Data from: Phylogeny and divergence times of lemurs inferred with recent and ancient fossils in the tree

Herrera JP, Dávalos LM

Date Published: March 31, 2016

DOI: http://dx.doi.org/10.5061/dryad.51f00

 

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Title Online Supplemental Materials v2
Downloaded 36 times
Description Description of online supplementary materials files, figures, tables, methods, results and morphological character descriptions.
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Title OSM File S1. Full 421 character morphological data matrix
Downloaded 35 times
Description Morphological data matrix in nexus format with all 421 characters coded for 81 taxa. The file can be opened in the software Mesquite for easy editing, or read directly with any text editor. Data are also available on MorphoBank project # 2167 (www.morphobank.org).
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Title OSM File S2. Character dissimilarity analysis code
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Description R code for running the character dissimilarity analysis described in the text. Comments throughout the code should allow the user to perform the analysis "out-of-the-box". Analysis used to identify characters with 0 dissimilarity, indicating they were possibly not independent.
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Title OSM File S3. Reduced 369 character morphological data matrix
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Description Reduced morphological data matrix of 369 characters after excluding those characters found to have 0 dissimilarity from the Gower analysis.
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Title OSM File S4. Morphological data sources GenBank accession numbers and dataset tabulations
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Description Sources of morphological and molecular data. Morphological data were either taken from the publication of Seiffert et al. 2015 or scored in this study. GenBank accession numbers are given for each gene used.
Download OSM File S4. Morphological data sources Ge....xlsx (17.45 Kb)
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Title OSM File S5. Concatenated molecular dataset w gene partitions
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Description Nexus file of DNA sequence alignments concatenated with the gene partitions indicated
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Title OSM File S6. Total evidence dataset with reduced morphological data matrix including MrBayes blocks for FBD and TD analyses
Downloaded 33 times
Description Nexus file with total evidence dataset (369 morphological characters, 5767 molecular characters) and the MrBayes blocks of code to run the tip-dating and fossilized birth-death process analyses described in the text. The optimal data partitions, including the two molecular partitions identified by PartitionFinder analysis, are specified. The codes for the divergence time analyses are included as comments (enclosed by square brackets []). The first block runs the fossilized birth-death process analysis, remove the [] to run. The second block includes the tip-dating analysis. The individual matrices and codes are also available in the MorphoBank project # 2167.
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Title OSM Fig S1 MCC FBD full morph
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Description PDF version of Figure 3 of the main text, enlarged. Mean clade credibility tree from the fossilized birth death process, total evidence dataset with full morphological dataset
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Title OSM Fig S2 MCC FBD reduced morph
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Description Maximum clade credibility tree from fossilized birth-death process with 369 morphological characters and 5767 molecular characters. Posterior probabilities of nodes are labelled.
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Title OSM Fig S3 MCC TD full morph
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Description Online Supplemental Material Figure S3. Maximum clade credibility tree from tip-dating method with 421 morphological characters and 5767 molecular characters posterior probabilities of nodes are labelled.
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Title OSM Fig S4 MCC TD reduced morph
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Description Maximum clade credibility tree from tip-dating method with 369 morphological characters and 5767 molecular characters posterior probabilities of nodes are labelled.
Download OSM Fig S4 MCC TD reduced morph.pdf (40.53 Mb)
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Title OSM Fig S5 Node age estimates with fixed and wide priors
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Description Comparison of node age estimates for 21 select nodes, using two divergence time estimation techniques, two datasets (full and reduced morphological datasets), and wide age range or fixed age priors
Download OSM Fig S5 Node age estimates with fixed ...rs.pdf (17.21 Kb)
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Title Online Supplemental Material File S7.
Downloaded 26 times
Description 1000 trees from the posterior distribution of trees inferred from the total evidence dataset (full morphological dataset) under the fossilized birth-death model in MrBayes.
Download 1000fbd421trees.tre (6.428 Mb)
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Title Online Supplemental Material File S8.
Downloaded 4 times
Description 1000 trees from the posterior distribution of trees inferred from the total evidence dataset (reduced morphological dataset) under the fossilized birth-death model in MrBayes.
Download 1000fbd369trees.tre (6.444 Mb)
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Title Online Supplemental Material File S9.
Downloaded 8 times
Description 1000 trees from the posterior distribution of trees inferred from the total evidence dataset (full morphological dataset) using tip-dating under the uniform clock model in MrBayes.
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Title Online Supplemental Material File S10.
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Description 1000 trees from the posterior distribution of trees inferred from the mtDNA dataset in MrBayes.
Download 1000mtdna_trees_combined.tre (5.202 Mb)
