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      Forty new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds

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          Abstract

          Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur–bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19 th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most complete morphological assessment of the postcranial skeleton of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds.

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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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            Creating the CIPRES Science Gateway for inference of large phylogenetic trees

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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
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                16 December 2022
                2022
                : 10
                : e13919
                Affiliations
                [1 ]Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath , Bath, United Kingdom
                [2 ]Department of Earth Sciences, University of Cambridge , Cambridge, Cambridgeshire, United Kingdom
                [3 ]Fort Hays State University, Sternberg Museum of Natural History and Department of Geosciences , Hays, Kansas, United States
                [4 ]Yale Peabody Museum of Natural History , New Haven, Conneticut, United States
                [5 ]Department of Earth & Planetary Sciences, Yale University , New Haven, Conneticut, United States
                [6 ]University of Kansas, Biodiversity Institute and Natural History Museum , Lawrence, Kansas, United States
                [7 ]University Museum of Zoology , Cambridge, United Kingdom
                Author information
                http://orcid.org/0000-0002-2671-9190
                http://orcid.org/0000-0002-1786-0352
                Article
                13919
                10.7717/peerj.13919
                9762251
                36545383
                4ca3dd03-e7f3-487a-b9f6-c88825671030
                © 2022 Benito et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 13 December 2021
                : 28 July 2022
                Funding
                Funded by: Cambridge Philosophical Society Research Studentship
                Funded by: University of Bath University Research Studenshipt Award
                Funded by: UKRI Future Leaders Fellowship
                Award ID: MR/S032177/1
                Juan Benito received support from the Palaeontographical Society Richard Owen Research fund, from a Cambridge Philosophical Society Research Studentship, and from the University of Bath University Research Studenshipt Award. Daniel J Field received support from the UKRI Future Leaders Fellowship MR/S032177/1. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Evolutionary Studies
                Paleontology
                Taxonomy
                Zoology

                ornithology,palaeontology,ornithurae,euornithes,ichthyornis,birds,skeleton,postcranial,mesozoic,avialae

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