX. 2008. Genetic control of rice plant architecture under domestication. Nat Genet. 40:1365-1369.
27. 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.
28. Kivisild T, Rootsi S, Metspalu M, Metspalu E, Parik J, Kaldama K, Usanga E, Mastana S, Papiha SS, Villems R. 2003. The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet. 72:313-332.
29. Kumar V, Langstieh BT, Madhavi KV, Naidu VM, Singh HP, Biswas S, Thangaraj K, Singh L, Reddy BM. 2006. Global patterns in human mitochondrial DNA and Y-chromosome variation caused by spatial instability of the local cultural processes. PLoS Genet. 2:e53.
30. Kumar V, Reddy ANS, Babu JP, Rao TN, Langstieh BT, Thangaraj K, Reddy AG, Singh L, Reddy BM. 2007. Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations. BMC Evol Biol. 7:47.
31. Lewis MP, editor. 2009. Ethnologue: languages of the world. Dallas (TX): SIL International. [Internet; cited 2010 Sep]. Available from: http://www.ethnologue.com/.
32. Li JZ, Absher DM, Tang H, et al. (10 co-authors). 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319:1100-1104.
33. Metspalu M, Kivisild T, Metspalu E, et al. (16 co-authors). 2004. Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet. 5:26.
34. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
35. Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genet. 2:e190.
36. Purcell S, Neale B, Todd-Brown K, et al. (11 co-authors). 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 81:559-575.
37. Purugganan MD, Fuller DQ. 2009. The nature of selection during plant domestication. Nature 457:843-848.
38. Ramachandran S, Deshpande O, Roseman C, Rosenberg N, Feldman M, Cavalli-Sforza L. 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. 102:15942.
39. Reddy BM, Langstieh BT, Kumar V, Nagaraja T, Reddy ANS, Meka A, Reddy AG, Thangaraj K, Singh L. 2007. Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia. PLoS One. 2:e1141.
40. Richards M, Macaulay V, Hickey E, et al. (36 co-authors). 2000. Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet. 67:1251-76.
41. Rootsi S, Zhivotovsky LA, Baldovic M, et al. (20 co-authors). 2007. A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe. Eur J Hum Genet. 15:204-211.
42. Sabeti PC, Varilly P, Fry B, et al. (99 co-authors). 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449:913-918.
43. Sahoo S, Singh A, Himabindu G, et al. (11 co-authors). 2006. A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. Proc Natl Acad Sci USA. 103:843-848.
44. Sengupta S, Zhivotovsky LA, King R, et al. (14 co-authors). 2006. Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet. 78:202-221.
45. Shi H, Dong YL, Wen B, Xiao CJ, Underhill PA, Shen PD, Chakraborty R, Jin L, Su B. 2005. Y-chromosome evidence of southern origin of the East Asian-specific haplogroup O3-M122. Am J Hum Genet. 77:408-419.
46. Tan L, Li X, Liu F, et al. (10 co-authors). 2008. Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet. 40:1360-1364.
47. Tang H, Peng J, Wang P, Risch NJ. 2005. Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol. 28:289-301.
48. Thangaraj K, Nandan A, Sharma V, et al. (11 co-authors). 2009. Deep rooting in-situ expansion of mtDNA Haplogroup R8 in South Asia. PloS One. 4:e6545.
49. Thangaraj K, Sridhar V, Kivisild T, et al. (20 co-authors). 2005. Different population histories of the Mundari- and Mon-Khmer-speaking Austro-Asiatic tribes inferred from the mtDNA 9-bp deletion/insertion polymorphism in Indian populations. Hum Genet. 116:507-517.
50. Weiss KM, Long JC. 2009. Non-Darwinian estimation: my ancestors, my genes' ancestors. Genome Res. 19:703-710.
51. Wright S. 1943. Isolation by distance. Genetics 28:114-138.
52. Xue Y, Zhang X, Huang N, et al. (14 co-authors). 2009. Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation. Genetics 183:1065-1077.
53. Zhivotovsky LA, Underhill PA, Cinnioglu C, et al. (16 co-authors). 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.