Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations

American Journal of Human Genetics

Volumn 99, Issue 6, 2016, Pages 1316-1324

  Haber, Marc ^a   Mezzavilla, Massimo ^a,b   Bergström, Anders ^a   Prado Martinez, Javier ^a   Hallast, Pille ^a,c   Saif Ali, Riyadh ^d   Al Habori, Molham ^d   Dedoussis, George ^e   Zeggini, Eleftheria ^a   Blue Smith, Jason ^f,j   Wells, R Spencer ^g   Xue, Yali ^a   Zalloua, Pierre A ^h,i   Tyler Smith, Chris ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF TRIESTE   (Italy)

^c UNIVERSITY OF TARTU   (Estonia)

^d SANA A UNIVERSITY   (Yemen)

^e HAROKOPIO UNIVERSITY   (Greece)

^f NATIONAL GEOGRAPHIC SOCIETY   (United States)

^g UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^h LEBANESE AMERICAN UNIVERSITY   (Lebanon)

ⁱ HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^j Karius   (United States)

more..

Author keywords

admixture; genetic isolate; genetic structure; genome wide SNPs; human population history; whole genome sequencing

Indexed keywords

AFRICAN; ARTICLE; CHAD; CONTROLLED STUDY; EVOLUTION; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HETEROZYGOSITY; HISTORY; HOLOCENE; HUMAN; HUMAN GENOME; MAJOR CLINICAL STUDY; MIGRATION; PRIORITY JOURNAL; Y CHROMOSOME; ANIMAL; ASIA; ETHIOPIA; ETHNOLOGY; EUROPE; GENE FLOW; GENETIC VARIATION; GENETICS; HETEROZYGOTE; HOMO NEANDERTHALENSIS; MIDDLE EAST; POPULATION DENSITY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; ASIA; CHAD; ETHIOPIA; EUROPE; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; HETEROZYGOTE; HISTORY, ANCIENT; HUMAN MIGRATION; HUMANS; LINKAGE DISEQUILIBRIUM; MIDDLE EAST; NEANDERTHALS; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DENSITY;

EID: 85004064487     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2016.10.012     Document Type: Article

References (43)

