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.

Usage Notes
dinosaur_MRP.tntThe MRP matrix submitted to TNT (Goloboff et al. 2008) for performing tree searches; in Hennig86/TNT format.dinosaur_tnt_1000_mpts.tre.zipThe 1,000 MPTs returned from the TNT tree searches; in Newick format (and zipped).dinosaur_str_1000_mpts.tre.zipThe 1,000 MPTs returned from the TNT tree searches with STR taxa reinserted; in Newick format (and zipped).dinosaur_dating_100_mpts.treThe 100 trees randomly sampled and taken forward for dating; in Newick format.consensus.treStrict consensus of the 1,000 MPTs of dinosaur_str_1000_mpts.tre.zip in Newick format.dinosaur_occurrences.xlsxThe dinosaur occurrences used for dating; in MS Excel format.dinosaur_occurrences.txtThe dinosaur occurrences used for dating; in plain text format.dinosaur_tipages.txtThe tip ages (hard lower bounds) used for dating; in plain text format.dinosaur_timelist.txtThe time list data used to generate the three rates used in the cal3 function; in plain text format.cal3_rates_code.RThe R code used to generate the three rates used in the cal3 dating code; in R code format.cal3_rates_code_11-11-16.Rcal3_dating_code.RThe R code used to perform the cal3 dating; in R code format.Hedman_code.RThe R code used to perform the Hedman dating; in R code format.Hedman_code.rcal3_dates.txtThe cal3 dates output from R; in plain text format.Hedman_dates.txtThe Hedman dates output from R; in plain text format.

分支长度——以字符变化量进行测量——是基于时钟的分歧估计的必要条件，无论所使用的化石校准数据代表的是节点还是末端。然而，在通常用于确定古生物学树状图的分歧时间的方法中，通常使用一组独立的方法，这些方法可能缺乏此类分支长度。在这些方法中，近年来已经出现了复杂的概率方法，与依赖于最小节点年龄的简单算法形成对比。在此，我们采用一种关于中生代恐龙的新型系统发育假设，应用两种此类方法来估计以下类群的分歧时间：（i）恐龙类，（ii）鸟类总纲（最早的鸟类）和（iii）新鸟亚纲（冠群鸟类）。我们发现：（i）恐龙起源于二叠纪的可能性取决于Nyasa恐龙是否是最古老的恐龙，（ii）无论将始祖鸟还是热河鸟视为第一只鸟，鸟类的飞行起源于中晚侏罗纪，以及（iii）新鸟亚纲起源于白垩纪晚期，这一结果与其他节点和末端日期估计结果广泛一致。进一步证明概率时间缩放法的可行性，进一步将分歧估计扩展到化石记录中灭绝生物多样性的丰富历史，即使在缺乏详细的特征数据的情况下。