Genetic history of Chad

American Journal of Physical Anthropology

Volumn 167, Issue 4, 2018, Pages 804-812

  Shriner, Daniel ^a   Rotimi, Charles N ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

Baggara Arabs; Berber; Chadic; genetic anthropology; Y DNA haplogroup R1b

Indexed keywords

ADULT; AGRICULTURAL WORKER; ANTHROPOLOGY; ARAB; ARTICLE; BURKINA FASO; CHADIAN (CITIZEN); EAST AFRICAN; FEMALE; GENE FLOW; GENE POOL; GENETIC VARIABILITY; HUMAN; HUMAN EXPERIMENT; LANGUAGE; MAJOR CLINICAL STUDY; MALE; MALI; PYGMY; SAHEL; SOUTH SUDAN; Y CHROMOSOME HAPLOGROUP; AFRICA SOUTH OF THE SAHARA; BLACK PERSON; CHAD; EPIDEMIOLOGY; GENETICS; HAPLOTYPE; PHYSICAL ANTHROPOLOGY; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; Y CHROMOSOME;

AFRICA SOUTH OF THE SAHARA; AFRICAN CONTINENTAL ANCESTRY GROUP; ANTHROPOLOGY, PHYSICAL; ARABS; CHAD; CHROMOSOMES, HUMAN, Y; GENE FLOW; GENETICS, POPULATION; HAPLOTYPES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 85053877257     PISSN: 00029483     EISSN: 10968644     Source Type: Journal    
DOI: 10.1002/ajpa.23711     Document Type: Article

References (47)

