A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations

Molecular Biology and Evolution

Volumn 27, Issue 2, 2010, Pages 385-393

  Shi, Wentao ^a,b   Ayub, Qasim ^a   Vermeulen, Mark ^c   Shao, Rong Guang ^b   Zuniga, Sofia ^d   Van Der Gaag, Kristiaan ^d   De Knijff, Peter ^d   Kayser, Manfred ^c   Xue, Yali ^a   Tyler Smith, Chris ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b INSTITUTE OF MEDICINAL BIOTECHNOLOGY   (China)

^c ERASMUS MEDICAL CENTER   (Netherlands)

^d LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

BATWING; HGDP CEPH; Male demographic history; Serial founder model; Y SNP; Y STR

Indexed keywords

AFRICA; ARTICLE; ASIA; BAYES THEOREM; DEMOGRAPHY; EUROPE; GENE MAPPING; GENETIC VARIABILITY; GROWTH RATE; HEALTH SURVEY; HISTORY; HUMAN; HUMAN EXPERIMENT; HUMAN GENOME PROJECT; MALE; PAKISTAN; PHYLOGENETIC TREE; POPULATION SIZE; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; WESTERN HEMISPHERE;

AFRICA, NORTHERN; CHROMOSOMES, HUMAN, Y; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HUMANS; MALE; MICROSATELLITE REPEATS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 74549133571     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp243     Document Type: Article

References (40)

