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Toledo-Rodriguez DA, Veglia A, Jimenez Marrero NM, Gomez-Samot JM, McFadden CS, Weil E, Schizas NV. Shadows over Caribbean reefs: Identification of a new invasive soft coral species, Xenia umbellata, in southwest Puerto Rico. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592775. [PMID: 38766101 PMCID: PMC11100662 DOI: 10.1101/2024.05.07.592775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
In October 2023, several colonies of an alien soft coral species were reported on shallow reefs in southwest Puerto Rico. The soft coral was identified as a xeniid octocoral (species undetermined), resembling the octocoral Unomia stolonifera, which has invaded and overgrown reefs in Venezuela in recent years. To conclusively characterize the species of the invading xeniid, we employed multilocus barcoding targeting four genes (ND2, mtMutS, COI, and 28S) of three separate colonies across three locations in southwest Puerto Rico. Sequence comparisons with xeniid sequences from GenBank, including those from the genera Xenia and Unomia, indicated a 100% sequence identity (>3,000 bp combined) with the species Xenia umbellata (Octocorallia : Malacalcyonacea : Xeniidae). Xenia umbellata is native to the Red Sea and to our knowledge, this represents the first confirmed case of this species as an invader on Caribbean reefs. Similar to U. stolonifera, X. umbellata is well known for its ability to rapidly overgrow substrate as well as tolerate environmental extremes. In addition, X. umbellata has recently been proposed as a model system for tissue regeneration having the ability to regenerate completely from a single tentacle. These characteristics greatly amplify X. umbellata's potential to adversely affect any reef it invades. Our findings necessitate continued collaborative action between local management agencies and stakeholders in Puerto Rico, as well as neighboring islands, to monitor and control this invasion prior to significant ecological perturbation.
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Affiliation(s)
- Daniel A. Toledo-Rodriguez
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA
- EcoAzul, HC01 Box 4729, Lajas, PR 00667, USA
| | - Alex Veglia
- EcoAzul, HC01 Box 4729, Lajas, PR 00667, USA
- Department of Biology, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA
| | - Nilda M. Jimenez Marrero
- Department of Natural and Environmental Resources, San José Industrial Park, 1375 Ave. Ponce de León, San Juan, PR 00926, USA
| | - Joyce M. Gomez-Samot
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA
| | | | - Ernesto Weil
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA
| | - Nikolaos V. Schizas
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA
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2
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Vicario S, Terraneo TI, Chimienti G, Maggioni D, Marchese F, Purkis SJ, Eweida AA, Rodrigue M, Benzoni F. Molecular diversity of black corals from the Saudi Arabian Red Sea: a first assessment. INVERTEBR SYST 2024; 38:IS23041. [PMID: 38744524 DOI: 10.1071/is23041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/12/2024] [Indexed: 05/16/2024]
Abstract
Black corals occur as part of benthic assemblages from shallow to deep waters in all oceans. Despite the importance in many benthic ecosystems, where these act as biodiversity aggregators, antipatharians remain poorly studied, with 75% of the known species occurring below recreational SCUBA diving depth limits. Currently, information regarding the diversity and evolutionary history is limited, with most studies focusing on Hawaii and the South Pacific Ocean. Other regions of the world have received less attention, such as the Red Sea, where only two black coral families and four genera have been recorded. We provide the first analysis of the molecular diversity of black corals in the eastern Gulf of Aqaba and the northern and central Saudi Arabian Red Sea, based on a dataset of 161 antipatharian colonies collected down to 627 m deep. Based on specimen morphology, we ascribed our material to 11 genera belonging to 4 of the 7 known Antipatharia families, i.e. Antipathidae, Aphanipathidae, Myriopathidae and Schizopathidae. The genus level phylogeny of three intergenic mitochondrial regions, the trnW-IGR-nad2 (IgrW ), nad5-IGR-nad1 (IgrN ) and cox3-IGR-cox1 was reconstructed including previously published material. Overall, we recovered six molecular clades that included exclusively Red Sea sequences, with the highest diversity occurring at mesophotic depths. This study highlights that diversity of black corals in the Red Sea is much higher than previously known, with seven new generic records, suggesting that this basin may be a hotspot for antipatharian diversity as is known for other taxa. Our results recovered unresolved relationships within the order at the familial and generic levels. This emphasises the urgent need for an integration of genomic-wide data with a re-examination of informative morphological features necessary to revise the systematics of the order at all taxonomic levels.
