DOI: 10.5061/dryad.74f2r
title: Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

description: Background: The taxonomy of pines (genus Pinus) is widely accepted and a
 robust gene tree based on entire plastome sequences exists. However, there
 is a large discrepancy in estimated divergence times of major pine clades
 among existing studies, mainly due to differences in fossil placement and
 dating methods used. We currently lack a dated molecular phylogeny that
 makes use of the rich pine fossil record, and this study is the first to
 estimate the divergence dates of pines based on a large number of fossils
 (21) evenly distributed across all major clades, in combination with
 applying both node and tip dating methods. Results: We present a range of
 molecular phylogenetic trees of Pinus generated within a Bayesian
 framework. We find the origin of pines is likely up to 30 Myr older (Early
 Cretaceous) than inferred in most previous studies (Late Cretaceous) and
 propose generally older divergence times for major clades within Pinus
 than previously thought. Our age estimates vary significantly between the
 different dating approaches, but the results generally agree on older
 divergence times. We present a revised list of 21 fossils that are
 suitable to use in dating or comparative analyses of pines. Conclusions:
 Reliable estimates of divergence times in pines are essential if we are to
 link diversification processes and functional adaptation of this genus to
 geological events or to changing climates. In addition to older divergence
 times in Pinus, our results also indicate that node age estimates in pines
 depend on dating approaches and the specific fossil sets used, reflecting
 inherent differences in various dating approaches. The sets of dated
 phylogenetic trees of pines presented here provide a way to account for
 uncertainties in age estimations when applying comparative phylogenetic
 methods.
description: Maximum clade
 credibility tree of FBDlThis 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.FBDl_MCC_commAnc.treSubsample of trees from FBDl analysisThis 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).FBDl_combined_extant.treesInput file for FBDl analysisThis 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.FBDl.xmlMaximum clade credibility tree of FBDsThis 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-fileFBDs_MCC_commAnc.treSubsample of trees from FBDs analysisThis 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).FBDs_combined_extant.treesInput file for FBDs analysisThis 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.FBDs.xmlMaximum clade credibility tree of NDblThis 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.NDbl_MCC_commAnc.treSubsample of trees from NDbl analysisThis 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).NDbl_combined.treesInput file NDbl analysisThis 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.NDbl.xmlSubsample of trees from NDbs analysisThis 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).NDbs_combined.treesMaximum clade credibility tree of NDbsThis 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.NDbs_MCC.treInput file NDbs analysisThis 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.NDbs.xmlSubsample of trees from NDnl analysisThis 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).NDnl_combined.treesMaximum clade credibility tree of NDnlThis 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.NDnl_MCC_commAnc.treInput file NDnl analysisThis 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.NDnl.xmlSubsample of trees from NDns analysisThis 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).NDns_combined.treesMaximum clade credibility tree of NDnsThis 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.NDns_MCC_commAnc.treInput file NDns analysisThis 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.NDns.xmlMaximum clade credibility tree of FBDl age rangeThis 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.FBDl_ageRange_MCC_extant_commAnc.treSubsample of trees from FBDl "age range" analysisThis 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).FBDl_ageRange_combined_extant.treesInput file for FBDl "age range" analysisThis 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.FBDl_ageRange.xmlMaximum clade credibility tree of FBDs age rangeThis 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.FBDs_ageRange_MCC_extant_commAnc.treSubsample of trees from FBDs "age range" analysisThis 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).FBDs_ageRange_combined_extant.treesInput file for FBDs "age range" analysisThis 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.FBDs_ageRange.xmlMaximum clade credibility tree of NDusThis 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.NDus_MCC_commAnc.treSubsample of trees from NDus analysisThis 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).NDus_combined.treesInput file for NDus analysisThis 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.NDus.xmlMaximum clade credibility tree of NDulThis 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.NDul_MCC_commAnc.treSubsample of trees from NDul analysisThis 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).NDul_combined.treesInput file for NDul analysisThis 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.NDul.xml