DOI: 10.5061/dryad.p65mc58
title: Data from: Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation

description: A primary challenge for modern phylogeography is understanding how ecology
 and geography, both contemporary and historical, shape the spatial
 distribution and evolutionary histories of species. Phylogeographic
 patterns are the result of many factors, including geology, climate,
 habitat, colonization history, and lineage-specific constraints. Assessing
 the relative influences of these factors is difficult because few species,
 regions, and environments are sampled in enough detail to compare
 competing hypotheses rigorously and because a particular phylogeographic
 pattern can potentially result from different evolutionary scenarios. The
 silky anoles (Anolis sericeus complex) of Central America and Mexico are
 abundant and found in all types of lowland terrestrial habitat, offering
 an excellent opportunity to test the relative influences of the factors
 affecting diversification. Here, we performed a range-wide statistical
 phylogeographic analysis on restriction-site associated DNA (RAD) markers
 from silky anoles and compared the phylogeographic patterns we recovered
 to historical and contemporary environmental and topographic data. We
 constructed niche models to compare niche overlap between sister lineages
 and conducted coalescent simulations to characterize how the major
 lineages of silky anoles have diverged. Our results revealed that the mode
 of divergence for major lineage diversification events was geographic
 isolation, resulting in ecological divergence between lineages, followed
 by secondary contact. Moreover, comparisons of parapatric sister lineages
 suggest that ecological niche divergence contributed to isolation by
 environment in this system, reflecting the natural history differences
 among populations in divergent environments.
description: ANSE_caribtehuanCaribbean silky anole localities used for Tehuantepec-only ENMsANSE_pactehuanPacific silky anole localities used for Tehuantepec-only ENMsANSE_RAxML_infileInfile for RAxML analyses for 75 silky anoles + 1 outgroup (Anolis laeviventris)ANSE_RAxML_resultOutput for RAxML analysis of 75 silky anoles + 1 outgroup (Anolis laeviventris)infile_ANSE_mrbayesInfile for MrBayes analyses for 75 silky anoles + 1 outgroup (Anolis laeviventris), including partitionsANSE_consensus_mrbayesMrBayes consensus results for analysis of 75 silky anoles + 1 outgroup (Anolis laeviventris)ANSE_samplingforDryadFile with coordinates and field/museum numbers for localities used in phylogeographic analyses and generating ecological niche models.DHL412_R1.fqRaw Illumina reads for DHL412DHL413_R1.fqRaw Illumina reads for DHL413FRMP94_R1.fqRaw Illumina reads for FRMP94JAC24546_R1.fqRaw Illumina reads for JAC24546AMH432_R1.fqRaw Illumina reads for AMH432RVG265_R1.fqRaw Illumina reads for RVG265RVG275_R1.fqRaw Illumina reads for RVG275LNG0029_R1.fqRaw Illumina reads for LNG0029POE4321_R1.fqRaw Illumina reads for POE4321POE4349_R1.fqRaw Illumina reads for POE4349POE4092_R1.fqRaw Illumina reads for POE4092LNG0172_R1.fqRaw Illumina reads for LNG0172LNG0173_R1.fqRaw Illumina reads for LNG0173LNG0170_R1.fqRaw Illumina reads for LNG0170LNG0179_R1.fqRaw Illumina reads for LNG0179LNG0177_R1.fqRaw Illumina reads for LNG0177LNG0174_R1.fqRaw Illumina reads for LNG0174LNG0186_R1.fqRaw Illumina reads for LNG0186LNG0171_R1.fqRaw Illumina reads for LNG0171LNG0169_R1.fqRaw Illumina reads for LNG0169LNG0168_R1.fqRaw Illumina reads for LNG0168POE4359_R1.fqRaw Illumina reads for POE4359POE4070_R1.fqRaw Illumina reads for POE4070POE4090_R1.fqRaw Illumina reads for POE4090ANMO1852_R1.fqRaw Illumina reads for ANMO1852POE4058_R1.fqRaw Illumina reads for POE4058POE4053_R1.fqRaw Illumina reads for POE4053POE4078_R1.fqRaw Illumina reads for POE4078LNG0068_R1.fqRaw Illumina reads for LNG0068LNG0106_R1.fqRaw Illumina reads for LNG0106LNG0105_R1.fqRaw Illumina reads for LNG0105LNG0104_R1.fqRaw Illumina reads for LNG0104LNG0066_R1.fqRaw Illumina reads for LNG0066LNG0103_R1.fqRaw Illumina reads for LNG0103LNG0092_R1.fqRaw Illumina reads for LNG0092LNG0095_R1.fqRaw Illumina reads for LNG0095LNG0102_R1.fqRaw Illumina reads for LNG0102LNG0100_R1.fqRaw Illumina reads for LNG0100POE4081_R1.fqRaw Illumina reads for POE4081POE3966_R1.fqRaw Illumina reads for POE3966LNG0062_R1.fqRaw Illumina reads for LNG0062LNG0067_R1.fqRaw Illumina reads for LNG0067LNG0122_R1.fqRaw Illumina reads for LNG0122LNG0113_R1.fqRaw Illumina reads for LNG0113LNG0123_R1.fqRaw Illumina reads for LNG0123LNG0055_R1.fqRaw Illumina reads for LNG0055LNG0071_R1.fqRaw Illumina reads for LNG0071LNG0094_R1.fqRaw Illumina reads for LNG0094LNG0112_R1.fqRaw Illumina reads for LNG0112LNG0076_R1.fqRaw Illumina reads for LNG0076LNG0130_R1.fqRaw Illumina reads for LNG0130LNG0074_R1.fqRaw Illumina reads for LNG0074LNG0056_R1.fqRaw Illumina reads for LNG0056LNG0143_R1.fqRaw Illumina reads for LNG0143LNG0142_R1.fqRaw Illumina reads for LNG0142LNG0144_R1.fqRaw Illumina reads for LNG0144LNG0145_R1.fqRaw Illumina reads for LNG0145LNG0147_R1.fqRaw Illumina reads for LNG0147LNG0146_R1.fqRaw Illumina reads for LNG0146POE4143_R1.fqRaw Illumina reads for POE4143POE4306_R1.fqRaw Illumina reads for POE4306POE4172_R1.fqRaw Illumina reads for POE4172POE4332_R1.fqRaw Illumina reads for POE4332LNG0082_R1.fqRaw Illumina reads for LNG0082LNG0081_R1.fqRaw Illumina reads for LNG0081POE3481_R1.fqRaw Illumina reads for POE3481POE3503_R1.fqRaw Illumina reads for POE3503POE3519_R1.fqRaw Illumina reads for POE3519POE3404_R1.fqRaw Illumina reads for POE3404POE4260_R1.fqRaw Illumina reads for POE4260POE3403_R1.fqRaw Illumina reads for POE3403POE3604_R1.fqRaw Illumina reads for POE3604POE3603_R1.fqRaw Illumina reads for POE3603POE3616_R1.fqRaw Illumina reads for POE3616JS818_R1.fqRaw Illumina reads for JS818