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      Evolutionary origins of the prolonged extant squamate radiation

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          Abstract

          Squamata is the most diverse clade of terrestrial vertebrates. Although the origin of pan-squamates lies in the Triassic, the oldest undisputed members of extant clades known from nearly complete, uncrushed material come from the Cretaceous. Here, we describe three-dimensionally preserved partial skulls of two new crown lizards from the Late Jurassic of North America. Both species are placed at the base of the skink, girdled, and night lizard clade Pan-Scincoidea, which consistently occupies a position deep inside the squamate crown in both morphological and molecular phylogenies. The new lizards show that several features uniting pan-scincoids with another major lizard clade, the pan-lacertoids, in trees using morphology were convergently acquired as predicted by molecular analyses. Further, the palate of one new lizard bears a handful of ancestral saurian characteristics lost in nearly all extant squamates, revealing an underappreciated degree of complex morphological evolution in the early squamate crown. We find strong evidence for close relationships between the two new species and Cretaceous taxa from Eurasia. Together, these results suggest that early crown squamates had a wide geographic distribution and experienced complicated morphological evolution even while the Rhynchocephalia, now solely represented by the tuatara, was the dominant clade of lepidosaurs.

          Abstract

          Here, the authors present two well preserved fossil lizard skulls from the Late Jurassic of North America. These fossils, placed at the base of the clade Pan-Scincoidea, suggest that squamates had a wide geographic distribution and preserve characteristics that show the complex early evolutionary history of squamate anatomy.

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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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            BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

            Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
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              TNT version 1.5, including a full implementation of phylogenetic morphometrics

              Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.
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                Author and article information

                Contributors
                chasethedinosaur@gmail.com
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                29 November 2022
                29 November 2022
                2022
                : 13
                : 7087
                Affiliations
                [1 ]GRID grid.47100.32, ISNI 0000000419368710, Department of Ecology and Evolutionary Biology, , Yale University, ; New Haven, CT USA
                [2 ]Stamford Museum and Nature Center, Stamford, CT USA
                [3 ]GRID grid.47100.32, ISNI 0000000419368710, Department of Earth and Planetary Sciences, , Yale University, ; New Haven, CT USA
                [4 ]GRID grid.299784.9, ISNI 0000 0001 0476 8496, Negaunee Integrative Research Center, , Field Museum of Natural History, ; Chicago, IL USA
                [5 ]GRID grid.47100.32, ISNI 0000000419368710, Yale Peabody Museum, , Yale University, ; New Haven, CT USA
                Author information
                http://orcid.org/0000-0003-4514-9565
                http://orcid.org/0000-0002-1257-1594
                http://orcid.org/0000-0002-0838-8068
                Article
                34217
                10.1038/s41467-022-34217-5
                9708687
                36446761
                0c2d6bed-1d4c-4346-990e-7bb3113d1594
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 1 June 2022
                : 18 October 2022
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                © The Author(s) 2022

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                palaeontology,phylogenetics,taxonomy
                Uncategorized
                palaeontology, phylogenetics, taxonomy

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