Combined Effects of Isolation by Distance, Ecology and Resistance on Population Genetic Divergence in Rana kukunoris From Qinghai‐Tibetan Plateau

ABSTRACT Investigation of the impact of ecological and landscape processes on genetic population structuring and differentiation is critical for understanding adaptation to different environments. Several hypotheses, including isolation by distance (IBD), isolation by environment (IBE) and isolation by resistance (IBR), have been proposed to explain the spatial patterns of genetic diversity and differentiation among populations. However, these hypotheses have rarely been tested together, and the relative importance of these processes is still unclear. Here, we employed genome‐wide SNP data to investigate the genetic structure of 32 Rana kukunoris populations from the Qinghai‐Tibetan Plateau and explored the patterns and extent of genetic divergence among these populations in relation to the three aforementioned isolation patterns. The results indicated that the species was genetically highly structured ( F st values ranging from 0.03 to 0.80) and composed of three distinct lineages, with a high level of gene flow between the eastern lineage and the other two lineages (southern and western). Geographic isolation, environmental isolation and landscape resistance have all significantly influenced genetic differentiation among populations, as indicated by Mantel tests, suggesting that all three processes (viz. IBD, IBE and IBR) have shaped the degree of genetic differentiation. Variance partitioning (Varpart4) showed that IBD accounted for most of the variance (16.8%), followed by IBR (4.1%) and IBE (3.2%). The three most important environmental factors influencing genetic divergence among R. kukunoris populations, identified through multiple regression on distance matrices (MRM), were the occurrence of saline–alkali soil, road proximity and altitude. Interestingly, the relative contributions of isolation hypotheses varied regionally: MRM and varpart4 analyses revealed that IBE dominated in the north (85.2%), shaped by rivers and precipitation; IBR was strongest in the east (23.0%), driven by rivers, road proximity and distance; while IBD prevailed in the south (8.5%). These findings provide novel insights into the different factors and their relative importance in shaping the degree of genetic differentiation in high‐altitude amphibians.