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Data from: Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds
datasetposted on 2022-06-10, 03:03 authored by Graeme T. Lloyd, David W. Bapst, Matt Friedman, Katie E. Davis
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 Notesdinosaur_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.
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