Molecular Anthropology in the genomic era

Journal of Anthropological Sciences

Volumn 88, Issue , 2010, Pages 93-112

  Destro Bisol, Giovanni ^a,b   Jobling, Mark A ^c   Rocha, Jorge ^d   Novembre, John ^e   Richards, Martin B ^f   Mulligan, Connie ^g   Batini, Chiara ^b   Manni, Franz ^h  

^a Ist Ital di Paleontologia Um   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

^c UNIVERSITY OF LEICESTER   (United Kingdom)

^d UNIVERSITY OF PORTO   (Portugal)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF LEEDS   (United Kingdom)

^g University of Florida   (United States)

^h MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

Author keywords

Genetic variation; Genomics; Human populations; Interdisciplinary approaches

Indexed keywords

AFRICA; ANTHROPOLOGY; ASIA; DEMOGRAPHY; EUROPE; EVOLUTION; GENOMICS; HUMAN; MIGRATION; PROCEDURES; WESTERN HEMISPHERE;

AFRICA; AMERICAS; ANTHROPOLOGY; ASIA; BIOLOGICAL EVOLUTION; DEMOGRAPHY; EMIGRATION AND IMMIGRATION; EUROPE; GENOMICS; HUMANS;

EID: 77953941699     PISSN: 18274765     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (77)

