6
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      The skull of Sanajeh indicus, a Cretaceous snake with an upper temporal bar, and the origin of ophidian wide-gaped feeding

      , , ,
      Zoological Journal of the Linnean Society
      Oxford University Press (OUP)

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Recent phylogenetic analyses differ in their interpretations of the origin and interrelationships of snakes, resulting in polarized views of snake ecology, habit and acquisition of features associated with wide-gaped feeding (macrostomy). Here, we report a new specimen of the Late Cretaceous nest predator Sanajeh indicus that helps to resolve the origin of macrostomy. The new specimen preserves an ossified upper temporal bar and a posteriorly expanded otooccipital region that lacks a free-ending supratemporal bone and retains a lizard-like palatomaxillary arch that allows limited movements during swallowing. Phylogenetic analyses of a large-scale total evidence dataset resolve Sanajeh near the base of Pan-Serpentes, as the sister group of Najash, Dinilysia and crown-group Serpentes. The Cretaceous Tetrapodophis and Coniophis represent the earliest-diverging members of Pan-Serpentes. The Cretaceous hindlimbed pachyophiids and Cenozoic Australian ‘madtsoiids’ are inside crown Alethinophidia, whereas mosasaurs are recovered invariably within anguimorphs. Our results suggest that the wide-gape condition in mosasaurs and snakes might have evolved independently, as functionally distinct mechanisms of prey ingestion. The intermediate morphology preserved in Sanajeh indicates that ingestion of large prey items (macrophagy) preceded wide-gaped, unilateral feeding (macrostomy), which appeared 35 Myr later, in the common ancestor of pachyophiids, Cenozoic Australian ‘madtsoiids’ and alethinophidians.

          Related collections

          Most cited references139

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            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.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              phytools: an R package for phylogenetic comparative biology (and other things)

                Bookmark

                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                May 13 2022
                May 13 2022
                Article
                10.1093/zoolinnean/zlac001
                99f9cbb8-9020-4453-9df2-efa4f1acbec4
                © 2022

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

                History

                Comments

                Comment on this article