Data from: Large-scale phylogeny of chameleons suggests African origins and Eocene diversification

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 constrainedTime-calibrated BEAST output tree of all taxa studied (6 genes), monophyly of large Madagascar chameleons constrained (Calumma+Furcifer).0allcham_expOut20120319NoIntSum.treesMrBayes tree 6 genes Calumma+Furcifer constrainedBayesian 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).allcham_expOut20120319NoIntMadMonoB.conML tree, Calumma+Furcifer constrainedMaximum Likelihood tree of all taxa studied (6 genes, partition by genes), monophyly of large Madagascar chameleons constrained (Calumma+Furcifer).allcham_expOut2NoInt_MadMonoConstraint_bygene_a_boot.treesMrBayes tree, 13 genesBayesian Inference phylogenetic tree (50% majority rule consensus), reduced taxon sets, 13 genes, no topological constraints.ChamsReduced_13genesMB_20110229MBcon.treesBEAST tree, 13 genesBEAST output tree, time calibrated, no topological constraints, 13 genes / reduced set of taxaChamsReduced_13geneBEASTinputNoInt5sum.treesML tree, 13 genesMaximum Likelihood tree, reduced taxon sets, 13 genes, no topological constraints.ChamsRed_13genesIncD_20110229MLboot.treesML tree, 6 genes, no topological constraintMaximum Likelihood tree, 6-gene data set, all taxa, partition by gene, no topological constraint.allcham_expOut2NoInt_MLbygene_a_boot.treesBEAST tree, 6 genes, Calumma+Furcifer and position of Rampholeon constrainedTime calibrated BEAST tree, 6 genes, topological constraints enforced: Calumma+Furcifer and position of Rhampholeon as in 13-gene analysis.allcham_expOut20120319NoInt3sum.treesMrBayes tree 6 genes, no topological constraintBayesian Inference phylogenetic tree (50% majority rule consensus) calculated with MrBayes, partitioned analysis by gene, 6 genes, all taxa included, no topological constraint.allcham_expOut20120319con.treesBEAST tree, 6 genes, Calumma+Furcifer constrained, partitioned by CodonTime calibrated BEAST tree, 6 genes, Calumma+Furcifer constrained, partitioning scheme by codon.allchamExpOut20120319NoIntMadMono123SUM.trees6-gene alignment Alignment with MrBayes blockNEXUS format file of the 6-gene alignment with settings for MrBayes Bayesian Inference analysis.allcham_expOut20120319.nex13 gene Alignment with MrBayes blockNEXUS format file of 13-gene alignment with command block incluzding settings for MrBayes Bayesian Inference phylogenetic analysis.ChamsReduced_13genesMBbygene_20110229.nex