Genetic Basis of Human Biodiversity: An Update

Chapter

Abstract

The massive efforts to study the human genome in detail have produced extraordinary amounts of genetic data. Although we still fail to understand the molecular bases of most complex traits, including many common diseases, we now have a clearer idea of the degree of genetic resemblance between humans and other primate species. We also know that humans are genetically very close to each other, indeed more than any other primates, that most of our genetic diversity is accounted for by individual differences within populations, and that only a small fraction of the species’ genetic variance falls between populations and geographic groups thereof. However, population differences are large enough for patterns to emerge, and these patterns have been extremely useful to reconstruct the history of human migration and to recognise the effects of reproductive isolation. In many cases, crucial information about human demographic history has emerged from multidisciplinary analyses, which have stressed the importance of cultural, as well as geographical, barriers in causing local divergence of populations.

Notes

Acknowledgements

During the development of this paper, VC was supported by a MIUR (Italian Ministry of the Universities and Research) 2007 FIRB grant (The impact of biotechnological innovation of individual rights. An interdisciplinary study.) We thank Kenneth K. Kidd for the idea of Figure 6.3., based on material published at his website: http://info.med.yale.edu/genetics/kkidd/point.html.

References

  1. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C et al (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio ethnic group. Genome Res 19:1622–1629PubMedGoogle Scholar
  2. Auton A, Bryc K, Boyko AR et al (2009) Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res 19:795–803PubMedGoogle Scholar
  3. Barbujani G (2005) Human races: classifying people vs. understanding diversity. Curr Genomics 6:215–226Google Scholar
  4. Barbujani G, Belle EMS (2006) Genomic boundaries between human populations. Hum Hered 61:15–21PubMedGoogle Scholar
  5. Barbujani G, Colonna V (2010) Human genome diversity: frequently asked questions. Trends Genet 26:285–295Google Scholar
  6. Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL (1997) An apportionment of human DNA diversity. Proc Natl Acad Sci USA 94:4516–4519PubMedGoogle Scholar
  7. Barbujani G, Pilastro A (1993) Genetic evidence on origin and dispersal of human populations speaking languages of the Nostratic macrofamily. Proc Natl Acad Sci USA 90:4670–4673PubMedGoogle Scholar
  8. Barbujani G, Sokal RR (1990) Zones of sharp genetic change in Europe are also linguistic boundaries. Proc Natl Acad Sci USA 87:1816–1819PubMedGoogle Scholar
  9. Balaresque PL, Ballereau SJ, Jobling MA (2007) Challenges in human genetic diversity: demographic history and adaptation. Hum Mol Genet 16(2):R134–R139PubMedGoogle Scholar
  10. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L (2008) Natural selection has driven population differentiation in modern humans. Nat Genet 40:340–345PubMedGoogle Scholar
  11. Bastos-Rodrigues L, Pimenta JR, Pena SDJ (2006) The genetic structure of human populations studied through short insertion-deletion polymorphisms. Ann Hum Genet 70:658–665PubMedGoogle Scholar
  12. Belle EMS, Barbujani G (2007) A worldwide analysis of multiple microsatellites suggests that language diversity has a detectable influence on DNA diversity. Am J Phys Anthropol 133:1137–1146PubMedGoogle Scholar
  13. Belle EM, Benazzo A, Ghirotto S, Colonna V, Barbujani G (2009) Comparing models on the genealogical relationships among Neandertal, Cro-Magnoid and modern Europeans by serial coalescent simulations. Heredity 102:218–225PubMedGoogle Scholar
  14. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2010) GenBank. Nucl Acids Res 38:D46–D51PubMedGoogle Scholar
  15. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59PubMedGoogle Scholar
  16. Bernasconi R, Lott TL (2000) The idea of race. Hackett, Indianapolis/CambridgeGoogle Scholar
