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      CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges of the Family Irciniidae (Demospongiae: Dictyoceratida)

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          Abstract

          Background

          DNA barcoding is a promising tool to facilitate a rapid and unambiguous identification of sponge species. Demosponges of the order Dictyoceratida are particularly challenging to identify, but are of ecological as well as biochemical importance.

          Methodology/Principal Findings

          Here we apply DNA barcoding with the standard CO1-barcoding marker on selected Indo-Pacific specimens of two genera, Ircinia and Psammocinia of the family Irciniidae. We show that the CO1 marker identifies several species new to science, reveals separate radiation patterns of deep-sea Ircinia sponges and indicates dispersal patterns of Psammocinia species. However, some species cannot be unambiguously barcoded by solely this marker due to low evolutionary rates.

          Conclusions/Significance

          We support previous suggestions for a combination of the standard CO1 fragment with an additional fragment for sponge DNA barcoding.

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          Most cited references33

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          SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny.

          SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyon1.fr/pub/ mol_phylogeny or http:@acnuc.univ-lyon1.fr/, or by e-mail to galtier@biomserv.univ-lyon1.fr.
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            Sibling Species in the Sea

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              Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding.

              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
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2010
                1 April 2010
                : 5
                : 4
                : e9950
                Affiliations
                [1 ]Museum für Naturkunde, Department of Malacozoology, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Berlin, Germany
                [2 ]Biodiversity Program, Queensland Museum, South Brisbane, Australia
                [3 ]Department of Earth- and Environmental Sciences, Palaeontology and Geobiology & GeoBio-CenterLMU, Ludwig-Maximilians-University Munich, Munich, Germany
                University of Edinburgh, United Kingdom
                Author notes

                Conceived and designed the experiments: GW. Performed the experiments: JP. Analyzed the data: JP PS DE. Contributed reagents/materials/analysis tools: PS JH. Wrote the paper: JP DE.

                Article
                09-PONE-RA-11518R1
                10.1371/journal.pone.0009950
                2848591
                20376349
                f95c11f6-126a-4430-afde-26e42b8b9289
                Pöppe 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
                : 8 July 2009
                : 28 September 2009
                Page count
                Pages: 6
                Categories
                Research Article
                Evolutionary Biology
                Ecology/Marine and Freshwater Ecology
                Evolutionary Biology/Animal Genetics

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                Uncategorized

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