Forgotten in the taxonomic literature: resurrection of the scleractinian coral genus Sclerophyllia (Scleractinia, Lobophylliidae) from the Arabian Peninsula and its phylogenetic relationships
TL;DR: Phylogenetic trees and haplotype network analyses show that S. margariticola belongs to the family Lobophylliidae and that it is closely related to Acanthastrea maxima, an uncommon species from waters around the Arabian peninsula, and moves A. maxima into Sclerophyllia.
Abstract: The monospecific scleractinian coral genus Sclerophyllia Klunzinger, 1879 was originally described from Al-Qusayr (Egypt) in the Red Sea based on a series of solitary specimens. Thenceforth, it has been considered a junior synonym of Symphyllia and Cynarina based on corallum macromorphology. In this study, several specimens of Sclerophyllia margariticola were collected on the coasts of Saudi Arabia in the northern and central Red Sea. Four molecular markers were sequenced, COI and the intergenic spacer between COI and l-rRNA from mitochondrial DNA and Histone H3 and ribosomal ITS2 from nuclear DNA. Phylogenetic trees and haplotype network analyses show that S. margariticola belongs to the family Lobophylliidae and that it is closely related to Acanthastrea maxima, an uncommon species from waters around the Arabian peninsula (the Gulf of Aden, Arabian Sea, Gulf of Oman and Persian Gulf). Sclerophyllia margariticola and A. maxima share several macro- and micromorphological characters, such as the presence o...
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James Cook University1, University of Copenhagen2, Australian Institute of Marine Science3, Smithsonian Institution4, Wildlife Conservation Society5, University of Hawaii at Manoa6, National University of Singapore7, University of Queensland8, Macquarie University9, University of Auckland10, Curtin University11, Queensland Museum12, University of Warwick13
TL;DR: The overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.
Abstract: Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.
188 citations
01 Jan 2016
TL;DR: This synthesis of scleractinian phylogenetics and systematics is presented, focusing on the progress of the authors' phylogenetic understanding of this ecologically-significant clade, which today is supported by rich sets of molecular and morphological data.
Abstract: The taxonomy of scleractinian corals has traditionally been established based on morphology at the “macro” scale since the time of Carl Linnaeus. Taxa described using macromorphology are useful for classifying the myriad of growth forms, yet new molecular and small-scale morphological data have challenged the natural historicity of many familiar groups, motivating multiple revisions at every taxonomic level. In this synthesis of scleractinian phylogenetics and systematics, we present the most current state of affairs in the field covering both zooxanthellate and azooxanthellate taxa, focusing on the progress of our phylogenetic understanding of this ecologically-significant clade, which today is supported by rich sets of molecular and morphological data. It is worth noting that when DNA sequence data was first used to investigate coral evolution in the 1990s, there was no concerted effort to use phylogenetic information to delineate problematic taxa. In the last decade, however, the incompatibility of coral taxonomy with their evolutionary history has become much clearer, as molecular analyses for corals have been improved upon technically and expanded to all major scleractinian clades, shallow and deep. We describe these methodological developments and summarise new taxonomic revisions based on robust inferences of the coral tree of life. Despite these efforts, there are still unresolved sections of the scleractinian phylogeny, resulting in uncertain taxonomy for several taxa. We highlight these and propose a way forward for the taxonomy of corals.
90 citations
Cites background from "Forgotten in the taxonomic literatu..."
...2012b) and making separate estimations of gene trees (Benzoni et al. 2011, 2012a, 2014; Gittenberger et al. 2011; Bongaerts et al. 2013; Kitano et al. 2013, 2014; Huang et al. 2014a; Arrigoni et al. 2015)....
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...…(Huang et al. 2011; Addamo et al. 2012; Arrigoni et al. 2012, 2014a, b, c; Benzoni et al. 2012b) and making separate estimations of gene trees (Benzoni et al. 2011, 2012a, 2014; Gittenberger et al. 2011; Bongaerts et al. 2013; Kitano et al. 2013, 2014; Huang et al. 2014a; Arrigoni et al. 2015)....
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...(previously Acanthastrea) maxima that are endemic to waters surrounding the Arabian peninsula (Arrigoni et al. 2015)....