1. Aulchenko Y. S., Struchalin M. V., Belonogova N. M., Axenovich T. I., Weedon M. N., Hofman A., Uitterlinden A. G., Kayser M., Oostra B. A., van Duijn C. M., Janssens A. C. & Borodin P. M. 2009. Predicting human height by Victorian and genomic methods. Eur. J. Hum. Genet., 17:1070-1075.
2. Auton A., Bryc K., Boyko A. R., Lohmueller K. E., Novembre J., Reynolds A., Indap A., Wright M. H., Degenhardt J. D., Gutenkunst R. N., King K. S., Nelson M. R. & Bustamante C. D. 2009. Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res., 19:795-803.
3. Balloux F., Handley L. J., Jombart T., Liu H. & Manica A. 2009. Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. Proc. R. Soc. Lond. B. Sci., 276:3447-3455.
4. Barbujani G. & Goldstein D. B. 2004. Africans and Asians abroad: genetic diversity in Europe. Annu. Rev. Genomics Hum. Genet., 5:119-150.
5. Bellwood P. & Renfrew C. (eds) 2002. Examining the Farming/Language Dispersal Hypothesis. McDonald Institute for Archaeological Research, University of Cambridge, UK.
6. Bonatto S. L. & Salzano F. M. 1997. Diversity and age of the four major mtDNA haplogroups, and their implications for the peopling of the New World. Am. J. Hum. Genet., 61:1413-1423.
7. Bourgeois S., Yotova V., Wang S., Bourtoumieu S., Moreau C., Michalski R., Moisan J. P., Hill K., Hurtado A. M., Ruiz-Linares A. & Labuda D. 2009. X-chromosome lineages and the settlement of the Americas. Am. J. Phys. Anthropol., 140:417-428.
8. Cann H. M., de Toma C., Cazes L., Legrand M. F., Morel V., Piouffre L., Bodmer J., Bodmer W. F., Bonne-Tamir B., Cambon-Thomsen A., Chen Z., Chu J., Carcassi C., Contu L., Du R., Excoffier L., Ferrara G. B., Friedlaender J. S., Groot H., Gurwitz D., Jenkins T., Herrera R. J., Huang X., Kidd J., Kidd K. K., Langaney A., Lin A. A., Mehdi S. Q., Parham P., Piazza A., Pistillo M. P., Qian Y., Shu Q., Xu J., Zhu S., Weber J. L., Greely H. T., Feldman M. W., Thomas G., Dausset J. & Cavalli-Sforza L. L. 2002. A human genome diversity cell line panel. Science, 296:261-262.
9. Cann R. L., Stoneking M. & Wilson A. C. 1987. Mitochondrial DNA and human evolution. Nature, 325:31-36.
10. Cavalli-Sforza L. L. 2005. The Human Genome Diversity Project: past, present and future. Nature Rev. Genet., 6:333-340.
11. Cavalli-Sforza L. L., Menozzi P. & Piazza A. 1994. The history and geography of human genes. Princeton University Press, Princeton, New Jersey.
12. Chaubey G., Metspalu M., Kivisild T. & Villems R. 2006. Peopling of South Asia: investigating the caste-tribe contimuum in India. Bioessays, 29:91-100.
13. Coelho M., Sequeira F., Luiselli D., Beleza S. & Rocha J. 2009. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola. BMC Evol. Biol., 21:9-80.
14. Coop G., Pickrell J. K., Novembre J., Kudaravalli S., Li J., Absher D., Myers R. M., Cavalli-Sforza L. L., Feldman M. W. & Pritchard J. K. 2009. The role of geography in human adaptation. Plos Genet., 5:e1000500.
15. Cruciani F., Santolamazza P., Shen P., Macaulay V., Moral P., Olckers A., Modiano D., Holmes S., Destro-Bisol G., Coia V., Wallace D. C., Oefner P. J., Torroni A., Cavalli-Sforza L. L., Scozzari R. & Underhill P. A. 2002. A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am. J. Hum. Genet., 70:1197-1214.
16. Destro-Bisol G., Donati F., Coia V., Boschi I., Verginelli F., Caglià A., Tofanelli S., Spedini G. & Capelli C. 2004. Variation of female and male lineages in Sub-Saharian populations: the importance of sociocultural factors. Mol. Biol. Evol., 21:1673-1682.
