Data from: Likelihood of tree topologies with fossils and diversification rate estimation

Since the diversification process cannot be directly observed at the human scale, it has to be studied from the information available, namely the extant taxa and the fossil record. In this sense, phylogenetic trees including both extant taxa and fossils are the most complete representations of the diversification process that one can get. Such phylogenetic trees can be reconstructed from molecular and morphological data, to some extent. Among the temporal information of such phylogenetic trees, fossil ages are by far the most precisely known (divergence times are inferences calibrated mostly with fossils). We propose here a method to compute the likelihood of a phylogenetic tree with fossils in which the only considered time information is the fossil ages, and apply it to the estimation of the diversification rates from such data. Since it is required in our computation, we provide a method for determining the probability of a tree topology under the standard diversification model. Testing 21 our approach on simulated data shows that the maximum likelihood rate estimates from the phylogenetic tree topology and the fossil dates are almost as accurate as those obtained by taking into account all the data, including the divergence times. Moreover, they are substantially more accurate than the estimates obtained only from the exact divergence times (without taking into account the fossil record). We also provide an empirical example composed of 50 Permo-carboniferous eupelycosaur (early synapsid) taxa ranging in age from about 315 Ma (Late Carboniferous) to 270 Ma (shortly after the end of the Early Permian). Our analyses suggest a speciation (cladogenesis, or birth) rate of about 0.1 per lineage and per My, a marginally lower extinction rate, and a considerable hidden paleobiodiversity of early synapsids.由于物种多样化过程无法在人类可观测的尺度下直接观测，因此必须依托可获取的信息开展研究，即现生类群（extant taxa）与化石记录（fossil record）。就此而言，同时涵盖现生类群与化石的系统发育树（phylogenetic tree）是当前所能获得的、对物种多样化过程最为完整的表征形式。此类系统发育树可在一定程度上通过分子与形态学数据重建。在这类系统发育树的各类时间信息中，化石年代是目前已知精度最高的——物种分化时间（divergence times）大多需借助化石校准方可推断得出。 本文提出一种仅以化石年代作为时间信息的带化石系统发育树似然度（likelihood）计算方法，并将其应用于此类数据的物种多样化速率估算。鉴于该计算过程的需求，我们同时提供了一种基于标准物种多样化模型确定系统发育树拓扑结构（phylogenetic tree topology）概率的方法。我们在模拟数据上对所提方法进行验证后发现，基于系统发育树拓扑结构与化石年代得到的最大似然（maximum likelihood）速率估计值，其准确性几乎与纳入包括分化时间在内的全部数据时所得结果相当。不仅如此，该方法的估算精度也显著优于仅基于精确分化时间（未纳入化石记录）得到的结果。 我们还提供了一项实证案例，其包含50个石炭纪-二叠纪真盘龙类（eupelycosaur，早期合弓类synapsid）类群，年代跨度约为3.15亿年前（晚石炭世）至2.70亿年前（早二叠世结束后不久）。分析结果显示，其物种形成（分支成种，即诞生）速率约为每谱系每百万年0.1次，灭绝速率略低于成种速率，且早期合弓类存在相当可观的隐藏古生物多样性。