Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsReliable 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.
Highlights
The taxonomy of pines is widely accepted and a robust gene tree based on entire plastome sequences exists
In fossilized birth-death tree prior (FBD), the ages of the crown nodes within the two subgenera are dated to the Late Cretaceous to Eocene (FBDs: median subgenus Pinus: 64 Ma, 95% confidence interval (CI): 87– 52 Ma; median subgenus Strobus: 68 Ma, 95% CI: 89– 53 Ma; FBDl: median subgenus Pinus 69 Ma, 95% CI: 92–56 Ma; subgenus Strobus median: 71 Ma, 95% CI; 92–56 Ma)
While in node dating approaches (ND), the major split within subgenus Pinus is dated to the Paleocene to Eocene (NDbs: median: 50 Ma, 95% CI: 63–46 Ma; NDbl: median: 50 Ma, 95% CI: 63–46 Ma; narrow calibration densities (NDn) and NDnl: median: 45 Ma, 95% CI: 46–45 Ma)
Summary
The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. 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. In 2005, Gernandt et al [5] proposed a new classification based on phylogenetic trees inferred from two chloroplast genes, dividing the pines into two subgenera (Pinus and Strobus), four sections (sections Pinus and Trifoliae in subgenus Pinus and sections Parrya and Quinquefoliae in subgenus Strobus) and 11 subsections (Australes, Ponderosae, Contortae, Pinus, Pinaster, Strobus, Krempfianae, Cembroides, Balfourianae and Nelsoniae). Despite the detailed chloroplast data and the availability of potential fossil calibration points, comprehensive time-calibrated molecular phylogenetic trees remain lacking
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