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Benedict C, Delgado A, Pen I, Vaga C, Daly M, Quattrini AM. Sea anemone (Anthozoa, Actiniaria) diversity in Mo'orea (French Polynesia). Mol Phylogenet Evol 2024; 198:108118. [PMID: 38849066 DOI: 10.1016/j.ympev.2024.108118] [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: 01/05/2024] [Revised: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo'orea (French Polynesia) with the use of a dataset from the Mo'orea Biocode's "BioBlitz" initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo'orea's diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo'orea, spotlighting the area's ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.
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Affiliation(s)
- Charlotte Benedict
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA.
| | - Alonso Delgado
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | - Isabel Pen
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | - Claudia Vaga
- Department of Invertebrate Zoology, Smithsonian Institution's National Museum of Natural History, 10th and Constitution Ave NW, Washington, DC 20560, USA
| | - Marymegan Daly
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Rd, Columbus, OH 43212, USA
| | - Andrea M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution's National Museum of Natural History, 10th and Constitution Ave NW, Washington, DC 20560, USA
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2
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Miralles A, Puillandre N, Vences M. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy. Methods Mol Biol 2024; 2744:77-104. [PMID: 38683312 DOI: 10.1007/978-1-0716-3581-0_4] [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] [Indexed: 05/01/2024]
Abstract
Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.
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Affiliation(s)
- Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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3
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Núñez-Flores M, Solórzano A, Avaria-Llautureo J, Gomez-Uchida D, López-González PJ. Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum. Mol Phylogenet Evol 2024; 190:107945. [PMID: 37863452 DOI: 10.1016/j.ympev.2023.107945] [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: 03/10/2022] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.
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Affiliation(s)
- Mónica Núñez-Flores
- Centro de Investigación de Estudios Avanzados del Maule, Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca, Chile; Laboratorio Ecología de Abejas, Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile.
| | - Andrés Solórzano
- Escuela de Geología, Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile
| | | | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution, and Conservation Laboratory (GEECLAB), Department of Zoology, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Pablo J López-González
- Biodiversidad y Ecología Acuática. Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Reina Mercedes 6, 41012 Sevilla, Spain
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4
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Ling MK, Yap NWL, Iesa IB, Yip ZT, Huang D, Quek ZBR. Revisiting mitogenome evolution in Medusozoa with eight new mitochondrial genomes. iScience 2023; 26:108252. [PMID: 37965150 PMCID: PMC10641506 DOI: 10.1016/j.isci.2023.108252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Mitogenomics has improved our understanding of medusozoan phylogeny. However, sequenced medusozoan mitogenomes remain scarce, and Medusozoa phylogeny studies often analyze mitogenomic sequences without incorporating mitogenome rearrangements. To better understand medusozoan evolution, we analyzed Medusozoa mitogenome phylogeny by sequencing and assembling eight mitogenomes from three classes (Cubozoa, Hydrozoa, and Scyphozoa). We reconstructed the mitogenome phylogeny using these mitogenomes and 84 other existing cnidarian mitogenomes to study mitochondrial gene rearrangements. All reconstructed mitogenomes had 13 mitochondrial protein-coding genes and two ribosomal genes typical for Medusozoa. Non-cubozoan mitogenomes were all linear and had typical gene orders, while arrangement of genes in the fragmented Cubozoa (Morbakka sp.) mitogenome differed from other Cubozoa mitogenomes. Gene order comparisons and ancestral state reconstruction suggest minimal rearrangements within medusozoan classes except for Hydrozoa. Our findings support a staurozoan ancestral medusozoan gene order, expand the pool of available medusozoan mitogenomes, and enhance our understanding of medusozoan phylogenetic relationships.
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Affiliation(s)
- Min Kang Ling
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Nicholas Wei Liang Yap
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- St. John’s Island National Marine Laboratory, c/o Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Iffah Binte Iesa
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zhi Ting Yip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Singapore
| | - Zheng Bin Randolph Quek
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
- Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
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5
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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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6
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Xu YU, Zhan Z, Xu K. Studies on western Pacific gorgonians (Anthozoa: Octocorallia, Chrysogorgiidae). Part 1: a review of the genus Chrysogorgia, with description of a new genus and three new species. Zootaxa 2023; 5321:1-107. [PMID: 37518205 DOI: 10.11646/zootaxa.5321.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Members of Chrysogorgia Duchassaing & Michelotti, 1864, known as golden corals, are distributed in the deep sea worldwide. Based on specimens obtained from the tropical western Pacific and an integrated morphological-molecular approach, we established a new genus Parachrysogorgia, which includes 13 species separated from Chrysogorgia, and described nine species of Chrysogorgia including three new species C. arboriformis sp. nov., C. cylindrata sp. nov. and C. tenuis sp. nov., and two new combinations of Parachrysogorgia. The genus differs from Chrysogorgia by possessing a bare, sclerite-free area at the base of each tentacle and eight distinct projections beneath tentacles. Chrysogorgia cylindrata sp. nov. is distinguished by a slender bottlebrush-shaped colony in adults, elongate and lobed scales in coenenchyme, and warty and thick sclerites near the polyp mouth area. Chrysogorgia arboriformis sp. nov. is characterized by a tree-shaped colony with a long unbranched stem, slender and thin scales usually with large warts in coenenchyme. Chrysogorgia tenuis sp. nov. can be separated by a broad bottlebrush-shaped colony, long interbranch distance, elongate scales with broad lobes in polyp body wall. In contrast to the intraspecific variation of colony form, branch internodes, branching sequence and polyps, the sclerite forms and arrangement in different parts can be viewed as the most important character to separate Chrysogorgia species. For convenient identification, we divided the Chrysogorgia species into 12 morphological groups and divided Parachrysogorgia into three groups based on their sclerite forms and arrangement.
