DOI: 10.5061/dryad.51f00
title: Data from: Phylogeny and divergence times of lemurs inferred with recent and ancient fossils in the tree

description: Paleontological and neontological systematics seek to answer evolutionary
 questions with different data sets. Phylogenies inferred for combined
 extant and extinct taxa provide novel insights into the evolutionary
 history of life. Primates have an extensive, diverse fossil record and
 molecular data for living and extinct taxa are rapidly becoming available.
 We used two models to infer the phylogeny and divergence times for living
 and fossil primates, the tip-dating (TD) and fossilized birth–death
 process (FBD). We collected new morphological data, especially on the
 living and extinct endemic lemurs of Madagascar. We combined the
 morphological data with published DNA sequences to infer near-complete
 (88% of lemurs) time-calibrated phylogenies. The results suggest that
 primates originated around the Cretaceous–Tertiary boundary, slightly
 earlier than indicated by the fossil record and later than previously
 inferred from molecular data alone. We infer novel relationships among
 extinct lemurs, and strong support for relationships that were previously
 unresolved. Dates inferred with TD were significantly older than those
 inferred with FBD, most likely related to an assumption of a uniform
 branching process in the TD compared with a birth–death process assumed in
 the FBD. This is the first study to combine morphological and DNA sequence
 data from extinct and extant primates to infer evolutionary relationships
 and divergence times, and our results shed new light on the tempo of lemur
 evolution and the efficacy of combined phylogenetic analyses.
description: Online Supplemental
 Materials v2Description of online
 supplementary materials files, figures, tables, methods, results and
 morphological character descriptions.Online Supplemental
 Materials.docxOSM File S1. Full 421
 character morphological data matrixMorphological 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).OSM File S2. Character
 dissimilarity analysis codeR 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.OSM File S3. Reduced 369
 character morphological data matrixReduced morphological
 data matrix of 369 characters after excluding those characters found to
 have 0 dissimilarity from the Gower analysis.OSM File 3. Reduced 369
 character morphological data
 matrix.nexOSM File S4.
 Morphological data sources GenBank accession numbers and dataset
 tabulationsSources 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.OSM File S5.
 Concatenated molecular dataset w gene partitionsNexus file of DNA
 sequence alignments concatenated with the gene partitions
 indicatedOSM File S6. Total
 evidence dataset with reduced morphological data matrix including MrBayes
 blocks for FBD and TD analysesNexus 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.OSM Fig S1 MCC FBD full
 morphPDF 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 datasetOSM Fig S2 MCC FBD
 reduced morphMaximum clade
 credibility tree from fossilized birth-death process with 369
 morphological characters and 5767 molecular characters. Posterior
 probabilities of nodes are labelled.OSM Fig S3 MCC TD full
 morphOnline 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.OSM Fig 3 MCC TD full
 morph.pdfOSM Fig S4 MCC TD
 reduced morphMaximum clade
 credibility tree from tip-dating method with 369 morphological characters
 and 5767 molecular characters posterior probabilities of nodes are
 labelled.OSM Fig S5 Node age
 estimates with fixed and wide priorsComparison 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 priorsOnline Supplemental
 Material File S7.1000 trees from the
 posterior distribution of trees inferred from the total evidence dataset
 (full morphological dataset) under the fossilized birth-death model in
 MrBayes.1000fbd421trees.treOnline Supplemental Material File S8.1000 trees from the posterior distribution of trees inferred from the total evidence dataset (reduced morphological dataset) under the fossilized birth-death model in MrBayes.1000fbd369trees.treOnline Supplemental Material File S9.1000 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.1000td421trees.treOnline Supplemental Material File S10.1000 trees from the posterior distribution of trees inferred from the mtDNA dataset in MrBayes.1000mtdna_trees_combined.treOnline Supplemental Material File S11.1000 trees from the posterior distribution of trees inferred from the nDNA dataset in MrBayes.1000ndna_trees_combined.treOnline Supplemental Material File S12.1000 trees from the posterior distribution of trees inferred from the morphological dataset in MrBayes.1000morph_trees_combined.treOnline Supplemental Material File S13.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.PCT_rooted.treOnline Supplemental Material File S14.Tree topology inferred from total evidence dataset and reduced morphological dataset using maximum likelihood (RaxML).RAxML_bestTree_total_evidence.treeOnline Supplemental Material File S15.55 most parsimonious tree topologies inferred from total evidence dataset and reduced morphological dataset using the parsimony ratchet (TNT).pars_trees2.treOnline Supplemental Material Figure S6.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.mtDNA tree w node probs.pdfOnline Supplemental Material Figure S7.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.nDNA tree w node probs.pdfOnline Supplemental Material Figure S8.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.morph tree w node probs.pdfOnline Supplemental Material Figure S9.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.PCT w CFs.pdfOnline Supplemental Material Figure S10.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.box plot RF distances PCT vs other trees.pdfOnline Supplemental Material Figure S11.The tree topology with the highest likelihood found by RaxML with the bootstrap support values from 1000 pseudoreplicates indicated on branches.RaxML tree w bootstraps.pdfOnline Supplemental Material Figure S12.50% majority rule consensus of 55 most parsimonious tree topologies inferred from the total evidence dataset (reduced morphological dataset) using the parsimony ratchet (TNT).Parsimony 50 percent majority rule.pdfOnline Supplemental Material File S16Mean clade credibility tree from FBD analysis of full morphological and full molecular dataset.fbd421agerange.treOnline Supplemental Material File S17.Mean clade credibility tree from FBD analysis of reduced morphological and full molecular dataset.fbd369agerange_gooddates.treOnline Supplemental Material File S18.Mean clade credibility tree from TD analysis of full morphological and full molecular dataset.td421fixed.treOnline Supplemental Material File S19.Mean clade credibility tree from TD analysis of reduced morphological and full molecular dataset.td369fixed.treOnline Supplemental Material Figure S13.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).box plot RF distances ml pars bayes.pdf