Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Genomic resources are important for evaluating genetic diversity and supporting conservation efforts. The garden dormouse ( Eliomys quercinus ) is a small rodent that has experienced one of the most severe modern population declines in Europe. We present a high-quality haplotype-resolved reference genome for the garden dormouse, and combine comprehensive short and long-read transcriptomics datasets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome revealed a sharp population decline since the last interglacial, indicating that colder climates caused severe population declines prior to anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conducted the first population genomic analysis for this species to investigate patterns of connectivity between regions and factors explaining population declines. We found clear evidence for population structure across the species’ core Central European range. Notably, our data provide strong evidence that the Alpine population, characterized by strong differentiation likely due to habitat isolation, represents a differentiated evolutionary significant unit (ESU). Our data also show that the predominantly declining Eastern European populations show signs of recent isolation, a pattern consistent with a range expansion from Western to Eastern Europe during the Holocene, leaving relict populations now facing local extinction. Overall, our findings suggest that garden dormouse conservation may be enhanced in Europe through designation of ESUs.