17. Destro-Bisol G., Anagnostou P., Batini C., Battaggia C., Bertoncini S., Bottini A., Caciagli L., Calo C. M., Capelli C., Capocasa M., Castrì L., Ciani G., Coia V., Corrias L., Crivellaro F., Ghiani M. E., Luiselli D., Mela C., Melis A., Montano V., Paoli G., Sanna E., Rufo F., Sazzini M., Taglioli L., Tofanelli S., Useli A., Vona G. & Pettener D. 2008. Italian isolates today: geographic and linguistic factors shaping human biodiversity. J. Anthropol. Sci., 86:179-188.
18. Dillehay T. D. 2008. Probing deeper into first American studies. Proc. Natl. Acad. Sci. U. S. A., 106:971-978.
19. Endicott P. & Ho S. 2008. A Bayesian evaluation of human mitochondrial substitution rates. Am. J. Hum. Genet., 82:895-902.
20. Fagundes N. J. R., Ray N., Beaumont M., Neuenschwander S., Salzano F. M., Bonatto S. L. & Excoffier L. 2007. Statistical evaluation of alternative models of human evolution. Proc. Natl. Acad. Sci. U. S. A., 104:17614-17619.
21. Fagundes N. J. R., Kanitz R., Eckert R., Valls A. C. S., Bogo M. R., Salzano F. M., Smith D. G., Silva W. A. Jr, Zago M. A., Ribeiro-dos-Santos A. K., Santos S. E., Petzl-Erler M. L. & Bonatto S. L. 2008. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am. J. Hum. Genet., 82:583-592.
22. Fix A. G. 2004. Rapid deployment of the five founding Amerind mtNDA haplogroups via coastal and riverine colonization. Am. J. Phys. Anthropol., 128:430-436.
23. Forster P. & Renfrew C. (eds) 2006. Phylogenetic Methods and the Prehistory of Languages. McDonald Institute for Archaeological Research, University of Cambridge, UK.
24. Francois O., Currat M., Ray N., Han E., Excoffier L. & Novembre, J. 2009. Principal component analysis under population genetic models of range expansion and admixture (under review).
25. Garagnani P., Laayouni H., González-Neira A., Sikora M., Luiselli D., Bertranpetit J. & Calafell F. Isolated populations as treasure troves in genetic epidemiology: the case of the Basques. Eur. J. Hum Genet., 17:1490-1494.
26. Gutenkunst R. N., Hernandez R. D., Williamson S. H. & Bustamante C. D. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. Plos Genet., 5:e1000695.
27. Hammer M. F., Mendez F. L., Cox M. P., Woerner A. E. & Wall J. D. 2008. Sex-biased evolutionary forces shape genomic patterns of human diversity. Plos Genet., 4:e1000202.
28. Handley L. J., Manica A., Goudet J. & Balloux F. 2007. Going the distance: human population genetics in a clinal world. Trends Genet., 23:432-439.
29. Heath S. C., Gut I. G., Brennan P., McKay J. D., Bencko V., Fabianova E., Foretova L., Georges M., Janout V., Kabesch M., Krokan H. E., Elvestad M. B., Lissowska J., Mates D., Rudnai P., Skorpen F., Schreiber S., Soria J. M., Syvänen A., Meneton P., Herçberg S., Galan P., Szeszenia-Dabrowska N., Zaridze D., Génin E., Cardon L. R. & Lathrop M. 2008. Investigation of the fine structure of European populations with applications to disease association studies. Eur. J. Hum. Genet., 16:1413-1429.
30. Ilkilic I. & Paul. N. W. 2009. Ethical aspects of genome diversity research: genome research into cultural diversity or cultural diversity in genome research? Med. Health Care Philos., 12:25-34.
31. International HapMap Consortium 2003. The International HapMap Project. Nature, 426:789-796.
32. Jobling M., Hurles M & Tyler Smith C. 2004. Human Evolutionary Genetics: Origins, Peoples and Disease. Garland Science Publishing, New York.
33. Kimura R., Yamaguchi T., Takeda M., Kondo O., Toma T., Haneji K., Hanihara T., Matsukusa H., Kawamura S., Maki K., Osawa M., Ishida H. & Oota H. 2009. A common variation in EDAR is a genetic determinant of shovel-shaped incisors. Am. J. Hum. Genet., 85:528-535.
34. King T. E. & Jobling M. A. 2009. What's in a name? Y chromosomes, surnames and the genetic genealogy revolution. Trends Genet., 25:351-360.
