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      Fast-Evolving Mitochondrial DNA in Ceriantharia: A Reflection of Hexacorallia Paraphyly?

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          Abstract

          The low evolutionary rate of mitochondrial genes in Anthozoa has challenged their utility for phylogenetic and systematic purposes, especially for DNA barcoding. However, the evolutionary rate of Ceriantharia, one of the most enigmatic “orders” within Anthozoa, has never been specifically examined. In this study, the divergence of mitochondrial DNA of Ceriantharia was compared to members of other Anthozoa and Medusozoa groups. In addition, nuclear markers were used to check the relative phylogenetic position of Ceriantharia in relation to other Cnidaria members. The results demonstrated a pattern of divergence of mitochondrial DNA completely different from those estimated for other anthozoans, and phylogenetic analyses indicate that Ceriantharia is not included within hexacorallians in most performed analyses. Thus, we propose that the Ceriantharia should be addressed as a separate clade.

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          Multiple alignment of DNA sequences with MAFFT.

          Kazutaka Katoh, George Asimenos, Hiroyuki Toh (2009)
          Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.
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            The magnitude of global marine species diversity.

            Ward Appeltans, Shane Ahyong, Gary Anderson … (2012)
            The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000-72,000 species are collected but not yet described, and that 482,000-741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7-1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century. Copyright © 2012 Elsevier Ltd. All rights reserved.
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              Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding.

              Danwei Huang, Rudolf Meier, Peter Todd … (2008)
              The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found variation within and between species to be much lower in Porifera and Anthozoa compared to Medusozoa (Hydrozoa and Scyphozoa), which has divergences similar to typical metazoans. Given that recent evidence has shown that fungi also exhibit limited COI divergence, slow-evolving mtDNA is likely to be plesiomorphic for the Metazoa. Higher rates of evolution could have originated independently in Medusozoa and Bilateria or been acquired in the Cnidaria + Bilateria clade and lost in the Anthozoa. Low identification success and substantial overlap between intra- and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding. Caution is also advised for Porifera and Hydrozoa because of relatively low identification success rates as even threshold divergence that maximizes the "barcoding gap" does not improve identification success.
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                Author and article information

                Contributors
                Michael Schubert: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2014
                Publication date (Electronic): 27 January 2014
                Volume: 9
                Issue: 1
                Electronic Location Identifier: e86612
                Affiliations
                [1 ]Universidade Estadual Paulista “Júlio de Mesquita Filho”, Laboratório de Biologia Aquática - LABIA, Faculdade de Ciências e Letras de Assis, Departamento de Ciências Biológicas, Assis, São Paulo, Brazil
                [2 ]Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, São Paulo, Brazil
                [3 ]Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, São Paulo, Brazil
                [4 ]Universidade de São Paulo, Centro de Biologia Marinha, São Sebastião, São Paulo, Brazil
                [5 ]Molecular Invertebrate Systematics and Ecology Laboratory, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
                Laboratoire de Biologie du Développement de Villefranche-sur-Mer, France
                Author notes

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

                Conceived and designed the experiments: SNS MMM ACM. Performed the experiments: SNS MMM. Analyzed the data: SNS MMM MVK JDR ACM. Contributed reagents/materials/analysis tools: SNS MMM ACM. Wrote the paper: SNS MMM MVK JDR ACM.

                Article
                Publisher ID: PONE-D-13-35407
                DOI: 10.1371/journal.pone.0086612
                PMC ID: 3903554
                PubMed ID: 24475157
                SO-VID: 50dedcb7-7988-46ae-b9df-d5137702e1fa
                Copyright statement: Copyright @ 2014
                License:

                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
                Date received : 27 August 2013
                Date accepted : 12 December 2013
                Page count
                Pages: 10
                Funding
                This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 2012/01771, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, PROEX) through the Programa de Pós-Graduação em Zoologia do Departamento de Zoologia IB-USP and Conselho Nacional de Desenvolvimento Científico e Tecnológico - Universal 481549/2012-9 to SNS and JDR was supported by the Rising Star Program and the International Research Hub Project for Climate Change and Coral Reef/Island Dynamics at the University of the Ryukyus. This work was partly supported by grants 2012/01771 (SNS), 2010/50174-7 (ACM), 2006/56211-6(MMM) and 2011/17537 (MVK), São Paulo Research Foundation (FAPESP). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Biology
                Subject: Evolutionary Biology
                Subject: Evolutionary Systematics
                Subject: Phylogenetics
                Subject: Organismal Evolution
                Subject: Animal Evolution
                Subject: Comparative Genomics
                Subject: Evolutionary Genetics
                Subject: Genomic Evolution
                Subject: Genetics
                Subject: Animal Genetics
                Subject: Zoology
                Subject: Animal Phylogenetics

                ScienceOpen disciplines: Uncategorized
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                ScienceOpen disciplines: Uncategorized

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