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      A Palaeogene stem crotaphytid ( Aciprion formosum) and the phylogenetic affinities of early fossil pleurodontan iguanians

      research-article
      1 , 2 ,
      Royal Society Open Science
      The Royal Society
      squamata, phylogenetics, palaeontology, Palaeogene, Cretaceous

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          Abstract

          Pleurodonta is an ancient, diverse clade of iguanian lizard distributed primarily in the Western Hemisphere. Although the clade is a frequent subject of systematic research, phylogenetic resolution among the major pleurodontan clades is elusive. That uncertainty has complicated the interpretations of many fossil pleurodontans. I describe a fossil skull of a pleurodontan lizard from the Palaeogene of Wyoming that was previously allocated to the puzzling taxon Aciprion formosum, and provide an updated morphological matrix for iguanian lizards. Phylogenetic analyses using Bayesian inference demonstrate that the fossil skull is the oldest and first definitive stem member of Crotaphytidae (collared and leopard lizards), establishing the presence of that clade in North America during the Palaeogene. I also discuss new or revised hypotheses for the relationships of several early pleurodontans. In particular, I examine potential evidence for crown-Pleurodonta in the Cretaceous of Mongolia ( Polrussia), stem Pleurodonta in the Cretaceous of North America ( Magnuviator) and a stem anole in the Eocene of North America ( Afairiguana). I suggest that the placement of the fossil crotaphytid is stable to the uncertain phylogeny of Pleurodonta, but recognize the dynamic nature of fossil diagnosis and the potential for updated systematic hypotheses for the other fossils analysed here.

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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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              Creating the CIPRES Science Gateway for inference of large phylogenetic trees

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Journal
                R Soc Open Sci
                R Soc Open Sci
                RSOS
                royopensci
                Royal Society Open Science
                The Royal Society
                2054-5703
                January 10, 2024
                January 2024
                January 10, 2024
                : 11
                : 1
                : 221139
                Affiliations
                [ 1 ] Museum of Vertebrate Zoology, University of California Berkeley, , 3101 UC Berkeley Road, Berkeley, CA 94720, USA
                [ 2 ] Department of Environmental Science, University of San Francisco, , San Francisco, CA 94117, USA
                Author notes

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.6996726.

                Author information
                http://orcid.org/0000-0003-0976-9337
                Article
                rsos221139
                10.1098/rsos.221139
                10776235
                4544cc13-dc2d-40a7-ab16-f425ed37673f
                © 2024 The Authors.

                Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

                History
                : September 2, 2023
                : December 13, 2023
                Funding
                Funded by: National Science Foundation, http://dx.doi.org/10.13039/100000001;
                Award ID: 2109461
                Categories
                1001
                70
                144
                183
                Organismal and Evolutionary Biology
                Research Articles

                squamata,phylogenetics,palaeontology,palaeogene,cretaceous
                squamata, phylogenetics, palaeontology, palaeogene, cretaceous

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