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 data sets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the genome reveal a sharp population decline since the last interglacial, indicating an association between colder climates and population declines before anthropogenic influence. Using our genome and genetic data from 100 individuals, largely sampled in a citizen-science project across the contemporary range, we conduct the first population genomic analysis for this species. We find clear evidence for population structure across the species’ core Central European range. Notably, our data show that the Alpine population, characterized by strong differentiation and reduced genetic diversity, is reproductively isolated from other regions and likely represents a differentiated evolutionary significant unit (ESU). The predominantly declining Eastern European populations also 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 the designation of ESUs.

中文翻译：

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欧洲受威胁花园睡鼠的单倍型分辨基因组和群体基因组学


基因组资源对于评估遗传多样性和支持保护工作非常重要。花园睡鼠 （Eliomys quercinus） 是一种小型啮齿动物，经历了欧洲最严重的现代种群下降之一。我们提出了一个高质量的单倍型分辨的花园休眠小鼠参考基因组，并将全面的短读长转录组学数据集与基于同源性的方法相结合，以生成高度完整的基因注释。基因组的人口历史分析显示，自上次间冰期以来，种群数量急剧下降，这表明较冷的气候与人为影响之前的种群下降之间存在关联。利用我们来自 100 个个体的基因组和遗传数据，大部分是在当代范围内的一个公民科学项目中采样的，我们对该物种进行了第一次种群基因组分析。我们发现了该物种核心中欧分布区种群结构的明确证据。值得注意的是，我们的数据表明，以强分化和遗传多样性降低为特征的高山种群在生殖上与其他区域隔离，可能代表一个分化的进化显着单位 （ESU）。以下降为主的东欧种群也显示出近期孤立的迹象，这种模式与全新世期间从西欧到东欧的活动范围扩张一致，使遗留种群现在面临局部灭绝。总体而言，我们的研究结果表明，欧洲可能会通过指定 ESU 来加强花园睡鼠的保护。