Environmental drivers of genetic diversity and connectivity in a mountain ungulate across the European and Dinaric Alps

Global environmental change is reshaping biodiversity by altering species connectivity, genetic diversity, and long-term viability. A key challenge is to disentangle how historical, environmental, and anthropogenic factors jointly shape contemporary genetic patterns. Here, we combine population genomics with landscape ecology tools to investigate the drivers of levels of genetic diversity and patterns of population genetic structure using more than 20 k Single Nucleotide Polymorphisms (SNPs) in the Northern chamois (Rupicapra rupicapra), a wide-ranging Alpine ungulate. Based on 465 individuals sampled across the European and Dinaric Alps as well as the Tatra Mountains, we revealed a pronounced hierarchical genetic structure, with clusters showing marked geographic variation in genetic diversity across the species range. Our results show that current genetic diversity largely reflects the genetic legacy of past climatic conditions, with areas of long-term stability acting as reservoirs of genetic variation. At the same time, large Alpine rivers emerge as strong barriers to gene flow, emphasizing the powerful role of natural landscape features in shaping genetic structure. In contrast, recent anthropogenic infrastructures exerted limited detectable influence, suggesting that contemporary patterns are still predominantly driven by natural processes of population differentiation. By explicitly quantifying the relative contributions of long-term climatic stability and contemporary landscape features to genetic diversity and connectivity, this study demonstrates that historical processes outweigh recent anthropogenic fragmentation in shaping current genetic patterns in this mountain ungulate