Data from: Towards a self-updating platform for estimating rates of speciation and migration, ages, and relationships of taxa
Data files
Oct 25, 2016 version files 2.91 GB
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Fig_S1-Marker-thresholds.pdf
9.68 KB
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Fig_S2-Posterior-probabilities.pdf
4.99 KB
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Fig_S3-Primate-tree.pdf
805.03 KB
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Fig_S4-Arecaceae-tree.pdf
2.02 MB
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Fig_S5-SUPERSMART-Faurby-comparison.pdf
1.06 MB
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Fig_S6-Relative-dispersals.pdf
72.34 KB
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Fig_S7-BiogeoBEARS.pdf
985.70 KB
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Fig_S8-Simulated-Estimated-Trees.pdf
484.50 KB
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Fig_S9-Interactions.pdf
1.10 MB
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README_for_supersmart-palms.txt
2.77 KB
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README_for_supersmart-primates.txt
2.53 KB
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README_for_supersmart-simulations.txt
1.60 KB
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supersmart-palms.zip
1.28 GB
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supersmart-primates.zip
1.18 GB
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supersmart-simulations.zip
445.16 MB
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Table_S1-palm-fossil-calibrations.xlsx
126.50 KB
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Table_S2-palms-dates-comparison.xlsx
41.06 KB
Abstract
Rapidly growing biological data –including molecular sequences and fossils– hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyse these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive datasets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.