Abstract
Quaternary glacial cycles have been key drivers of diversification for Holarctic species, promoting divergence, isolation, and extinction processes in numerous taxa. These cycles facilitated evolutionary radiations in some groups but also erased much of the evolutionary history of species with northern origins. Here, we investigate the evolutionary and phylogeographic history of the Palmate Newt (Lissotriton helveticus), a widespread species in post-glacial ecosystems in Western Europe. We generate genome-wide ddRADseq for 205 individuals from 51 populations across the species range and reconstruct its phylogeographic and demographic history, assess population structure, and characterize ecological paleoniches for the species at different climatic periods. Results identify several distinct lineages exhibiting strong genetic differentiation, primarily driven by geographic barriers and isolation in historical refugia with admixture in transition zones. Phylogeographic reconstructions suggest that the main glacial refugium for L. helveticus was most likely located in northern Iberia. Two main dispersal routes were identified: one extending eastward through the Ebro River Basin and a second, following a northeastward pathway across the Pyrenees and into Europe. We specifically pinpoint the origin of Europe's recolonization route to a specific set of localities surrounding Andorra, where L. helveticus probably expanded along tributaries to the Garonne River into southern and western France over warm periods. By integrating genomic, geographic, and paleoclimatic data, this study provides an in-depth understanding of how climate shaped the evolutionary history of this temperate species and reinforces the importance of waterways for amphibian dispersal dynamics.