Data from: Vicariance divergence and gene flow among islet populations of an endemic lizard

Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species which inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet–mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene flow estimates from the mainland to the islet populations was positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.DataDescriptionRunemark et alA file describing the headers and contents of the other uploaded filesMicrosatellite_data_Runemark_et_alMicrosatellite data of the individuals included in the study. The first column entitled population includes the abbreviation for population affinity of the individuals, see Fig. 1 in the paper. The following columns contain allele 1 and 2 for each loci used in the analysis; Lv319 1 is the first allele and Lv319 2 is the second.Microsatellite_data_Runemark_et_alMicrosatellite data of the individuals included in the study. The first column entitled population includes the abbreviation for population affinity of the individuals, see Fig. 1 in the paper. The following columns contain allele 1 and 2 for each loci used in the analysis.Geographic_locals_Runemark_et_alContains a table with full population names in the first column (the names of the islets or names from the geographic locals or churches nearby), the population abbreviations used in the microsatellite files and in Fig. 1 in the manuscript in the second, habitat (i. e. if it is an islet or mainland local) in the third column, and the coordinates (latitude,longitude) in the fourth column