DOI: 10.5061/dryad.m81b5
title: Data from: Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling

description: Until recently, most phylogeographic approaches have been unable to
 distinguish between demographic and range expansion processes, making it
 difficult to test for the possibility of range expansion without
 population growth and vice versa. In this study, we applied a Bayesian
 phylogeographic approach to reconstruct both demographic and range
 expansion in the lizard Liolaemus darwinii of the Monte Desert in Central
 Argentina, during the Late Quaternary. Based on analysis of 14 anonymous
 nuclear loci and the cytochrome b mitochondrial DNA gene, we detected
 signals of demographic expansion starting at ~55 ka based on Bayesian
 Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial
 diffusion suggested that range expansion occurred only between ~95 and 55
 ka, and more recently, diffusion rates were very low during demographic
 expansion. The possibility of population growth without substantial range
 expansion could account for the shared patterns of demographic expansion
 during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and
 other lizards of the Monte Desert. We found substantial variation in
 diffusion rates over time, and very high rates during the range expansion
 phase, consistent with a rapidly advancing expansion front towards the
 southeast shown by palaeo-distribution models. Furthermore, the estimated
 diffusion rates are congruent with observed dispersal rates of lizards in
 field conditions and therefore provide additional confidence to the
 temporal scale of inferred phylogeographic patterns. Our study highlights
 how the integration of phylogeography with palaeo-distribution models can
 shed light on both demographic and range expansion processes and their
 potential causes.
description: Nexus_filesCompressed zip file containing the alignments of DNA sequences for cyt b and phased alleles of 14 anonymous nuclear loci in nexus formatPhase_filesCompressed zip file containing the input and output files of PHASE analyses for each of 14 anonymous nuclear lociTCS_filesCompressed zip file containing the output log files of TCS analyses for cyt b and for phased alleles of 14 anonymous nuclear lociBeast_filesCompressed zip file containing the input files of Extended Bayesian Skyline Plot (EBSP), Standard Random Walk (SRW), and Relaxed Random Walk (RRW) analyses in BEAST. Log files for marginal likelihood estimation (MLE), the maximum credibility tree (MCC), and the KML file for visualization in Google Earth are also included for SRW and RRW analyses.Structure_filesCompressed zip file containing the input and output files of STRUCTURE analyses for all loci and for cyt b only.Geneland_filesCompressed zip file containing the input and output files of GENELAND analyses for all loci.Beast_strict_clock_filesCompressed zip file containing the input files of Extended Bayesian Skyline Plot (EBSP), Standard Random Walk (SRW), and Relaxed Random Walk (RRW) analyses in BEAST using a strict molecular clock for the substitution rate of cyt b. Log files for marginal likelihood estimation (MLE), the maximum credibility tree (MCC), and the KML file for visualization in Google Earth are also included for SRW and RRW analyses.0k_patagoniaBioclimatic layers for current conditions obtained from WorldClim used in species-distribution modeling with Maxent21k_CCSM_PatagoniaBioclimatic layers for past conditions (21 kya, CCSM model) obtained from WorldClim used in species-distribution modeling with Maxent21k_MIROC_PatagoniaBioclimatic layers for past conditions (21 kya, MIROC model) obtained from WorldClim used in species-distribution modeling with Maxent120k_PatagoniaBioclimatic layers for past conditions (120 kya) obtained from WorldClim used in species-distribution modeling with MaxentGeoreferenced localitiesGeographic coordinates of sampled localities used in species-distribution modeling with Maxentlocalities.csv