Data from: Phylogeny and divergence times of lemurs inferred with recent and ancient fossils in the tree
Data files
Mar 31, 2016 version files 197.69 MB
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1000fbd369trees.tre
6.44 MB
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1000fbd421trees.tre
6.43 MB
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1000morph_trees_combined.tre
3.57 MB
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1000mtdna_trees_combined.tre
5.20 MB
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1000ndna_trees_combined.tre
3.23 MB
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1000td421trees.tre
6.38 MB
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box plot RF distances ml pars bayes.pdf
20.74 KB
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box plot RF distances PCT vs other trees.pdf
5.87 KB
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fbd369agerange_gooddates.tre
221.54 KB
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fbd421agerange.tre
221.54 KB
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morph tree w node probs.pdf
444.21 KB
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mtDNA tree w node probs.pdf
330.02 KB
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nDNA tree w node probs.pdf
377.52 KB
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Online Supplemental Materials.docx
80.18 KB
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OSM Fig 3 MCC TD full morph.pdf
40.21 MB
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OSM Fig S1 MCC FBD full morph.pdf
40.55 MB
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OSM Fig S2 MCC FBD reduced morph.pdf
40.56 MB
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OSM Fig S4 MCC TD reduced morph.pdf
40.54 MB
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OSM Fig S5 Node age estimates with fixed and wide priors.pdf
17.21 KB
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OSM File 3. Reduced 369 character morphological data matrix.nex
100.80 KB
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OSM File S1. Full 421 character morphological data matrix.nex
115.19 KB
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OSM File S2. Character dissimilarity analysis code.txt
2.57 KB
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OSM File S4. Morphological data sources GenBank accession numbers and dataset tabulations.xlsx
17.45 KB
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OSM File S5. Concatenated molecular dataset w gene partitions.nex
698.64 KB
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OSM File S6. Total evidence dataset with reduced morphological data matrix including MrBayes blocks for FBD and TD analyses.nex
921.20 KB
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pars_trees2.tre
180.12 KB
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Parsimony 50 percent majority rule.pdf
15.57 KB
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PCT w CFs.pdf
6.45 KB
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PCT_rooted.tre
1.10 KB
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RaxML tree w bootstraps.pdf
350.27 KB
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RAxML_bestTree_total_evidence.tree
6.67 KB
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td369fixed.tre
221.53 KB
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td421fixed.tre
221.53 KB
Abstract
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.