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（Pinus）的分类学已被广泛认可，且已有基于完整质体基因组序列构建的稳健基因树。然而，现有研究对松属主要支系的分化时间估算存在较大分歧，这主要源于所用化石校准位点与定年方法的差异。目前学界仍缺乏利用丰富松类化石记录构建的带定年分子系统发育树，本研究首次基于均匀分布于所有主要支系的21枚化石，并结合节点定年与末端定年两种方法，估算了松属的分化时间。
结果：本研究构建了一系列基于贝叶斯框架的松属分子系统发育树。研究发现，松属的起源时间可能比多数既往研究的估算结果（晚白垩世）早至多30百万年（早白垩世），且松属主要支系的分化时间普遍早于此前认知。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。本研究还修订了适用于松属定年或比较分析的21枚化石清单。
结论：若要将松属的多样化进程与功能适应性与地质事件或气候变化相关联，可靠的松属分化时间估算至关重要。本研究除得出更古老的松属分化时间外，结果还表明，松属的节点年代估算结果依赖于所用的定年方法与特定化石数据集，这反映了不同定年方法的固有差异。本研究提供的一系列带定年的松属系统发育树，为应用比较系统发育方法时处理年代估算的不确定性提供了可行途径。