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Affiliation(s)
- Silvia Vicario
- Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; and Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Tullia Isotta Terraneo
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Giovanni Chimienti
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia; and Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Davide Maggioni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; and Marine Research and Higher Education (MaRHE) Center, University of Milano-Bicocca, Faafu Magoodhoo, Maldives
| | - Fabio Marchese
- Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Sam J Purkis
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL 33149, USA; and Khaled bin Sultan Living Oceans Foundation, Annapolis, USA
| | | | | | - Francesca Benzoni
- Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; and Division of Biological and Environmental Science and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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3
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Combosch DJ, Burdick D, Primov K, Rios D, Rios K, Fernandez J. Barcoding and mitochondrial phylogenetics of Porites corals. PLoS One 2024; 19:e0290505. [PMID: 38359055 PMCID: PMC10868756 DOI: 10.1371/journal.pone.0290505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/10/2023] [Indexed: 02/17/2024] Open
Abstract
Coral reefs are the most diverse ecosystem on the planet based on the abundance and diversity of phyla and higher taxa. However, it is still difficult to assess the diversity of lower taxa, especially at the species level. One tool for improving the identification of lower taxa are genetic markers that can distinguish cryptic species and assess species boundaries. Here, we present one such approach for an important and challenging group of reef-building corals. Porites corals are the main reef-builders of many coral reefs in the Indo-Pacific, owing to the massive growth forms of some species. The current number of valid Porites species is controversial, inflated with many synonymies, and often based on gross colony morphology although several morphospecies believed to be widespread and common can only be distinguished based on detailed microstructure analyses by taxonomic experts. Here, we test the suitability of multiple regions of mtDNA as genetic barcodes to identify suitable markers for species differentiation and unambiguous identification. Resulting sequencing data was further used for the first phylogenetic analysis of Guam's Porites species. We tested eight different mitochondrial markers and analyzed four in detail for 135 Porites specimens: mtDNA markers were amplified for 67 Porites specimens from Guam, representing 12 nominal Porites species, and combined with 69 mitochondrial genomes, mostly from Hawaii. The combination of all 4 markers distinguished 10 common and 7 uncommon Central-West Pacific Porites species. Most clades separate species along taxonomic boundaries, which is uncommon for Porites corals and testifies to the suitability of our multi-marker approach, and a combination of the two most promising barcodes distinguished 8/10 common species. These barcodes are thus suitable to distinguish virtually cryptic species in one of the most important and challenging coral genera. They offer a cheap, fast and reliable way to identify Porites species for species-level research, monitoring and conservation.