1. Abu-Amero, K. K., Hellani, A., González, A. M., Larruga, J. M., Cabrera, V. M., & Underhill, P. A. (2009). Saudi Arabian Y-chromosome diversity and its relationship with nearby regions. BMC Genetics, 10, 59.
2. Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19, 1655–1664.
3. Baker, J. L., Rotimi, C. N., & Shriner, D. (2017). Human ancestry correlates with language and reveals that race is not an objective genomic classifier. Scientific Reports, 7, 1572.
4. Bandelt, H.-J., Alves-Silva, J., Guimarães, P. E. M., Santos, M. S., Brehm, A., Pereira, L., … Pena, S. D. J. (2001). Phylogeography of the human mitochondrial haplogroup L3e: A snapshot of African prehistory and Atlantic slave trade. Annals of Human Genetics, 65, 549–563.
5. Bekada, A., Fregel, R., Cabrera, V. M., Larruga, J. M., Pestano, J., Benhamamouch, S., & González, A. M. (2013). Introducing the Algerian mitochondrial DNA and Y-chromosome profiles into the North African landscape. PLoS One, 8, e56775.
6. Blench, R. (1999). The westward wandering of Cushitic pastoralists: Explorations in the prehistory of Central Africa. In C. Baroin & J. Boutrais (Eds.), Man and animal in the Lake Chad Basin: Proceedings of the Mega-Chad Network Symposium (pp. 39–80). Orléans: Research Institute for Development.
7. Blench, R. (2006). Archaeology, language, and the African past. In Lanham. Maryland: AltaMira Press.
8. Braukämper, U. (1994). Notes on the origin of Baggara Arab culture with special reference to the Shuwa. In J. Owens (Ed.), Arabs and Arabic in the Lake Chad region. Koln. Germany: Rüdiger Köppe Verlag.
9. Bučková, J., Černý, V., & Novelletto, A. (2013). Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel. American Journal of Physical Anthropology, 151, 10–21.
10. Cadenas, A. M., Zhivotovsky, L. A., Cavalli-Sforza, L. L., Underhill, P. A., & Herrera, R. J. (2008). Y-chromosome diversity characterizes the Gulf of Oman. European Journal of Human Genetics, 16, 374–386.
11. Černý, V., Fernandes, V., Costa, M. D., Hájek, M., Mulligan, C. J., & Pereira, L. (2009). Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup. BMC Evolutionary Biology, 9, 63.
12. Chiaroni, J., King, R. J., Myres, N. M., Henn, B. M., Ducourneau, A., Mitchell, M. J., … Underhill, P. A. (2010). The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations. European Journal of Human Genetics, 18, 348–353.
13. Cruciani, F., Santolamazza, P., Shen, P., Macaulay, V., Moral, P., Olckers, A., … Underhill, P. A. (2002). A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. American Journal of Human Genetics, 70, 1197–1214.
14. Cruciani, F., Trombetta, B., Sellitto, D., Massaia, A., Destro-Bisol, G., Watson, E., … Scozzari, R. (2010a). Human Y chromosome haplogroup R-V88: A paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. European Journal of Human Genetics, 18, 800–807.
15. Cruciani, F., Trombetta, B., Sellitto, D., Massaia, A., Destro-Bisol, G., Watson, E., … Scozzari, R. (2010b). Reply to Lancaster. European Journal of Human Genetics, 18, 1186–1187.
16. DeLancey, M. W., & DeLancey, M. D. (2000). Historical dictionary of the Republic of Cameroon. Lanham, Maryland: The Scarecrow Press.
17. Dobon, B., Hassan, H. Y., Laayouni, H., Luisi, P., Ricaño-Ponce, I., Zhernakova, A., … Bertranpetit, J. (2015). The genetics of east African populations: A Nilo-Saharan component in the African genetic landscape. Scientific Reports, 5, 9996.
18. Ehret, C. (2002). The civilizations of Africa: A history to 1800. Virginia: The University Press of Virginia.
19. Fenner, J. N. (2005). Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. American Journal of Physical Anthropology, 128, 415–423.
20. Haber, M., Mezzavilla, M., Bergström, A., Prado-Martinez, J., Hallast, P., … Tyler-Smith, C. (2016). Chad genetic diversity reveals an African history marked by multiple Holocene Eurasian migrations. American Journal of Human Genetics, 99, 1316–1324.
21. Harich, N., Costa, M. D., Fernandes, V., Kandil, M., Pereira, J. B., Silva, N. M., & Pereira, L. (2010). The trans-Saharan slave trade—Clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages. BMC Evolutionary Biology, 10, 138.
22. Hassan, H. Y., Underhill, P. A., Cavalli-Sforza, L. L., & Ibrahim, M. E. (2008). Y-chromosome variation among Sudanese: Restricted gene flow, concordance with language, geography, and history. American Journal of Physical Anthropology, 137, 316–323.
23. Hathaway, J. (1997). The politics of households in Ottoman Egypt: The rise of the Qazdağlis. Cambridge, United Kingdom: Cambridge University Press.