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Affiliation(s)
- Y U Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny; Qingdao Key Laboratory of Marine Biodiversity and Conservation; Shandong Province Key Laboratory of Experimental Marine Biology; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071; China.
| | - Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny; Qingdao Key Laboratory of Marine Biodiversity and Conservation; Shandong Province Key Laboratory of Experimental Marine Biology; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071; China.
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny; Qingdao Key Laboratory of Marine Biodiversity and Conservation; Shandong Province Key Laboratory of Experimental Marine Biology; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071; China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai); Zhuhai 519082; China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai); Zhuhai 519082; China.
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7
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Breedy O, McFadden CS, Cortés J. An enigmatic new octocoral species (Anthozoa, Octocorallia, Malacalcyonacea) from Isla del Coco National Park. Zookeys 2023; 1169:317-331. [PMID: 37502774 PMCID: PMC10369172 DOI: 10.3897/zookeys.1169.100576] [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: 01/15/2023] [Accepted: 06/16/2023] [Indexed: 07/29/2023] Open
Abstract
Alienaparvagen. et sp. nov. is described from Cocos Island, Costa Rica. The species was found at various islets and rocky outcrops north and northwest of the island, 20-30 m in depth. The genus is characterised by polyps, retracting into calyces, that form thin encrusting mats extending on dead or live substrates. Sclerites are mostly asymmetrical spindles. Anthocodial rods are arranged in points, not forming a collaret. Colonies and coenenchymal sclerites are red, and polyps are transparent. Using an integrative taxonomic approach, we found the new genus to morphologically and genetically differ from all other described taxa. The molecular phylogenetic analyses provide strong support for the placement of this new genus in the family Pterogorgiidae. Morphologically it is unlike any of the other members of this family, necessitating an amendment to the diagnosis of Pterogorgiidae. Like several other known taxa of octocorals with encrusting growth forms, Alienagen. nov. appears to have evolved from a gorgonian ancestor by loss of an internal skeletal axis. It is the first member of Pterogorgiidae to be reported from the eastern Pacific, contributing further to the knowledge of marine biodiversity in the eastern tropical Pacific and to the octocoral biodiversity of Cocos Island in particular.
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Affiliation(s)
- Odalisca Breedy
- Centro de Investigación en Ciencias del Mar y Limnología; Museo de Zoología, Centro de Investigación en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, P.O. Box 11501-2060, San José, Costa Rica
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica
| | | | - Jorge Cortés
- Centro de Investigación en Ciencias del Mar y Limnología; Museo de Zoología, Centro de Investigación en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, P.O. Box 11501-2060, San José, Costa Rica
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8
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Tödter L, Worsaae K, Schmidt-Rhaesa A. Comparative molecular and morphological species delineation of Halammohydra Remane, 1927 (Hydrozoa)—with the description of four new species. ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-023-00606-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Abstract
Whereas most cnidarians are macrofaunal, a few microscopic lineages have evolved, and some of them inhabit marine sediments. The meiofaunal genus with the most species is Halammohydra, comprising nine nominal species. Species are described with high intraspecific variability in, e.g., the number of tentacles and statocysts and the shape and length of tentacles and body, complicating morphological identification to species level. Additionally, there is not much molecular data available. This study aims to revise already described species with morphological and molecular methods, as well as, to delineate potential new species answering questions about their geographical distribution. For this, specimens were sampled at 16 locations in the Northwest Atlantic and two localities in the East Atlantic, documented with light microscopy, and fixed individually for sequencing (16S, 18S, and CO1). Herewith, morphological characters were linked to a specific sequence, enabling the testing of character variation within one molecular phylogenetic group. Phylogenetic analyses were conducted (Bayesian Interference and Maximum Likelihood) in combination with species delimitation tests (ABGD, GMYC, and bPTP). Four already described species were identified in the data sets, and all of these were found at multiple localities. Four new species are described. Overall, the combined molecular and morphological data acquisition revealed multiple new species and a high degree of sympatry in Halammohydra. This, together with the confirmed excessive intraspecific variation in morphological traits, underlines the necessity of molecular sequencing for the taxonomy and species identification of Halammohydra.
