DOI: 10.5061/dryad.27q72
title: Data from: Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (Genus Oplurus)

description: Understanding the remarkably high species diversity and levels of endemism
 found among Madagascar’s flora and fauna has been the focus of many
 studies. One hypothesis that has received much attention proposes that
 Pleistocene climate fluctuations spurred diversification. However, while
 spatial patterns of distribution and phylogenetic relationships can
 provide support for biogeographic predictions, temporal estimates of
 divergence are required to determine the fit of these geospatial patterns
 to climatic or biogeographic mechanisms. We use multilocus DNA sequence
 data to test whether divergence times among Malagasy iguanid lizards of
 the subfamily Oplurinae are compatible with a hypotheses of Quaternary
 diversification. We estimate the oplurine species tree and associated
 divergence times under a relaxed clock model. In addition, we examine the
 phylogeographic structure and population divergence times within two
 sister-species of Oplurus primarily distributed in the northwest and
 southwest of Madagascar (O. cuvieri and O. cyclurus, respectively). We
 find that divergence events among oplurine lineages occurred in the
 Oligocene and Miocene and are thus far older and incompatible with the
 hypothesis that recent climate fluctuations are related to current species
 diversity. However, the timing of intraspecific divergences and spatial
 patterns of population genetic structure within O. cuvieri and O. cyclurus
 suggest a role for both intrinsic barriers and recent climate fluctuations
 at population-level divergences. Integrating information across spatial
 and temporal scales allows us to identify and better understand the
 mechanisms generating patterns diversity.
description: BEAST infile for Iguania
 ND1 dataXML formatted infile for
 fossil calibrated analysis of Iguania ND1 data in BEASTND1yule01.xml*BEAST infile for Species Tree Estimation of Subset AXML formated infile for species tree estimation of subset A dataset in *BEAST. Includes ND1, ND1 flanking regions, PRLR, and UBN1 sequences.subA01.xml*BEAST infile for Species Tree Estimation of Subset BXML formated infile for species tree estimation of subset B dataset in *BEAST. Includes ND1, ND1 flanking regions, PRLR, and UBN1 sequences.subB01.xmlBEAST infile for Oplurus cuvieri, constant pop sizeXML formated infile for estimation of Oplurus cuvieri gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes constant population size model.ocuvND1con02b.xmlBEAST infile for Oplurus cuvieri, exponential growthXML formated infile for estimation of Oplurus cuvieri gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes exponential growth model.ocuvND1exp02b.xmlBEAST infile for Oplurus cyclurus, constant pop sizeXML formated infile for estimation of Oplurus cyclurus gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes constant growth model.ocycND1con_ucld02b.xmlBEAST infile for Oplurus cyclurus, exponential growthXML formated infile for estimation of Oplurus cyclurus gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes exponential growth model.ocycND1exp_ucld02b.xmlBEAST infile for Oplurus cuvieri, Watershed Model Zone 8XML formated infile for extended Bayesian skyline plot analysis of Oplurus cuvieri from watershed model (Wilme et al. 2006) Zone 8 in BEAST 1.6.2. Includes sequence data for ND1, ND1 flanking regions, PRLR, and UBN1.cuvWilmeZ8a.xmlBEAST infile for Oplurus cyclurus, Watershed Model Zone 6XML formated infile for extended Bayesian skyline plot analysis of Oplurus cyclurus from watershed model (Wilme et al. 2006) Zone 6 in BEAST 1.6.2. Includes sequence data for ND1, ND1 flanking regions, PRLR, and UBN1.ocycWilmeZ6a.xmlBEAST infile for Oplurus cyclurus, Watershed Model Zone EXML formated infile for extended Bayesian skyline plot analysis of Oplurus cyclurus from watershed model (Wilme et al. 2006) Zone E in BEAST 1.6.2. Includes sequence data for ND1, ND1 flanking regions, PRLR, and UBN1.ocycWilmeZEa.xmlND1 alignmentAlignment of sequence data for ND1 and ND1 flanking regions from all oplurine taxa included in this study.oplurineND1.nexPRLR alignmentAlignment of sequence data for PRLR from all oplurine taxa included in this study. Alleles were determined either through TA cloning or computationally using the program PHASE.oplurinePRLR.nexUBN1 alignmentAlignment of sequence data for UBN1 from all oplurine taxa included in this study. Alleles were determined either through TA cloning or computationally using the program PHASE.oplurineUBN1.nex