Molecular Ecology (2004) 13, 3477–3487 doi: 10.1111/j.1365-294X.2004.02311.x © 2004 Blackwell Publishing Ltd Blackwell Publishing, Ltd. Admixture and diversity in West African cattle populations A. R. FREEMAN,*† C. M. MEGHEN,†‡ D. E. M ac HUGH,§ R. T. LOFTUS,‡ M. D. ACHUKWI,¶ A. BADO,** B. SAUVEROCHE †† and D. G. BRADLEY * *Department of Genetics, Smurfit Institute, Trinity College, Dublin 2, Ireland, ‡Identigen Ltd, Unit 9, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland, §Department of Animal Science and Production and Conway Institute of Biomolecular and Biomedical Research, Faculty of Agriculture, University College Dublin, Belfield, Dublin 4, Ireland, ¶Institute of Agricultural Research for Development, Wakwa Regional Centre, PO Box 65, Ngaoundere, Cameroon, **Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES), 01 BP 454, Burkina Faso, ††FAO Regional Project, Banjul, The Gambia Abstract We present a population genetic analysis of microsatellite variation in 16 West African cattle populations. West Africa represents a unique juxtaposition of different climatic and ecological zones in a relatively small geographical area. While more humid coastal regions are inhabited by the tsetse fly, a vector which spreads trypanosomiasis among cattle, the disease is not transmitted in the drier areas outside this zone. This is the most thorough study of genetic diversity in cattle within this area, which contains genetically important trypanotolerant Bos taurus breeds. Genetic relationships among the many breeds are exam- ined and levels of diversity are assessed. Admixture levels were determined using a variety of methods. Ancestry informative or population-associated alleles (PAAs) were selected using populations from India, the Near East and Europe. Multivariate analysis, the ADMIX program and model-based Bayesian admixture analysis approaches were also employed. These analyses reveal the direct impact of ecological factors and the profound effect of admixture on the cattle of this region. They also highlight the importance of efforts to pre- vent further dilution of African taurine breeds by B. indicus cattle. Keywords: admixture, Bos indicus, Bos taurus, gene flow, microsatellite, trypanosomiasis Received 23 March 2004; revision received 29 June 2004; accepted 9 July 2004 Introduction The original cattle of Africa were Bos taurus (taurine), the humpless descendants of aurochs that were domesticated in either the Near East or on the African continent itself (Clutton-Brock 1989; Bradley et al. 1996; Hanotte et al. 2002). Subsequently, waves of migrations of humped zebu B. indicus (indicine) cattle have changed the genetic landscape of African cattle profoundly (MacHugh et al. 1997; Hanotte et al. 2000; Hanotte et al. 2002). Molecular genetic surveys of autosomal microsatellite markers reveal that most extant cattle breeds in the Sahel savannah region have had substantial zebu genetic input. However, further south in the humid forested areas a number of relic African taurine populations remain relatively intact due to the presence of high tsetse densities that preclude trypanosusceptible cattle without veterinary intervention (Bradley et al. 1994; MacHugh et al. 1997; Hanotte et al. 2002). Notwithstanding the complex patterns of admixture in Sahelian breeds, the finding that all African cattle surveyed to date have B. taurus-type mitochondrial DNA reveals their original ancestry (Troy et al. 2001). Payne & Hodges (1997) define three indigenous West African cattle types: first, longhorn N’Dama of the far west forest savannah; second, West African shorthorn such as Baoule; and third, the massive-horned Kuri from the wetland areas of Lake Chad. It is likely that these African taurine populations are the descendants of the original B. taurus shorthorns that may have been domesticated in North Africa, possibly after initial introductions of taurine cattle from the Fertile Crescent. Available archaeological evidence suggests that pastoralists herding shorthorn cattle had migrated to and penetrated West African forests by about 4000 bp (MacDonald & Hutton MacDonald 2000; Marshall & Hildebrand 2002). N’Dama and West African Correspondence: Dan Bradley, Department of Genetics, Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland. Fax: 00 353 1679 8558; E-mail: daniel.bradley@tcd.i.e. †These authors contributed equally to this work.