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...…as Arrigoni et al. (2014b) considered Australomussa as a junior synonym of Parascolymia, and also resurrected Sclerophyllia to accommodate S. margariticola and its sister species S. (previously Acanthastrea) maxima that are endemic to waters surrounding the Arabian peninsula (Arrigoni et al. 2015)....
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TL;DR: The efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches are demonstrated as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.
42 citations
TL;DR: The authors thank M. Baird and M. Dreyfus (IRD) for collections in New Caledonia, and the Niugini Biodiversity Expedition and P. Dutrieux (CREOCEAN) and C. Chaineau (Total SA) for samples from Yemen.
40 citations
Cites background or methods or result from "Forgotten in the taxonomic literatu..."
...However, the most recent phylogenetic analysis by Arrigoni et al. (2015), supported by our results here (Fig....
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...The major change over the most recent proposals by Arrigoni et al. (2014b, 2015) is the placement of all members of subclade I (sensu Arrigoni et al., 2014c) in Lobophyllia; our results show neither genetic nor morphological separation amongst Lobophyllia, Parascolymia, and Symphyllia....
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...Sclerophyllia is restricted to reefs of the Arabian Peninsula and Arabian Sea (Sheppard & Sheppard, 1991; Veron, 2000; Arrigoni et al., 2015)....
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...Arrigoni et al. (2015) then swiftly moved Ac. maxima Sheppard & Salm, 1988: 276, into the revived Sclerophyllia Klunzinger, 1879: 4....
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...Sclerophyllia maxima (Sheppard & Salm, 1988: 276, figs 4, 5); holotype: NHMUK 1986.11.17.2 (dry specimen); type locality: Muscat, Oman (14 m depth); phylogenetic data: molecular (see also Arrigoni et al., 2015) and morphology....
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TL;DR: This work uses the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea, and proposes a consistent species definition method for corals based on the combination of genomic, morphological, morphometric, and distributional data.
Abstract: Accurate delimitation of species and their relationships is a fundamental issue in evolutionary biology and taxonomy and provides essential implications for conservation management. Scleractinian corals are difficult to identify because of their ecophenotypic and geographic variation and their morphological plasticity. Furthermore, phylogenies based on traditional loci are often unresolved at the species level because of uninformative loci. Here, we attempted to resolve these issues and proposed a consistent species definition method for corals by applying the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea. We collected 77 colonies from nine localities of the Indo-Pacific and subjected them to genomic analyses. Based on de novo clustering, we obtained 44,162 SNPs (3701 loci) from the holobiont dataset and 62,728 SNPs (9573 loci) from the reads that map to coral transcriptome to reconstruct a robust phylogenetic hypothesis of the genus. Moreover, nearly complete mitochondrial genomes and ribosomal DNA arrays were retrieved by reference mapping. We combined concatenation-based phylogenetic analyses with coalescent-based species tree and species delimitation methods. Phylogenies suggest the presence of six distinct species, three corresponding to known taxa, namely Leptastrea bottae, Leptastrea inaequalis, Leptastrea transversa, one characterized by a remarkable skeletal variability encompassing the typical morphologies of Leptastrea purpurea and Leptastrea pruinosa, and two distinct and currently undescribed species. Therefore, based on the combination of genomic, morphological, morphometric, and distributional data, we herein described Leptastrea gibbosa sp. n. from the Pacific Ocean and Leptastrea magaloni sp. n. from the southwestern Indian Ocean and formally considered L. pruinosa as a junior synonym of L. purpurea. Notably, mitogenomes and rDNA yielded a concordant yet less resolved phylogeny reconstruction compared to the ones based on SNPs. This aspect demonstrates the strength and utility of RADseq technology for disentangling species boundaries in closely related species and in a challenging group such as scleractinian corals.
36 citations
Cites background from "Forgotten in the taxonomic literatu..."
...…the last decade, combined morpho-molecular approaches described new genera and species endemic to the northern and/or western Indian Ocean, thus increasing the coral biodiversity of this area (Benzoni and Stefani 2012; Benzoni et al. 2012; Terraneo et al. 2014; Arrigoni et al. 2015, 2016b, 2016c)....
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References
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TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Abstract: Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
39,110 citations
35,309 citations
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Abstract: We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
27,771 citations
01 Jan 1990
26,241 citations