  17. Biswas S, Scheinfeldt LB, Akey JM (2009) Genome-wide insights into the patterns and determinants of fine-scale population structure in humans. Am J Hum Genet 84:641–645PubMedGoogle Scholar
  18. Brown RA, Armelagos GJ (2001) Apportionment of racial diversity: a review. Evol Anthropol 10:34–40Google Scholar
  19. Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM, Wambebe C, Tishkoff SA, Bustamante CD (2010) Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci USA 107:786–791PubMedGoogle Scholar
  20. Calafell F, Bertranpetit J (1994) Principal component analysis of gene frequencies and the origin of Basques. Am J Phys Anthropol 93:201–215PubMedGoogle Scholar
  21. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A et al (2002) A human genome diversity cell line panel. Science 296:261–262PubMedGoogle Scholar
  22. Cavalli-Sforza LL (1966) Population structure and human evolution. Proc R Soc Lond B Biol Sci 164:362–379PubMedGoogle Scholar
  23. Cavalli-Sforza LL (2005) The Human Genome Diversity Project: past, present and future. Nat Rev Genet 6(4):333–340PubMedGoogle Scholar
  24. Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Am J Hum Genet 19:233–257PubMedGoogle Scholar
  25. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, PrincetonGoogle Scholar
  26. Cavalli-Sforza LL, Piazza A, Menozzi P, Mountain J (1988) Reconstruction of human evolution: bringing together genetic, archaeological, and linguistic data. Proc Natl Acad Sci USA 85:6002–6006PubMedGoogle Scholar
  27. Chen J, Sokal RR, Ruhlen M (1995) Worldwide analysis of genetic and linguistic relationships of human populations. Hum Biol 67:595–612PubMedGoogle Scholar
  28. Chen J, Zheng H, Bei JX, Sun L, Jia WH, Li T, Zhang F, Seielstad M, Zeng YX, Zhang X, Liu J (2009) Genetic structure of the Han Chinese population revealed by genome-wide SNP variation. Am J Hum Genet 85(6):775–785PubMedGoogle Scholar
  29. Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong P, Wilson RK, Pääbo S et al (2005) A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437:88–93PubMedGoogle Scholar
  30. Chikhi L, Destro-Bisol G, Bertorelle G, Pascali V, Barbujani G (1998) Clines of nuclear DNA markers suggest a largely Neolithic ancestry of the European gene pool. Proc Natl Acad Sci USA 95:9053–9058PubMedGoogle Scholar
  31. Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437:69–87Google Scholar
  32. Cohen C (1991) Les races humaines en histoire des sciences. In: Hublin JJ, Tillier AM (eds) Aux origines d’Homo sapiens. Presses Universitaries de France, Paris, pp 9–47Google Scholar
  33. Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, Pritchard JK (2009) The role of geography in human adaptation. PLoS Genet 5:e1000500PubMedGoogle Scholar
  34. Corander J, Waldmann P, Marttinen P, Sillanpää MJ (2004) BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20(15):2363–2369PubMedGoogle Scholar
  35. Cordaux R, Aunger R, Bentley G, Nasidze I, Sirajuddin SM, Stoneking M (2004) Independent origins of Indian caste and tribal paternal lineages. Curr Biol 14:231–235PubMedGoogle Scholar
  36. Currat M, Excoffier L (2004) Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol 2:e421PubMedGoogle Scholar
  37. Darwin CR (1871) Descent of man and selection in relation to sex. John Murray, LondonGoogle Scholar
  38. Degiorgio M, Jakobsson M, Rosenberg NA (2009) Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proc Natl Acad Sci USA 106:16057–16062PubMedGoogle Scholar
  39. de la Chapelle A (1993) Disease gene mapping in isolated human populations: the example of Finland. J Med Genet 30:857–865PubMedGoogle Scholar
  40. Deshpande O, Batzoglou S, Feldman MW, Cavalli-Sforza LL (2009) A serial founder effect model for human settlement out of Africa. Proc Biol Sci 276:291–300PubMedGoogle Scholar
  41. Diamond J, Bellwood P (2003) Farmers and their languages: the first expansions. Science 300:597–603PubMedGoogle Scholar
  42. Dobzhansky T (1967) On types, genotypes, and the genetic diversity in populations. In: Spuhler JN (ed) Genetic diversity and human behavior. Wenner-Gren Foundation for Anthropological Research, New York, pp 1–19Google Scholar
