Selective Breeding Programs for Rare Alleles: Examples from the Przewalski's Horse and California Condor Pedigrees

As extinction due to loss of habitat grows more imminent for a wide variety of species, population management has been recognized as an important means toward species survival and recovery in the wild. Genetic management practices generally seek to preserve population variation at the level of the genome. It has been proposed, however, that such efforts should instead be directed to specific loci harboring alleles with particular selective benefits. This strategy may in fact result in greater loss of variation in the rest of the genome, potentially threatening population viability. Pedigrees of Przewalski's horse ( Equus prezewalskii ) and the California Condor ( Gymnogyps californianus ) were used to evaluate a "rare kinship" management strategy in which a single individual known to carry a unique allele is repeatedly bred to mates chosen by mean kinship in order to increase the frequency of the rare allele. This strategy led to increased population mean kinship and reduced gene diversity and founder genome equivalents relative to a no-management control pedigree and performed considerably worse than a pedigree managed for mean kinship. Reduced success in the breeding program can be directly attributed to significant deviations of founders' representations from their respective target values. As a result, a strategy for increasing the frequency of rare alleles cannot be generally recommended for management of captive populations. Under strict conditions, however, limited use of this strategy may be applicable only if used for a short time under careful monitoring by pedigree analysis. Even if these conditions are met, managing by a more conventional method such as mean kinship is preferable. These results illustrate the utility of thoughtful analysis of pedigree information to successful population management.