The aim of the doctoral thesis was to check the current state of grayling in the Soča River basin, to assess the levels of introgression and previous conservation efforts, and to develop an improved genotyping test to determine the native genomic proportion based on species-specific SNP markers. The test was made based on museum specimens of T. aeliani (originating before anthropogenic translocations) and extant populations of this species from the Sesia and Adige Rivers, which were compared with populations of T. thymallus from the Danube basin, that represent a source of translocations into the Adriatic grayling species range. Using the NGS ddRAD method, we obtained 112k polymorphic nuclear markers on 40k ddRAD-tags. The test enables distinction between native alleles of the Adriatic grayling in Soča river and non-native alleles of the European grayling from Sava River, based on 21k ddRAD-tags. We conclude that extant populations in Soča River is a hybrid swarm in which continuous native gene complexes, could not be detected. During the study, a significant decline of grayling population in Soča River was detected. The rescue of the Adriatic grayling in the Soča River is thus only possible by translocation of suitable population from the Sesia River, in which specimens with intact native genome for T. aeliani were observed. Only a small proportion of allelic variants (3k / 40k) characteristic of the native Adriatic grayling genome from the Soča River, found in museum specimens, is absent in grayling from Sesia. This suggests high suitability for translocation, but high FST (0.37) at polymorphic sites between these two populations calls for attention during this action. Analysis of adaptive loci revealed 58 potential adaptive loci where the frequency of alleles between these two populations were inconsistent (FST '> 0). Most of these loci are responsible for immune response, i.e., resistance to locally present pathogens.
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