Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

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.

背景：松属（genus Pinus）植物的分类学方案已被广泛接受，且已有基于完整质体基因组（plastome）全序列构建的可靠基因树。但现有研究对松属主要演化支（clade）的分化时间估算存在显著差异，这主要源于所采用的化石校准位点与定年方法的不同。目前学界尚未有利用丰富松属化石记录构建的校准分子系统发育树，本研究首次基于均匀分布于所有主要演化支的21枚化石，并结合节点定年法（node dating）与末端定年法（tip dating）两种方法，对松属的分化时间进行估算。
研究结果：本研究基于贝叶斯（Bayesian）框架构建了一系列松属分子系统发育树。我们发现松属的起源时间可能比多数既往研究估算的晚白垩世（Late Cretaceous）早至少30百万年（Myr），即早白垩世（Early Cretaceous），且松属内主要演化支的分化时间整体也比此前认为的更古老。不同定年方法得到的年代估算结果存在显著差异，但整体均支持更古老的分化时间。本研究还修订了一套共21枚适合用于松属定年或比较分析的化石名录。
研究结论：若要将松属的物种分化过程与功能适应性与地质事件或气候变化相联系，可靠的松属分化时间估算至关重要。除了松属分化时间整体更古老这一结论外，本研究结果还表明，松属的节点年代估算结果依赖于所采用的定年方法与特定化石集，这反映了不同定年方法间的固有差异。本研究提供的一系列松属校准系统发育树，为在应用比较系统发育学方法时处理年代估算的不确定性提供了可行途径。