African Pastoralism: Genetic Imprints of Origins and Migrations

The taxonomy of the North African subspecies of the wild cattle or aurochs Bos primigenius, the ancestor of the domesticated cattle, is unclear due to large variation in osteological characters of the fossils. It is sometimes referred to in the literature as B. p. africanus, B. p. mauritanicus, or even B. p. opisthonomus. Consequently, here we stick to the species name of the ancestral species, B. primigenius.

K. C. MacDonald, in The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics and Ethnography, R. M. Blench, K. C. MacDonald, Eds. (Univ. College London Press, London, 2000), pp. 2–17.

Wendorf F., Schild R., J. Anthropol. Archeol. 17, 93 (1998).

Bradley D. G., MacHugh D. E., Cunningham P., Loftus R. T., Proc. Natl. Acad. Sci. U.S.A. 93, 5131 (1996).

D. G. Bradley, R. Loftus, in The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics and Ethnography, R. M. Blench, K. C. MacDonald, Eds. (Univ. College London Press, London, 2000), pp. 244–250.

C. Grigson, in The Beginnings of Agriculture, A. Milles, D. Williams, G. Gardner, Eds. (British Archaeological Reports International Series 496, Oxford, 1989), pp. 77–109.

MacHugh D. E., Shriver M. D., Loftus R. T., Cunningham P., Bradley D. G., Genetics 146, 1071 (1997).

Hanotte O., et al., Mol. Ecol. 9, 387 (2000).

F. A. Hassan, in The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics and Ethnography, R. M. Blench, K. C. MacDonald, Eds. (Univ. College London Press, London, 2000), pp. 61–86.

A. Muzzolini, thesis, University of Provence Aix-Marseille (1983).

H. Epstein, The Origins of the Domestic Animals of Africa, vol. 1 (Africana Publishing Corporation, London, 1971).

F. Marshall, in The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics and Ethnography, R. M. Blench, K. C. MacDonald, Eds. (Univ. College London Press, London, 2000), pp. 191–221.

J. E. O. Rege, C. V. Yapi-Gnaoré, C. L. Tawah, in Proceedings of the 2nd Africa Conference on Animal Agriculture, Pretoria, Republic of South Africa, 1 to 4 April 1996, H. H. Meissner, Ed. (South African Society of Animal Science, Irene, South Africa, 1996).

Supplementary details of experimental procedures and tables are available on Science Online at www.sciencemag.org/cgi/content/full/296/5566/336/DC1. Population allele frequencies are available from the corresponding author.

P. C. Nderito, K. O. Adeniji, Africa Distribution of Cattle by OAU/STRC (Inter Africa Bureau for Animal Resources, Nairobi, ed. 1, 1976).

The PC scores interpolation maps were drawn using the “Spatial Analyst Extension” of ArcView version 3.2 (Fig. 1, B through D), available at: www.esri.com/software/arcview/. The “Inverse Distance Weighted” (IDW) option with a power of two was selected for the interpolation of the surface. IDW assumes that each input point has a local influence that diminishes with distance. The area of sampling of each breed was used as geographic coordinates (Fig. 1A), and the six nearest neighbors were used for the calculation. Interpolation surfaces were divided into eight equal classes. The Madagascar Zebu population was excluded for the calculation of the continental African interpolation map.

C. Troy, thesis, Trinity College Dublin (2000).

Admixture coefficient mR, a least-squares frequency estimator (19), was calculated using the program Admix 1.0, available at: www.unife.it/genetica/Giorgio/giorgio.html. Mean values after 100 bootstraps were used (14).

Roberts D. F., Hiorns R. W., Hum. Biol. 37, 38 (1965).

Similarly, we observe a very high and significant correlation between PC1 values and the mean frequency of zebu-specific alleles (r = 0.96, P < 0.001), as well as between PC1 values and the average genetic distances (Da) with the Ongole, Nelore, and Sahiwal zebu reference populations (r = 0.96, P < 0.001).

The geographic coordinates of the African taurine Baladi (latitude, 29°03′11"; longitude, 30°59′76") and the African zebu Ogaden (latitude, 7°37′05", longitude, 46°22′80") were used as the reference point for the calculation of the distance from the Isthmus of Suez and the Horn of Africa, respectively. The median point (latitude, 23°20′0", longitude, 32°30′6") between the geographic coordinates of the taurine Baladi and the African zebu Butana (latitude, 17°70′75", longitude, 34°39′05") was used as the reference point for the origin of African pastoralism in the eastern Sahara.

