# Pleistocene island connectivity did not enhance dispersal or impact population size change in Galápagos geckos [https://doi.org/10.5061/dryad.vx0k6dk0n](https://doi.org/10.5061/dryad.vx0k6dk0n) The data contained here are the assembled genomic data needed to reconstruct the phylogenetic trees, test for phylogentic reticulation, and reconstruct the demographic history of each species. ## Description of the data and file structure Concatenated, unlinked SNPs in phylip format. These files can be used to reconstruct the maximum likelihood of concatenated trees and dated phylogenetic trees from BEAST presented in the paper. These alignments can be viewed in a text editor or commonly used Geneious software: Alignment for all species, including outgroups: all_taxa_09122022.usnps Alignment of the *galapagensis* group only: galapagensis_taxa_09122022.usnps Variant calling format file with all SNPs, these files were used for population structure analyses (e.g., PCA), the species tree estimation (in the software PoMo), and demographic reconstructions. These files can be manipulated in R (e.g., with the vcfR library) or using command line tools (e.g., vcftools): vcf file for all species, including outgroups: all_taxa_09122022.vcf vcf file for the *galapagensis* group only: galapagensis_taxa_09122022.vcf Input data for Snaq analyses. This includes the input quartet file and the starting phylogeny: Quartet file: Phyllo_02152024_Quart_all.csv Starting phylogeny: Phyllo_start_tree_Snaq_02152024.tre Input files and Jupyter notebooks for Phylogeographic Temporal Analysis: Jupyter notebook to create the mSFS input file: PTA-GalapagosGeckos-Create-mSFS.ipynb Jupyter notebooks to run the three PTA analyses: PTA-GalapagosGeckos-AllPops-Expansion.ipynb; PTA-GalapagosGeckos-4pop-RecentExpansion.ipynb; PTA-GalapagosGeckos-4pop-AncientExpansion.ipynb Site-frequency spectrum files for all *galapagensis* species: sfs_files.zip

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.