Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese

Human Genetics

Volumn 136, Issue 5, 2017, Pages 499-510

  Mondal, Mayukh ^a   Bergström, Anders ^b   Xue, Yali ^b   Calafell, Francesc ^a   Laayouni, Hafid ^a,c   Casals, Ferran ^a   Majumder, Partha P ^d   Tyler Smith, Chris ^b   Bertranpetit, Jaume ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c GiGa   (Spain)

^d NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ANCESTRY GROUP; ANDAMANESE (PEOPLE); ARTICLE; HAPLOGROUP; HAPLOTYPE; HUMAN; INDIA; PHYLOGENY; POPULATION MIGRATION; POPULATION STRUCTURE; PRIORITY JOURNAL; Y CHROMOSOME; CAUCASIAN; DNA SEQUENCE; GENETIC DATABASE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOMES, HUMAN, Y; DATABASES, GENETIC; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETICS, POPULATION; GENOME, HUMAN; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDIA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 85018239165     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-017-1800-0     Document Type: Article

References (50)

1. Aghakhanian F, Yunus Y, Naidu R et al (2015) Unravelling the genetic history of Negritos and Indigenous populations of Southeast Asia. Genome Biol Evol 7:1206–1215. doi:10.1093/gbe/evv065
2. ArunKumar G, Soria-Hernanz DF, Kavitha VJ et al (2012) Population differentiation of southern indian male lineages correlates with agricultural expansions predating the caste system. PLoS ONE. doi:10.1371/journal.pone.0050269
3. Barbujani G, Bertorelle G, Chikhi L (1998) Evidence for Paleolithic and Neolithic gene flow in Europe. Am J Hum Genet 62:488–492. doi:10.1086/301719
4. Basu A, Mukherjee N, Roy S et al (2003) Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res 13:2277–2290. doi:10.1101/gr.1413403
5. Basu A, Sarkar-Roy N, Majumder PP (2015) Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. PNAS 113:201513197. doi:10.1073/pnas.1513197113
6. Batini C, Hallast P, Zadik D et al (2015) Large-scale recent expansion of European patrilineages shown by population resequencing. Nat Commun Commun. doi:10.1038/ncomms8152
7. Carvalho-Silva DR, Zerjal T, Tyler-Smith C (2006) Ancient Indian roots? J Biosci 31:1–2. doi:10.1007/BF02705228
8. Chaubey G, Endicott P (2013) The Andaman Islanders in a Regional Genetic Context: Reexamining the Evidence for an Early Peopling of the Archipelago from South Asia. Hum. Biol. 85
9. Cordaux R, Aunger R, Bentley G et al (2004) Independent origins of indian caste and tribal paternal lineages. Curr Biol 14:231–235. doi:10.1016/S0960-9822(04)00040-5
10. Danecek P, Auton A, Abecasis G et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158. doi:10.1093/bioinformatics/btr330
11. Fu Q, Li H, Moorjani P et al (2014) Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514:445–449. doi:10.1038/nature13810
12. Gayden T, Cadenas AM, Regueiro M et al (2007) The Himalayas as a directional barrier to gene flow. Am J Hum Genet 80:884–894. doi:10.1086/516757
13. Haak W, Lazaridis I, Patterson N et al (2015) Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522:207–211. doi:10.1038/nature14317
14. Hallast P, Batini C, Zadik D et al (2014) The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol Biol Evol 32:661–673. doi:10.1093/molbev/msu327
15. Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337–338. doi:10.1093/bioinformatics/18.2.337
16. Jobling MA, Tyler-Smith C (2003) The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet 4:598–612. doi:10.1038/nrg1124
17. Juyal G, Mondal M, Luisi P et al (2014) Population and genomic lessons from genetic analysis of two Indian populations. Hum Genet 133:1273–1287. doi:10.1007/s00439-014-1462-0
18. Karmin M, Saag L, Vicente M et al (2015) A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res 25:459–466. doi:10.1101/gr.186684.114
19. Kivisild T, Rootsi S, Metspalu M et al (2003) The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 72:313–332. doi:10.1086/346068
20. Lazaridis I, Nadel D, Rollefson G et al (2016) Genomic insights into the origin of farming in the ancient Near East. Nature 536:1–22. doi:10.1038/nature19310