  43. Edwards AWF (2003) Human genetic diversity: Lewontin’s fallacy. Bioessays 25:798–801PubMedGoogle Scholar
  44. Enattah NS, Jensen TG, Nielsen M, Lewinski R, Kuokkanen M, Rasinpera H, El-Shanti H, Seo JK, Alifrangis M, Khalil IF et al (2008) Independent introduction of two lactase-persistence alleles into human populations reflects different history of adaptation to milk culture. Am J Hum Genet 82:57–72PubMedGoogle Scholar
  45. Excoffier L, Hamilton G (2003) Comment on “Genetic structure of human populations”. Science 300:1877PubMedGoogle Scholar
  46. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491PubMedGoogle Scholar
  47. Fagundes NJ, Ray N, Beaumont M, Neuenschwander S, Salzano FM, Bonatto SL, Excoffier L (2007) Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci USA 104:17614–17619PubMedGoogle Scholar
  48. Fischer A, Wiebe V, Pääbo S, Przeworski M (2004) Evidence for a complex demographic history of chimpanzees. Mol Biol Evol 5:799–808Google Scholar
  49. Fischer A, Pollack J, Thalmann O, Nickel B, Paabo S (2006) Demographic history and genetic differentiation in apes. Curr Biol 16:1133–1138PubMedGoogle Scholar
  50. Foley R (1998) The context of human genetic evolution. Genome Res 8:339–347PubMedGoogle Scholar
  51. Frazer KA, Murray SS, Schork NJ, Topol EJ (2009) Human genetic variation and its contribution to complex traits. Nat Rev Genet 10:241–251PubMedGoogle Scholar
  52. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M et al (2002) The structure of haplotype blocks in the human genome. Science 296(5576):2225–2229PubMedGoogle Scholar
  53. Gagneux P, Varki A (2001) Genetic differences between humans and great apes. Mol Phylogenet Evol 18:2–13PubMedGoogle Scholar
  54. Garcia-Bailo B, Toguri C, Eny KM, El-Sohemy A (2009) Genetic variation in taste and its influence on food selection. OMICS 13:69–80PubMedGoogle Scholar
  55. Ghirotto S, Tassi F, Benazzo A, Barbujani G (2011) No evidence of Neandertal admixture in the mitochondrial genomes of early European modern humans and contemporary Europeans. Am J Phys Anthropol (in the press)Google Scholar
  56. Glasgow J (2009) A theory of race. Routledge, New York and LondonGoogle Scholar
  57. Glatt SJ, Chayavichitsilp P, Schork NJ, Jeste DV (2007) Successful aging: from phenotype to genotype. Biol Psychiatry 62:282–293PubMedGoogle Scholar
  58. Goebel T, Waters MR, O'Rourke DH (2008) The late Pleistocene dispersal of modern humans in the Americas. Science 319:1497–1502PubMedGoogle Scholar
  59. Goldman D, Giri PR, O’Brien SJ (1987) A molecular phylogeny of the hominoid primates as indicated by two-dimensional protein electrophoresis. Proc Natl Acad Sci USA 84:3307–3311PubMedGoogle Scholar
  60. Goldstein DB (2009) Common genetic variation and human traits. N Engl J Med 360:1696–1698PubMedGoogle Scholar
  61. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. (2010) A draft sequence of the Neandertal genome. Science 328:710–722Google Scholar
  62. Greenberg JH, Turner CG, Zegura SL (1986) The settlement of the Americas: a comparison of the linguistic, dental and genetic evidence. Curr Anthropol 27:477–497Google Scholar
  63. Harris EE, Meyer D (2006) The molecular signature of selection underlying human adaptations. Am J Phys Anthropol 43:89–130PubMedGoogle Scholar
  64. Heyer E, Balaresque P, Jobling MA, Quintana-Murci L, Chaix R, Segurel L, Aldashev A, Hegay T (2009) Genetic diversity and the emergence of ethnic groups in Central Asia. BMC Genet 10:49PubMedGoogle Scholar
  65. Hofer T, Ray N, Wegmann D, Excoffier L (2009) Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Ann Hum Genet 73:95–108PubMedGoogle Scholar
  66. Hunley KL, Cabana GS, Merriwether DA, Long JC (2007) A formal test of linguistic and genetic coevolution in native Central and South America. Am J Phys Anthropol 132(4):622–631PubMedGoogle Scholar
  67. Hunley KL, Healy ME, Long JC (2009) The global pattern of gene identity variation reveals a history of long-range migrations, bottlenecks, and local mate exchange: implications for biological race. Am J Phys Anthropol 139:35–46PubMedGoogle Scholar
