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      Dominance of the coral Pocillopora acuta around Phuket Island in the Andaman Sea, Thailand

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          Abstract

          Pocillopora damicornis (Linnaeus, 1758), a species complex, consists of several genetic lineages, some of which likely represent reproductively isolated species, including the species Pocillopora acuta Lamarck, 1816. Pocillopora acuta can exhibit similar morphological characteristics as P. damicornis, thus making it difficult to identify species‐level taxonomic units. To determine whether the P. damicornis‐like colonies on the reefs in the Andaman Sea (previously often identified as P. damicornis) consist of different species, we sampled individual colonies at five sites along a 50 km coastal stretch at Phuket Island and four island sites towards Krabi Province, Thailand. We sequenced 210 coral samples for the mitochondrial open reading frame and identified six distinct haplotypes, all belonging to P. acuta according to the literature. Recently, P. acuta was observed to efficiently recolonize heat‐damaged reefs in Thailand as well as globally, making it a potentially important coral species in future reefs. Specifically in the light of global change, this study underscores the importance of high‐resolution molecular species recognition, since taxonomic units are important factors for population genetic studies, and the latter are crucial for management and conservation efforts.

          Abstract

          Pocillopora damicornis (Linnaeus, 1758), a species complex, consists of several genetic lineages, some of which likely represent reproductively isolated species, including the species Pocillopora acuta Lamarck, 1816. P. acuta can exhibit similar morphological characteristics as P. damicornis, thus making it difficult to identify species‐level taxonomic units. To determine whether the P. damicornis‐like colonies on the reefs in the Andaman Sea (previously often identified as P. damicornis) consist of different species, we sampled individual colonies at five sites along a 50 km coastal stretch at Phuket Island and four island sites towards Krabi Province, Thailand. We sequenced 210 coral samples for the mitochondrial open reading frame and identified six distinct haplotypes, all belonging to P. acuta according to the literature.

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          DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.

          We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.
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            Molecular Evolutionary Genetics Analysis (MEGA) for macOS

            The Molecular Evolutionary Genetics Analysis (MEGA) software enables comparative analysis of molecular sequences in phylogenetics and evolutionary medicine. Here, we introduce the macOS version of the MEGA software. This new version eliminates the need for virtualization and emulation programs previously required to use MEGA on Apple computers. MEGA for macOS utilizes memory and computing resources efficiently for conducting evolutionary analyses on macOS. It has a native Cocoa graphical user interface that is programmed to provide a consistent user experience across macOS, Windows, and Linux. MEGA for macOS is available from www.megasoftware.net free of charge.
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              Median-joining networks for inferring intraspecific phylogenies.

              Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
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                Author and article information

                Contributors
                anna.fiesinger@uni-konstanz.de
                mwall@geomar.de
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                13 November 2023
                November 2023
                : 13
                : 11 ( doiID: 10.1002/ece3.v13.11 )
                : e10724
                Affiliations
                [ 1 ] GEOMAR Helmholtz Centre for Ocean Research Kiel Kiel Germany
                [ 2 ] Department of Biology University of Konstanz Konstanz Germany
                [ 3 ] Alfred‐Wegener‐Institut Helmholtz‐Zentrum für Polar‐ und Meeresforschung Bremerhaven Germany
                [ 4 ] Cooperative Institute for Marine and Atmospheric Research University of Hawai‘i at Manoa Honolulu Honolulu USA
                [ 5 ] Phuket Marine Biological Centre Phuket Thailand
                Author notes
                [*] [* ] Correspondence

                Anna Fiesinger, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany.

                Email: anna.fiesinger@ 123456uni-konstanz.de

                Marlene Wall, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße 1‐3, 24148 Kiel, Germany.

                Email: mwall@ 123456geomar.de

                Author information
                https://orcid.org/0000-0001-5543-1703
                Article
                ECE310724 ECE-2023-05-00815.R2
                10.1002/ece3.10724
                10643679
                46d3dfec-0208-4a8c-a1a5-2352c08d197f
                © 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 19 October 2023
                : 17 May 2023
                : 30 October 2023
                Page count
                Figures: 3, Tables: 0, Pages: 8, Words: 6250
                Funding
                Funded by: VW Foundation
                Award ID: #AZ 95 842
                Categories
                Genetics
                Nature Notes
                Nature Notes
                Custom metadata
                2.0
                November 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.3.4 mode:remove_FC converted:14.11.2023

                Evolutionary Biology
                biodiversity,haplotypes,indian ocean,pocillopora,species delimitation,species diversity

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