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9
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Gaurisas DY, Bernardino AF. Benthic biogeographic patterns on the deep Brazilian margin. PeerJ 2023; 11:e14585. [PMID: 36874960 PMCID: PMC9979832 DOI: 10.7717/peerj.14585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/28/2022] [Indexed: 03/02/2023] Open
Abstract
The Brazilian continental margin (BCM) extends from the Tropical to the Subtropical Atlantic Ocean, with much of its seafloor within deep waters, supporting rich geomorphological features and under wide productivity gradients. Deep-sea biogeographic boundaries on the BCM have been limited to studies that used water mass and salinity properties of deep-water masses, partly as a result of historical under sampling and a lack of consolidation of available biological and ecological datasets. The aim of this study was to consolidate benthic assemblage datasets and test current oceanographic biogeographical deep-sea boundaries (200-5,000 m) using available faunal distributions. We retrieved over 4,000 benthic data records from open-access databases and used cluster analysis to examine assemblage distributions against the deep-sea biogeographical classification scheme from Watling et al. (2013). Starting from the assumption that vertical and horizontal distribution patterns can vary regionally, we test other schemes incorporating latitudinal and water masses stratification within the Brazilian margin. As expected, the classification scheme based on benthic biodiversity is in overall agreement with the general boundaries proposed by Watling et al. (2013). However, our analysis allowed much refinement in the former boundaries, and here we propose the use of two biogeographic realms, two provinces and seven bathyal ecoregions (200-3,500 m), and three abyssal provinces (>3,500 m) along the BCM. The main driver for these units seems to be latitudinal gradients as well as water mass characteristics such as temperature. Our study provides a significant improvement of benthic biogeographic ranges along the Brazilian continental margin allowing a more detailed recognition of its biodiversity and ecological value, and also supports the needed spatial management for industrial activities occurring in its deep waters.
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Affiliation(s)
- Daniela Y. Gaurisas
- Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Angelo F. Bernardino
- Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
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10
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Glon H, Häussermann V, Brewin PE, Brickle P, Kong S, Smith ML, Daly M. There and Back Again: The Unexpected Journeys of Metridium de Blainville, 1824 between the Old Oceans and throughout the Modern World. THE BIOLOGICAL BULLETIN 2023; 244:9-24. [PMID: 37167618 DOI: 10.1086/723800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
AbstractMembers of the sea anemone genus Metridium are abundant in temperate rocky habitats and fouling communities. Their biogeographic history is expected to reflect changes in currents and habitats that have influenced benthic communities, such as the climate-influenced changes that occurred during the Last Glacial Maximum. More recently, however, anthropogenic influences such as shipping transportation and the creation of artificial habitat have altered and affected the composition of modern-day marine communities. Here we use sequence-capture data to examine the genetic structure of Metridium across its shallow-water distribution to (1) evaluate species boundaries within Metridium, (2) elucidate the dispersal history of Metridium between and among oceans, and (3) assess the influence of anthropogenic movement on modern-day populations. We find strong evidence for two species within Metridium: M. farcimen and M. senile. Dispersal from the Pacific to the Atlantic included a subsequent isolation of a small population in or above the Bering Sea, which has presumably moved southward. Within the native range of M. senile, admixture is prevalent even between oceans as a result of anthropogenic activities. The nonnative populations in Chile and the Falkland Islands came from at least two distinct introduction events originating from both coasts of the United States in the North Pacific and North Atlantic Oceans. Hybridization between M. senile and M. farcimen is documented as occurring in anthropogenically influenced habitats. The heavy influence from anthropogenic activities will continue to impact our understanding of marine organisms, particularly within the native range and for those that are easily transported across long distances.
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11
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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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12
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Rogers AD, Appeltans W, Assis J, Ballance LT, Cury P, Duarte C, Favoretto F, Hynes LA, Kumagai JA, Lovelock CE, Miloslavich P, Niamir A, Obura D, O'Leary BC, Ramirez-Llodra E, Reygondeau G, Roberts C, Sadovy Y, Steeds O, Sutton T, Tittensor DP, Velarde E, Woodall L, Aburto-Oropeza O. Discovering marine biodiversity in the 21st century. ADVANCES IN MARINE BIOLOGY 2022; 93:23-115. [PMID: 36435592 DOI: 10.1016/bs.amb.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.
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Affiliation(s)
- Alex D Rogers
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom.
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
| | - Jorge Assis
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Lisa T Ballance
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | | | - Carlos Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Fabio Favoretto
- Autonomous University of Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Lisa A Hynes
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Joy A Kumagai
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Patricia Miloslavich
- Scientific Committee on Oceanic Research (SCOR), College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States; Departamento de Estudios Ambientales, Universidad Simón Bolívar, Venezuela & Scientific Committee for Oceanic Research (SCOR), Newark, DE, United States
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | | | - Bethan C O'Leary
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom; Department of Environment and Geography, University of York, York, United Kingdom
| | - Eva Ramirez-Llodra
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Gabriel Reygondeau
- Yale Center for Biodiversity Movement and Global Change, Yale University, New Haven, CT, United States; Nippon Foundation-Nereus Program, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Callum Roberts
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Yvonne Sadovy
- School of Biological Sciences, Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Oliver Steeds
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Tracey Sutton
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL, United States
| | | | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Veracruz, Mexico
| | - Lucy Woodall
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom; Department of Zoology, University of Oxford, Oxford, United Kingdom
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New Records of the Cryptogenic Soft Coral Genus Stragulum (Tubiporidae) from the Eastern Caribbean and the Persian Gulf. DIVERSITY 2022. [DOI: 10.3390/d14110909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The monotypic soft coral genus Stragulum van Ofwegen and Haddad, 2011 (Octocorallia: Malacalcyonacea: Tubiporidae) was originally described from Brazil, southwest Atlantic Ocean. Here, we report the first records of the genus from the eastern Caribbean and the Persian Gulf in the northwest Indian Ocean. We compare the morphological features of specimens, together with molecular data from three commonly used barcoding markers (COI, mtMutS, 28S rDNA) and 308 ultraconserved elements (UCE) and exon loci sequenced using a target-enrichment approach. The molecular and morphological data together suggest that specimens from all three localities are the same species, i.e., Stragulum bicolor van Ofwegen and Haddad, 2011. It is still not possible to establish the native range of the species or determine whether it may be an introduced species due to the limited number of specimens included in this study. However, the lack of historical records, its fouling abilities on artificial substrates, and a growing number of observations support the invasive nature of the species in Brazilian and Caribbean waters and therefore suggest that it may have been introduced into the Atlantic from elsewhere. Interestingly, the species has not shown any invasive behaviour in the Persian Gulf, where it has been found only on natural, rocky substrates. The aim of the present report is to create awareness of this taxon with the hope that this will lead to new records from other localities and help to establish its native range.
