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      Cutting the Gordian knot: a historical and taxonomic revision of the Jurassic crocodylomorph Metriorhynchus

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          Abstract

          Metriorhynchidae was a clade of extinct crocodylomorphs that adapted to a pelagic lifestyle, becoming a key component of Mesozoic lagoonal and coastal marine ecosystems. The type genus Metriorhynchus is one of the best-known genera of Mesozoic crocodylomorphs, and since the mid-19th century, the ‘concept’ of Metriorhynchus has become associated with the referred species Me. superciliosus. Historically Metriorhynchus has been the most species-rich genus in Metriorhynchidae, with most Middle Jurassic species and many Late Jurassic species referred to the genus at some point in their history. However, the type species Me. geoffroyii has largely been omitted in the literature. Its type series is a chimera of multiple metriorhynchid species, and a type specimen has never been designated. Moreover, phylogenetic analyses have repeatedly shown that the 19th–20th century concept of Metriorhynchus is not monophyletic – to the point where only referring every metriorhynchid species, and some basal metriorhynchoids, to the genus would render it monophyletic. Herein we designate a lectotype for Me. geoffroyii, re-describe it and restrict the genus Metriorhynchus to the type species. We also establish the new genus Thalattosuchus for Me. superciliosus, thereby cutting the ‘Gordian knot’ of Metriorhynchus with Th. superciliosus.

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          MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

          Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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            Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

            Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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              ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data

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                Author and article information

                Contributors
                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                November 03 2020
                November 03 2020
                Affiliations
                [1 ]School of GeoSciences, Grant Institute, The King’s Buildings, University of Edinburgh, Edinburgh, UK
                [2 ]5, Villa Jeanne-d’Arc, Bourg-la-Reine, France
                [3 ]Naturkunde-Museum Bielefeld, Abteilung Geowissenschaften, Bielefeld, Germany
                [4 ]Niedersächsisches Landesmuseum Hannover, Hannover, Germany
                [5 ]Department of Natural Sciences, National Museums Scotland, Chambers St, Edinburgh, Edinburgh, UK
                [6 ]School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
                [7 ]Department of Earth Sciences, Natural History Museum, London, UK
                Article
                10.1093/zoolinnean/zlaa092
                927b56fc-dc8c-412e-9360-13cc87b9c40a
                © 2020

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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