  68. Hunley K, Long JC (2005) Gene flow across linguistic boundaries in native North American populations. Proc Natl Acad Sci USA 102:1312–1317PubMedGoogle Scholar
  69. Indian Genome Variation Consortium (2008) Genetic landscape of the people of India: a canvas for disease gene exploration. J Genet 87:3–20Google Scholar
  70. International Hap Map Consortium (2005) A haplotype map of the human genome. Nature 437:1299–1320Google Scholar
  71. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921Google Scholar
  72. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R et al (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998–1003PubMedGoogle Scholar
  73. Jauch A, Wienberg J, Stanyon R, Arnold N, Tofanelli S, Ishida T, Cremer T (1992) Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting. Proc Natl Acad Sci USA 89:8611–8615PubMedGoogle Scholar
  74. Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA (2000) The distribution of human genetic diversity: a comparison of mitochondrial, autosomal and Y-chromosome data. Am J Hum Genet 66:979–988PubMedGoogle Scholar
  75. Kaessmann H, Wiebe V, Weiss G, Paabo S (2001) Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat Genet 27:155–156PubMedGoogle Scholar
  76. Kehrer-Sawatzki H, Cooper DN (2007) Structural divergence between the human and chimpanzee genomes. Hum Genet 120:759–778PubMedGoogle Scholar
  77. Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ et al (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011–1015PubMedGoogle Scholar
  78. Krause J, Fu Q, Good JM, Viola B, Shunkov MB, Derevianko AP, Pääbo S (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:894–897PubMedGoogle Scholar
  79. Lahr MM, Foley R (1994) Multiple dispersals and modern human origins. Evol Anthropol 3:48–60Google Scholar
  80. Latter BDH (1980) Genetic differences within and between populations of the major human subgroups. Am Nat 116:220–237Google Scholar
  81. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G et al (2007) The diploid genome sequence of an individual human. PLoS Biol 5:e254PubMedGoogle Scholar
  82. Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398Google Scholar
  83. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319:1100–1104PubMedGoogle Scholar
  84. Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, Falush D, Stamer C, Prugnolle F, van der Merwe SW et al (2007) An African origin for the intimate association between humans and Helicobacter pylori. Nature 445:915–918PubMedGoogle Scholar
  85. Liu H, Prugnolle F, Manica A, Balloux F (2006) A geographically explicit genetic model of worldwide human-settlement history. Am J Hum Genet 79:230–237PubMedGoogle Scholar
  86. Livingstone FB (1962) On the nonexistence of human races. Curr Anthropol 3:279–281Google Scholar
  87. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F et al (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034–1036PubMedGoogle Scholar
  88. Madrigal L, Barbujani G (2007) Partitioning of genetic variation in human populations and the concept of race. In: Crawford MH (ed) Anthropological genetics. Theory, methods and applications. Cambridge University Press, Cambridge, pp 19–37Google Scholar
  89. Manica A, Amos W, Balloux F, Hanihara T (2007) The effect of ancient population bottlenecks on human phenotypic variation. Nature 448:346–348PubMedGoogle Scholar
  90. Marques-Bonet T, Girirajan S, Eichler EE (2009a) The origins and impact of primate segmental duplications. Trends Genet 25:443–454PubMedGoogle Scholar
  91. Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, Hillier LW, Jiang Z, Baker C, Malfavon-Borja R, Fulton LA et al (2009b) A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457:877–881PubMedGoogle Scholar
  92. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC et al (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19:1527–1541PubMedGoogle Scholar
  93. Menozzi P, Piazza A, Cavalli-Sforza L (1978) Synthetic maps of human gene frequencies in Europeans. Science 201:786–792PubMedGoogle Scholar
  94. Meyer D, Single RM, Mack SJ, Erlich HA, Thomson G (2006) Signatures of demographic history and natural selection in the human major histocompatibility complex Loci. Genetics 173:2121–2142PubMedGoogle Scholar