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14
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A Demonstration of DNA Barcoding-Based Identification of Blade-Form Ulva (Ulvophyceae, Chlorophyta) Species from Three Site in the San Juan Islands, Washington, USA. DIVERSITY 2022. [DOI: 10.3390/d14110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Marine macroalgae are foundation species that play a critical ecological role in coastal communities as primary producers. The macroalgal genus Ulva is vital in intertidal communities, serving as a food source and shelter for organisms, but these species also form environment-damaging nuisance blooms. This project aimed to demonstrate the utility of DNA barcoding for determining the diversity of Ulva species in the San Juan Islands (Washington, DC, USA). Blade-form Ulva (Ulvophyceae) specimens were collected from the lower, mid, and upper intertidal zones at three sites experiencing different levels of wave exposure. Sequences of plastid-encoded tufA were generated for each specimen and cluster analyses revealed the presence of four species at the collection sites. Two species were positively identified as Ulva expansa and Ulva fenestrata based on their sharing identical tufA sequences with those of the holotype specimens. Sequences of plastid-encoded rbcL and the nuclear-encoded ribosomal ITS regions of representative specimens were used to identify the other two species as Ulva prolifera and Ulva californica based on their similarity to epitype and topotype specimen sequences, respectively. Additional types of specimen sequencing efforts are needed to increase the number of Ulva species that can be accurately identified and realize their true biodiversity.
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15
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Mondino A, Crovadore J, Lefort F, Ursenbacher S. Impact of invading species on biodiversity: Diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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16
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Guo M, Yuan C, Tao L, Cai Y, Zhang W. Life barcoded by DNA barcodes. CONSERV GENET RESOUR 2022; 14:351-365. [PMID: 35991367 PMCID: PMC9377290 DOI: 10.1007/s12686-022-01291-2] [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: 07/15/2021] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.
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17
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Bribiesca-Contreras G, Dahlgren TG, Amon DJ, Cairns S, Drennan R, Durden JM, Eléaume MP, Hosie AM, Kremenetskaia A, McQuaid K, O’Hara TD, Rabone M, Simon-Lledó E, Smith CR, Watling L, Wiklund H, Glover AG. Benthic megafauna of the western Clarion-Clipperton Zone, Pacific Ocean. Zookeys 2022; 1113:1-110. [PMID: 36762231 PMCID: PMC9848802 DOI: 10.3897/zookeys.1113.82172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/05/2022] [Indexed: 11/12/2022] Open
Abstract
There is a growing interest in the exploitation of deep-sea mineral deposits, particularly on the abyssal seafloor of the central Pacific Clarion-Clipperton Zone (CCZ), which is rich in polymetallic nodules. In order to effectively manage potential exploitation activities, a thorough understanding of the biodiversity, community structure, species ranges, connectivity, and ecosystem functions across a range of scales is needed. The benthic megafauna plays an important role in the functioning of deep-sea ecosystems and represents an important component of the biodiversity. While megafaunal surveys using video and still images have provided insight into CCZ biodiversity, the collection of faunal samples is needed to confirm species identifications to accurately estimate species richness and species ranges, but faunal collections are very rarely carried out. Using a Remotely Operated Vehicle, 55 specimens of benthic megafauna were collected from seamounts and abyssal plains in three Areas of Particular Environmental Interest (APEI 1, APEI 4, and APEI 7) at 3100-5100 m depth in the western CCZ. Using both morphological and molecular evidence, 48 different morphotypes belonging to five phyla were found, only nine referrable to known species, and 39 species potentially new to science. This work highlights the need for detailed taxonomic studies incorporating genetic data, not only within the CCZ, but in other bathyal, abyssal, and hadal regions, as representative genetic reference libraries that could facilitate the generation of species inventories.
