Challenging the loss of genetic variability in Italian brown bears (Ursus arctos) - A genome-wide approach

The first part of this PhD thesis is devoted to the application of molecular genetics to describe demographic trends, geographic distribution patterns and genetic status of the Alpine population 15 years after the reintroduction program. In order to achieve the first objective we a) increased the number of STR markers (from 10 to 15 loci) in the Alpine population to raise the informativity content for population genetics studies, and possibly resolve uncertain parentage assignments; b) presented an annual overview of the demographic status of the Alpine population for a long-term monitoring program; c) measured the genetic diversity over generations, highlighting possible trends d) identified parentage relationships and provided a pedigree reconstruction, showing if there is an increase of inbreeding events over generations; e) estimated the effective population size; f) verified whether or not a connection between the reintroduced population in the central Alps and the Dinaric population was established. We furthermore provided considerations for conservation and management of this species in the Alps, taking into account the emerged demographic, spatial and genetic aspects. The second part is methodological and is about developing a new set of SNP markers to enhance the resolution power for population genetics analysis of the Alpine and Apennine populations. In order to identify reliable and informative SNPs we a) tested the effectiveness of an existing SNP panel, developed for the Scandinavian brown bear populations, on the two Italian brown bear subspecies, identifying a set of SNPs that has potential for a SNP-based individual and sex identification system. I took into consideration the ascertainment bias that arises when transferring SNP markers across populations; and b) tested the selected subset of SNPs for parentage assignments in the Alpine population, comparing its resolution power with that derived from STRs.