Loftus R. T., et al., Mol. Ecol. 8, 2015 (1999).

J. Clutton-Brock, in The Archaeology of Africa: Food, Metals and Towns, T. Shaw, P. J. J. Sinclair, B. Andah, A. Okpoko, Eds. (Routledge, London, 1993), pp. 61–70.

J. R. Harlan, in The Archaeology of Africa: Food, Metals and Towns, T. Shaw, P. J. J. Sinclair, B. Andah, A. Okpoko, Eds. (Routledge, London, 1993), pp. 53–60.

J. L. Newman, The Peopling of Africa: A Geographic Interpretation (Yale Univ. Press, New Haven, CT, 1995).

Gifford-Gonzalez D., Afr. Archaeol. Rev. 17, 95 (2000).

Regional dates used for correlation analysis involving the advent of cattle herding were as follows: eastern Sahara, 7800 BP; central Sahara, 7200 BP; northern Sahara, 5600 BP; West African river basins, 4000 BP; Ethiopia/Eritrea, 4800 BP; Great Lakes region, 3700 BP; Southern Africa, 1600 BP (9, 10, 26).

Smith A. B., Annu. Rev. Anthropol. 21, 125 (1992).

Also, we observe a very high and significant negative correlation between PC3 and the average frequencies of alleles present at relatively high frequencies in African taurine but not in the European–Near East taurine breeds (r = –0.65, P < 0.001).

Wade M. J., McCauley D. E., Evolution 42, 995 (1988).

Barbujani G., Sokal R. R., Oden N. L., Am. J. Phys. Anthropol. 2, 109 (1995).

Fix A. G., Hum. Biol. 5, 663 (1997).

The corrected index of diversity was the observed mean number of alleles (MNAO) minus the expected MNA (MNAE) given the estimated level of zebu introgression in each population. This was obtained by taking the average of 500 simulated samples from the Asian Bos indicus and European B. taurus reference populations in proportion to the fraction of zebu ancestry.

A. B. Smith, in The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics and Ethnography, R. M. Blench, K. C. MacDonald, Eds. (Univ. College London Press, London, 2000), pp. 222–238.

J. Denbow Afr. Archaeol. Rev. 8, 139 (1990).

ILRI research is principally funded by program grants from the United Kingdom, Japan, The European Union, Ireland, and France, as well as unrestricted funding from other donors to the Consultative Group on International Agricultural Research (CGIAR). This project was funded in large part through a special grant from the African Development Bank. We thank C. L. Tawah, M. Stear, R. Loftus, D. MacHugh, C. Meghen, B. Sauveroche, S. Dunner (Retinta), L. R. Ritz, and C. Gaillard (Nelore and Ongole breeds); CIRDES (Baoulé) and the following people who coordinated the sampling in their respective countries: R. Mosi, A. M. Okeyo and M. Okomo (Kenya), Esubalew Abate (Ethiopia), P. Gwakisa (Tanzania), S. Maciel (Mozambique), J. Els (Namibia), K. Ramsay and A. Kotze (South Africa), O. A. El Khidir (Sudan), F. Mbuza (Uganda), W. N. M. Mwenya and G. B. M. Phiri (Zambia), S. Moyo and K. Dzama (Zimbabwe), V. N. Tanya and M. D. Achui-Kwi (Cameroon), L. Kamwanja (Malawi), U. Ghebremicael (Eritrea), K. Agyemang (ILRI-Nigeria), L. O. Ngere (Nigeria), R. Sow (Senegal), G. Kana (Chad), L. Gnaho (Benin), B. Fye (The Gambia), M. Diallo (Guinea), H. Djata (Guinea-Bissau), L. Ouragh (Morocco), R. Rakotozandrindrainy (Madagascar), and M.A.A. El-Barody (Egypt). The figures (maps) were drawn with the help of R. Kruska. Useful comments on the manuscript and/or support during the study were provided by H. Fitzhugh, D. Taylor, J. Gibson, D. MacHugh, J Clutton-Brock, D. Gifford-Gonzales, D. Desmond Clark, A. Teale, N. Pavitt, J. Bailey, M. Okomo, J. Rowlands, S. Nagda, S. Park, D. Mburu, and A. R. Freeman. We also thank the anonymous reviewers for their constructive criticisms. This is ILRI-publication 200164.