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Affiliation(s)
- Guadalupe Bribiesca-Contreras
- Life Sciences Department, Natural History Museum, London, UK Life Sciences Department, Natural History MuseumLondonUnited Kingdom
| | - Thomas G. Dahlgren
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SwedenUniversity of GothenburgGothenburgSweden,Norwegian Research Centre, NORCE, Bergen, NorwayNorwegian Research Centre, NORCEBergenNorway
| | - Diva J. Amon
- SpeSeas, D’Abadie, Trinidad and TobagoSpeSeasD’AbadieTrinidad and Tobago
| | - Stephen Cairns
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Regan Drennan
- National Oceanography Centre, Southampton, UKLife Sciences Department, Natural History MuseumLondonUnited Kingdom
| | - Jennifer M. Durden
- UMR ISYEB, Départment Origines et Évolution, Muséum national d’Histoire Naturelle, Paris, FranceNational Oceanography CentreSouthamptonUnited Kingdom
| | - Marc P. Eléaume
- Collections & Research, Western Australia Museum, Perth, AustraliaDépartment Origines et Évolution, Muséum national d’Histoire NaturelleParisFrance
| | - Andrew M. Hosie
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, RussiaCollections & Research, Western Australia MuseumPerthAustralia
| | - Antonina Kremenetskaia
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UKShirshov Institute of Oceanology, Russian Academy of SciencesMoscowRussia
| | - Kirsty McQuaid
- Museums Victoria, Melbourne, AustraliaUniversity of PlymouthPlymouthUnited Kingdom
| | - Timothy D. O’Hara
- Department of Oceanography, University of Hawai’i at Mānoa, Honolulu, USAMuseums VictoriaMelbourneAustralia
| | - Muriel Rabone
- National Oceanography Centre, Southampton, UKLife Sciences Department, Natural History MuseumLondonUnited Kingdom
| | - Erik Simon-Lledó
- UMR ISYEB, Départment Origines et Évolution, Muséum national d’Histoire Naturelle, Paris, FranceNational Oceanography CentreSouthamptonUnited Kingdom
| | - Craig R. Smith
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, USAUniversity of Hawai’i at MānoaHonoluluUnited States of America
| | - Les Watling
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, USAUniversity of Hawai’i at MānoaHonoluluUnited States of America
| | - Helena Wiklund
- Department of Marine Sciences, University of Gothenburg, Gothenburg, SwedenUniversity of GothenburgGothenburgSweden
| | - Adrian G. Glover
- National Oceanography Centre, Southampton, UKLife Sciences Department, Natural History MuseumLondonUnited Kingdom
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18
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CARPINELLI ÁGATHANASCIMENTO, CORDEIRO RALFTARCISOSILVA, CASTRO CLOVISBARREIRA, KITAHARA MARCELOVISENTINI. Thesea pyrrha sp. nov., a new shallow-water octocoral (Cnidaria, Anthozoa) from southwestern Atlantic, and implications on the systematics of the genus. Zootaxa 2022; 5116:89-106. [DOI: 10.11646/zootaxa.5116.1.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 11/04/2022]
Abstract
The family Plexauridae Gray, 1859 is characterized by grouping octocorals that have thick branches and coenenchyme. However, due to their relatively simple body plan, the establishment of homologous and, therefore, systematically informative morphological characters is a challenge for the systematics of Octocorallia. During the last decade, molecular studies suggested that Plexauridae is polyphyletic, with representatives grouping with Acanthogorgiidae Gray, 1859 and also Gorgoniidae Lamouroux, 1812. Represented by 22 extant species, mostly of which occur in the Atlantic Ocean, the plexaurid genus Thesea Duchassaing & Michelotti, 1860 has also been purported to be polyphyletic, with a Pacific lineage related to the former “Paramuriceidae” and an Atlantic lineage more closely related to Gorgoniidae. Thus, aiming to further improve our understanding of the evolutionary position of the Southwestern Atlantic Thesea, sequencing of the extended Octocorallia barcode reinforces the need for a re-evaluation of the position of the genus within plexaurids. Molecular and macro and micromorphological analyzes indicate the occurrence of an undescribed species distributed from Rio de Janeiro to Santa Catarina, here named Thesea pyrrha sp. nov. Results presented herein also suggest that T. pyrrha is close related to Adelogorgia and Psammogorgia, both genera exclusive to the Pacific Ocean.
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19
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Tu TH, Dai CF. A new species of anthothelid octocoral (Cnidaria, Alcyonacea) discovered on an algal reef of Taiwan. Zookeys 2022; 1089:37-51. [PMID: 35586606 PMCID: PMC8942965 DOI: 10.3897/zookeys.1089.77273] [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: 10/29/2021] [Accepted: 02/23/2022] [Indexed: 11/12/2022] Open
Abstract
A molecular phylogenetic analysis of 132 octocoral species reveals a close relationship between specimens collected from the intertidal pools of the Datan Algal Reef, Taoyuan, Taiwan, and Erythropodium caribaeorum (Duchassaing & Michelotti, 1860), but the two species have distinct morphological features. On the basis of morphological differences in polyps and sclerites, we identify and describe a new Erythropodium species: E. taoyuanensissp. nov. The distinct identifying features of E. taoyuanensissp. nov. include the upright contractile polyps from thin encrusting membranes and abundant 6-radiate sclerites. Using an integrative approach, we present the findings of morphological comparisons and molecular phylogenetic analyses to demonstrate that E. taoyuanensissp. nov. is distinct from other Erythropodium species. Our study contributes to the knowledge of octocoral biodiversity in marginal habitats.
