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）通常通过对照化石记录校准内部节点来完成定年。此类方法依赖间接手段，在极端情况下可能会误释化石信息。本研究对比了此类节点定年法（node dating）与一种整合化石与现存类群（extant taxa）的贝叶斯全证据分析（Bayesian total-evidence analysis）策略。作为测试案例，我们聚焦于膜翅目（Hymenoptera）的早期辐射演化，该类群的化石记录多为保存较差的印痕化石（impression fossils），难以进行系统发育定位。具体而言，我们比较了两种定年方法：一是利用来自化石记录的9个校准点（calibration points）开展节点定年；二是基于针对45件化石标本（完整度为4%~20%）与68个现存类群所编码的343个形态特征（morphological characters）开展全证据定年。两种方法均针对现存类群使用了来自7个分子标记（约5 kb）的分子数据（molecular data）。由于难以精准模拟物种形成、灭绝、采样与化石保存的真实过程，我们为包含化石的时钟树构建了一种简单的均匀先验分布，并采用宽松分子钟模型（relaxed clock models）以适配进化树内部的进化速率变异。尽管多数化石的系统发育定位存在较大不确定性，但我们发现，在全证据分析中，化石数据对分化时间（divergence times）的估算具有显著贡献。具体而言，分化时间的后验分布（posterior distributions）对先验假设的敏感性更低，且相较于节点定年法，其结果更为精确。全证据分析还显示，节点定年法中所使用的7个膜翅目校准点里，有4个背后关于化石定位的假设可能存在错误或存疑。针对膜翅目早期辐射演化这一科学问题，我们的研究结果表明，其冠群（crown group）可追溯至石炭纪（Carboniferous），距今约309 Ma（95%置信区间：291–347 Ma），且其主要现存类群的分化时间远早于此前认知，早在三叠纪（Triassic）之前就已完成。