  95. Molnar S (1998) Human variation. Races, types, and ethnic groups, 4th edn. Prentice Hall, Upper Saddle River, NJGoogle Scholar
  96. Nettle D, Harriss L (2003) Genetic and linguistic affinities between human populations in Eurasia and West Africa. Hum Biol 75:331–344PubMedGoogle Scholar
  97. Novembre J, Di Rienzo A (2009) Spatial patterns of variation due to natural selection in humans. Nat Rev Genet 10:745–755PubMedGoogle Scholar
  98. O’Connell J, Allen J (2004) Dating the colonization of the Sahul (Pleistocene Australia – New Guinea): a review of recent research. J Archaeol Sci 31:835–853Google Scholar
  99. O’Rourke DH, Suarez BK (1985) Pattern and correlates of genetic variation in South Amerindians. Ann Hum Biol 13:13–32Google Scholar
  100. Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2:e190PubMedGoogle Scholar
  101. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  102. Ragoussis J (2009) Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet 10:117–133PubMedGoogle Scholar
  103. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL (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 102:15942–15947PubMedGoogle Scholar
  104. Ramachandran S, Rosenberg NA, Zhivotovsky LA, Feldman MW (2004) Robustness of the inference of human population structure: a comparison of X-chromosomal and autosomal microsatellites. Hum Genomics 1:87–97PubMedGoogle Scholar
  105. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W et al (2006) Global variation in copy number in the human genome. Nature 444:444–454PubMedGoogle Scholar
  106. Reed FA, Tishkoff SA (2006) African human diversity, origins and migrations. Curr Opin Genet Dev 16:597–605PubMedGoogle Scholar
  107. Reich D, Price AL, Patterson N (2008) Principal component analysis of genetic data. Nat Genet 40(5):491–492PubMedGoogle Scholar
  108. Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461:489–494PubMedGoogle Scholar
  109. Relethford JH (2008) Genetic evidence and the modern human origins debate. Heredity 100:555–563PubMedGoogle Scholar
  110. Romualdi C, Balding D, Nasidze IS, Risch G, Robichaux M, Sherry S, Stoneking M, Batzer M, Barbujani G (2002) Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 12:602–612PubMedGoogle Scholar
  111. Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005) Clines, clusters, and the effects of study design on the inference of human population structure. PloS Genet 6:e70Google Scholar
  112. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298:2381–2385PubMedGoogle Scholar
  113. Rothhammer F, Silva C, Callegari-Jacques SM, Llop E, Salzano FM (1997) Gradients of HLA diversity in South American Indians. Ann Hum Biol 24:197–208PubMedGoogle Scholar
  114. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES (2006) Positive natural selection in the human lineage. Science 312:1614–1620PubMedGoogle Scholar
  115. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J et al (2010) Complete Khoisan and Bantu geomes from Southern Africa. Nature 463:943–947PubMedGoogle Scholar
  116. Semino O, Passarino G, Oefner PJ, Lin AA, Arbuzova S, Beckman LE, De Benedictis G, Francalacci P, Kouvatsi A, Limborska S et al (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. Science 290:1155–1159PubMedGoogle Scholar
  117. Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G (2000) Geographic patterns of mtDNA diversity in Europe. Am J Hum Genet 66:262–278PubMedGoogle Scholar
  118. Soares P, Achilli A, Semino O, Davies W, Macaulay V, Bandelt HJ, Torroni A, Richards MB (2010) The archaeogenetics of Europe. Curr Biol 20:R174–R183PubMedGoogle Scholar
  119. Sokal RR (1988) Genetic, geographic, and linguistic distances in Europe. Proc Natl Acad Sci USA 85:1722–1726PubMedGoogle Scholar
  120. Sokal RR, Oden NL, Legendre P, Fortin MJ, Kim J, Thomson BA, Vaudor A, Harding RM, Barbujani G (1990) Genetics and language in European populations. Am Nat 135:157–175Google Scholar
  121. Sokal RR, Oden NL, Thomson BA (1988) Genetic changes across language boundaries in Europe. Am J Phys Anthropol 76:337–361PubMedGoogle Scholar