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20
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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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21
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Lendvay B, Cartier LE, Costantini F, Iwasaki N, Everett MV, Krzemnicki MS, Kratzer A, Morf NV. Coral-ID: A forensically validated genetic test to identify precious coral material and its application to objects seized from illegal traffic. Forensic Sci Int Genet 2022; 58:102663. [DOI: 10.1016/j.fsigen.2022.102663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/01/2022]
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22
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Hayes JM, Abdul-Rahman NH, Gerdes MJ, Musah RA. Coral Genus Differentiation Based on Direct Analysis in Real Time-High Resolution Mass Spectrometry-Derived Chemical Fingerprints. Anal Chem 2021; 93:15306-15314. [PMID: 34761917 DOI: 10.1021/acs.analchem.1c02519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coral reefs are one of the most biologically diverse ecosystems, and the accurate identification of the species is essential for diversity assessment and conservation. Current genus determination approaches are time-consuming and resource-intensive and can be highly subjective. To explore the hypothesis that the small-molecule profiles of coral are genus-specific and can be used as a rapid tool to catalogue and distinguish between coral genera, the small-molecule chemical fingerprints of the species Acanthastrea echinata, Catalaphyllia jardinei, Duncanopsammia axifuga, Echinopora lamellosa, Euphyllia divisa, Euphyllia paraancora, Euphyllia paradivisa, Galaxea fascicularis, Herpolitha limax, Montipora confusa, Monitpora digitata, Montipora setosa, Pachyseris rugosa, Pavona cactus, Plerogyra sinuosa, Pocillopora acuta, Seriatopora hystrix, Sinularia dura, Turbinaria peltata, Turbinaria reniformis, Xenia elongata, and Xenia umbellata were generated using direct analysis in real time-high resolution mass spectrometry (DART-HRMS). It is demonstrated here that the mass spectrum-derived small-molecule profiles for coral of different genera are distinct. Multivariate statistical analysis processing of the DART-HRMS data enabled rapid genus-level differentiation based on the chemical composition of the coral. Coral samples were analyzed with no sample preparation required, making the approach rapid and efficient. The resulting spectra were subjected to kernel discriminant analysis (KDA), which furnished accurate genus differentiation of the coral. Leave-one-out cross-validation (LOOCV) was carried out to determine the classification accuracy of each model and confirm that this approach can be used for coral genus attribution with prediction accuracies ranging from 86.67 to 97.33%. The advantages and application of the statistical analysis to DART-HRMS-derived coral chemical signatures for genus-level differentiation are discussed.
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Affiliation(s)
- Jessica M Hayes
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nana-Hawwa Abdul-Rahman
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Michael J Gerdes
- CapitalCorals Inc., 20 Colvin Avenue, Albany, New York 12206, United States
| | - Rabi A Musah
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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23
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Strohecker J, Golladay J, Paramo M, Paramo M, El Rahmany W, Blackstone NW. Reactive Oxygen Species and the Stress Response in Octocorals. Physiol Biochem Zool 2021; 94:394-410. [PMID: 34542375 DOI: 10.1086/716857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractReactive oxygen species (ROS) may damage cellular components but may also contribute to signaling that mitigates damage. In this context, the role of ROS in the stress response that leads to coral bleaching was investigated in three series of experiments with octocorals Sarcothelia sp. and Sympodium sp. Using video and fluorescent microscopy, the first experiments examined ROS and symbiont migration. Colonies mildly stressed with increased temperature and light showed increases in both ROS and numbers of migrating symbionts compared with stress-free controls. Symbionts migrating in the gastrovascular lumen may escape programmed cell death and provide a reservoir of healthy symbionts once conditions return to normal. In the second series of experiments, colonies were mildly stressed with elevated temperature and light. During stress, treated colonies were incubated in seawater enriched with two concentrations of bicarbonate (1 and 3 mmol/L), while controls were incubated in normal seawater. Bicarbonate enrichment provides additional carbon for photosynthesis and at some concentrations diminished the ROS emissions of stressed colonies of Sympodium sp. and Sarcothelia sp. In all experiments, the latter species tended to exhibit more ROS. Sympodium sp. contains Cladocopium sp. symbionts, which are less tolerant of stress, while Sarcothelia sp. contains the more resistant Durusdinium sp. Indeed, in direct comparisons, Sarcothelia sp. experienced higher levels of ROS under stress-free conditions and thus is conditioned to endure the stress associated with bleaching. Generally, ROS levels provide important insight into the cnidarian stress response and should be measured more often in studies of this response.
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24
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Grinblat M, Cooke I, Shlesinger T, Ben-Zvi O, Loya Y, Miller DJ, Cowman PF. Biogeography, reproductive biology and phylogenetic divergence within the Fungiidae (mushroom corals). Mol Phylogenet Evol 2021; 164:107265. [PMID: 34274488 DOI: 10.1016/j.ympev.2021.107265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/15/2022]
Abstract
While the escalating impacts of climate change and other anthropogenic pressures on coral reefs are well documented at the coral community level, studies of species-specific trends are less common, owing mostly to the difficulties and uncertainties in delineating coral species. It has also become clear that traditional coral taxonomy based largely on skeletal macromorphology has underestimated the diversity of many coral families. Here, we use targeted enrichment methods to sequence 2476 ultraconserved elements (UCEs) and exonic loci to investigate the relationship between populations of Fungia fungites from Okinawa, Japan, where this species reproduces by brooding (i.e., internal fertilization), and Papua New Guinea and Australia, where it reproduces by broadcast-spawning (i.e., external fertilization). Moreover, we analyzed the relationships between populations of additional fungiid species (Herpolitha limax and Ctenactis spp.) that reproduce only by broadcast-spawning. Our phylogenetic and species delimitation analyses reveal strong biogeographic structuring in both F. fungites and Herpolitha limax, consistent with cryptic speciation in Okinawa in both species and additionally for H. limax in the Red Sea. By combining UCE/exon data and mitochondrial sequences captured in off-target reads, we reinforce earlier findings that Ctenactis, a genus consisting of three nominal morphospecies, is not a natural group. Our results highlight the need for taxonomic and systematic re-evaluations of some species and genera within the family Fungiidae. This work demonstrates that sequence data generated by the application of targeted capture methods can provide objective criteria by which we can test phylogenetic hypotheses based on morphological and/or life history traits.
