Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

Saladin B, Leslie AB, Wueest RO, Litsios G, Conti E, Salamin N, Zimmermann NE

Date Published: March 20, 2017

DOI: http://dx.doi.org/10.5061/dryad.74f2r.2

 

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Title Maximum clade credibility tree of FBDl
Downloaded 17 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 21 fossils, resulting from the beast2 analysis using the FBDl.xml input-file.
Download FBDl_MCC_commAnc.tre (86.53 Kb)
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Title Subsample of trees from FBDl analysis
Downloaded 8 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 21 fossils (see FBDl.xml file for detailed settings of the Bayesian analysis).
Download FBDl_combined_extant.trees (6.721 Mb)
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Title Input file for FBDl analysis
Downloaded 12 times
Description This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 21 fossils (FBDl). The file was generated in BEAUti 2.3.1.
Download FBDl.xml (887.0 Kb)
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Title Maximum clade credibility tree of FBDs
Downloaded 9 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 14 fossils, resulting from the beast2 analysis using the FBDs.xml input-file
Download FBDs_MCC_commAnc.tre (86.21 Kb)
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Title Subsample of trees from FBDs analysis
Downloaded 7 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 14 fossils (see FBDs.xml file for detailed settings of the Bayesian analysis).
Download FBDs_combined_extant.trees (6.730 Mb)
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Title Input file for FBDs analysis
Downloaded 13 times
Description This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 14 fossils (FBDs). The file was generated in BEAUti 2.3.1.
Download FBDs.xml (837.7 Kb)
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Title Maximum clade credibility tree of NDbl
Downloaded 4 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with broad calibration densities), using 15 fossils; resulting from the beast2 analysis using the NDbl.xml input-file.
Download NDbl_MCC_commAnc.tre (124.4 Kb)
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Title Subsample of trees from NDbl analysis
Downloaded 5 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with broad calibration densities) using 15 fossils (see NDbl.xml file for detailed settings of the Bayesian analysis).
Download NDbl_combined.trees (15.38 Mb)
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Title Input file NDbl analysis
Downloaded 8 times
Description This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with broad prior calibration densities. This approach included 15 calibration constraints based on fossil information (NDbl). The file was generated in BEAUti 2.3.1.
Download NDbl.xml (736.8 Kb)
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Title Subsample of trees from NDbs analysis
Downloaded 3 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with broad calibration densities) using 12 fossils (see NDbs.xml file for detailed settings of the Bayesian analysis).
Download NDbs_combined.trees (15.37 Mb)
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Title Maximum clade credibility tree of NDbs
Downloaded 3 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with broad calibration densities) using 12 fossils, resulting from the beast2 analysis using the NDbs.xml input-file.
Download NDbs_MCC.tre (125.0 Kb)
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Title Input file NDbs analysis
Downloaded 6 times
Description This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with broad prior calibration densities. This approach included 12 calibration constraints based on fossil information (NDbs). The file was generated in BEAUti 2.3.1.
Download NDbs.xml (732.9 Kb)
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Title Subsample of trees from NDnl analysis
Downloaded 3 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with narrow calibration densities) using 15 fossils (see NDnl.xml file for detailed settings of the Bayesian analysis).
Download NDnl_combined.trees (15.37 Mb)
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Title Maximum clade credibility tree of NDnl
Downloaded 5 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with narrow calibration densities), using 15 fossils; resulting from the beast2 analysis using the NDnl.xml input-file.
Download NDnl_MCC_commAnc.tre (124.4 Kb)
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Title Input file NDnl analysis
Downloaded 8 times
Description This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with narrow prior calibration densities. This approach included 15 calibration constraints based on fossil information (NDnl). The file was generated in BEAUti 2.3.1.
Download NDnl.xml (736.8 Kb)
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Title Subsample of trees from NDns analysis
Downloaded 3 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with narrow calibration densities) using 12 fossils (see NDns.xml file for detailed settings of the Bayesian analysis).
