Evaluating the importance of translocations in rescuing the genetic diversity of the endemic Saimaa ringed seal

Abstract Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1,000 generations, is alarmingly low. The population is further divided into semi-isolated subpopulations in the labyrinthine landscape of the lake, which exposes the population to deleterious genomic effects. We performed whole-genome sequencing on Saimaa ringed seals (N=30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p<0.001). We found a general signal of differentiation in homozygosity within Lake Saimaa subpopulations (p<0.05) and detected thousands of unique single-nucleotide polymorphisms (SNPs) in all subpopulations. The observed high levels of inbreeding and the risk of losing indispensable SNPs may directly affect fitness in individuals. These results support augmented gene flow as a genetic conservation action. Based on our results, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.