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Affiliation(s)
- Mila Grinblat
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Ira Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Tom Shlesinger
- Institute for Global Ecology, Florida Institute of Technology, Melbourne, FL, USA
| | - Or Ben-Zvi
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel; The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Yossi Loya
- School of Zoology, Tel-Aviv University, Tel-Aviv, Israel
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia; Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, Queensland, Australia.
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25
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Xu Y, Zhan Z, Xu K. Morphological and Molecular Characterization of Five Species Including Three New Species of Golden Gorgonians (Cnidaria: Octocorallia) from Seamounts in the Western Pacific. BIOLOGY 2021; 10:588. [PMID: 34206888 PMCID: PMC8301098 DOI: 10.3390/biology10070588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022]
Abstract
Members of genus Iridogorgia Verrill, 1883 are the typical deep-sea megabenthos with only seven species reported. Based on an integrated morphological-molecular approach, eight sampled specimens of Iridogorgia from seamounts in the tropical Western Pacific are identified as three new species, and two known species I. magnispiralis Watling, 2007 and I. densispicula Xu, Zhan, Li and Xu, 2020. Iridogorgia flexilis sp. nov. is unique in having a very broad polyp body base with stout and thick scales. Iridogorgia densispiralis sp. nov. can be distinguished by rods present in both polyps and coenenchyme, and I. verrucosa sp. nov. is characterized by having numerous verrucae in coenenchyme and irregular spindles and scales in the polyp body wall. Phylogenetic analysis based on the nuclear 28S rDNA indicated that I. densispiralis sp. nov. showed close relationships with I. splendens Watling, 2007 and I. verrucosa sp. nov., and I. flexilis sp. nov. formed a sister clade with I. magnispiralis. In addition, due to Rhodaniridogorgia fragilis Watling, 2007 nested into the Iridogorgia clade in mtMutS-COI trees and shared highly similar morphology to the latter, we propose to eliminate the genus Rhodaniridogorgia by establishing a new combination Iridogorgia fragilis (Watling, 2007) comb. nov. and resurrecting I. superba Nutting, 1908.
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Affiliation(s)
- Yu Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.X.); (Z.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.X.); (Z.Z.)
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.X.); (Z.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans. Mol Phylogenet Evol 2021; 163:107233. [PMID: 34139346 DOI: 10.1016/j.ympev.2021.107233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Genome-level sequencing is the next step in understanding species-level relationships within Anthozoa (soft corals, anemones, stony corals, and their kin) as morphological and PCR-directed (single-locus) sequencing methods often fall short of differentiating species. The sea anemone genus Metridium is a common northern temperate sea anemone whose species are difficult to differentiate using morphology alone. Here we use Metridium as a case study to confirm the low level of information available in six loci for species differentiation commonly sequenced for Actiniaria and explore and compare the efficacy of ddRAD and sequence-capture methods in species-level systematics and biogeographic studies. We produce phylogenetic trees from concatenated datasets and perform DAPC and STRUCTURE analyses using SNP data. The six conventional loci are not able to consistently differentiate species within Metridium. The sequence-capture dataset resulted in high support and resolution for both current species and relationships between geographic areas. The ddRAD datasets displayed ambiguity among species, and support between major geographic groupings was not as high as the sequence-capture datasets. The level of resolution and support resulting from the sequence-capture data, combined with the ability to add additional individuals and expand beyond the genus Metridium over time, emphasizes the utility of sequence-capture methods for both systematics and future biogeographic studies within anthozoans. We discuss the strengths and weaknesses of the genomic approaches in light of our findings and suggest potential implications for the biogeography of Metridium based on our sampling.
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Genetic Divergence and Polyphyly in the Octocoral Genus Swiftia [Cnidaria: Octocorallia], Including a Species Impacted by the DWH Oil Spill. DIVERSITY 2021. [DOI: 10.3390/d13040172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mesophotic coral ecosystems (MCEs) are recognized around the world as diverse and ecologically important habitats. In the northern Gulf of Mexico (GoMx), MCEs are rocky reefs with abundant black corals and octocorals, including the species Swiftia exserta. Surveys following the Deepwater Horizon (DWH) oil spill in 2010 revealed significant injury to these and other species, the restoration of which requires an in-depth understanding of the biology, ecology, and genetic diversity of each species. To support a larger population connectivity study of impacted octocorals in the GoMx, this study combined sequences of mtMutS and nuclear 28S rDNA to confirm the identity of Swiftia sea fans in the GoMx, compare these markers for different polyp colors in the GoMx and Atlantic, and examine the phylogeny of the genus. Two mtMutS haplotypes were identified, one seemingly endemic to the northern GoMx. Compared to other North Atlantic Swiftia, S. exserta, the type of the genus was found to be extremely divergent and distinct from the two other Swiftia at both loci, with strong evidence of polyphyly in the genus. This information refines our understanding of the geographical distribution of injured coral and highlights how little is known about MCEs. Substantial taxonomic revisions may be needed for several taxa injured by the DWH oil spill.
