Genomic signatures of population isolation in an endangered European rodent

The garden dormouse (Eliomys quercinus) is one of the fastest-declining mammals in Europe, and action is needed to prevent further population losses. The primary causes of declines are not well-understood, as the species experiences variable conditions and threats across its range, but likely include habitat fragmentation and loss. Previous genetic studies have provided evidence of highly structured garden dormouse populations in Western Europe, despite this region having been defined as a single clade with mitochondrial DNA analysis. Within Western Europe, the magnitude of declines has been recognized to be greater on the eastern edge of the species' range, which could explain differentiation within the clade as resulting from diversity loss and genetic drift for regions under greater risk of extirpation. Here, we focus on fine-scale genomic differentiation across the Western European clade to explore the consequences of genomic erosion on the eastern region and to help identify mechanisms driving genetic differentiation within this species.

We found genetic differentiation both between and within major geographic regions. Populations located in the eastern edge of the species' range showed stronger signs of population isolation, including structure between spatially distant populations, lower genetic diversity, and greater rates of inbreeding. However, all populations exhibited signals of recent rapid population decline. Outlier analyses indicated that differentiation between regions was primarily due to genetic drift resulting from isolation-by-distance rather than adaptive differentiation. We also found genetic structuring between populations within the Rhine Valley, despite apparent lack of physical barriers preventing dispersal among groups within this region.

Our findings indicate that population isolation following habitat loss and fragmentation has likely been a major contributor to garden dormouse declines. Dispersal among disparate garden dormouse sampling regions is restricted-even across local spatial scales-leading to loss of genetic diversity and potential erosion of evolutionary potential. With 21st century declines expected to continue across the species' range, even relatively common and well-connected populations are likely to follow the trajectory of the eastern populations, with increasing loss of diversity as populations contract and become more isolated.