UNCORRECTED PROOF Genetic evaluation of the captive breeding program of the Persian wild ass R. K. Nielsen 1 , C. Pertoldi 1,2 & V. Loeschcke 1 1 Department of Ecology and Genetics, Institute of Biological Science, University of Aarhus, Ny Munkegade, Aarhus C, Denmark. 2 Department of Landscape Ecology, National Environmental Research Institute, Kalø, Rønde, Denmark. Keywords conservation; microsatellites; genetic structure; relatedness; effective population size; bottleneck. Correspondence Rikke Kruse Nielsen, Department of Ecology and Genetics, Institute of Biological Science, University of Aarhus, Ny Munkegade, Building 1540, DK-8000 Aarhus C, Denmark. Fax: +45 894 22722 Email: rikke.kruse@biology.au.dk Received 11 September 2006; accepted 28 November 2006 doi:10.1111/j.1469-7998.2007.00294.x Abstract During the last century, many species have become endangered and conservation in terms of captive breeding has been crucial for their survival. Classical manage- ment of captive species is based on recorded genealogies. However, if pedigrees are incomplete or inaccurate, it can bias the interpretation of the results obtained from analyses based on such data. In this investigation, 12 microsatellite loci were investigated to evaluate the studbook information of the critically endangered Persian wild ass Equus hemionus onager. Relatedness and inbreeding coefficients were calculated in order to compare the same coefficients estimated from the recorded studbook. A significant correlation between coefficients obtained by microsatellites and the studbook validates the recorded studbook as a reasonable tool for future genetic management. Furthermore, a Bayesian-based method divided the captive onager population into four subgroups that indicate departure from random mating, and thus minor rotation of animals between zoos. Lastly, analyses for inferring past demographic changes revealed a gradual population decline and inbreeding over several generations. This may indicate a low genetic load in captive onagers as a consequence of some degree of purging. Consequently, the risk of inbreeding depression should currently be minimal in the captive breeding program. Therefore, it is recommended to increase the connectivity between the four subgroups of onagers in order to reduce the risk of demographic and genetic stochasticity. This study underlines the importance of using molecular markers to evaluate genetic management of captive breeding programs. Introduction Many species have become endangered in the last century and require active management to ensure their survival (Olech & Perzanowski, 2002; Wisely, McDonald & Buskirk, 2003; Wilson et al., 2005). Genetic variation is a primary component of adaptive evolution, and its loss or reduction will decrease the long-term survival probability of popula- tions. Therefore, maintaining genetic variation has been a major goal in captive breeding programs (Reed & Frank- ham, 2003). Minimizing kinship, which involves choosing individuals with the lowest mean kinship to be parents of subsequent generations, has been a strategy used in various breeding programs to maximize the retention of genetic variation. Minimizing kinship reduces the overall level of relatedness and maximizes founder representation in captive populations, and additionally minimizes the expression of deleterious alleles in inbred animals (Montgomery et al., 1997). Deleterious alleles are expressed through consanguineous mating and through random genetic drift in small popula- tions in which deleterious alleles can be fixed (Hedrick & Kalinowski, 2000). This increases the risk of inbreeding depression in populations, which can reduce individual fitness (Seymour et al., 2001). Removal of deleterious alleles by natural selection (purging) has become increasingly interesting in breeding programs, especially in cases when the number of founders is low and inbreeding unavoidable. However, as deliberate inbreeding to purge deleterious alleles causes a further reduction in fitness, ‘maximum avoidance of inbreeding’ is the currently accepted breeding strategy for eliminating inbreeding depression in captive species (Hedrick & Kalinowski, 2000). In many breeding programs, the complete pedigrees are often unknown. When the ancestry of founders is unspeci- fied, they are assumed to be non-inbred and unrelated, referred to as ‘founder assumption’ (Russello & Amato, 2004). This may lead to an underestimation of relatedness within the population and result in incorrect calculations of mean kinship and inbreeding coefficients that conservation decisions normally rely on (Russello & Amato, 2004). However, Willis (2001) showed that it is more appropriate to underestimate than overestimate relatedness in unpedi- greed populations in order to maintain genetic variation. Application of polymorphic molecular markers has allowed ‘black holes’ in pedigrees to be eliminated and to infer JZO 294 B Dispatch: 19.1.07 Journal: JZO CE: Chandrika Journal Name Manuscript No. Author Received: No. of pages: 9 TE: Rathna/Suresh Journal of Zoology (2007) c  2007 The Authors. Journal compilation c  2007 The Zoological Society of London 1 Journal of Zoology. Print ISSN 0952-8369 JZO 294 (BWUK JZO 294.PDF 19-Jan-07 19:55 196527 Bytes 9 PAGES n operator=Suresh Babu)