Reconstructing the complex colonisation histories of lizards across Mediterranean archipelagos

Aim: The Mediterranean Basin is a global biodiversity hotspot and has one of the longest histories of human–biota interactions. Islands host a large fraction of Mediterranean diversity and endemism, but the relative importance of natural versus human-mediated colonisation processes in shaping the distribution and genetic structure of Mediterranean island fauna remains poorly understood. Here, we combine population genomics, demographic models and palaeoshoreline reconstructions to establish the island-colonisation dynamics of wall lizards in Mediterranean archipelagos. Location: Four Mediterranean archipelagos in Italy and Croatia. Taxon: The wall lizard Podarcis siculus. Methods: We used ddRAD sequencing to genotype 140 lizards from 23 island and mainland populations. Analyses of admixture and site frequency spectra were used to reconstruct population structure, demographic history and variation of gene flow through time. Genomic results were integrated with palaeogeographical reconstructions and were compared to archaeological evidence of human presence on these islands. Results: Although many island populations of this species are assumed to be non-native, we find that many islands were colonised long before any known human settlements (230,000–12,000 years ago). This natural colonisation most likely occurred through land bridges during glacial marine regression or by over-sea rafting. On the other hand, islands distant from the continent were often colonised recently, and some of the estimated island colonisation times match historical records of human arrival. We also determine that long-established island populations generally show lower genetic diversity compared to proximate mainland populations, contrary to recently colonised islands that must have experienced higher rates of post-colonisation gene flow. Main Conclusion: Our integrated approach provides us with the power to accurately quantify the origin, timing and mode of island colonisation. This framework helps to clarify the biogeographical and evolutionary history of island populations, with important implications for conservation and management of island biodiversity.