10.5061/DRYAD.11350
Tolley, Krystal A.
South African National Biodiversity Institute
Townsend, Ted M.
San Diego State University
Vences, Miguel
Technische Universität Braunschweig
Data from: Large-scale phylogeny of chameleons suggests African origins
and Eocene diversification
Dryad
dataset
2013
Oligocene
overeseas dispersal
Squamata
Eocene
Chamaeleonidae
Holocene
2013-04-11T14:43:00Z
2013-04-11T14:43:00Z
en
https://doi.org/10.1098/rspb.2013.0184
2762578 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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
Africa
Seychelles
Madagascar