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Title Online Supplemental Material File S11.
Downloaded 5 times
Description 1000 trees from the posterior distribution of trees inferred from the nDNA dataset in MrBayes.
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Title Online Supplemental Material File S12.
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Description 1000 trees from the posterior distribution of trees inferred from the morphological dataset in MrBayes.
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Title Online Supplemental Material File S13.
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Description The primary concordance tree inferred using Bayesian concordance analysis (BUCKy) of the posterior distributions of trees inferred from individual analysis of the mtDNA, nDNA and morphology.
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Title Online Supplemental Material File S14.
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Description Tree topology inferred from total evidence dataset and reduced morphological dataset using maximum likelihood (RaxML).
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Title Online Supplemental Material File S15.
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Description 55 most parsimonious tree topologies inferred from total evidence dataset and reduced morphological dataset using the parsimony ratchet (TNT).
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Title Online Supplemental Material Figure S6.
Downloaded 71 times
Description Maximum clade credibility tree topology for unconstrained (non-clock) Bayesian analysis of mtDNA in MrBayes. Circles on nodes represent the posterior probability of that node. The tree was rooted for drawing purposes only.
Download mtDNA tree w node probs.pdf (330.0 Kb)
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Title Online Supplemental Material Figure S7.
Downloaded 47 times
Description Maximum clade credibility tree topology for unconstrained (non-clock) Bayesian analysis of nDNA in MrBayes. Circles on nodes represent the posterior probability of that node. The tree was rooted for drawing purposes only.
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Title Online Supplemental Material Figure S8.
Downloaded 40 times
Description Maximum clade credibility tree topology for unconstrained (non-clock) Bayesian analysis of the reduced morphological dataset (369 characters) in MrBayes. Circles on nodes represent the posterior probability of that node. The tree was rooted for drawing purposes only.
Download morph tree w node probs.pdf (444.2 Kb)
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Title Online Supplemental Material Figure S9.
Downloaded 57 times
Description The primary concordance tree topology inferred using Bayesian concordance analysis (BUCKy) of the posterior distributions of trees inferred from individual analysis of the mtDNA, nDNA and morphology. Numbers on branches indicate the concordance factor, a measure of the average number of data types that support the given branch. The tree was rooted for drawing purposes only.
Download PCT w CFs.pdf (6.452 Kb)
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Title Online Supplemental Material Figure S10.
Downloaded 64 times
Description Box plots of Robinson-Foulds distances (RF) from the primary concordance tree (PCT) for tree sets inferred from different data types. mtDNA = mitochondrial DNA, nDNA = nuclear DNA, TE = total evidence, Null1 and Null2 = randomized trees to generate null distributions. See main text for further details.
Download box plot RF distances PCT vs other trees.pdf (5.866 Kb)
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Title Online Supplemental Material Figure S11.
Downloaded 15 times
Description The tree topology with the highest likelihood found by RaxML with the bootstrap support values from 1000 pseudoreplicates indicated on branches.
Download RaxML tree w bootstraps.pdf (350.2 Kb)
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Title Online Supplemental Material Figure S12.
Downloaded 53 times
Description 50% majority rule consensus of 55 most parsimonious tree topologies inferred from the total evidence dataset (reduced morphological dataset) using the parsimony ratchet (TNT).
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Title Online Supplemental Material File S16
Downloaded 9 times
Description Mean clade credibility tree from FBD analysis of full morphological and full molecular dataset.
Download fbd421agerange.tre (221.5 Kb)
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Title Online Supplemental Material File S17.
Downloaded 11 times
Description Mean clade credibility tree from FBD analysis of reduced morphological and full molecular dataset.
Download fbd369agerange_gooddates.tre (221.5 Kb)
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Title Online Supplemental Material File S18.
Downloaded 10 times
Description Mean clade credibility tree from TD analysis of full morphological and full molecular dataset.
Download td421fixed.tre (221.5 Kb)
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Title Online Supplemental Material File S19.
Downloaded 11 times
Description Mean clade credibility tree from TD analysis of reduced morphological and full molecular dataset.
Download td369fixed.tre (221.5 Kb)
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Title Online Supplemental Material Figure S13.
Downloaded 57 times
Description Box plots of Robinson-Foulds distances (RF) among trees inferred from the total evidence dataset using different tree inference techniques. ML = maximum likelihood (using RaxML), parsimony = maximum parsimony (using TNT, 55 most parsimonious trees), Bayes = Bayesian inference (using MrBayes v3.2.6).
Download box plot RF distances ml pars bayes.pdf (20.73 Kb)
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When using this data, please cite the original publication:

Herrera JP, Davalos LM (2016) Phylogeny and divergence times of lemurs inferred with recent and ancient fossils in the tree. Systematic Biology 65(5): 772-791. http://dx.doi.org/10.1093/sysbio/syw035

Additionally, please cite the Dryad data package:

Herrera JP, Dávalos LM (2016) Data from: Phylogeny and divergence times of lemurs inferred with recent and ancient fossils in the tree. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.51f00
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