Genome sequencing uncovers the history of the Russian desman’s gradual population decline and contributes to the evolutionary history of Talpidae

BACKGROUND: The Russian desman (Desmana moschata) is a critically endangered, elusive semi-aquatic mammal. While understanding its historical population dynamics is crucial for conservation, genomic data on its evolutionary and demographic history remain scarce. RESULTS: Here, we present a comprehensive whole-genome phylogenetic analysis of Desmana moschata within the Talpidae family, including heterozygosity assessments and inferred population size changes, as determined by PSMC and MSMC analyses. Our results demonstrate that, similar to its closest relative the Pyrenean desman (Galemys pyrenaicus), this species has undergone a long-term population decline preceding significant human influence. The phylogenetic component of our study involved a multigene analysis based on over 2,000 exons, producing a well-resolved, dated phylogeny of the Talpidae family at the tribal level. CONCLUSIONS: Although anthropogenic factors have undoubtedly contributed to recent declines, our data reveal that the reduction in the desman population is primarily an ancient process driven by natural causes. This has resulted in persistent declines in both effective population size and geographic range and then subsequent evolutionary extinction of ancient taxa with limited adaptive capabilities. These findings lay the groundwork for future genomic conservation studies, incorporating expanded sampling and targeted investigation of specific genomic features.