Data from: Reconstructing the complex colonization 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 vs. human-mediated colonization 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-colonization 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
paleogeographic 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 colonized long before any known human settlements
(230,000–12,000 years ago). This natural colonization 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
colonized recently, and some of the estimated island colonization 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 colonized
islands that must have experienced higher rates of post-colonization gene
flow. Main conclusion: Our integrated approach provides us with the power
to accurately quantify the origin, timing, and mode of island
colonization. This framework helps to clarify the biogeographic and
evolutionary history of island populations, with important implications
for conservation and management of island biodiversity.