DOI: 10.5061/dryad.n34d4m7
title: Data from: The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

description: A primary goal of biogeography is to understand how large-scale
 environmental processes, like climate change, affect diversification. One
 often-invoked but seldom tested process is the so-called
 ''species-pump'' model, in which repeated bouts of
 co-speciation is driven by oscillating climate-induced habitat
 connectivity cycles. For example, over the past three million years, the
 landscape of the Philippine Islands has repeatedly coalesced and
 fragmented due to sea-level changes associated with the glacial cycles.
 This repeated climate-driven vicariance has been proposed as a model of
 speciation across evolutionary lineages codistributed throughout the
 islands. This model predicts speciation times that are temporally
 clustered around the times when interglacial rises in sea level fragmented
 the islands. Given the significance and conceptual impact the model has
 shown, surprisingly few tests of this prediction have been provided. We
 collected comparative genomic data from 16 pairs of insular gecko
 populations to test the prediction of temporally clustered divergences.
 Specifically, we analyze these data in a full-likelihood, Bayesian
 model-choice framework to test for shared divergence times among the
 pairs. Our results provide support against the species-pump model
 prediction in favor of an alternative interpretation, namely that each
 pair of gecko populations diverged independently. These results suggest
 the repeated bouts of climate-driven landscape fragmentation has not been
 an important mechanism of speciation for gekkonid lizards on the
 Philippine Islands. Interpretations of shared mechanisms of
 diversification historically have been pervasive in biogeography, often
 advanced on the basis of taxonomy-based depictions of species
 distributions. Our results call for possible re-evaluation of other,
 classic co-diversification studies in a variety of geographic systems.
description: Project
 repositoryAn archived version of
 the project git repository. The archive is in Zenodo; the original
 repository is hosted on GitHub.NCBI
 BioProjectThis NCBI BioProject
 includes the raw (demultiplexed) sequence reads that were used in the
 paper.Supplemental Table
 1The
 data for all samples included in the three RADseq
 libraries.msg-samples-edited.txtSupplemental Table 2The data for all samples included in the 16 pairs of populations analyzed in this study. This is a subset of the data in Supplemental Table 1.comparison-samples-edited.txtAnimation from Supplemental Figure 2Animation of approximate sea-level changes in the Philippine Islands over the last 430,000 years. Sea-level estimates are from the projection of Spratt and Lisiecki (2016) based on seven reconstructions. Bathymetry data are from the ETOPO1 1-arc-minute global relief model (Amante and Eakins, 2009). Animation generated using marmap version 1.0.2 (Pante and Simon-Bouhet, 2013), ggplot2 Version 2.2.1 (Wickham, 2009), ImageMagick Version 6.9.10-8 Q16 x86_64 20180723, and FFmpeg Version 4.0.2-2. The source code for generating the plot is available at https://github.com/phyletica/animating-sea-level-change. This animation can also be viewed at https://youtu.be/NjGdCezUvw8.animated-bathymetry.mp4