Patterns of biodiversity on remote archipelagos are largely shaped by intra-archipelago colonization followed by in situ 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 (Phyllodactylus) endemic to the Galápagos. Consistent with previous studies, we found that present diversity of Galápagos Phyllodactylus stems from three independent dispersal events. Contrary to the hypothesis of Pleistocene-driven diversification, we found no correspondence between lineage divergence, island ages, and island connectivity. Furthermore, we found no evidence of introgression, demographic modeling indicated that all species increased rapidly in effective population size between 20–150 kya, 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 Phyllodactylus and underscore the need for additional population genomic studies of terrestrial taxa to understand the impact of past climate cycles on Galápagos island communities.

This is a RADseq data set generated for the Phyllodactylus species of the Galapagos islands. We used ipyrad to assemble the raw sequence data, estimated phylogenetic trees using both concatenation, species tree, and multispecies coalescent network based approaches, and lastly reconstructed demographic histories for each species and in a hierarchical model to assess shared population size changes through time.