34
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Species delimitation in Amblyosyllis (Annelida, Syllidae)

      research-article

      Read this article at

          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

          Amblyosyllis is a worldwide distributed group of annelids mainly found in coastal environments. It is well known among the polychaete specialists mostly because of its notable beauty, showing bright colourful patterns and outstanding long and coiled appendices. Amblyosyllis is a monophyletic genus easy to identify due to its distinct diagnostic features; however, the species and their boundaries are, in most cases, not well defined. Herein, we provide an extensive sample of Amblyosyllis material (115 specimens) from several world geographic areas. We have studied the morphological features of each specimen and photographed them alive. Two mitochondrial DNA markers (COI and 16S) and one nuclear gene fragment (28S, D1 region) were sequenced. We performed phylogenetic analyses based on each DNA partition, as well as the combined data sets, obtaining congruent results. Species delimitation methods such as distance analyses, statistical parsimony networks and multi-rate Poisson tree processes were also applied. The combined results obtained from different methodologies and data sets are used to differentiate between, at least, 19 lineages compatible with the separately evolving meta-populations species concept. Four of these lineages are identified as nominal species, including the type species of Amblyosyllis, A. rhombeata. For three other lineages previously synonymized names are recovered, and seven lineages are described as new species. All of these species are described and supported by appropriate iconography. We recognize several morphological characters useful to identify species of Amblyosyllis, which in some cases should also be combined with molecular methods for species delineation. The genetic divergence in the genus is high, contrary to the morphological homogeneity observed. Two species show a wide geographical distribution, while the rest have a more restricted distribution. There are several examples of species with overlapping distribution patterns.

          Related collections

          Most cited references171

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

          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
              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

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: Visualization
                Role: Data curationRole: InvestigationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: VisualizationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: VisualizationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                10 April 2019
                2019
                : 14
                : 4
                : e0214211
                Affiliations
                [1 ] Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
                [2 ] Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-Universität Göttingen, Göttingen, Germany
                [3 ] Departament de Biologia, Universitat de les Illes Balears, Palma, Illes Balears, Spain
                [4 ] NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
                [5 ] Laboratório de Ecologia e Evolução, Escola de Artes, Ciências e Humanidades (EACH), Universidade de São Paulo, São Paulo, São Paulo, Brazil
                [6 ] Centre of Marine Sciences, CCMAR, University of Algarve, Faro, Portugal
                [7 ] Centre d’Estudis Avançats de Blanes, CEAB-CSIC, Blanes, Girona, Spain
                [8 ] Department of Marine Science, The Faculty of Science, University of Gothenburg, Tjärnö, Strömstad, Sweden
                [9 ] Sjöfartsmuseet Akvariet, Gothenburg, Sweden
                Universidad de Sevilla, SPAIN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-5063-7961
                http://orcid.org/0000-0002-1856-3333
                http://orcid.org/0000-0001-5761-8803
                Article
                PONE-D-18-21574
                10.1371/journal.pone.0214211
                6457521
                30970025
                ab1fc02b-2f7a-4684-928c-39fcbef3f118
                © 2019 Aguado et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 20 July 2018
                : 8 March 2019
                Page count
                Figures: 33, Tables: 2, Pages: 71
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100010198, Ministerio de Economía, Industria y Competitividad, Gobierno de España;
                Award ID: CGL2015-63593-P
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100005416, Norges Forskningsråd;
                Award ID: 248799
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100009123, Norges Teknisk-Naturvitenskapelige Universitet;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003176, Ministerio de Educación, Cultura y Deporte;
                Award ID: RYC-2016-20799
                Award Recipient :
                This study is a contribution of the project “Macroevolutionary transitions in Syllidae” CGL2015-63593-P supported by MINECO ( http://www.mineco.gob.es)/FEDER, UE funds, PI: MTA. Funding was also provided by the ForBio Research School (supported by the Research Council of Norway ( https://forskningsradet.no, project no. 248799) and the Norwegian Taxonomy Initiative ( https://artsdatabanken.no, project no. 70184215); and the Ramon y Cajal program (RYC-2016-20799) funded by Spanish MINECO, Agencia Estatal de Investigación, Comunidad Autónoma de las Islas Baleares and the European Social Fund to MC. Financial support was provided to AN by the Norwegian Taxonomy Initiative (Cryptic polychaete species in Norwegian waters, (project no. 70184228, and by Kungliga Fysiografiska sällskapet Nilsson-Ehle donationerna ( https://fysiografen.se). NTNU publication fund ( http://ntnu.edu) to MC covered the publication costs. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Anatomy
                Digestive System
                Teeth
                Medicine and Health Sciences
                Anatomy
                Digestive System
                Teeth
                Biology and Life Sciences
                Anatomy
                Head
                Jaw
                Teeth
                Medicine and Health Sciences
                Anatomy
                Head
                Jaw
                Teeth
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Species Delimitation
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Cryptic Speciation
                Biology and Life Sciences
                Taxonomy
                New Species Reports
                Computer and Information Sciences
                Data Management
                Taxonomy
                New Species Reports
                Research and analysis methods
                Database and informatics methods
                Bioinformatics
                Sequence analysis
                DNA sequence analysis
                Earth sciences
                Marine and aquatic sciences
                Bodies of water
                Oceans
                Mediterranean Sea
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

                Uncategorized
                Uncategorized

                Comments

                Comment on this article