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      An intermediate crocodylian linking two extant gharials from the Bronze Age of China and its human-induced extinction

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          Abstract

          A solid phylogenetic framework is the basis of biological studies, yet higher level relationships are still unresolved in some major vertebrate lineages. One such group is Crocodylia, where the branching pattern of three major families (Alligatoridae, Crocodylidae and Gavialidae) has been disputed over decades due to the uncertain relationship of two slender-snouted lineages, gavialines and tomistomines. Here, we report a bizarre crocodylian from the Bronze Age of China, which shows a mosaic of gavialine and tomistomine features across the skeleton, rendering support to their sister taxon relationship as molecular works have consistently postulated. Gavialine characters of the new Chinese crocodylian include a novel configuration of the pterygoid bulla, a vocal structure known in mature male Indian gharials. Extinct gavialines have repeatedly evolved potentially male-only acoustic apparatus of various shapes, illuminating the deep history of sexual selection on acoustic signalling in a slender-snouted group of crocodylians. Lastly, a cutmark analysis combined with accelerator mass spectrometry (AMS) radiocarbon dating of bone remains demonstrated that two individuals from Shang and Zhou dynasties in Guangdong, China, suffered head injuries and decapitation. Archaeological evidence together with historical accounts suggests the human-induced extinction of this unique crocodylian only a few hundred years ago.

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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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            THE INTCAL20 NORTHERN HEMISPHERE RADIOCARBON AGE CALIBRATION CURVE (0–55 CAL kBP)

            Radiocarbon ( 14 C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric 14 C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international 14 C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable 14 C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the 14 C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine 14 C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
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              Bayesian Analysis of Radiocarbon Dates

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Writing – review & editing
                Role: Writing – review & editing
                Role: Writing – review & editing
                Role: InvestigationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Journal
                Proc Biol Sci
                Proc Biol Sci
                RSPB
                royprsb
                Proceedings of the Royal Society B: Biological Sciences
                The Royal Society
                0962-8452
                1471-2954
                March 9, 2022
                March 9, 2022
                March 9, 2022
                : 289
                : 1970
                : 20220085
                Affiliations
                [ 1 ] School of Resource and Environmental Engineering, Hefei University of Technology, , 193 Tunxi Road, Baohe, Hefei, Anhui 230009, People's Republic of China
                [ 2 ] Department of Biological Sciences, Clemson University, , Clemson, SC 29634, USA
                [ 3 ] Nagoya University Museum, Furocho, Chikusa-Ku, , Nagoya, Aichi 464-8601, Japan
                [ 4 ] Xinhui Museum, , 12 Gongyuan Road, Xinhui, Jiangmen, Guangdong 529199, People's Republic of China
                [ 5 ] Shunde Museum, , Bishui Road, Shunde, Foshan, Guangdong 528300, People's Republic of China
                [ 6 ] The University Museum, The University of Tokyo, , Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
                Author notes

                Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.5870758.

                Author information
                http://orcid.org/0000-0003-2701-0391
                http://orcid.org/0000-0003-0129-8921
                http://orcid.org/0000-0001-7859-5209
                Article
                rspb20220085
                10.1098/rspb.2022.0085
                8905159
                35259993
                9ee567c8-59fd-406b-b421-4aaa339c5fdd
                © 2022 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
                : January 15, 2022
                : Feburary 4, 2022
                Funding
                Funded by: National Natural Science Foundation of China, http://dx.doi.org/10.13039/501100001809;
                Award ID: 41772003
                Award ID: 42172026
                Funded by: Fundamental Research Funds for the Central Universities of China;
                Award ID: PA2020GDKC0022
                Funded by: Japan Society for the Promotion of Science, http://dx.doi.org/10.13039/501100001691;
                Award ID: 15H05969
                Award ID: 19J00701
                Award ID: 20H05821
                Funded by: China Scholarship Council, http://dx.doi.org/10.13039/501100004543;
                Award ID: 202106690044
                Funded by: Department of Natural Resources of Anhui Province;
                Award ID: 2021-g-216
                Categories
                1001
                70
                144
                183
                Palaeobiology
                Research Articles
                Custom metadata
                March 9, 2022

                Life sciences
                phylogeny,crocodylia,acoustics,sexual selection,extinction,holocene
                Life sciences
                phylogeny, crocodylia, acoustics, sexual selection, extinction, holocene

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