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      Stolonifera from shallow waters in the north-western Pacific: a description of a new genus and two new species within the Arulidae (Anthozoa, Octocorallia)

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          Abstract

          Abstract

          A new genus and two new species of stoloniferous octocorals ( Alcyonacea ) within the family Arulidae are described based on specimens collected from Okinawa (Japan), Palau and Dongsha Atoll (Taiwan). Hana gen. n. is erected within Arulidae . Hana hanagasa sp. n. is characterised by large spindle-like table-radiates and Hana hanataba sp. n. is characterised by having ornamented rods. The distinction of these new taxa is also supported by molecular phylogenetic analyses. The support values resulting from maximum likelihood and Bayesian inference analyses for the genus Hana and new species H. hanagasa and H. hanataba are 82/1.0, 97/1.0 and 61/0.98, respectively. Hana hanagasa sp. n. and Hana hanataba sp. n. are the first arulid records for Okinawa, Palau, and Dongsha Atoll, and represent species of the second genus within the family Arulidae .

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

          We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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              ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

              Modern sequencing technology now allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary trees. We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on data sets of arbitrary size. Our software introduces a nonblocking parallelization of Metropolis-coupled chains, modifications for efficient analyses of data sets comprising thousands of partitions and memory saving techniques. We report on first experiences with Bayesian inferences at the whole-genome level using the SuperMUC supercomputer and simulated data.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                ZooKeys
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2018
                15 October 2018
                : 790
                : 1-19
                Affiliations
                [1 ] Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0123, Japan
                [2 ] Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
                [3 ] Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0123, Japan
                Author notes
                Corresponding author: James Davis Reimer ( jreimer@ 123456sci.u-ryukyu.ac.jp )

                Academic editor: B.W. Hoeksema

                Article
                10.3897/zookeys.790.28875
                6198026
                c7eb4e03-ca7e-4772-9617-82ab28ed60bb
                Yee Wah Lau, Frank Robert Stokvis, Leendert Pieter van Ofwegen, James Davis Reimer

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 August 2018
                : 10 September 2018
                Categories
                Research Article
                Anthozoa
                Biodiversity & Conservation
                Systematics
                Asia
                Oceans
                Pacific

                Animal science & Zoology
                arulidae ,coi,molecular phylogeny,mtmuts,north-western pacific,octocoral,28s rdna, stolonifera ,taxonomy,animalia,alcyonacea,arulidae

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