24. Hollfelder, N., Schlebusch, C. M., Günther, T., Babiker, H., Hassan, H. Y., & Jakobsson, M. (2017). Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLoS Genetics, 13, e1006976.
25. Lange, D. (1987). A Sudanic chronicle: the Borno expeditions of Idris Alauma (1564-1576) according to the account of Ahmad B. Furtu: Arabic text, English translation, commentary, and geographical gazetteer. Stuttgart, Germany: F. Steiner Verlag Wiesbaden.
26. Jostins, L., Xue, Y., McCarthy, S., Ayub, Q., Durbin, R., Barrett, J., & Tyler-Smith, C. (2014). YFitter: Maximum likelihood assignment of Y chromosome haplogroups from low-coverage sequence data. arXiv. 1407.7988.
27. Kulichová, I., Fernandes, V., Deme, A., Nováčková, J., Stenzl, V., Novelletto, A., … Černý, V. (2017). Internal diversification of non-sub-Saharan haplogroups in Sahelian populations and the spread of pastoralism beyond the Sahara. American Journal of Physical Anthropology, 164, 424–434.
28. Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., … Myers, R. M. (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science, 319, 1100–1104.
29. Loh, P.-R., Lipson, M., Patterson, N., Moorjani, P., Pickrell, J. K., Reich, D., & Berger, B. (2013). Inferring admixture histories of human populations using linkage disequilibrium. Genetics, 193, 1233–1254.
30. McGregor, A. (2006). A military history of modern Egypt: From the Ottoman conquest to the Ramadan war. Westport, CT: Praeger Security International.
31. Mohammad, T., Xue, Y., Evison, M., & Tyler-Smith, C. (2009). Genetic structure of nomadic Bedouin from Kuwait. Heredity, 103, 425–433.
32. Moorjani, P., Sankararaman, S., Fu, Q., Przeworski, M., Patterson, N., & Reich, D. (2016). A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proceedings of the National Academy of Sciences of the United States of America, 113, 5652–5657.
33. Owens, J. (1994). Arabs and Arabic in the Lake Chad region. Köln, Germany: Rüdiger Köppe Verlag.
34. Philipp, T., & Haarmann, U. (Eds.) (1998). The Mamluks in Egyptian politics and society. Cambridge, UK: Cambridge University Press.
35. Pickrell, J. K., Patterson, N., Loh, P.-R., Lipson, M., Berger, B., Stoneking, M., … Reich, D. (2014). Ancient west Eurasian ancestry in southern and eastern Africa. Proceedings of the National Academy of Sciences of the United States of America, 111, 2632–2637.
36. Priehodová, E., Abdelsawy, A., Heyer, E., & Černý, V. (2014). Lactase persistence variants in Arabia and in the African Arabs. Human Biology, 86, 7–18.
37. Shriner, D., Tekola-Ayele, F., Adeyemo, A., & Rotimi, C. N. (2014). Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry. Scientific Reports, 4, 6055.
38. Silva, M., Alshamali, F., Silva, P., Carrilho, C., Mandlate, F., Jesus Trovoada, M., … Soares, P. (2015). 60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Scientific Reports, 5, 12526.
39. Soares, P., Alshamali, F., Pereira, J. B., Fernandes, V., Silva, N. M., Afonso, C., … Pereira, L. (2012). The expansion of mtDNA Haplogroup L3 within and out of Africa. Molecular Biology and Evolution, 29, 915–927.
40. Tishkoff, S. A., Reed, F. A., Friedlaender, F. R., Ehret, C., Ranciaro, A., Froment, A., … Williams, S. M. (2009). The genetic structure and history of Africans and African Americans. Science, 324, 1035–1044.
41. Triska, P., Soares, P., Patin, E., Fernandes, V., Cerny, V., & Pereira, L. (2015). Extensive admixture and selective pressure across the Sahel Belt. Genome Biology and Evolution, 7, 3484–3495.
42. Underhill, P. A., Shen, P., Lin, A. A., Jin, L., Passarino, G., Yang, W. H., … Oefner, P. J. (2000). Y chromosome sequence variation and the history of human populations. Nature Genetics, 26, 358–361.
43. Urasin, V. (2017a). R YTree. Retrieved from https://www.yfull.com/tree/R. Accessed August 11, 2017.
44. Urasin, V. (2017b). R-V88 YTree. Retrieved from https://www.yfull.com/tree/R-V88. Accessed August 11, 2017.
45. Vianello, D., Sevini, F., Castellani, G., Lomartire, L., Capri, M., & Franceschi, C. (2013). HAPLOFIND: A new method for high-throughput mtDNA haplogroup assignment. Human Mutation, 34, 1189–1194.
46. Wilson, C. W. (1888). On the tribes of the Nile Valley, north of Khartúm. Journal of the Anthropological Institute of Great Britain and Ireland, 17, 3–25.
47. Yunusbayev, B., Metspalu, M., Järve, M., Kutuev, I., Rootsi, S., Metspalu, E., … Villems, R. (2012). The Caucasus as an asymmetric semipermeable barrier to ancient human migrations. Molecular Biology and Evolution, 29, 359–365.