Download NDns_combined.trees (15.40 Mb)
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Title Maximum clade credibility tree of NDns
Downloaded 4 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with narrow calibration densities), using 12 fossils; resulting from the beast2 analysis using the NDns.xml input-file.
Download NDns_MCC_commAnc.tre (125.0 Kb)
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Title Input file NDns analysis
Downloaded 5 times
Description This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with narrow prior calibration densities. This approach included 12 calibration constraints based on fossil information (NDns). The file was generated in BEAUti 2.3.1.
Download NDns.xml (732.9 Kb)
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Title Maximum clade credibility tree of FBDl age range
Downloaded 5 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 21 fossils, resulting from the beast2 analysis using the FBDl_ageRange.xml input-file.
Download FBDl_ageRange_MCC_extant_commAnc.tre (86.28 Kb)
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Title Subsample of trees from FBDl "age range" analysis
Downloaded 6 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 21 fossils (see FBDl_ageRange.xml file for detailed settings of the Bayesian analysis).
Download FBDl_ageRange_combined_extant.trees (6.709 Mb)
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Title Input file for FBDl "age range" analysis
Downloaded 9 times
Description This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 21 fossils, based on an "age range" dating approach (FBDl_ageRange). The file was generated in BEAUti 2.3.1.
Download FBDl_ageRange.xml (891.3 Kb)
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Title Maximum clade credibility tree of FBDs age range
Downloaded 7 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 14 fossils, resulting from the beast2 analysis using the FBDs_ageRange.xml input-file.
Download FBDs_ageRange_MCC_extant_commAnc.tre (86.05 Kb)
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Title Subsample of trees from FBDs "age range" analysis
Downloaded 7 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 14 fossils (see FBDs_ageRange.xml file for detailed settings of the Bayesian analysis).
Download FBDs_ageRange_combined_extant.trees (6.718 Mb)
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Title Input file for FBDs "age range" analysis
Downloaded 11 times
Description This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 14 fossils, based on an "age range" dating approach (FBDs_ageRange). The file was generated in BEAUti 2.3.1.
Download FBDs_ageRange.xml (840.7 Kb)
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Title Maximum clade credibility tree of NDus
Downloaded 6 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis using 12 fossils (based on an uniform density prior), resulting from the beast2 analysis using the NDus.xml input-file.
Download NDus_MCC_commAnc.tre (125.9 Kb)
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Title Subsample of trees from NDus analysis
Downloaded 8 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis using 12 fossils (see NDus.xml file for detailed settings of the Bayesian analysis).
Download NDus_combined.trees (11.52 Mb)
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Title Input file for NDus analysis
Downloaded 10 times
Description This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the node dating approach including 12 fossils and an uniform calibration prior (NDus). The file was generated in BEAUti 2.3.1.
Download NDus.xml (729.9 Kb)
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Title Maximum clade credibility tree of NDul
Downloaded 6 times
Description This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis using 15 fossils (based on an uniform density prior), resulting from the beast2 analysis using the NDul.xml input-file.
Download NDul_MCC_commAnc.tre (124.5 Kb)
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Title Subsample of trees from NDul analysis
Downloaded 7 times
Description This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis using 15 fossils and an uniform calibration prior (see NDul.xml file for detailed settings of the Bayesian analysis).
Download NDul_combined.trees (11.53 Mb)
Details View File Details
Title Input file for NDul analysis
Downloaded 11 times
Description This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the node dating approach including 15 fossils and an uniform calibration prior (NDul). The file was generated in BEAUti 2.3.1.
Download NDul.xml (737.9 Kb)
Details View File Details

When using this data, please cite the original publication:

Saladin B, Leslie AB, Wüest RO, Litsios G, Conti E, Salamin N, Zimmermann NE (2017) Fossils matter: improved estimates of divergence times in Pinus reveal older diversification. BMC Evolutionary Biology 17(1): null. http://dx.doi.org/10.1186/s12862-017-0941-z

Additionally, please cite the Dryad data package:

Saladin B, Leslie AB, Wueest RO, Litsios G, Conti E, Salamin N, Zimmermann NE (2017) Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.74f2r.2
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