1. 1 Central Intelligence Agency. (2014). The World Factbook 2014. https://www.cia.gov/library/publications/the-world-factbook/index.html.
2. 2 Kröpelin, S., Verschuren, D., Lézine, A.M., Eggermont, H., Cocquyt, C., Francus, P., Cazet, J.P., Fagot, M., Rumes, B., Russell, J.M., et al. Climate-driven ecosystem succession in the Sahara: the past 6000 years. Science 320 (2008), 765–768.
3. 3 Löhr, D., Lake Chad and the migratory routes to Borno: A linguistic trail. Tourneaux, H., (eds.) Migrations and Spatial Mobility in the Lake Chad Basin, XIIIth Mega-Chad Conference, 2009, Editions de l'IRD, 665–681.
4. 4 Pagani, L., Kivisild, T., Tarekegn, A., Ekong, R., Plaster, C., Gallego Romero, I., Ayub, Q., Mehdi, S.Q., Thomas, M.G., Luiselli, D., et al. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. Am. J. Hum. Genet. 91 (2012), 83–96.
5. 5 Gallego Llorente, M., Jones, E.R., Eriksson, A., Siska, V., Arthur, K.W., Arthur, J.W., Curtis, M.C., Stock, J.T., Coltorti, M., Pieruccini, P., et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350 (2015), 820–822.
6. 6 Cerný, V., Fernandes, V., Costa, M.D., Hájek, M., Mulligan, C.J., Pereira, L., Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup. BMC Evol. Biol., 9, 2009, 63.
7. 7 Cerezo, M., Černý, V., Carracedo, Á., Salas, A., New insights into the Lake Chad Basin population structure revealed by high-throughput genotyping of mitochondrial DNA coding SNPs. PLoS ONE, 6, 2011, e18682.
8. 8 Cruciani, F., Trombetta, B., Sellitto, D., Massaia, A., Destro-Bisol, G., Watson, E., Beraud Colomb, E., Dugoujon, J.M., Moral, P., Scozzari, R., Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. Eur. J. Hum. Genet. 18 (2010), 800–807.
9. 9 Triska, P., Soares, P., Patin, E., Fernandes, V., Cerny, V., Pereira, L., Extensive Admixture and Selective Pressure Across the Sahel Belt. Genome Biol. Evol. 7 (2015), 3484–3495.
10. 10 Gurdasani, D., Carstensen, T., Tekola-Ayele, F., Pagani, L., Tachmazidou, I., Hatzikotoulas, K., Karthikeyan, S., Iles, L., Pollard, M.O., Choudhury, A., et al. The African Genome Variation Project shapes medical genetics in Africa. Nature 517 (2015), 327–332.
11. 11 Abecasis, G.R., Altshuler, D., Auton, A., Brooks, L.D., Durbin, R.M., Gibbs, R.A., Hurles, M.E., McVean, G.A., 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467 (2010), 1061–1073.
12. 12 Pagani, L., Schiffels, S., Gurdasani, D., Danecek, P., Scally, A., Chen, Y., Xue, Y., Haber, M., Ekong, R., Oljira, T., et al. Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am. J. Hum. Genet. 96 (2015), 986–991.
13. 13 Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522 (2015), 207–211.
14. 14 Drmanac, R., Sparks, A.B., Callow, M.J., Halpern, A.L., Burns, N.L., Kermani, B.G., Carnevali, P., Nazarenko, I., Nilsen, G.B., Yeung, G., et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327 (2010), 78–81.
15. 15 Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J., Sham, P.C., PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81 (2007), 559–575.
16. 16 Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 (2009), 2078–2079.
17. 17 Delaneau, O., Zagury, J.F., Marchini, J., Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods 10 (2013), 5–6.
18. 18 Auton, A., Brooks, L.D., Durbin, R.M., Garrison, E.P., Kang, H.M., Korbel, J.O., Marchini, J.L., McCarthy, S., McVean, G.A., Abecasis, G.R., 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526 (2015), 68–74.
19. 19 Patterson, N., Price, A.L., Reich, D., Population structure and eigenanalysis. PLoS Genet., 2, 2006, e190.
20. 20 Schiffels, S., Durbin, R., Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46 (2014), 919–925.
21. 21 Brisbin, A., Bryc, K., Byrnes, J., Zakharia, F., Omberg, L., Degenhardt, J., Reynolds, A., Ostrer, H., Mezey, J.G., Bustamante, C.D., PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations. Hum. Biol. 84 (2012), 343–364.
22. 22 Bergström, A., Nagle, N., Chen, Y., McCarthy, S., Pollard, M.O., Ayub, Q., Wilcox, S., Wilcox, L., van Oorschot, R.A., McAllister, P., et al. Deep roots for Aboriginal Australian Y chromosomes. Curr. Biol. 26 (2016), 809–813.
23. 23 Forster, P., Harding, R., Torroni, A., Bandelt, H.J., Origin and evolution of Native American mtDNA variation: a reappraisal. Am. J. Hum. Genet. 59 (1996), 935–945.
24. 24 Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S.M., Bondarev, A.A., Johnson, P.L., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514 (2014), 445–449.
25. 25 Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., Reich, D., Ancient admixture in human history. Genetics 192 (2012), 1065–1093.
26. 26 Alexander, D.H., Novembre, J., Lange, K., Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19 (2009), 1655–1664.
27. 27 Loh, P.R., Lipson, M., Patterson, N., Moorjani, P., Pickrell, J.K., Reich, D., Berger, B., Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193 (2013), 1233–1254.
28. 28 Pickrell, J.K., Patterson, N., Loh, P.R., Lipson, M., Berger, B., Stoneking, M., Pakendorf, B., Reich, D., Ancient west Eurasian ancestry in southern and eastern Africa. Proc. Natl. Acad. Sci. USA 111 (2014), 2632–2637.
29. 29 Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al., 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics 27 (2011), 2156–2158.
30. 30 Peng, B., Kimmel, M., simuPOP: a forward-time population genetics simulation environment. Bioinformatics 21 (2005), 3686–3687.
31. 31 Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z.X., Pool, J.E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T.S., et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329 (2010), 75–78.
32. 32 Ayub, Q., Mezzavilla, M., Pagani, L., Haber, M., Mohyuddin, A., Khaliq, S., Mehdi, S.Q., Tyler-Smith, C., The Kalash genetic isolate: ancient divergence, drift, and selection. Am. J. Hum. Genet. 96 (2015), 775–783.
33. 33 Li, H., Durbin, R., Inference of human population history from individual whole-genome sequences. Nature 475 (2011), 493–496.
34. 34 Enattah, N.S., Sahi, T., Savilahti, E., Terwilliger, J.D., Peltonen, L., Järvelä, I., Identification of a variant associated with adult-type hypolactasia. Nat. Genet. 30 (2002), 233–237.
35. 35 Sturm, R.A., Duffy, D.L., Zhao, Z.Z., Leite, F.P., Stark, M.S., Hayward, N.K., Martin, N.G., Montgomery, G.W., A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Am. J. Hum. Genet. 82 (2008), 424–431.
36. 36 Stokowski, R.P., Pant, P.V., Dadd, T., Fereday, A., Hinds, D.A., Jarman, C., Filsell, W., Ginger, R.S., Green, M.R., van der Ouderaa, F.J., Cox, D.R., A genomewide association study of skin pigmentation in a South Asian population. Am. J. Hum. Genet. 81 (2007), 1119–1132.
37. 37 deMenocal, P.B., Tierney, J.E., Green Sahara: African Humid Periods paced by Earth's orbital changes. Nature Education Knowledge, 3, 2012, 12.
38. 38 Larrasoaña, J.C., Roberts, A.P., Rohling, E.J., Dynamics of green Sahara periods and their role in hominin evolution. PLoS ONE, 8, 2013, e76514.
39. 39 Balaresque, P., Bowden, G.R., Adams, S.M., Leung, H.Y., King, T.E., Rosser, Z.H., Goodwin, J., Moisan, J.P., Richard, C., Millward, A., et al. A predominantly neolithic origin for European paternal lineages. PLoS Biol., 8, 2010, e1000285.
40. 40 Batini, C., Hallast, P., Zadik, D., Delser, P.M., Benazzo, A., Ghirotto, S., Arroyo-Pardo, E., Cavalleri, G.L., de Knijff, P., Dupuy, B.M., et al. Large-scale recent expansion of European patrilineages shown by population resequencing. Nat. Commun., 6, 2015, 7152.
41. 41 Haber, M., Gauguier, D., Youhanna, S., Patterson, N., Moorjani, P., Botigué, L.R., Platt, D.E., Matisoo-Smith, E., Soria-Hernanz, D.F., Wells, R.S., et al. Genome-wide diversity in the levant reveals recent structuring by culture. PLoS Genet., 9, 2013, e1003316.
42. 42 Rodriguez-Flores, J.L., Fakhro, K., Agosto-Perez, F., Ramstetter, M.D., Arbiza, L., Vincent, T.L., Robay, A., Malek, J.A., Suhre, K., Chouchane, L., et al. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res. 26 (2016), 151–162.
43. 43 Haber, M., Mezzavilla, M., Xue, Y., Tyler-Smith, C., Ancient DNA and the rewriting of human history: be sparing with Occam's razor. Genome Biol., 17, 2016, 1.