Pleistocene island connectivity did not enhance dispersal or impact population size change in Galápagos geckos

Patterns of biodiversity on remote archipelagos are largely shaped by intra-archipelago colonization followed by <i>in situ</i> diversification. Pleistocene sea-level fluctuations purportedly enhanced gene flow among terrestrial organisms by increasing connectivity during periods of lower sea level. Furthermore, changes in sea-level are hypothesized to impact population sizes as a result of fluctuations in island sizes. Here, we used genomic data to test the role of Pleistocene island connectivity on the diversification and demographics of leaf-toed geckos (<i>Phyllodactylus</i>) endemic to the Galápagos. Consistent with previous studies, we found that present diversity of Galápagos <i>Phyllodactylus</i> stems from three independent dispersal events. Contrary to the hypothesis of Pleistocene-driven diversification, we found no correspondence between lineage divergence and island connectivity. Furthermore, we found no evidence of introgression; demographic modelling indicated that all species increased rapidly in effective population size in the period 20-150 ka, and these inferred demographic expansions were largely asynchronous and apparently unassociated with species or island age. Collectively, these results indicate that more complex abiotic and/or biotic factors may better explain the recent demographic history of <i>Phyllodactylus</i> and underscore the need for additional population genomic studies of terrestrial taxa to understand the impact of past climate cycles on Galápagos island communities.