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 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.由于演化分异过程无法在人类观测尺度下直接被观测，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 trees）是当前所能获得的、对演化分异过程最完整的呈现形式。这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得到。在这类系统发育树的各类时间信息中，化石年代是目前精度最高的已知信息——分化时间（divergence times）的推断大多以化石作为校准依据。本文提出一种仅以化石年代作为时间信息约束条件、计算含化石系统发育树似然值的方法，并将其应用于基于此类数据的演化分异速率估计。由于该计算过程有此需求，我们同时提供了一种基于标准演化分异模型，确定树拓扑结构（tree topology）概率的方法。在模拟数据集上对本方法进行测试的结果表明，基于系统发育树拓扑结构与化石年代得到的最大似然速率估计值，其精度几乎与纳入所有数据（包括分化时间）时得到的结果相当。此外，该方法的估计精度显著优于仅基于精确分化时间（未纳入化石记录）得到的估计结果。我们还提供了一个实证案例：包含50个二叠-石炭纪（Permo-carboniferous）真盘龙类（eupelycosaur，早期合弓类synapsid）类群，其年代跨度约为3.15亿年前（315 Ma，晚石炭世（Late Carboniferous））至2.7亿年前（270 Ma，早二叠世（Early Permian）结束后不久）。本研究的分析结果显示，早期合弓类的物种形成（分支演化cladogenesis，即起源birth）速率约为每支系每百万年（My）0.1次，灭绝速率略低于物种形成速率，且存在相当规模的隐性古生物多样性（paleobiodiversity）。