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Affiliation(s)
| | - David Burdick
- Marine Laboratory, University of Guam, Mangilao, Guam
| | - Karim Primov
- Marine Laboratory, University of Guam, Mangilao, Guam
| | - Dareon Rios
- Marine Laboratory, University of Guam, Mangilao, Guam
| | - Kireon Rios
- Marine Laboratory, University of Guam, Mangilao, Guam
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4
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Morrissey D, Gordon JD, Saso E, Bilewitch JP, Taylor ML, Hayes V, McFadden CS, Quattrini AM, Allcock AL. Bamboozled! Resolving deep evolutionary nodes within the phylogeny of bamboo corals (Octocorallia: Scleralcyonacea: Keratoisididae). Mol Phylogenet Evol 2023; 188:107910. [PMID: 37640170 DOI: 10.1016/j.ympev.2023.107910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/22/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough signal to explore the relationships among groups. Using increased phylogenomic resolution generated from Ultraconserved Elements and exons (i.e. conserved elements), we aim to resolve deeper nodes within the family and investigate the relationships among those predefined groups. In total, 109 libraries of conserved elements were generated from individuals representing both the genetic and morphological diversity of our keratoisidids. In addition, the conserved element data of 12 individuals from previous studies were included. Our taxon sampling included 11 of the 12 keratoisidid groups. We present two phylogenies, constructed from a 75% (231 loci) and 50% (1729 loci) taxon occupancy matrix respectively, using both Maximum Likelihood and Multiple Species Coalescence methods. These trees were congruent at deep nodes. As expected, S1 keratoisidids were recovered as a well-supported sister clade to the rest of the bamboo corals. S1 corals do not share the same mitochondrial gene arrangement found in other members of Keratoisididae. All other bamboo corals were recovered within two major clades. Clade I comprises individuals assigned to alphanumeric groups B1, C1, D1&D2, F1, H1, I4, and J3 while Clade II contains representatives from A1, I1, and M1. By combining genomics with already published morphological data, we provide evidence that group H1 is not monophyletic, and that the division between other groups - D1 and D2, and A1 and M1 - needs to be reconsidered. Overall, there is a lack of robust morphological markers within Keratoisididae, but subtle characters such as sclerite microstructure and ornamentation seem to be shared within groups and warrant further investigation as taxonomically diagnostic characters.
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Affiliation(s)
- Declan Morrissey
- Ryan Institute & School of Natural Sciences, University of Galway, University Road, Galway, Ireland.
| | - Jessica D Gordon
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Emma Saso
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Jaret P Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA), 301 Evans Bay Parade, Wellington 6021, New Zealand
| | - Michelle L Taylor
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Vonda Hayes
- Department of Fisheries and Oceans, St. John's, Newfoundland and Labrador, Canada
| | - Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711, USA
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - A Louise Allcock
- Ryan Institute & School of Natural Sciences, University of Galway, University Road, Galway, Ireland
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5
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Coelho MAG, Pearson GA, Boavida JRH, Paulo D, Aurelle D, Arnaud‐Haond S, Gómez‐Gras D, Bensoussan N, López‐Sendino P, Cerrano C, Kipson S, Bakran‐Petricioli T, Ferretti E, Linares C, Garrabou J, Serrão EA, Ledoux J. Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification. Ecol Evol 2023; 13:e9740. [PMID: 36789139 PMCID: PMC9912747 DOI: 10.1002/ece3.9740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/31/2023] Open
Abstract
The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.
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Affiliation(s)
- Márcio A. G. Coelho
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,MARE – Marine and Environmental Sciences CentreISPA‐Instituto UniversitárioLisboaPortugal
| | | | | | - Diogo Paulo
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal
| | - Didier Aurelle
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne UniversitéParisFrance
| | - Sophie Arnaud‐Haond
- MARBEC (Marine Biodiversity, Exploitation and Conservation)Univ. Montpellier, IFREMER, CNRS, IRDSète CedexFrance
| | - Daniel Gómez‐Gras
- Hawai‘i Institute of Marine BiologyUniversity of Hawai‘i at MānoaKaneoheHawaiiUSA,Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Nathaniel Bensoussan
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Paula López‐Sendino
- Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Carlo Cerrano
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA)Università Politecnica delle MarcheAnconaItaly,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomeItaly,Stazione Zoologica Anton DohrnNaplesItaly,Fano Marine CenterFanoItaly
| | - Silvija Kipson
- Department of Biology, Faculty of ScienceUniversity of ZagrebZagrebCroatia,SEAFAN – Marine Research & ConsultancyZagrebCroatia
| | | | - Eliana Ferretti
- Studio Associato GAIA s.n.c.GenoaItaly,Institute of Marine ScienceThe University of AucklandAucklandNew Zealand
| | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Joaquim Garrabou
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Ester A. Serrão
