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.
BEAST infile for Iguania ND1 data
XML formatted infile for fossil calibrated analysis of Iguania ND1 data in BEAST
ND1yule01.xml
*BEAST infile for Species Tree Estimation of Subset A
XML 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 B
XML formated infile for species tree estimation of subset B dataset in *BEAST. Includes ND1, ND1 flanking regions, PRLR, and UBN1 sequences.
subB01.xml
BEAST infile for Oplurus cuvieri, constant pop size
XML 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.xml
BEAST infile for Oplurus cuvieri, exponential growth
XML 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.xml
BEAST infile for Oplurus cyclurus, constant pop size
XML 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.xml
BEAST infile for Oplurus cyclurus, exponential growth
XML 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.xml
BEAST infile for Oplurus cuvieri, Watershed Model Zone 8
XML 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.xml
BEAST infile for Oplurus cyclurus, Watershed Model Zone 6
XML 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.xml
BEAST infile for Oplurus cyclurus, Watershed Model Zone E
XML 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.xml
ND1 alignment
Alignment of sequence data for ND1 and ND1 flanking regions from all oplurine taxa included in this study.
oplurineND1.nex
PRLR alignment
Alignment 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.nex
UBN1 alignment
Alignment 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