Data from: Multiple morphological clocks and total-evidence tip-dating in mammals

Lee M

Date Published: September 13, 2016

DOI: http://dx.doi.org/10.5061/dryad.3h4m5.2

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Description of All Data Files on Dryad
Downloaded 18 times
Description Description of All Data Files on Dryad (docx); this is also available on on the Biology Letters website. All numbered refs, such as [6], in the descriptions below refer to citations in the main Biology Letters paper or in this document.
Download Description.docx (149.9 Kb)
Details View File Details
Title A1_CharacterPartitions
Downloaded 17 times
Description File_A1 (Excel). Table describing the 28 partitions (25 morphological, 3 molecular) and listing the included characters. Character numbering is based on the matrix from [6], available as MorphoBank Project 773 (http://dx.doi.org/10.7934/P773).
Download A1_CharacterPartitions.xlsx (53.35 Kb)
Details View File Details
Title B1_TreeRef6_MrBayesFile_Morph1-25
Downloaded 15 times
Description File_B1 (plain text). The MrBayes [10] executable file to infer branch lengths for the 25 candidate morphological partitions, using the total-evidence Maximum Likelihood topology from [6]. The matrix consists of only the 46 extant taxa from [6], since molecular branch lengths (to which these morphological branch lengths have to be compared) cannot be ascertained for extinct taxa.
Download B1_TreeRef6_MrBayesFile_Morph1-25.mrb (223.3 Kb)
Details View File Details
Title B2_TreeRef6_MrBayesFile_Codons1-3
Downloaded 12 times
Description File_B2 (plain text). The MrBayes executable file to infer branch lengths for the 3 candidate molecular partitions (and overall morphological branch lengths), using the total-evidence Maximum Likelihood topology from [6]. The matrix consists of the 46 extant taxa from [6].
Download B2_TreeRef6_MrBayesFile_Codons1-3.mrb (1.917 Mb)
Details View File Details
Title B3_TreeRef6_Parts1-28branchlengths_newick
Downloaded 12 times
Description File_B3 (newick format). The ClockstaR [3] treefile containing the trees with the branch lengths for the 28 candidate partitions obtained from the MrBayes analysis in files B1, B2. Note: ClockstaR treats all trees as unrooted, so different rootings of trees are of no consequence.
Download B3_TreeRef6_Parts1-28branchlengths_newick.trees (74.24 Kb)
Details View File Details
Title B4_TreeRef9_MrBayesFile_Morph1-25
Downloaded 12 times
Description File_B4 (plain text). The MrBayes [10] executable file to infer branch lengths for the 25 candidate morphological partitions, using the topology from [9]. The matrix consists of only the 46 extant taxa from [6], since molecular branch lengths (to which these morphological branch lengths have to be compared) cannot be ascertained for extinct taxa.
Download B4_TreeRef9_MrBayesFile_Morph1-25.mrb (223.0 Kb)
Details View File Details
Title B5_TreeRef9_MrBayesFile_Codons1-3
Downloaded 11 times
Description File_B5 (plain text). The MrBayes executable file to infer branch lengths for the 3 candidate molecular partitions (and overall morphological branch lengths), using the topology from [9]. The matrix consists of the 46 extant taxa from [6].
Download B5_TreeRef9_MrBayesFile_Codons1-3.mrb (1.917 Mb)
Details View File Details
Title B6_TreeRef9_Parts1-28branchlengths_newick
Downloaded 7 times
Description File_B6 (newick format). The ClockstaR treefile containing the trees with the branch lengths for the 28 candidate partitions obtained from the MrBayes analysis in files B4, B5. Note: ClockstaR treats all trees as unrooted, so different rootings of trees are of no consequence.
Download B6_TreeRef9_Parts1-28branchlengths_newick.trees (54.85 Kb)
Details View File Details
Title B7_ClockstarResults
Downloaded 64 times
Description File_B7 (pdf). ClockstaR partition matrices and gap statistics for analyses using the guide tree from ref [6] (upper panels) and ref [9] (lower panels). From the 28 candidate partitions, both analyses identified an optimal number of 8 clock-partitions (pacemakers) of similar composition. Note that the order of partitions in these tables (molecular partitions uppermost) is different to that in Fig. 1, but the same as in Fig. B10.
Download B7_ClockstarResults.pdf (327.5 Kb)
Details View File Details
Title B8_Randomised_TOLMorph25p_TOL_Gam
Downloaded 6 times
Description File_B8 (plain text). The MrBayes [10] executable file to infer branch lengths for the 25 randomised morphological partitions. The partitions were of the same size as the 25 original partitions (42-553 characters); morphological characters were randomly shuffled in Excel. The molecular data were not randomised. The matrix otherwise is identical to that in File B1.
Download B8_Randomised_TOLMorph25p_TOL_Gam.mrb (244.1 Kb)
Details View File Details