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,CIBIO/InBIO‐Centro de Investigação em Biodiversidade e Recursos GenéticosVairãoPortugal
| | - Jean‐Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e AmbientalUniversidade do PortoPortoPortugal
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6
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Kessel GM, Alderslade P, Bilewitch JP, Schnabel KE, Gardner JPA. The use of integrative taxonomy in Octocorallia (Cnidaria: Anthozoa): a literature survey. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abstract
Octocorals are problematic in their systematics, and the extent of their biodiversity is poorly understood. Integrative taxonomy (the use of two or more lines of evidence for the delimitation and description of taxa) is seen as a promising way to produce more robust species hypotheses and achieve taxonomic progress in this group. However, many octocoral descriptions continue to rely on morphological evidence alone, and the prevalence of integrative methods is unclear. Here, a literature survey was conducted to gain an overview of historical description rates and to examine trends in the publication of integrative descriptions between the years 2000 and 2020. We find that recent description rates are among the highest in the history of octocoral taxonomy, and although increasing, integrative taxon descriptions remain in the minority overall. We also find that integrative taxonomy has been applied unevenly across octocoral groups and geographical regions. Description rates show no signs of slowing, and no ceiling of total species richness has yet come into view. Coupled with a continued overreliance on morphological variation, particularly at the species level, this suggests that we might be adding to the workload of taxa requiring future revision faster than such instances can be resolved.
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Affiliation(s)
- Gustav M Kessel
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
| | - Philip Alderslade
- CSIRO Oceans and Atmosphere , Castray Esplanade, Hobart, TAS 7000 , Australia
| | - Jaret P Bilewitch
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Kareen E Schnabel
- National Institute of Water & Atmospheric Research Ltd (NIWA) , 301 Evans Bay Parade, Wellington 6021 , New Zealand
| | - Jonathan P A Gardner
- School of Biological Sciences, Te Toki a Rata Building L2, Victoria University of Wellington , Gate 7 Kelburn Parade, Wellington 6012 , New Zealand
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7
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Koido T, Imahara Y, Fukami H. Xenia konohana sp. nov. (Cnidaria, Octocorallia, Alcyonacea), a new soft coral species in the family Xeniidae from Miyazaki, Japan. Zookeys 2022; 1085:29-49. [PMID: 35210904 PMCID: PMC8831390 DOI: 10.3897/zookeys.1085.77924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/18/2022] [Indexed: 11/12/2022] Open
Abstract
A new soft coral species, Xeniakonohanasp. nov. (Alcyonacea, Xeniidae), is described from Miyazaki in the warm-temperate region of Japan. This new species has conspicuous and unique spindle sclerites in addition to the simple ellipsoid platelet-shaped sclerites typically found in the genus Xenia. These unique spindles are a specific key morphological characteristic for this new species and for differentiating this species among congeneric species.
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8
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Drake JL, Benayahu Y, Polishchuk I, Pokroy B, Pinkas I, Mass T. Sclerites of the soft coral Ovabunda macrospiculata (Xeniidae) are predominantly the metastable CaCO 3 polymorph vaterite. Acta Biomater 2021; 135:663-670. [PMID: 34492373 DOI: 10.1016/j.actbio.2021.08.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 11/25/2022]
Abstract
Soft corals (Cnidaria, Anthozoa, Octocorallia, Alcyonacea) produce internal sclerites of calcium carbonate previously shown to be composed of calcite, the most stable calcium carbonate polymorph. Here we apply multiple imaging and physical chemistry analyses to extracted and in-vivo sclerites of the abundant Red Sea soft coral, Ovabunda macrospiculata, to detail their mineralogy. We show that this species' sclerites are comprised predominantly of the less stable calcium carbonate polymorph vaterite (> 95%), with much smaller components of aragonite and calcite. Use of this mineral, which is typically considered to be metastable, by these soft corals has implications for how it is formed as well as how it will persist during the anticipated anthropogenic climate change in the coming decades. This first documentation of vaterite dominating the mineral composition of O. macrospiculata sclerites is likely just the beginning of establishing its presence in other soft corals. STATEMENT OF SIGNIFICANCE: Vaterite is typically considered to be a metastable polymorph of calcium carbonate. While calcium carbonate structures formed within the tissues of octocorals (phylum Cnidaria), have previously been reported to be composed of the more stable polymorphs aragonite and calcite, we observed that vaterite dominates the mineralogy of sclerites of Ovabunda macrospiculata from the Red Sea. Based on electron microscopy, Raman spectroscopy, and X-ray diffraction analysis, vaterite appears to be the dominant polymorph in sclerites both in the tissue and after extraction and preservation. Although this is the first documentation of vaterite in soft coral sclerites, it likely will be found in sclerites of other related taxa as well.
