Application of individual increase in inbreeding to estimate realized effective sizes from real pedigrees.

Abstract

The objective of this study was to test the performance of a recently proposed methodology for the estimation of realized effective size (Ne) based on individual increase in inbreeding (DFi) on several real pedigrees: (a) an experimental mice population; (b) a closed pedigree of fighting bulls; (c) the Spanish Purebred (SPB, Andalusian) horse pedigree; (d) the Carthusian strain of SPB pedigree; (e) the Spanish Arab horse pedigree; and (f) the Spanish Anglo-Arab horse pedigree. Several reference subpopulations were defined on the basis of generation length in order to consider only animals in the last generation, to assess the influence of the pedigree content on the estimates of Ne. The estimates of realized Ne computed from DFi (Ne) tended to be higher than those obtained from regression on equivalent generations. The new parameter Ne remained approximately stable when pedigree depth achieved about five equivalent generations. Estimates of Ne take into account the genetic history of the populations, the size of their founder population, and the mating policy or bottlenecks caused by poor use of reproducing individuals. The usefulness of the realized Ne computed from individual increase in inbreeding in real pedigrees is also discussed.