Analysis of genetic diversity for the management of conserved subdivided populations

Recent studies in the literature have applied phylogenetic methods based on genetic distances to set priorities for conservation of domestic animal breeds. While these methods may be appropriate for between-species conservation, they are clearly inappropriate for within-species breed conservation, because they ignore within-breed variation. In this paper we show the basic tools to analyse genetic diversity in subdivided populations within species, and illustrate the errors incurred by applying methods based exclusively on genetic distances. We also show that maximisation of genetic diversity (minimisation of coancestry or kinship) is equivalent to maximisation of effective population size, as in undivided populations, and derive a generalisation of previous equations for the prediction of effective size. Finally, we discuss the strategies for conservation in the light of the theory.