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9
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Ramírez-Portilla C, Baird AH, Cowman PF, Quattrini AM, Harii S, Sinniger F, Flot JF. Solving the Coral Species Delimitation Conundrum. Syst Biol 2021; 71:461-475. [PMID: 34542634 DOI: 10.1093/sysbio/syab077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022] Open
Abstract
Distinguishing coral species is not only crucial for physiological, ecological and evolutionary studies, but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that inter-specific hybridization might be responsible for this apparent conundrum. Here, we used three lines of evidence - morphology, breeding trials and molecular approaches - to identify species boundaries in a group of ecologically important tabular Acropora corals. In contrast to previous studies, our morphological analyses yielded groups that were congruent with experimental crosses as well as with coalescent-based and allele sharing-based multilocus approaches to species delimitation. Our results suggest that species of the genus Acropora are reproductively isolated and independently evolving units that can be distinguished morphologically. These findings not only pave the way for a taxonomic revision of coral species, but also outline an approach that can provide a solid basis to address species delimitation and provide conservation support to a wide variety of keystone organisms.
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Affiliation(s)
- Catalina Ramírez-Portilla
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, B-1050, Belgium.,Systematics & Biodiversity, Justus-Liebig University, Giessen, D-35392, Germany
| | - Andrew H Baird
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Peter F Cowman
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - Saki Harii
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Frederic Sinniger
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels, B-1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)2, Brussels, B-1050, Belgium
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10
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Reverter M, Jackson M, Rohde S, Moeller M, Bara R, Lasut MT, Segre Reinach M, Schupp PJ. High taxonomic resolution surveys and trait-based analyses reveal multiple benthic regimes in North Sulawesi (Indonesia). Sci Rep 2021; 11:16554. [PMID: 34400684 PMCID: PMC8367970 DOI: 10.1038/s41598-021-95905-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
As coral reef communities change and reorganise in response to increasing disturbances, there is a growing need for understanding species regimes and their contribution to ecosystem processes. Using a case study on coral reefs at the epicentre of tropical marine biodiversity (North Sulawesi, Indonesia), we explored how application of different biodiversity approaches (i.e., use of major taxonomic categories, high taxonomic resolution categories and trait-based approaches) affects the detection of distinct fish and benthic communities. Our results show that using major categories fails to identify distinct coral reef regimes. We also show that monitoring of only scleractinian coral communities is insufficient to detect different benthic regimes, especially communities dominated by non-coral organisms, and that all types of benthic organisms need to be considered. We have implemented the use of a trait-based approach to study the functional diversity of whole coral reef benthic assemblages, which allowed us to detect five different community regimes, only one of which was dominated by scleractinian corals. Furthermore, by the parallel study of benthic and fish communities we provide new insights into key processes and functions that might dominate or be compromised in the different community regimes.