35. Kitchen D., Miyamoto M. M. & Mulligan C. J. 2008. A three-stage colonization model for the peopling of the Americas, Plos One, 2:e1596.
36. Laayouni H., Calafell F., Bertranpetit J. 2010. A genome-wide survey does not show the genetic distinctiveness of Basques. Hum Genet., 127:455-458.
37. Lao O., Lu T. T., Nothnagel M., Junge O., Freitag-Wolf S., Caliebe A., Balascakova M., Bertranpetit J., Bindoff L. A., Comas D., Holmlund G., Kouvatsi A., Macek M., Mollet I., Parson W., Palo J., Ploski R., Sajantila A., Tagliabracci A., Gether U., Werge T., Rivadeneira F., Hofman A., Uitterlinden A. G., Gieger C., Wichmann H. E., Rüther A., Schreiber S., Becker C., Nürnberg P., Nelson M. R., Krawczak M. & Kayser M. 2008. Correlation between genetic and geographic structure in Europe. Curr. Biol., 18:1241-1248.
38. Macaulay V., Hill C., Achilli A., Rengo C., Clarke D., Meehan W., Blackburn J., Semino O., Scozzari R., Cruciani F., Taha A., Shaari N. K., Raja J. M., Ismail P., Zainuddin Z. A., Goodwin W., Bulbeck D., Bandelt H.-J., Oppenheimer S., Torroni A. & Richards M. 2005. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science, 308:1034-1036.
39. Manolio T. A., Collins F. S., Cox N. J., Goldstein D. B., Hindorff L. A., Hunter D. J., McCarthy M. I., Ramos E. M., Cardon L. R., Chakravarti A., Cho J. H., Guttmacher A. E., Kong A., Kruglyak L., Mardis E., Rotimi C. N., Slatkin M., Valle D., Whittemore A. S., Boehnke M., Clark A. G., Eichler E. E., Gibson G., Haines J. L., Mackay T. F., McCarroll S. A. & Visscher P. M. 2009. Finding the missing heritability of complex diseases. Nature, 461:747-753.
40. McVean G. 2009. A genealogical interpretation of principal components analysis. Plos Genet., 5:e1000686.
41. Mellars P. 2006. Going East: New genetic and archaeological perspectives on the modern human colonization of Eurasia. Science, 313:796-800.
42. Menozzi P., Piazza A., Cavalli-Sforza L. 1978. Synthetic maps of human gene frequencies in Europeans. Science, 201:786-792.
43. Metspalu M., Kivisild T., Bandelt H. J., Richards M. & Villems R. 2006. The pioneer settlement of modern humans in Asia. In H. J. Bandelt, V. Macaulay & M. Richards (eds): Human mitochondrial DNA and the evolution of Homo sapiens, pp 181-199. Springer, Berlin.
44. Migliano A. B., Vinicius L. & Lahr M. M. 2007. Life history trade-offs explain the evolution of human pygmies. Proc. Natl. Acad. Sci. U. S. A., 104:20216-20219.
45. Mulligan C. J., Hunley K., Cole S., Long J. C. 2004. Population genetics, history, and health patterns in native Americans. Annu. Rev. Genom. Hum. Genet., 5:295-315.
46. Mulligan C. J., Kitchen A. & Miyamoto M. M. 2008. Updated three-stage model for the peopling of the Americas. Plos One, 3: e3199.
47. Need A. C. & Goldstein D. B. 2009. Next generation disparities in human genomics: concerns and remedies. Trends Genet., 25:489-494.
48. Nelson M. R., Bryc K., King K. S., Indap A., Boyko A. R., Novembre J., Briley L. P., Maruyama Y., Waterworth D. M., Waeber G., Vollenweider P., Oksenberg J. R., Hauser S. L., Stirnadel H. A., Kooner J. S., Chambers J. C., Jones B., Mooser V., Bustamante C. D., Roses A. D., Burns D. K., Ehm M. G. & Lai E. H. 2008. The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am. J. Hum. Genet., 83:347-358.
49. Novembre J., Johnson T., Bryc K., Kutalik Z., Boyko A. R., Auton A., Indap A., King K. S., Bergmann S., Nelson M. R., Stephens M. & Bustamante C. D. 2008. Genes mirror geography within Europe. Nature, 456:98-101.
50. Novembre J. & Stephens M. 2008. Interpreting principal component analyses of spatial population genetic variation. Nature Genet., 40:646-649.