  122. Stone AC, Griffiths RC, Zegura SL, Hammer MF (2002) High levels of Y-chromosome nucleotide diversity in the genus Pan. Proc Natl Acad Sci USA 99:43–48PubMedGoogle Scholar
  123. Tang H, Peng J, Wang P, Risch NJ (2005) Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 28(4):289–301PubMedGoogle Scholar
  124. Tattersall I (2009) Out of Africa: modern human origins special feature: human origins. Proc Natl Acad Sci USA 106:16018–16021PubMedGoogle Scholar
  125. Terrell JE, Kelly KM, Rainbird P (2001) Foregone conclusions? In search of “Papuans” and “Austronesians”. Curr Anthropol 42:97–124Google Scholar
  126. Thalmann O, Fischer A, Lankester F, Paabo S, Vigilant L (2007) The complex evolutionary history of gorillas: insights from genomic data. Mol Biol Evol 24:146–158PubMedGoogle Scholar
  127. Thanseem I, Thangaraj K, Chaubey G, Singh VK, Bhaskar LV, Reddy BM, Reddy AG, Singh L (2006) Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA. BMC Genet 7:42PubMedGoogle Scholar
  128. Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo JM, Doumbo O et al (2009) The genetic structure and history of Africans and African Americans. Science 324:1035–1044PubMedGoogle Scholar
  129. Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M et al (2007) Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet 39:31–40PubMedGoogle Scholar
  130. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J et al (2008) The diploid genome sequence of an Asian individual. Nature 456:60–65PubMedGoogle Scholar
  131. Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending HC, Rogers AR, Jorde LB (2001) Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms. Am J Hum Genet 68:738–752PubMedGoogle Scholar
  132. Watkins WS, Thara R, Mowry BJ, Zhang Y, Witherspoon DJ, Tolpinrud W, Bamshad MJ, Tirupati S, Padmavati R, Smith H et al (2008) Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms. BMC Genet 9:86PubMedGoogle Scholar
  133. Watson JD, Jordan E (1989) The Human Genome Program at the National Institutes of Health. Genomics 5:654–656PubMedGoogle Scholar
  134. Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, Mangino M, Freathy RM, Perry JR, Stevens S, Hall AS et al (2008) Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet 40:575–583PubMedGoogle Scholar
  135. Weir BS, Cardon LR, Anderson AD, Nielsen DM, Hill WG (2005) Measures of human population structure show heterogeneity among genomic regions. Genome Res 15:1468–1476PubMedGoogle Scholar
  136. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–876PubMedGoogle Scholar
  137. Witherspoon DJ, Wooding S, Rogers AR, Marchani EE, Watkins WS, Batzer MA, Jorde LB (2007) Genetic similarities within and between human populations. Genetics 176(1):351–359PubMedGoogle Scholar
  138. Wolpoff MH, Hawks J, Frayer DW, Hunley K (2001) Modern human ancestry at the peripheries: a test of the replacement theory. Science 291:293–297PubMedGoogle Scholar
  139. Xing J, Watkins WS, Witherspoon DJ, Zhang Y, Guthery SL, Thara R, Mowry BJ, Bulayeva K, Weiss RB, Jorde LB (2009) Fine-scaled human genetic structure revealed by SNP microarrays. Genome Res 19:815–825PubMedGoogle Scholar
  140. Xu S, Yin X, Li S, Jin W, Lou H, Yang L, Gong X, Wang H, Shen Y, Pan X et al (2009) Genomic dissection of population substructure of Han Chinese and its implication in association studies. Am J Hum Genet 85(6):762–774PubMedGoogle Scholar
  141. Yu N, Chen FC, Ota S, Jorde LB, Pamilo P, Patthy L, Ramsay M, Jenkins T, Shyue SK, Li WH (2002) Larger genetic differences within Africans than between Africans and Eurasians. Genetics 161:269–274PubMedGoogle Scholar
  142. Zerjal T, Pandya A, Thangaraj K, Ling EY, Kearley J, Bertoneri S, Paracchini S, Singh L, Tyler-Smith C (2007) Y-chromosomal insights into the genetic impact of the caste system in India. Hum Genet 121:137–144PubMedGoogle Scholar

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Authors and Affiliations

  1. 1.Department of Biology and EvolutionUniversity of FerraraFerraraItaly
  2. 2.Institute of Genetics and Biophysics “A. Buzzati-Traverso”National Research Council (CNR)NaplesItaly

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