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Affiliation(s)
- Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment (ICBM) at the Carl Von Ossietzky University of Oldenburg, Wilhelmshaven, Germany.
| | - Matthew Jackson
- Institute for Chemistry and Biology of the Marine Environment (ICBM) at the Carl Von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | - Sven Rohde
- Institute for Chemistry and Biology of the Marine Environment (ICBM) at the Carl Von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | - Mareen Moeller
- Institute for Chemistry and Biology of the Marine Environment (ICBM) at the Carl Von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | - Robert Bara
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Jl. Kampus UNSRAT Bahu, 95115, Manado, Sulawesi Utara, Indonesia
| | - Markus T Lasut
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Jl. Kampus UNSRAT Bahu, 95115, Manado, Sulawesi Utara, Indonesia
| | | | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM) at the Carl Von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
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11
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Terraneo TI, Benzoni F, Arrigoni R, Baird AH, Mariappan KG, Forsman ZH, Wooster MK, Bouwmeester J, Marshell A, Berumen ML. Phylogenomics of Porites from the Arabian Peninsula. Mol Phylogenet Evol 2021; 161:107173. [PMID: 33813021 DOI: 10.1016/j.ympev.2021.107173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.
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Affiliation(s)
- Tullia I Terraneo
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia.
| | - Francesca Benzoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Roberto Arrigoni
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; European Commission, Joint Research Centre (JRC), Ispra, Italy; Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Napoli, Italy
| | - Andrew H Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, QLD, Australia
| | - Kiruthiga G Mariappan
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zac H Forsman
- Hawaii Institute of Marine Biology, Kaneohe 96744, HI, USA
| | - Michael K Wooster
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Michael L Berumen
- Red Sea Research Centre, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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12
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Gómez‐Corrales M, Prada C. Cryptic lineages respond differently to coral bleaching. Mol Ecol 2020; 29:4265-4273. [DOI: 10.1111/mec.15631] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Matías Gómez‐Corrales
- College of the Environment and Life Sciences University of Rhode Island Kingston RI USA
| | - Carlos Prada
- College of the Environment and Life Sciences University of Rhode Island Kingston RI USA
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13
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Erickson KL, Pentico A, Quattrini AM, McFadden CS. New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons. Mol Ecol Resour 2020; 21:78-92. [PMID: 32786110 DOI: 10.1111/1755-0998.13241] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/04/2020] [Indexed: 01/06/2023]
Abstract
As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,181 baits) to target-capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered single nucleotide polymorphisms delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using restriction site associated DNA sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow timescales in corals.
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Affiliation(s)
| | - Alicia Pentico
- Department of Biology, Harvey Mudd College, Claremont, CA, USA
| | - Andrea M Quattrini
- Department of Biology, Harvey Mudd College, Claremont, CA, USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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14
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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15
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Bryant PJ, Arehart TE. Diversity and life-cycle analysis of Pacific Ocean zooplankton by videomicroscopy and DNA barcoding: Hydrozoa. PLoS One 2019; 14:e0218848. [PMID: 31652271 PMCID: PMC6814237 DOI: 10.1371/journal.pone.0218848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 10/11/2019] [Indexed: 11/18/2022] Open
Abstract
Most, but not all cnidarian species in the class Hydrozoa have a life cycle in which a colonial, asexually reproducing hydroid phase alternates with a free-swimming, sexually reproducing medusa phase. They are not well known, in part because many of them are microscopic, at least in the medusa phase. Matching the two phases has previously required rearing of the organism from one phase to another, which has not often been possible. Here we show that DNA barcoding makes it possible to easily link life-cycle phases without the need for laboratory rearing. Hydrozoan medusae were collected by zooplankton tows in Newport Bay and the Pacific Ocean near Newport Beach, California, and hydroid colonies were collected from solid substrates in the same areas. Specimens were documented by videomicroscopy, preserved in ethanol, and sent to the Canadian Centre for DNA Barcoding at the University of Guelph, Ontario, Canada for sequencing of the COI DNA barcode. In the order Anthoathecata (athecate hydroids), DNA barcoding allowed for the discrimination between the medusae of eight putative species of Bougainvillia, and the hydroid stages were documented for two of these. The medusae of three putative species of Amphinema were identified, and the hydroid stages were identified for two of them. DNA barcodes were obtained from medusae of one species of Cladonema, one adult of the by-the wind Sailor, Velella velella, five putative species of Corymorpha with the matching hydroid phase for one; and Coryne eximia, Turritopsis dohrnii and Turritopsis nutricula with the corresponding hydroid phases. The actinula larvae and hydroid for the pink-hearted hydroid Ectopleura crocea were identified and linked by DNA barcoding. In the order Leptothecata (thecate hydroids) medusae were identified for Clytia elsaeoswaldae, Clytia gracilis and Clytia sp. 701 AC and matched with the hydroid phases for the latter two species. Medusae were matched with the hydroid phases for two species of Obelia (including O. dichotoma) and Eucheilota bakeri. Obelia geniculata was collected as a single hydroid. DNA barcodes were obtained for hydroids of Orthopyxis everta and three other species of Orthopyxis. One member of the family Solmarisidae, representing the order Narcomedusae, and one member (Liriope tetraphylla) of the order Trachymedusae were recognized as medusae. The results show the utility of DNA barcoding for matching life-cycle stages as well as for documenting the diversity of this class of organisms.
