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      Species delimitation in Amblyosyllis (Annelida, Syllidae)

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          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.

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          Cryptic species as a window on diversity and conservation.

          The taxonomic challenge posed by cryptic species (two or more distinct species classified as a single species) has been recognized for nearly 300 years, but the advent of relatively inexpensive and rapid DNA sequencing has given biologists a new tool for detecting and differentiating morphologically similar species. Here, we synthesize the literature on cryptic and sibling species and discuss trends in their discovery. However, a lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups. The discovery of cryptic species is likely to be non-random with regard to taxon and biome and, hence, could have profound implications for evolutionary theory, biogeography and conservation planning.
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            A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.

            We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.
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                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
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                Phylogenetic Analysis
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                Computer and Information Sciences
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                Taxonomy
                Evolutionary Systematics
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                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
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                Computer and Information Sciences
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                Earth sciences
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