Data from: The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?

The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950–1,259 million years ago (Mya), animals diverged from choanoflagellates 761–957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642–761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be ≈100 million years more ancient than the Cambrian boundary.

核苷酸与氨基酸序列的应用，有助于更深入地理解地球生命演化事件的发生时序。不过，基于分子序列的分化时间估算仍存在争议，且通常比化石记录所揭示的时间更为古老。已研究的基因与物种数量有限，以及演化速率普遍存在差异，正是这类分歧最可能的成因。本研究对36种真核生物的129种蛋白质的串联氨基酸序列进行比对，以确定多个主要演化支的分化时间，涵盖动物界、真菌界、植物界以及各类原生生物。考虑到演化速率存在显著差异，同时为了处理化石记录的不确定性，本研究采用了经6项古生物学约束条件同时校准的贝叶斯宽松分子钟（Bayesian relaxed molecular clock）方法。研究结果显示，基于95%置信区间，真核生物各界的分化发生在9.5亿至12.59亿年前（百万年前，Mya）；动物与领鞭毛虫的分化时间为7.61亿至9.57亿年前；存在争议的原口动物与后口动物分化事件则发生在6.42亿至7.61亿年前。上述分化时间估计结果对先验假设与古生物学校准均表现出较强的稳健性。值得注意的是，相较于基于全局分子钟假设得到的估算结果，本研究采用宽松分子钟得到的时间估计更为年轻；但两侧对称动物的分化时间仍比寒武纪界限早约1亿年。