Multiple processes - including dispersal, morphological innovation, and habitat change - are frequently cited as catalysts for increased diversification. We investigate these processes and the causal linkages among them in the genus Cyphostemma (Vitaceae), a clade comprising ~200 species that is unique in the Vitaceae for its diversity of growth habits. We reconstruct time-calibrated evolutionary relationships among 64 species in the genus using five nuclear and chloroplast markers, and infer the group’s morphological and biogeographic history. We test for changes in speciation rate, and evaluate the temporal association and sequencing of events with respect to dispersal, habitat change, and morphological evolution using a Monte Carlo simulation approach. In Cyphostemma, neither dispersal nor morphological evolution is associated with shifts in speciation rate, but dispersal is associated with evolutionary shifts in growth form. Evolution of stem succulence, in particular, is associated with adaptation to local, pre-existing conditions following long-distance dispersal, not habitat change in situ. We suggest that the pattern of association between dispersal, morphological innovation, and diversification may depend on the particular characters under study. Lineages with evolutionarily labile characters, such as stem succulence, do not necessarily conform to the notion of niche conservatism and instead demonstrate remarkable morphological adaptation to local climate and edaphic conditions following dispersal.
Readme
Consult this master Readme for information about all files in this Dryad repository.
BEAST_3Partition_NormalPriors_DivergenceTimeEstimation
The XML file provides the full set of parameters used to run a Bayesian analysis of phylogeny and divergence times using the program BEAST 2. Parameters include normally distributed priors on fossil constraints and three data partitions
BEAST_5Partition_ExpPriors_DivergenceTimeEstimation
The XML file provides the full set of parameters used to run a Bayesian analysis of phylogeny and divergence times using the program BEAST 2. This file contains exponentially distributed minimum age priors on fossil age constraints and data in 5 partitions from PartitionFinder 2.
RAxML_CyphostemmaAndOutgroup_MLPhylogeny.phy
This text file provides data partitions for the RAxML analysis.
RAxML_CyphostemmaAndOutgroup_Partitions
This text file provides data partitions for the RAxML analysis.
Mesquite_CyphostemmaMorphology_AncestralCharacterStateReconstructions.nex
This NEXUS file has a single tree (MCCT) and categorical data for the species of Cyphostemma used to reconstruct ancestral character states. The evolutionary history of the character states for the 'stem' and 'tendril' characters were reconstructed using parsimony and maximum likelihood by Mesquite.
MrBayes_CyphostemmaAndOutgroup_BayesianPhylogeny.nex
The NEXUS file provides the data alignment and the Mr Bayes block to run the analysis. Additional information concerning the locus positions in the alignment are provided by the comments in the file.
Lagrange_Cyphostemma_DEC_noConstraints
This file is a Python script that is run using Python to carry out a DEC analysis based on the data contained in the provided script. This script was generated by the online Lagrange configurator(http://www.reelab.net/lagrange/configurator/index). This script enforces no constraints on the ancestral provinces and no constraints on the paths of dispersal between provinces.
Lagrange_Cyphostemma_DEC_wConstraints
This file is a Python script that is run using Python to carry out a DEC analysis based on the data contained in the provided script. This script was generated by the online Lagrange configurator(http://www.reelab.net/lagrange/configurator/index). This script enforces constraints on the paths of dispersal between provinces.
Additional_SampleLabelTranslations
Data files provided at Dryad were the untouched data files used for analyses. In some cases, the taxon labels in the files do not match the taxon labels in figures in the manuscript. This file provides the translations between the taxon labels in the data files and the taxon labels in the manuscript.