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Affiliation(s)
- Peter J. Bryant
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States of America
- * E-mail:
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16
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Iguchi A, Yoshioka Y, Forsman ZH, Knapp ISS, Toonen RJ, Hongo Y, Nagai S, Yasuda N. RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea). BMC Evol Biol 2019; 19:187. [PMID: 31615417 PMCID: PMC6794731 DOI: 10.1186/s12862-019-1522-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/27/2019] [Indexed: 01/06/2023] Open
Abstract
Background Heliopora coerulea, the blue coral, is the octocoral characterized by its blue skeleton. Recently, two Heliopora species were delimited by DNA markers: HC-A and HC-B. To clarify the genomic divergence of these Heliopora species (HC-A and HC-B) from sympatric and allopatric populations in Okinawa, Japan, we used a high throughput reduced representation genomic DNA sequencing approach (ezRAD). Results We found 6742 biallelic SNPs shared among all target populations, which successfully distinguished the HC-A and HC-B species in both the sympatric and allopatric populations, with no evidence of hybridization between the two. In addition, we detected 410 fixed SNPs linking functional gene differences, including heat resilience and reproductive timing, between HC-A and HC-B. Conclusions We confirmed clear genomic divergence between Heliopora species and found possible genes related to stress-responses and reproduction, which may shed light on the speciation process and ecological divergence of coral species.
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Affiliation(s)
- Akira Iguchi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago-City, Okinawa, 905-2192, Japan. .,Present address: Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago-City, Okinawa, 905-2192, Japan
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, Kaneohe, HI, USA
| | | | | | - Yuki Hongo
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Satoshi Nagai
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nina Yasuda
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen- kibanadai-nishi-1-1, Miyazaki, 889-2192, Japan.
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17
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Quattrini AM, Wu T, Soong K, Jeng MS, Benayahu Y, McFadden CS. A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals. BMC Evol Biol 2019; 19:116. [PMID: 31170912 PMCID: PMC6555025 DOI: 10.1186/s12862-019-1427-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. RESULTS Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. CONCLUSIONS A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.
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Affiliation(s)
- Andrea M. Quattrini
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
| | - Tiana Wu
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
| | - Keryea Soong
- Institute of Marine Biology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ming-Shiou Jeng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yehuda Benayahu
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Catherine S. McFadden
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
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18
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Gong S, Ding Y, Wang Y, Jiang G, Zhu C. Advances in DNA Barcoding of Toxic Marine Organisms. Int J Mol Sci 2018; 19:E2931. [PMID: 30261656 PMCID: PMC6213214 DOI: 10.3390/ijms19102931] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/28/2018] [Accepted: 09/20/2018] [Indexed: 01/10/2023] Open
Abstract
There are more than 200,000 marine species worldwide. These include many important economic species, such as large yellow croaker, ribbonfish, tuna, and salmon, but also many potentially toxic species, such as blue-green algae, diatoms, cnidarians, ctenophores, Nassarius spp., and pufferfish. However, some edible and toxic species may look similar, and the correct identification of marine species is thus a major issue. The failure of traditional classification methods in certain species has promoted the use of DNA barcoding, which uses short, standard DNA fragments to assist with species identification. In this review, we summarize recent advances in DNA barcoding of toxic marine species such as jellyfish and pufferfish, using genes including cytochrome oxidase I gene (COI), cytochrome b gene (cytb), 16S rDNA, internal transcribed spacer (ITS), and Ribulose-1,5-bisphosphate carboxylase oxygenase gene (rbcL). We also discuss the application of this technique for improving the identification of marine species. The use of DNA barcoding can benefit the studies of biological diversity, biogeography, food safety, and the detection of both invasive and new species. However, the technique has limitations, particularly for the analysis of complex objects and the selection of standard DNA barcodes. The development of high-throughput methods may offer solutions to some of these issues.
