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.

支长（Branch lengths）以性状改变（character changes）为度量单位，是基于进化钟的分化时间估算（clock-based divergence estimation）的必要前提，无论所用化石校准（fossil calibrations）对应系统发育节点（nodes）还是分类单元末端（tips）。然而，古生物学系统发育树（palaeontological trees）往往缺失此类支长信息，因此学界通常需采用另一套分化时间分析方法。此类方法中，近年涌现出了复杂的概率性分析框架，与依赖最小节点年龄（minimum node ages）的简易算法形成鲜明对比。本研究基于一项全新的中生代恐龙（Mesozoic dinosaurs）系统发育假说，运用两种此类方法估算了三类类群的分化时间：(i) 恐龙总目（Dinosauria）、(ii) 鸟翼类（Avialae，即最早鸟类）以及(iii) 今鸟亚纲（Neornithes，即冠群鸟类）。研究结果表明：(i) 恐龙是否起源于二叠纪（Permian），取决于尼亚萨龙（Nyasasaurus）是否为已知最古老的恐龙；(ii) 鸟类飞行的起源时间为中侏罗世至晚侏罗世（Middle to Late Jurassic），无论将始祖鸟（Archaeopteryx）还是曙光鸟（Aurornis）认定为最早的鸟类；(iii) 今鸟亚纲起源于晚白垩世（Late Cretaceous），该结果与其他节点定年及末端定年（node- and tip-dating）的估算结果大体一致。本研究证实了概率性时间标度法（probabilistic time-scaling）的可行性，进一步拓展了分化时间估算的应用边界，可用于解析化石记录中蕴藏的丰富已灭绝生物多样性（extinct biodiversity）历史，即便缺乏详细的性状数据（character data）亦然。