Oceanic dispersal has emerged as an important factor contributing to biogeographic patterns in numerous taxa. Chameleons are a clear example of this, as they are primarily found in Africa and Madagascar, but the age of the family is post-Gondwanan break-up. A Malagasy origin for the family has been suggested, yet this hypothesis has not been tested using modern biogeographic methods with a dated phylogeny. To examine competing hypotheses of African and Malagasy origins, we generated a dated phylogeny using between six and 13 genetic markers, for up to 174 taxa representing greater than 90 per cent of all named species. Using three different ancestral-state reconstruction methods (Bayesian and likelihood approaches), we show that the family most probably originated in Africa, with two separate oceanic dispersals to Madagascar during the Palaeocene and the Oligocene, when prevailing oceanic currents would have favoured eastward dispersal. Diversification of genus-level clades took place in the Eocene, and species-level diversification occurred primarily in the Oligocene. Plio-Pleistocene speciation is rare, resulting in a phylogeny dominated by palaeo-endemic species. We suggest that contraction and fragmentation of the Pan-African forest coupled to an increase in open habitats (savannah, grassland, heathland), since the Oligocene played a key role in diversification of this group through vicariance.
BEAST tree 6 genes Calumma+Furcifer constrained
Time-calibrated BEAST output tree of all taxa studied (6 genes), monophyly of large Madagascar chameleons constrained (Calumma+Furcifer).
MrBayes tree 6 genes Calumma+Furcifer constrained
Bayesian Inference phylogenetic tree of all taxa studied (6 genes, calculated with MrBayes (50% majority rule consensus), partition by gene, monophyly of large Madagascar chameleons constrained (Calumma+Furcifer).
ML tree, Calumma+Furcifer constrained
Maximum Likelihood tree of all taxa studied (6 genes, partition by genes), monophyly of large Madagascar chameleons constrained (Calumma+Furcifer).
MrBayes tree, 13 genes
Bayesian Inference phylogenetic tree (50% majority rule consensus), reduced taxon sets, 13 genes, no topological constraints.
BEAST tree, 13 genes
BEAST output tree, time calibrated, no topological constraints, 13 genes / reduced set of taxa
ML tree, 13 genes
Maximum Likelihood tree, reduced taxon sets, 13 genes, no topological constraints.
ML tree, 6 genes, no topological constraint
Maximum Likelihood tree, 6-gene data set, all taxa, partition by gene, no topological constraint.
BEAST tree, 6 genes, Calumma+Furcifer and position of Rampholeon constrained
Time calibrated BEAST tree, 6 genes, topological constraints enforced: Calumma+Furcifer and position of Rhampholeon as in 13-gene analysis.
MrBayes tree 6 genes, no topological constraint
Bayesian Inference phylogenetic tree (50% majority rule consensus) calculated with MrBayes, partitioned analysis by gene, 6 genes, all taxa included, no topological constraint.
BEAST tree, 6 genes, Calumma+Furcifer constrained, partitioned by Codon
Time calibrated BEAST tree, 6 genes, Calumma+Furcifer constrained, partitioning scheme by codon.
6-gene alignment Alignment with MrBayes block
NEXUS format file of the 6-gene alignment with settings for MrBayes Bayesian Inference analysis.
13 gene Alignment with MrBayes block
NEXUS format file of 13-gene alignment with command block incluzding settings for MrBayes Bayesian Inference phylogenetic analysis.