Genetic Legacy of the Last Ice Age Shapes Shallow Phylogeographic Structure in a Widespread Mediterranean Snake

Aim: Mediterranean peninsulas typically harbour high intraspecific genetic diversity associated with long-term persistence in multiple glacial refugia. However, some widespread taxa show unexpectedly shallow phylogeographic structure. Here, we investigate which historical processes can generate a pattern of strong genetic depletion within a classic southern European refugial region. Location: Iberian Peninsula and southern France. Taxon: A widespread Mediterranean colubrid snake (Zamenis scalaris). Methods: We combined range-wide multilocus genetic data (mitochondrial and nuclear markers) with coalescent-based demographic inference, species distribution modelling under present and Last Glacial Maximum climatic conditions, and Pliocene–Pleistocene fossil evidence. This integrative framework was used to reconstruct refugial history, post-glacial expansion dynamics, and spatial patterns of genetic diversity. Results: Both mitochondrial and nuclear markers indicate very low genetic variation across most of the species' range, with rare, derived haplotypes geographically clustered in southeastern and eastern Iberia. This pattern, combined with demographic reconstructions, indicates persistence through the Late Pleistocene in a single, spatially restricted refugium with reduced effective population size, followed by rapid post-glacial expansion around ~20 ka. Climatic suitability models and fossil records independently support this scenario, showing persistent suitable conditions confined to eastern–southeastern Iberia during glacial phases and a broad east-to-west temporal gradient of fossil occurrences consistent with long-term eastern persistence and subsequent westward expansion. Main Conclusions: Despite its long-term presence in Iberia, Zamenis scalaris lacks the multilayered phylogeographic structure typical of many Mediterranean vertebrates. Its genetic legacy is consistent with strong Late Pleistocene contraction that overrode deeper evolutionary history. This study highlights how glacial dynamics can erode genetic complexity even in widespread taxa within classical refugial regions, with broader implications for comparative phylogeography and the interpretation of genetic diversity patterns in southern Europe.