48
views
0
recommends
+1 Recommend
1 collections
    0
    shares

      Publish your biodiversity research with us!

      Submit your article here.

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

      Hidden in plain sight: two co-occurring cryptic species of Supplanaxis in the Caribbean ( Cerithioidea , Planaxidae )

      research-article
      1 , , 2
      ZooKeys
      Pensoft Publishers
      distribution, radular morphology, shell morphology, synonymy

      Read this article at

      ScienceOpenPublisherPMC
          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

          The cerithioid Supplanaxis nucleus (Bruguière, 1789) is widespread in the Caribbean, where it lives in often dense aggregates on hard surfaces in the middle-high intertidal. Molecular evidence shows that it comprises two species that are in fact morphologically diagnosable. We fix the nomenclature of Supplanaxis nucleus by designating a sequenced neotype from Bruguière’s historical locality of Barbados, and identify the second, cryptic species as S. nancyae (Petuch, 2013). The two live syntopically across the Caribbean and form a closely related species group with the Panamic S. planicostatus (G.B. Sowerby I, 1825). Planaxis nucleola Mörch, 1876, described from St Croix, in the Virgin Islands, never again recorded in the literature but listed as a synonym of S. nucleus in taxonomic authority lists, is recognized as a valid species of Hinea Gray, 1847. Proplanaxis Thiele, 1929 and Supplanaxis Thiele, 1929, are synonyms and the latter is given precedence over the former.

          Related collections

          Most cited references35

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

          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
                Bookmark

                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2020
                11 November 2020
                : 991
                : 85-109
                Affiliations
                [1 ] National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 163, Washington, DC 20013-7012, USA Smithsonian Institution Washington United States of America
                [2 ] Institut de Systématique, Évolution, Biodiversité, ISYEB, UMR7205 (CNRS, EPHE, MNHN, UPMC), Muséum National d’Histoire Naturelle, Sorbonne Universités, 43 Rue Cuvier, 75231 Paris Cedex 05, France Sorbonne Universités Paris France
                Author notes
                Corresponding author: Ellen E. Strong ( StrongE@ 123456si.edu )

                Academic editor: T. Backeljau

                Author information
                https://orcid.org/0000-0001-7181-4114
                Article
                PMC7674383 PMC7674383 7674383 57521
                10.3897/zookeys.991.57521
                7674383
                33223900
                25c266f3-1728-4756-9e7f-6b23d6310931

                This is an open access article distributed under the terms of the CC0 Public Domain Dedication.

                History
                : 11 August 2020
                : 17 September 2020
                Categories
                Research Article
                Planaxidae
                Nomenclature
                Phylogeny
                Taxonomy
                Atlantic Ocean

                distribution,synonymy,shell morphology,radular morphology

                Comments

                Comment on this article