1. Atkinson QD, Gray RD, Drummond AJ. 2008. mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory. Mol Biol Evol. 25:468-474.
2. Bandelt HJ, Forster P, Sykes BC, Richards MB. 1995. Mitochondrial portraits of human populations using median networks. Genetics 141:743-753.
3. Behar DM, Villems R, Soodyall H, et al. (16 co-authors). 2008. The dawn of human matrilineal diversity. Am J Hum Genet. 82:1130-1140.
4. Berniell-Lee G, Calafell F, Bosch E, Heyer E, Sica L, Mouguiama-Daouda P, van der Veen L, Hombert JM, Quintana-Murci L, Comas D. 2009. Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages. Mol Biol Evol. 26:1581-1589.
5. Cann HM, de Toma C, Cazes L, et al. (41 co-authors). 2002. A human genome diversity cell line panel. Science 296:261-262.
6. Cavalli-Sforza LL 2007. Human evolution and its relevance for genetic epidemiology. Annu Rev Genomics Hum Genet. 8:1-15.
7. Cavalli-Sforza LL, Menozzi P, Piazza A 1994. The history and geography of human genes. Princeton (NJ): Princeton University Press. Decker AE, Kline MC, Redman JW, Reid TM, Butler JM. 2008. Analysis of mutations in father-son pairs with 17 Y-STR loci. Forensic Sci Int Genet. 2:e31-e35.
8. Dupuy BM, Stenersen M, Egeland T, Olaisen B. 2004. Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci. Hum Mutat. 23: 117-124.
9. Goedbloed M, Vermeulen M, Fang RN, et al. (17 co-authors). 2009. Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTR® Yfiler® PCR amplification kit. IntJ Legal Med. 123:471-482.
10. Gusmao L, Sanchez-Diz P, Calafell F, et al. (42 co-authors). 2005. Mutation rates at Y chromosome specific microsatellites. Hum Mutat. 26:520-528.
11. Hellenthal G, Auton, Falush D. 2008. Inferring human colonization history using a copying model. PLoS Genet. 4:e1000078.
12. Jakobsson M, Scholz SW, Scheet P, et al. (24 co-authors). 2008. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998-1003.
13. Jobling MA, Hurles ME, Tyler-Smith C. 2004. Human evolutionary genetics. New York and Abingdon. Garland Science
14. Jobling MA, Tyler-Smith C. 2003. The human Y chromosome: an evolutionary marker comes of age. Nat Rev Genet. 4:598-612.
15. Kayser M, Kittler R, Erler A, et al. (12 co-authors). 2004. A comprehensive survey of human Y-chromosomal microsatel-lites. Am J Hum Genet. 74:1183-1197.
16. Kim SH, Kim NY, Kim KS, Kim JJ, Park JT, Chung KW, Han MS, Kim W. 2009. Population genetics and mutational events at 6 Y-STRs in Korean population. Forensic Sci Int Genet. 3:e53-e54.
17. Lee HY, Park MJ, Chung U, Lee HY, Yang WI, Cho SH, Shin KJ. 2007. Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father-son pairs. Int J Legal Med. 121:128-135.
18. Li JZ, Absher DM, Tang H, et al. (11 co-authors). 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319:1100-1104.
19. Lim SK, Xue Y, Parkin EJ, Tyler-Smith C. 2007. Variation of 52 new Y-STR loci in the Y Chromosome Consortium worldwide panel of 76 diverse individuals. Int J Legal Med. 121:124-127.
20. Macpherson JM, Ramachandran S, Diamond L, Feldman MW. 2004. Demographic estimates from Y chromosome microsatellite polymorphisms: analysis of a worldwide sample. Hum Genomics. 1:345-354.
21. Padilla-Gutierrez JR, Valle Y, Quintero-Ramos A, Hernandez G, Rodarte K, Ortiz RO, Olivares N, Rivas F. 2008. Population data and mutation rate of nine Y-STRs in a mestizo Mexican population from Guadalajara, Jalisco, Mexico. Leg Med (Tokyo). 10:319-320.
22. Pakendorf B, Novgorodov IN, Osakovskij VL, Danilova AP, Protod'jakonov AP, Stoneking M. 2006. Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts. Hum Genet. 120:334-353.
23. Pickrell JK, Coop G, Novembre J, et al. (11 co-authors). 2009. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19:826-837.
24. Powell GT, Yang H, Tyler-Smith C, Xue Y. 2007. The population history of the Xibe in northern China: a comparison of autosomal, mtDNA and Y-chromosomal analyses of migration and gene flow. FSI Genetics 1:115-119.
25. Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW. 1999. Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol. 16:1791-1798.
26. Prugnolle F, Manica A, Balloux F. 2005. Geography predicts neutral genetic diversity of human populations. Curr Biol. 15:R159-R160.
27. Rosenberg NA. 2006. Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet. 70:841-847.
28. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. 2002. Genetic structure of human populations. Science 298:2381-2385.
29. Sanchez JJ, Borsting C, Hallenberg C, Buchard A, Hernandez A, Morling N. 2003. Multiplex PCR and minisequencing of SNPs\-a model with 35 Y chromosome SNPs. Forensic Sci Int. 137:74-84.
30. Shi MS, Tang JP, Bai RF, Yu XJ, Lv JY, Hu B. 2007. Haplotypes of 20 Y-chromosomal STRs in a population sample from southeast China (Chaoshan area). Int J Legal Med. 121:455-462.
31. Toscanini U, Gusmao L, Berardi G, Amorim A, Carracedo A, Salas A, Raimondi E. 2008. Y chromosome microsatellite genetic variation in two Native American populations from Argentina: population stratification and mutation data. Forensic Sci Int Genet. 2:274-280.
32. Vermeulen M, Wollstein A, Gaag Kvd, et al. (11 co-authors). 2009. Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms. Forensic Sci Int Genet. 3:205-213.
33. Weale ME, Yepiskoposyan L, Jager RF, Hovhannisyan N, Khudoyan A, Burbage-Hall O, Bradman N, Thomas MG. 2001. Armenian Y chromosome haplotypes reveal strong regional structure within a single ethno-national group. Hum Genet. 109:659-674.
34. Wilson IJ, Weale ME, Balding DJ. 2003. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. J R Stat Soc Series A (Stat Soc). 166: 155-188.
35. Xue Y, Daly A, Yngvadottir B, et al. (14 co-authors). 2006. Spread of an inactive form of caspase-12 in humans is due to recent positive selection. Am J Hum Genet. 78:659-670.
36. Xue Y, Zerjal T, Bao W, et al. (11 co-authors). 2006. Male demography in East Asia: a north-south contrast in human population expansion times. Genetics 172:2431-2439.
37. Xue Y, Zerjal T, Bao W, et al. 2008. (13 co-authors). 2008. Modelling male prehistory in East Asia using BATWING. In: Matsumura S, Forster P, Renfrew C, editors. Simulations, genetics and prehistory: a focus on islands. Cambridge: McDonald Institute. p. 81-90.
38. Zerjal T, Dashnyam B, Pandya A, et al. (18 co-authors). 1997. Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. Am J Hum Genet. 60:1174-1183.
39. Zhivotovsky LA, Rosenberg NA, Feldman MW. 2003. Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet. 72:1171-1186.
40. Zhivotovsky LA, Underhill PA, Cinnioglu C, et al. (17 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.