Dating the time of origin of major clades c a wunderlich violin dating
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.
There remains a great need to include a larger number of carefully evaluated fossil constraints, preferably evenly distributed across all major clades, in order to improve our understanding of pine evolution.
Although Bayesian methods using a relaxed molecular clock are widely accepted for time calibration of molecular trees, there is ongoing debate regarding the best strategy to convert fossil information into calibration information [33–36] and methods are still under development .
More specifically, our objectives are to: (1) provide a revised and well-supported time-scale for the evolution of major subsections of pines; (2) test the sensitivity of age estimates to different dating methods and fossil sets; and (3) provide a revised list of fossils and their phylogenetic placement within the genus for use in further studies on pine evolution.
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.
Despite a rich fossil record, most recent time calibrations of pine divergences have used very few (usually 1–3) fossils [11, 13, 15, 16, 18] (but see ).
Some of these fossils are controversial regarding their phylogenetic assignment and age (e.g. belgica as discussed in ), leading to inconsistent age estimates of the origin of pines and divergence times of subsections therein.
However, there is no objective way to define the calibration densities and researchers have used different approaches to define them [19, 37, 38, 40].
Recently, the fossilized birth-death (FBD, hereafter) method has been introduced as a new approach for time calibration of molecular phylogenetic trees [41, 42].