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Affiliation(s)
- Shaohua Gong
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Yanfei Ding
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Yi Wang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Guangze Jiang
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Cheng Zhu
- Key Laboratory of Marine, Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
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19
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Benayahu Y, van Ofwegen LP, McFadden CS. Evaluating the genus Cespitularia MilneEdwards & Haime, 1850 with descriptions of new genera of the family Xeniidae (Octocorallia, Alcyonacea). Zookeys 2018:63-101. [PMID: 29755257 PMCID: PMC5943446 DOI: 10.3897/zookeys.754.23368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/22/2018] [Indexed: 11/12/2022] Open
Abstract
Several species of the family Xeniidae, previously assigned to the genus Cespitularia Milne Edwards & Haime, 1850 are revised. Based on the problematical identity and status of the type of this genus, it became apparent that the literature has introduced misperceptions concerning its diagnosis. A consequent examination of the type colonies of Cespitularia coerulea May, 1898 has led to the establishment of the new genus Conglomeratuscleragen. n. and similarly to the assignment of Cespitularia simplex Thomson & Dean, 1931 to the new genus, Caementabundagen. n. Both new genera are described and depicted and both feature unique sclerite morphology, further highlighting the importance of sclerite microstructure for generic position among Xeniidae. Freshly collected material was subjected to molecular phylogenetic analysis, whose results substantiated the taxonomic assignment of the new genera, as well as the synonymies of several others.
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Affiliation(s)
- Yehuda Benayahu
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Leen P van Ofwegen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
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20
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Quattrini AM, Faircloth BC, Dueñas LF, Bridge TCL, Brugler MR, Calixto‐Botía IF, DeLeo DM, Forêt S, Herrera S, Lee SMY, Miller DJ, Prada C, Rádis‐Baptista G, Ramírez‐Portilla C, Sánchez JA, Rodríguez E, McFadden CS. Universal target‐enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long‐standing problems. Mol Ecol Resour 2017; 18:281-295. [DOI: 10.1111/1755-0998.12736] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/28/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA USA
| | - Luisa F. Dueñas
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Tom C. L. Bridge
- Queensland Museum Network Townsville QLD Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Mercer R. Brugler
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
- Biological Sciences Department NYC College of Technology City University of New York Brooklyn NY USA
| | - Iván F. Calixto‐Botía
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Danielle M. DeLeo
- Department of Biological Sciences Florida International University North Miami FL USA
- Biology Department Temple University Philadelphia PA USA
| | - Sylvain Forêt
- Research School of Biology Australian National University Canberra ACT Australia
| | - Santiago Herrera
- Department of Biological Sciences Lehigh University Bethlehem PA USA
| | - Simon M. Y. Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences University of Macau Macao China
| | - David J. Miller
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD Australia
| | - Carlos Prada
- Department of Biological Sciences University of Rhode Island Kingston RI USA
| | | | - Catalina Ramírez‐Portilla
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
- Department of Animal Ecology and Systematics Justus Liebig Universität Giessen Germany
| | - Juan A. Sánchez
- Departamento de Ciencias Biológicas‐Facultad de Ciencias Laboratorio de Biología Molecular Marina (BIOMMAR) Universidad de los Andes Bogotá Colombia
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
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