Phylogeography, evolutionary history, and effects of glaciations in a species (Zootoca vivipara) inhabiting multiple biogeographic regions

[Aim]: During glaciations, the distribution of temperate species inhabiting the Northern Hemisphere generally contracts into southern refugia; and in boreo‐alpine species of the Northern Hemisphere, expansion from Northern refugia is the general rule. Little is known about the drivers explaining vast distributions of species inhabiting multiple biogeographic regions (major biogeographic regions defined by the European Environmental Agency). Here we investigate the fine‐scale phylogeography and evolutionary history of the Eurasian common lizard (Zootoca vivipara), the terrestrial reptile with the world's widest and highest latitudinal distribution, that inhabits multiple biogeographic regions.[Location]: Eurasia.[Methods]: We generated the largest molecular dataset to date of Z. vivipara, ran phylogenetic analyses, reconstructed its evolutionary history, determined the location of glacial refuges and reconstructed ancestral biogeographic regions.[Results]: The phylogenetic analyses revealed a complex evolutionary history, driven by expansions and contractions of the distribution due to glacials and interglacials, and the colonization of new biogeographic regions by all lineages of Z. vivipara. Many glacial refugia were detected, most were located close to the southern limit of the Last Glacial Maximum. Two subclades recolonized large areas covered by permafrost during the last glaciation: namely, Western and Northern Europe and North‐Eastern Europe and Asia.[Main conclusions]: In Z. vivipara, most of the glacial refugia were located in the South of their current distribution. Previous studies suggested the existence of Northern refuges, but the species' inability to overwinter on permafrost and the lack of genetic support suggest that the presence of a refugia in the north of the Alps is unlikely. This species currently inhabits boreo‐alpine climates and retracted during previous glaciations into southern refugia, as temperate species. Two clades exhibited enormous geographic expansion that started from two distinct glacial refugia. These phylogeographic patterns were highly congruent with those of Vipera berus. Together they suggest that glacial retraction, the location of the refugia and absence of competition may have promoted the enormous geographic expansion of two clades.We thank M. Urieta for help during sampling of Z. vivipara. J.L. Horreo was supported by two Spanish MINECO post‐doc grants (FPDI‐2013‐16116 and IJCI‐2015‐23618). W. Mayer and M.L.A. Ceirans provided samples. Project funds were provided by the Swiss National Science Foundation (PPOOP3_128375, PP00P3_152929/1 to P.S.F.), the Spanish Ministry of Education and Science (CGL2008‐01522, CGL2012‐32459, CGL2016‐76918 to P.S.F.), and the Academy of Finland (grant no. 7108955 to T. Oksanen).Peer Reviewe