title: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification.
abstract: 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.
  
  
  
  We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of crown Pinus 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.
  
  
  
  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.
authors.affiliation: Swiss Federal Research Institute WSL, Birmensdorf, Switzerland. bianca.saladin@wsl.ch.
authors.forename: Bianca
authors.identifier: 0000-0002-4544-6562
authors.initials: B
authors.lastname: Saladin
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, USA.
authors.forename: Andrew B
authors.initials: AB
authors.lastname: Leslie
authors.affiliation: Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
authors.forename: Rafael O
authors.initials: RO
authors.lastname: Wüest
authors.affiliation: Department of Computational Biology, Biophore building, University of Lausanne, Lausanne, Switzerland.|Species, Ecosystems, Landscapes Division, Federal Office for the Environment FOEN, Bern, Switzerland.
authors.forename: Glenn
authors.initials: G
authors.lastname: Litsios
authors.affiliation: Department of Systematic and Evolutionary Botany and Botanical Garden, University of Zurich, Zurich, Switzerland.
authors.forename: Elena
authors.initials: E
authors.lastname: Conti
authors.affiliation: Department of Computational Biology, Biophore building, University of Lausanne, Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Quartier Sorge, University of Lausanne, Lausanne, Switzerland.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Salamin
authors.affiliation: Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
authors.forename: Niklaus E
authors.initials: NE
authors.lastname: Zimmermann
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D019143:Evolution, Molecular; D005580:Fossils; D049810:Genetic Speciation; D010802:Phylogeny; D028223:Pinus / Q000145:classification / Q000235:genetics*
keywords: Bayesian clock dating; Fossil calibration; Fossilized birth-death; Molecular clock calibration; Node dating; Phylogeny; Pines