Data from: Tightly congruent bursts of lineage and phenotypic diversification identified in a continental ant radiation

Price SL, Etienne RS, Powell S

Date Published: February 29, 2016

DOI: http://dx.doi.org/10.5061/dryad.ff2p0

 

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Title Body length data (log transformed) in Cephalotes
Downloaded 14 times
Description Maximum reported body length measurements from the worker caste of Cephalotes species. Data are log transformed. Data are from multiple museum collections, most of which are in de Andrade and Baroni-Urbani (1999). Data for C. specularis are from Brandão et al. (2014), measurements for C_sp3 came from data from a reproductively mature colony (S. Powell, in press), and data for C_sp2 came from one individual (S. Powell, unpublished data).
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Title Molecular and morphological data matrix with MrBayes block
Downloaded 26 times
Description Nexus file that includes the sequence alignment of 5 genes (from Price et al. 2014) and a morphological dataset (from de Andrade and Baroni-Urbani 1999). About 50% of species have molecular data, and morphological data are included for all known Cephalotes species, including extinct species. A MrBayes blocks is included for the analyses for Figure S1 (extinct and extant species phylogram) and Figure S2 (extant species phylogram).
Download Ceph_phylogram.nex (564.8 Kb)
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Title Nexus file for divergence time estimation (node-calibrated and tip-dated)
Downloaded 25 times
Description Nexus file used for divergence time estimation analyses. It includes molecular data from Price et al. (2014) and morphological data from de Andrade and Baroni-Urbani (1999). MrBayes blocks are included for total evidence tip-dating (Figure S3)and node-calibration (Figure S4) analyses.
Download Ceph_time_calibration.nex (707.6 Kb)
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Title BAMM control file for lineage diversification
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Description This is the input file (called the control file) for lineage diversification analysis in BAMM. The file was directly adapted from the documentation on the BAMM website (http://bamm-project.org/).
Download lineage_controlfile.txt (9.34 Kb)
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Title BAMM control file for trait evolution
Downloaded 13 times
Description This is the input file (called the control file) for analysis of trait evolution in BAMM. The file was directly adapted from the documentation on the BAMM website (http://bamm-project.org/).
Download trait_controlfile.txt (8.628 Kb)
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Title BAMMtools R script for lineage diversification
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Description Script used in the R program BAMMtools for the analysis and visualization of lineage diversification results in BAMM. The script was adapted from documentation on the BAMM website (http://bamm-project.org/).
Download BAMMtools_lineage_script.R (3.819 Kb)
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Title BAMMtools R script for trait evolution
Downloaded 23 times
Description Script used in the R program BAMMtools for the analysis and visualization of trait evolution, specifically body size evolution, results in BAMM. The script was adapted from documentation on the BAMM website (http://bamm-project.org/).
Download BAMMtools_trait_script.R (3.912 Kb)
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Title R script for gamma and MCCR analyses
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Description Script for conducting gamma/MCCR analyses in Laser in R.
Download gamma_MCCR.R (1.135 Kb)
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Title R script for DDD analyses
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Description R script for performing DDD analyses on the phylogeny. It does the likelihood optimization from two different sets of starting values of the parameters, for the most parameter-rich models.
Download MLkeyinnCephalotes.R (8.89 Kb)
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Title R script for DDD settings
Downloaded 7 times
Description The R script loads the turtle ant data and calls the function MLkeyinnCephalotes to perform the DDD analyses. It provides all the settings which are then passed to this function.
Download MLkeyinnCephalotes2.R (3.568 Kb)
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Title Node-calibrated MCC tree
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Description Node-calibrated maximum clade credibility (MCC) tree for Cephalotes.
Download Cephalotes_node_calibration.tre (3.915 Kb)
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Title Tip-dated MCC tree
Downloaded 18 times
Description Tip-dated maximum clade credibility (MCC) tree for Cephalotes.
Download Cephalotes_tip_dating.tre (3.992 Kb)
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When using this data, please cite the original publication:

Price SL, Etienne RS, Powell S (2016) Tightly congruent bursts of lineage and phenotypic diversification identified in a continental ant radiation. Evolution 70(4): 903–912. http://dx.doi.org/10.1111/evo.12894

Additionally, please cite the Dryad data package:

Price SL, Etienne RS, Powell S (2016) Data from: Tightly congruent bursts of lineage and phenotypic diversification identified in a continental ant radiation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ff2p0
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