51. Patin E., Laval G., Barreiro L. B., Salas A., Semino O., Santachiara-Benerecetti S., Kidd K. K., Kidd J. R., Van der Veen L., Hombert J. M., Gessain A., Froment A., Bahuchet S., Heyer E. & Quintana-Murci L. 2009. Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set. Plos Genet., 4:e1000448.
52. Perego U. A., Achilli A., Angerhofer N., Accetturo M., Pala M., Olivieri A., Kashani B. H., Ritchie K. H., Scozzari R., Kong Q. P., Myres N. M., Salas A., Semino O., Bandelt H. J., Woodward S. R. & Torroni A. 2009. Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr. Biol., 19:1-8.
53. Price A. L., Patterson N. J., Plenge R. M., Weinblatt M. E., Shadick N. A. & Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nature Genet., 38:904-909.
54. Ramachandran S., Deshpande O., Roseman C. C., Rosenberg N. A., Feldman M. W. & Cavalli-Sforza L. 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. U. S. A., 102:15942-15947.
55. Relethford J. H. 1998. Genetics of modern human origins and diversity. Annu. Rev. Anthropol., 27:1-23.
56. Renfrew C. & Boyle K. (eds) 2000. Archaeogenetics: DNA and the Population Prehistory of Europe. McDonald Institute for Archaeological Research, University of Cambridge, UK.
57. Richards M., Bandelt H. J., Kivisild T. & Oppenheimer S. 2006. A model for the dispersal of modern humans out of Africa. In H. J. Bandelt, V. Macaulay & M. Richards (eds): Human mitochondrial DNA and the evolution of Homo sapiens, pp. 225-265. Springer, Berlin.
58. Rosenberg N. A., Mahajan S., Gonzalez-Quevedo C., Blum M. G., Nino-Rosales L., Ninis V., Das P., Hegde M., Molinari L., Zapata G., Weber J. L., Belmont J. W. & Patel P. I. 2006. Low levels of genetic divergence across geographically and linguistically diverse populations from India. Plos Genet., 2: e215.
59. Sabatti C., Service S. K., Hartikainen A. L., Pouta A., Ripatti S., Brodsky J., Jones C. G., Zaitlen N. A., Varilo T., Kaakinen M., Sovio U., Ruokonen A., Laitinen J., Jakkula E., Coin L., Hoggart C., Collins A., Turunen H., Gabriel S., Elliot P., McCarthy M. I., Daly M. J., Järvelin M. R., Freimer N. B. & Peltonen L. 2009. Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. Nature Genet., 41:35-46.
60. Salas A., Richards M., De la Fe T., Lareu M. V., Sobrino B., Sanchez-Diz P., Macaulay V. & Carracedo A. 2002. The making of the African mtDNA landscape. Am. J. Hum. Genet., 71:1082-1111.
61. Samuels D. C., Burn D. J. & Chinnery P. F. 2009. Detecting new neurodegenerative disease genes: does phenotype accuracy limit the horizon? Trends Genet., 25:486-488.
62. Schuster S. C., Miller W., Ratan A., Tomsho L. P., Giardine B., Kasson L. R., Harris R. S., Petersen D. C., Zhao F., Qi J., Alkan C., Kidd J. M., Sun Y., Drautz D. I., Bouffard P., Muzny D. M., Reid J. G., Nazareth L. V., Wang Q., Burhans R., Riemer C., Wittekindt N. E., Moorjani P., Tindall E. A., Danko C. G., Teo W. S., Buboltz A. M., Zhang Z., Ma Q., Oosthuysen A., Steenkamp A. W., Oostuisen H., Venter P., Gajewski J., Zhang Y., Pugh B. F., Makova K. D., Nekrutenko A., Mardis E. R., Patterson N., Pringle T. H., Chiaromonte F., Mullikin J. C., Eichler E. E., Hardison R. C., Gibbs R. A., Harkins T. T. & Hayes V. M. 2010. Complete Khoisan and Bantu genomes from southern Africa. Nature, 463:943-947
63. Soares P., Ermini L., Thomson N., Mormina M., Rito T., Röhl A., Salas A., Oppenheimer S., Macaulay V. & Richards M. B. 2009. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am. J. Hum. Genet., 84:740-759.
