Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4–20% complete) and 68 extant taxa. In both cases we use molecular data from seven markers (about 5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, approximately 309 Ma (95% interval: 291–347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic.系统发育树（Phylogenies）的定年通常通过参照化石记录校准其内部节点来实现。此类方法依赖间接手段，极端情况下可能会误读化石所承载的信息。本研究将此类节点定年法（node dating），与一种将化石与现生类群（extant taxa）一同纳入贝叶斯（Bayesian）总证据分析（total-evidence analysis）的方法进行对比。本研究以膜翅目（Hymenoptera）的早期辐射演化作为测试案例，该类群的化石记录多为保存欠佳的印痕化石（impression fossils），难以确定其系统发育位置。具体而言，我们对比了两种定年策略：其一为利用9个源自化石记录的校准点（calibration points）实施的节点定年法；其二为基于343项形态特征（morphological characters）的总证据定年法，该特征矩阵针对45件化石（完整度为4%~20%）与68个现生类群完成特征编码。两类策略均针对现生类群使用了来自7个分子标记（molecular markers，总长约5 kb）的分子数据。由于难以精准模拟物种形成、灭绝、采样过程以及化石保存的真实情况，我们为包含化石的钟型树构建了简洁的均匀先验分布（prior），并采用宽松分子钟模型（relaxed clock models）以适配树内不同分支的进化速率异质性。尽管多数化石的系统发育位置仍存在较大不确定性，但我们发现，在总证据分析中，化石数据对分歧时间的估算具有显著贡献。具体而言，分歧时间的后验分布（posterior distributions）对先验假设的敏感性更低，且相较于节点定年法，其估算结果往往更为精确。此外，总证据分析还显示，节点定年法中所使用的7个膜翅目校准点里，有4个很可能是基于对化石系统发育位置的错误或存疑假设得到的。针对膜翅目的早期辐射演化，我们的研究结果显示，该类群的冠群（crown group）可追溯至约309 Ma的石炭纪（Carboniferous，95%置信区间：291–347 Ma），且其主要现生支系的分化时间远早于此前的认知，甚至早于三叠纪（Triassic）。