Title B9_Randomised_TreeRef6_Parts1-28branchlengths_newick
Downloaded 7 times
Description File_B9 (newick format). The ClockstaR [3] treefile containing the trees with the branch lengths for the 25 randomised morphological partitions, and the original (not randomised) 3 molecular partitions obtained from the MrBayes analysis as per file B2. Note: ClockstaR treats all trees as unrooted, so different rootings of trees are of no consequence.
Download B9_Randomised_TreeRef6_Parts1-28branchleng...trees (54.81 Kb)
Details View File Details
Title B10_Randomised_clockstar_Results
Downloaded 52 times
Description File_B10 (pdf). ClockstaR partition matrices and gap statistics for analysis using randomised morphological partitions, using the guide tree from ref [6]. From the 28 candidate partitions, the analysis preferred very many, or very few, morphological partitions, unlike the corresponding analysis of the original data (File B7, top) which preferred an intermediate number. Note that the order of partitions in these tables (molecular partitions uppermost) is different to that in Fig. 1, but the same as in Fig. B7.
Download B10_Randomised_clockstar_Results.pdf (185.5 Kb)
Details View File Details
Title B11_ClockstaR_script
Downloaded 9 times
Description File_B11 (plain text). ClockstaR R script (and output) for the above analysis. Note filenames and paths need to be changed as appropriate.
Download B11_ClockstaR_script.txt (6.465 Kb)
Details View File Details
Title C1_PartitionFinder
Downloaded 9 times
Description File_C1 (zipped, plain text). Matrix with molecular data for 46 extant taxa (extracted from [6]), in Phylip format (mammals.phy); PartitionFinder [12] command file (cfg) with 71 candidate partitions (by genes and by codons, with noncoding genes treated as single candidate partitions); best scheme with 7 partitions requiring separate substitution models, found by PartitionFinder using the Bayesian Information Criterion with unlinked branch lengths.
Download C1_PartitionFinder.zip (418.1 Kb)
Details View File Details
Title C2_1clock - MrBayes file
Downloaded 22 times
Description File_C2 (plain text). MrBayes executable file for a total-evidence dating analysis of all 86 taxa in the matrix in [6], using a single relaxed (independent gamma rates) clock for all traits (morphological and molecular). The sampled ancestor birth-death tree prior [17], and the Markov model of morphological evolution [18,19], were used. Optimal substitution models and substitution-model-partitions were found with PartitionFinder for molecular data (see C1) and with stepping-stone analysis in MrBayes for morphological data as implemented in [10]. Numerous (>20) MCMC runs were initially performed for 5 million generations to investigate tuning, mixing and convergence. The final analysis was then performed with 4 runs of 20 million generations, with the first 30% of samples discarded as burnin.
Download C2_1clock.mrb (3.710 Mb)
Details View File Details
Title C3_1clock_PostburninTrees&Params_folder
Downloaded 12 times
Description File_C3 (zipped, plain text). The full MCMC tree and parameter output files from the MrBayes analysis in file C1. Only post-burnin samples are included to reduce file sizes. Run the MrBayes file in C2 (after disabling the MCMC command and setting burnin to 0) to generate consensus trees and statistics from these files.
Download C3_1clock_PostburninTrees&Params_folder.zip (3.420 Mb)
Details View File Details
Title C4_1clock_con_fig
Downloaded 16 times
Description File_C4 (approximate nexus format). The majority-rule consensus tree from the MrBayes analysis in files C1-2. Note: the wrong file was previously uploaded onto Dryad; I thank Joseph Brown for pointing this out.
Download C4_1clock_con_fig.tre (124.1 Kb)
Details View File Details
Title C5_1clock_topologyConvergence
Downloaded 43 times
Description File_C5 (pdf). Convergence diagnostics for tree topologies sampled in C2. (A) AWTY [20] plots demonstrating similar posterior probabilities for all clades across 4 runs, and (B) at different stages in a single run. The topology convergence statistics from MrBayes and AWTY (standard deviation of split frequencies across runs) were also good ie low, being <0.031 across all comparisons (see top right cells of panel A). These patterns are consistent with good convergence. The kink in one of the fitted lines appears to be an artefact of a glitch in AWTY.
Download C5_1clock_topologyConvergence.pdf (396.0 Kb)
Details View File Details
Title C6_1clock_paramConvergence
Downloaded 10 times
Description File_C6 (plain text). Convergence diagnostics for numerical parameters from MrBayes [9] for the analysis in Files C2-4. PSRFs (ratio of within-run to between-run variance) is approximately 1 for all parameters, consistent with the view the MCMC runs are sampling from the same posterior and consistent with good convergence [10].