21. Letunic I, Bork P (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39:W475–W478. doi:10.1093/nar/gkr201
22. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079. doi:10.1093/bioinformatics/btp352
23. Lischer HEL, Excoffier L (2012) PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28:298–299. doi:10.1093/bioinformatics/btr642
24. Lu D, Lou H, Yuan K, et al (2016) Ancestral origins and genetic history of Tibetan Highlanders. 1–15. doi:10.1016/j.ajhg.2016.07.002
25. McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. doi:10.1101/gr.107524.110
26. Metspalu M, Kivisild T, Metspalu E et al (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. doi:10.1186/1471-2156-5-26
27. Metspalu M, Romero IG, Yunusbayev B et al (2011) Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. Am J Hum Genet 89:731–744. doi:10.1016/j.ajhg.2011.11.010
28. Mondal M, Casals F, Xu T et al (2016) Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat Genet 48:1066–1070. doi:10.1038/ng.3621
29. Moorjani P, Thangaraj K, Patterson N et al (2013) Genetic evidence for recent population mixture in India. Am J Hum Genet 93:422–438. doi:10.1016/j.ajhg.2013.07.006
30. Ning C, Yan S, Hu K et al (2016) Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134. Eur J Hum Genet 24:307–309. doi:10.1038/ejhg.2015.183
31. Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290. doi:10.1093/bioinformatics/btg412
32. Patterson N, Moorjani P, Luo Y et al (2012) Ancient admixture in human history. Genetics 192:1065–1093. doi:10.1534/genetics.112.145037
33. Poznik GD, Henn BM, Yee M-C et al (2013) Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341:562–565. doi:10.1126/science.1237619
34. Poznik GD, Xue Y, Mendez FL et al (2016) Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet 12:593–599. doi:10.1038/ng.3559
35. Reich D, Thangaraj K, Patterson N et al (2009) Reconstructing Indian population history. Nature 461:489–494. doi:10.1038/nature08365
36. Sahoo S, Singh A, Himabindu G et al (2006) A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. Proc Natl Acad Sci USA 103:843–848. doi:10.1073/pnas.0507714103
37. Scally A, Durbin R (2012) Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 13:745–753. doi:10.1038/nrg3295
38. Semino O (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: a Y Chromosome perspective. Science 290:1155–1159. doi:10.1126/science.290.5494.1155
39. Sengupta S, Zhivotovsky LA, King R et al (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. doi:10.1086/499411
40. Sherry ST, Ward MH, Kholodov M et al (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311. doi:10.1093/nar/29.1.308
41. Shi H, Zhong H, Peng Y et al (2008) Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biol 6:45. doi:10.1186/1741-7007-6-45
42. Singh S, Singh A, Rajkumar R et al (2016) Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep 6:19157. doi:10.1038/srep19157
43. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. doi:10.1093/bioinformatics/btu033
44. Thangaraj K, Chaubey G, Kivisild T et al (2005) Reconstructing the origin of Andaman Islanders. Science 308:996. doi:10.1126/science.1109987
45. Thangaraj K, Singh L, Reddy AG et al (2003) Genetic Affinities of the Andaman Islanders, a vanishing human population. Curr Biol 13:86–93. doi:10.1016/S0960-9822(02)01336-2
46. Thanseem I, Thangaraj K, Chaubey G et al (2006) Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA. BMC Genet 7:42. doi:10.1186/1471-2156-7-42
47. Thapar R (2014) Can genetics help us understand Indian social history? Cold Spring Harb Perspect Biol 6(11):a008599
48. The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation. Nature 526:68–74. doi:10.1038/nature15393
49. Wei W, Ayub Q, Chen Y et al (2013) A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 23:388–395. doi:10.1101/gr.143198.112
50. Willems T, Gymrek M, Poznik GD et al (2016) Population-scale sequencing data enable precise estimates of Y-STR mutation rates. Am J Hum Genet 98:919–933. doi:10.1016/j.ajhg.2016.04.001