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）通常通过以化石记录校准内部节点的方式进行定年。此类方法依赖间接手段，极端情况下可能歪曲化石所承载的信息。本研究对比了这类节点定年（node dating）方法，与一种将化石与现存类群一同纳入贝叶斯全证据分析（Bayesian total-evidence analysis）的分析策略。
作为测试案例，本研究聚焦膜翅目（Hymenoptera）的早期辐射演化——该类群的化石记录多为保存欠佳的印痕化石，难以开展精准的系统发育定位。具体而言，我们比较了两种定年方案：一是利用化石记录推导的9个校准点（calibration points）进行节点定年；二是基于为45件化石（完整度4%~20%）与68个现存类群编码的343个形态特征（morphological characters）开展全证据定年。两种方案均针对所有现存类群，使用了来自7个总长度约5kb的分子标记的分子数据。
由于难以精准模拟物种形成、灭绝、采样及化石保存的真实过程，我们针对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）以适配进化树内的演化速率异质性。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，化石对分化时间（divergence times）的估算贡献显著。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，且相比节点定年结果，其精度更高。
全证据分析还显示，节点定年中使用的7个膜翅目校准点中，有4个很可能基于对化石系统发育定位的错误或存疑假设。针对膜翅目早期辐射演化，本研究结果表明：其冠群可追溯至约3.09亿年前的石炭纪（Carboniferous，95%置信区间：291~347 Ma），且现存主要类群的分化时间远早于此前认知，早在三叠纪（Triassic）之前就已完成多样化。