64. Soares P., Trejaut J. A., Loo J.-H., Hill C., Mormina M., Lee C. L., Chen Y. M., Hudjashov G., Forster P., Macaulay V., Bulbeck D., Oppenheimer S., Lin M. & Richards M. B. 2008. Climate change and post-glacial human dispersals in Southeast Asia. Mol Biol. Evol., 25:1209-1218.
65. Sommer M. 2008. History in the gene: Negotiations Between Molecular and organismal anthropology. J. Hist. Biol., 41:473-528
66. Stringer C. & Andrews P. 1998. Genetic and fossil evidence for the origin of modern humans. Science, 239:1263-1268.
67. Sun C., Kong Q. P., Palanichamy M. G., Agrawal S., Bandelt H. J., Yao Y. G., Khan F., Zhu C. L., K. Chaudhuri T. & Zhang Y. P. 2006. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Mol. Biol. Evol., 23:683-690.
68. Tamm E., Kivisild T., Reidla M., Metspalu M., Smith D. G., Mulligan C. J., Bravi C. M., Rickards O., Martinez-Labarga C., Khusnutdinova E. K., Fedorova S. A., Golubenko M. V., Stepanov V. A., Gubina M. A., Zhadanov S. I., Ossipova L. P., Damba L., Voevoda M. I., Dipierri J. E., Villems R. & Malhi R. S. 2007. Beringian standstill and spread of Native American founders. Plos One, 2: e829.
69. Templeton A. R. 1992. Human origins and analysis of mitochondrial DNA sequences. Science, 255:737.
70. Terwilliger J. D. & Lee J. H. 2007. Natural experiments in human gene mapping: the intersection of anthropological genetics and genetic epidemiology. In Crawford M. H. (ed): Anthropological Genetics: theory, methods and applications, pp 38-76. Cambridge University Press, Cambridge.
71. Tishkoff S. A., Reed F. A., Friedlaender F. R., Ehret C., Ranciaro A., Froment A., Hirbo J. B., Awomoyi A. A., Bodo J. M., Doumbo O., Ibrahim M., Juma A. T., Kotze M. J., Lema G., Moore J. H., Mortensen H., Nyambo T. B., Omar S. A., Powell K., Pretorius G. S., Smith M. W., Thera M. A., Wambebe C., Weber J. L. & Williams S. M. 2009. The genetic structure and history of Africans and African Americans. Science, 22:1035-1044.
72. Verdu P., Austerlitz F., Estoup A., Vitalis R., Georges M., Théry S., Froment A., Le Bomin S., Gessain A., Hombert J. M., Van der Veen L., Quintana-Murci L., Bahuchet S. & Heyer E. 2009. Origins and genetic diversity of pygmy hunter-gatherers from Western Central Africa. Curr. Biol., 19:312-318.
73. Via M., Gignoux C. & Burchard E. G. 2010. The 1000 Genomes Project: new opportunities for research and social challenges. Genome Med., 2:3.
74. Vigilant L., Stoneking M., Harpending H., Hawkes K. & Wilson A. C. 1991. African populations and the evolution of human mitochondrial DNA. Science, 253:1503-1507.
75. Wang S., Lewis C. M., Jakobsson M., Ramachandran S., Ray N., Bedoya G., Rojas W., Parra M. V., Molina J. A., Gallo C., Mazzotti G., Poletti G., Hill K., Hurtado A. M., Labuda D., Klitz W., Barrantes R., Bortolini M. C., Salzano F. M., Petzl-Erler M. L., Tsuneto L. T., Llop E., Rothhammer F., Excoffier L., Feldman M. W., Rosenberg N. A. & Ruiz-Linares A. 2007. Genetic variation and population structure in Native Americans. Plos Genet., 3:e185.
76. Wells R. S., Yuldasheva N., Ruzibakiev R., Underhill P. A., Evseeva I., Blue-Smith J., Jin L., Su B., Pitchappan R., Shanmugalakshmi S., Balakrishnan K., Read M., Pearson N. M., Zerja L. T., Webster M. T., Zholoshvili I., Jamarjashvili E., Gambarov S., Nikbin B., Dostiev A., Aknazarov O., Zalloua P., Tsoy I., Kitaev M., Mirrakhimov M., Chariev A. & Bodmer W. F. 2001. The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc. Natl. Acad. Sci. U. S. A., 98:10244-10249.
77. Xue Y., Wang Q., Long Q., Ng B. L., Swerdlow H., Burton J., Skuce C., Taylor R., Abdellah Z., Zhao Y., Asan, MacArthur D. G., Quail M. A., Carter N. P., Yang H. & Tyler-Smith C. 2009. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr. Biol., 19:1453-1457.