Molecular Ecology (2006) 15, 3787–3799 doi: 10.1111/j.1365-294X.2006.03059.x © 2006 The Authors Journal compilation © 2006 Blackwell Publishing Ltd Blackwell Publishing Ltd Hybridization between subspecies of waterbuck (Kobus ellipsiprymnus) in zones of overlap with limited introgression ELINE D. LORENZEN,* BO T. SIMONSEN,† PIETER W. KAT,‡ PETER ARCTANDER § and HANS R. SIEGISMUND * * Institute of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark, † Department of Forensic Genetics, University of Copenhagen, Frederik V’s Vej 11, DK-2100 Copenhagen Ø, Denmark, ‡ Lion Research, Private Bag 13, Maun, Botswana, § Institute of Molecular Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark Abstract Two subspecies of waterbuck (Kobus ellipsiprymnus), common (Kobus ellipsiprymnus ellipsiprymnus) and defassa (Kobus ellipsiprymnus defassa), are recognized based on differ- ences in rump pattern, coat colour and geographical distribution. These forms are para- patrically distributed with an area of range overlap in East Africa, where phenotypically intermediate populations occur. Variation in 478 bp of the mitochondrial DNA control region and 14 polymorphic microsatellite loci were used to describe the genetic structure and phylogeographical pattern of the species, and to assess if the intermediate populations are the results of hybridization. In total, 186 individuals from 11 localities were analysed. A high degree of genetic differentiation was found between subspecies, although this was most evident from the microsatellite data. Hybridization was suggested in the phenotypically and geographically intermediate Nairobi NP population in Kenya. A neighbour-joining (NJ) tree based on microsatellite population genetic distances grouped Nairobi between the common and defassa populations, and a Bayesian analysis clearly showed introgression. Individuals sampled in Samburu NP, Kenya, had a common waterbuck phenotype, but introgression was suggested by both markers. Although a high degree of maternal defassa input was indicated from the sequence data, the Samburu population grouped with the common waterbuck in the microsatellite population genetic distance tree, with high support. Analyses of linkage disequilibrium and maximum-likelihood estimates of genetic drift suggested that admixture between subspecies is a recent event. The fact that introgression is limited between subspecies could be caused by chromosomal differences, hindering gene flow between common and defassa waterbuck. Keywords: hybridization, introgression, Kobus ellipsiprymnus, microsatellites, mtDNA, waterbuck Received 4 April 2006; revision received 30 May 2006; accepted 19 June 2006 Introduction In the past decade, population genetic and phylogeographic studies of African bovids have revealed various patterns and stages of population differentiation, taxonomic sub- division and admixture (Arctander et al . 1999; van Hooft et al . 2002; Alpers et al . 2004; Lorenzen et al . 2006). In the inference of species evolutionary history, most studies support one main hypothesis. Major refugial areas with persistent savanna habitat are believed to have existed in Africa during the climatic fluctuations of the Pleistocene (deMenocal 1995; Partridge et al . 1995). These isolated areas have enabled the survival of many savanna species, influencing and shaping their ecology, distribution and morphology (Arctander et al . 1999; van Hooft et al . 2002; Muwanika et al . 2003; Alpers et al . 2004; Lorenzen & Siegismund 2004; Okello et al . 2005; Lorenzen et al . 2006). In the process of evolution, populations that have become differentiated due to a period of isolation can come into Correspondence: Eline Deirdre Lorenzen, Fax: (+45) 3532 1300; E-mail: edlorenzen@bi.ku.dk