Download C6_1clock_paramConvergence.txt (12.83 Kb)
Details View File Details
Title C7_8clocks MrBayes file
Downloaded 14 times
Description File_C7 (plain text). MrBayes executable file for a total-evidence dating analysis of all 86 taxa in the matrix in [6], using 8 separate relaxed clocks (independent gamma rates; 7 for morphology and 1 for molecular data), as found in analysis B-3. The sampled ancestor birth-death tree prior [17], and the Markov model of morphological evolution [18,19], were used. Optimal substitution models and substitution-model-partitions were found with PartitionFinder for molecular data (see C1) and with stepping-stone analysis in MrBayes for morphological data [10]. Numerous (>20) MCMC runs were initially performed for 20 million generations to investigate tuning, mixing and convergence. The final analysis was then performed with 4 runs and the trees from 10 million post-burnin generations retained Note: The burnin for each run varies considerably due to variation in time to reach (apparent) stationarity, from 20 million to 50 million. For computational efficiency, the 4 runs were performed separately and in all cases, the last 10 million steps (after stationarity) were retained. However, the step numbers have been readjusted in file C8 below so they are all identical across runs (ie to a common burnin of 50 million), to facilitate downstream analyses e.g. generating summary statistics in MrBayes.
Download C7_8clocks.mrb (3.711 Mb)
Details View File Details
Title C8_8clocks_PostburninTrees&Params_folder
Downloaded 9 times
Description File_C8 (zipped, plain text). The full MCMC tree and parameter output files from the MrBayes analysis in file C7. Only post-burnin samples for each of the 4 runs (last 10 million, see below) are included to reduce file sizes. Run the MrBayes file in C7 (first disabling the MCMC command) and setting burnin to 0 to generate consensus trees and statistics. Run the relevant MrBayes file (disabling the MCMC command) and setting burnin to 0 to generate consensus statistics.
Download C8_8clocks_PostburninTrees&Params_folder.zip (10.32 Mb)
Details View File Details
Title C9_8clocks_con_fig
Downloaded 11 times
Description File_C9 (approximate nexus format). The majority-rule consensus tree from the MrBayes analysis in files C6-7.
Download C9_8clocks_con_fig.tree (387.2 Kb)
Details View File Details
Title C10_8clocks_topolConvergence
Downloaded 69 times
Description File_C10 (pdf). Convergence diagnostics for tree topologies sampled in C8. (A) AWTY [20] plots demonstrating relatively good correlation (albeit with substantial variance) for all clades across 4 runs, and (A) high variation at different stages in a single run, but no obvious directional trends. The topology convergence statistics from MrBayes and AWTY (standard deviation of split frequencies across runs) were also relatively good ie being <0.093 across all comparisons (see top right cells of panel A). These results are consistent with convergence or near-convergence, i.e. runs sampling similar distributions but cycling very slowly through parameter space.
Download C10_8clocks_topolConvergence.pdf (416.7 Kb)
Details View File Details
Title C11_8clocks_param_summary
Downloaded 11 times
Description File_C11 (plain text). Convergence diagnostics for numerical parameters from MrBayes [10] for the analysis in Files C7-9. PSRFs (ratio of within-run to between-run variance) is very 1 for most numerical parameters, but approaches ~1.7 for a single parameter (due to variance in 1 run). This single outlier is slightly higher than desirable. These diagnostics do not indicate convergence, though are consistent with convergence being approached.
Download C11_8clocks_param_summary.txt (13.74 Kb)
Details View File Details
Title C12_NodeAges
Downloaded 18 times
Description File_C12 (Word docx). Comparison of divergence dates obtained from the single-clock and multi-clock analyses, and two previous studies [6,9]. Numerical dates were not published in [9] so dates were retrieved from a detailed time-tree (Figure S1) and are thus shown as estimated (e.g. ~56).
Download C12_NodeAges.docx (79.67 Kb)
Details View File Details

When using this data, please cite the original publication:

Lee MSY (2016) Multiple morphological clocks and total-evidence tip-dating in mammals. Biology Letters 12(7): 20160033. http://dx.doi.org/10.1098/rsbl.2016.0033

Additionally, please cite the Dryad data package:

Lee M (2016) Data from: Multiple morphological clocks and total-evidence tip-dating in mammals. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3h4m5.2
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Version History

Item Version Date Summary

* Selected Version

Search for data

Be part of Dryad

We encourage organizations to: