Data from: Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds

Branch lengths—measured in character changes—are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips. However, a separate set of divergence time approaches are typically used to date palaeontological trees, which may lack such branch lengths. Among these methods, sophisticated probabilistic approaches have recently emerged, in contrast with simpler algorithms relying on minimum node ages. Here, using a novel phylogenetic hypothesis for Mesozoic dinosaurs, we apply two such approaches to estimate divergence times for: (i) Dinosauria, (ii) Avialae (the earliest birds) and (iii) Neornithes (crown birds). We find: (i) the plausibility of a Permian origin for dinosaurs to be dependent on whether Nyasasaurus is the oldest dinosaur, (ii) a Middle to Late Jurassic origin of avian flight regardless of whether Archaeopteryx or Aurornis is considered the first bird and (iii) a Late Cretaceous origin for Neornithes that is broadly congruent with other node- and tip-dating estimates. Demonstrating the feasibility of probabilistic time-scaling further opens up divergence estimation to the rich histories of extinct biodiversity in the fossil record, even in the absence of detailed character data.以字符替换数计量的支长（branch length），是基于演化钟的分歧时间估计的核心必要条件，无论所用化石校准针对的是系统发育节点还是枝尖。 然而，针对古生物系统发育树的定年通常需采用另一套分歧时间分析方法，这类树往往缺乏上述支长数据。 在这类方法中，相较于依赖最小节点年龄的简易算法，复杂概率模型方法近年得以发展。 本研究基于一项全新的中生代恐龙系统发育假说，采用上述两类方法对三类类群的分歧时间进行估计：（1）恐龙总目（Dinosauria）；（2）鸟翼类（Avialae，即最早的鸟类）；（3）今鸟亚纲（Neornithes，即冠群鸟类）。 本研究得到如下结论：（1）恐龙总目起源于二叠纪的合理性，取决于尼亚萨龙（Nyasasaurus）是否为迄今已知最古老的恐龙；（2）鸟类飞行能力的起源时间为中侏罗世至晚侏罗世，无论将始祖鸟（Archaeopteryx）还是曙光鸟（Aurornis）视作最早的鸟类；（3）今鸟亚纲起源于晚白垩世，这一结果与其他节点定年及枝尖定年的估计结果基本一致。 本研究证实了概率时序定标的可行性，即便缺乏详细的字符数据，该方法仍可拓展应用于化石记录中各类灭绝生物多样性的演化历史分歧时间估计。