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.
Maximum clade credibility tree of FBDl
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.
FBDl_MCC_commAnc.tre
Subsample of trees from FBDl analysis
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).
FBDl_combined_extant.trees
Input file for FBDl analysis
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.
FBDl.xml
Maximum clade credibility tree of FBDs
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
FBDs_MCC_commAnc.tre
Subsample of trees from FBDs analysis
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).
FBDs_combined_extant.trees
Input file for FBDs analysis
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.
FBDs.xml
Maximum clade credibility tree of NDbl
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.
NDbl_MCC_commAnc.tre
Subsample of trees from NDbl analysis
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).
NDbl_combined.trees
Input file NDbl analysis
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.
NDbl.xml
Subsample of trees from NDbs analysis
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).
NDbs_combined.trees
Maximum clade credibility tree of NDbs
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.
NDbs_MCC.tre
Input file NDbs analysis
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.
NDbs.xml
Subsample of trees from NDnl analysis
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).
NDnl_combined.trees
Maximum clade credibility tree of NDnl
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.
NDnl_MCC_commAnc.tre
Input file NDnl analysis
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.
NDnl.xml
Subsample of trees from NDns analysis
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).
NDns_combined.trees
Maximum clade credibility tree of NDns
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.
NDns_MCC_commAnc.tre
Input file NDns analysis
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.
NDns.xml
Maximum clade credibility tree of FBDl age range
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.
FBDl_ageRange_MCC_extant_commAnc.tre
Subsample of trees from FBDl "age range" analysis
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).
FBDl_ageRange_combined_extant.trees
Input file for FBDl "age range" analysis
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.
FBDl_ageRange.xml
Maximum clade credibility tree of FBDs age range
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.
FBDs_ageRange_MCC_extant_commAnc.tre
Subsample of trees from FBDs "age range" analysis
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).
FBDs_ageRange_combined_extant.trees
Input file for FBDs "age range" analysis
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.
FBDs_ageRange.xml
Maximum clade credibility tree of NDus
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.
NDus_MCC_commAnc.tre
Subsample of trees from NDus analysis
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).
NDus_combined.trees
Input file for NDus analysis
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.
NDus.xml
Maximum clade credibility tree of NDul
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.
NDul_MCC_commAnc.tre
Subsample of trees from NDul analysis
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).
NDul_combined.trees
Input file for NDul analysis
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.
NDul.xml