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Effective population size (Ne) is one of the most important tools used to assess genetic diversity for conservation purposes. Using pedigree data of three Croatian autochthonous cattle breeds (Busa, Istrian and Slavonian Syrmian Podolian) the effective maternal (NeF), paternal (NeM) and combined maternal-paternal (NeFM) population size was estimated. Additionally, we estimated the effective population size based on the census population sex ratio (Nes), the effective population size from the individual increase in inbreeding (NeFi) and the effective population size from individual increase in coancestry (NeCi). We compared these sizes with the values obtained for 20 additional cattle populations, as well as with the newly calculated NeFM. The effective population sizes calculated for three autochthonous breeds were consistently the lowest in amongst all considered cattle breeds. Utilisation of extremely small numbers of breeding males is the main reason for the observed reduction in the effective population size. The decomposition of effective population size into maternal and paternal components is shown to be an informative parameter in detecting the reduction of the effective population size as a consequence of unequal sex contribution. Still, the impact of the pedigree depth and completeness on the NeF, NeM and NeFM estimation remain to be analysed. We observed a large deviation between Nes and all other methods of Ne estimation and it is our recommendation that breeders and stakeholders should consider using alternative methods of Ne estimation when planning breeding programmes as well as in the determination of the endangered status of animal populations.

GENEALOGICAL DECOMPOSITION OF THE EFFECTIVE POPULATION SIZE: A CASE STUDY ON CROATIAN AUTOCHTHONOUS CATTLE BREEDS