The value of using probabilities of gene origin to measure genetic variability in a population

The increase in inbreeding can be used to derive the realized effective size of a population. However, this method reflects mainly long term effects of selection choices and is very sensitive to incomplete pedigree information. Three parameters derived from the probabilities of gene origin could be a valuable and complementary alternative. Two of these parameters, the effective number of founders and the effective number of remaining founder genomes, are commonly used in wild populations but are less frequently used by animal breeders. The third method, developed in this paper, provides an effective number of ancestors, accounting for the bottlenecks in a pedigree. These parameters are illustrated and compared with simple examples, in a simulated population, and in three large French bovine populations. Their properties, their relationship with the effective population size, and their possible applications are discussed.