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Sikorskaya TV, Efimova KV, Imbs AB. Lipidomes of phylogenetically different symbiotic dinoflagellates of corals. PHYTOCHEMISTRY 2021; 181:112579. [PMID: 33166751 DOI: 10.1016/j.phytochem.2020.112579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
The structural base of all membranes of symbiotic dinoflagellates (SD) is composed of glycolipids and betaine lipids, whereas triacylglycerols (TG) constitute an energy reserve and are involved in biosynthesis of glycolipids. Since data on the SD lipidome and the host's influence on symbionts' lipidome are scanty, we analyzed and compared the lipidomes of SD isolated from the zoantharian Palythoa tuberculosa and the alcyonarian Sinularia heterospiculata. A sequencing of nuclear gene regions showed that both cnidarians hosted the dinoflagellates Cladocopium sp. (subclades C1 and C3), but the zoantharian also contained the dinoflagellates Durusdinium trenchii (clade D). The presence of the thermotolerant D. trenchii resulted in a higher unsaturation of mono- and digalactosyldiacylglycerols (MGDG and DGDG), but a lower unsaturation of sulfoquinovosyldiacylglycerol (SQDG). The same features were earlier described for same SD from a reef-building coral. Hence, the profile of glycolipid molecules, which form SD thylakoid membranes, seems to be species-specific and does not depend on the host's taxonomic position. In contrast, the betaine lipid molecular species profile of diacylglyceryl-3-O-carboxyhydroxymethylcholine (DGCC), which forms SD cell membranes, can be influenced by the host. The profiles of the TG molecular species from freshly isolated SD have been determined for the first time. These molecular species can be divided on the basis of the acyl group in sn-2 position. The TG with 16:0 acyl group in sn-2 position may enrich total TG of a cnidarian colony and originate from SD cytoplasm. In contrast, TG 18:3/18:4/18:3 may be biosynthetically related with DGDG and concentrated in SD plastoglobules. Our data may be useful for further investigations of natural and technogenic variations in microalgal lipids and symbiont-host interactions in marine ecosystems.
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Affiliation(s)
- Tatyana V Sikorskaya
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russian Federation.
| | - Kseniya V Efimova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russian Federation; Laboratory of Ecology and Evolutionary Biology of Aquatic Organisms, Far Eastern Federal University, 690091, Vladivostok, Russian Federation
| | - Andrey B Imbs
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041, Vladivostok, Russian Federation
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29
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Cordeiro RTS, McFadden CS, Sanchez JA, Pérez CD. Revision of the genus Plexaurella Kölliker, 1865 (Anthozoa: Octocorallia) and resurrection of Plexaurellidae Verrill, 1912 new rank. INVERTEBR SYST 2021. [DOI: 10.1071/is21003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The current knowledge on the diversity of the genus Plexaurella is based on a series of dated revisions, often with no examination of types. Although being common octocorals in western Atlantic reefs, there is no consensus on an exact number of valid species. Furthermore, phylogenetic reconstructions do not support the current classification of Plexaurella within the family Plexauridae. Thus, this study reviews the genus based on examination of available types and assesses monophyly using mitochondrial (COI+igr, mtMutS) and nuclear (28S) markers, mostly from available molecular data. Until now, up to six species were considered valid. Our results show that the group is composed of at least seven previously described species: P. dichotoma, P. nutans, P. grisea, P. teres, P. grandiflora, P. regia and P. obesa; and one new species: Plexaurella rastrera sp. nov. An illustrated key to the valid species and a list of all available names are provided and the current classification of the genus is discussed. Based on congruent phylogenetic reconstructions and genetic distances, we propose the elevation of the former plexaurid subfamily Plexaurellinae to family level. Finally, based on examination of types, we propose the synonymy between Pseudoplexaura crucis and Plexaurella tenuis under Pseudoplexaura tenuis new comb.
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30
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Poliseno A, Altuna A, Puetz LC, Mak SST, Ríos P, Petroni E, McFadden CS, Sørensen MV, Gilbert MTP. An integrated morphological–molecular approach reveals new insights on the systematics of the octocoral Telestula humilis (Thomson, 1927) (Octocorallia:Alcyonacea:Clavulariidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Telestula humilis (Thomson, 1927) is a rare deep-sea stoloniferan octocoral distributed in the eastern Atlantic. Here we compared seven putative colonies of this species collected off Spain with the lectotype from the Oceanographic Museum of Monaco and found them to be identical morphologically. Phylogenetic analyses on both full mitogenomes and a concatenated alignment containing two mtDNA genes (mtMutS and Cox1) and nuclear 28S rRNA gene recovered Telestula humilis sister to Incrustatus and Inconstantia rather than to other species of Telestula. This therefore supports its taxonomic reassignment to Pseudotelestula gen. nov. as Pseudotelestula humilis comb. nov. The taxonomic reassignment is also supported by subtle differences observed between the morphology of the colony and the sclerome of Pseudotelestula humilis comb. nov. and the two sister genera. The occurrence of an intrusion tissue with sclerites in the basal part of the gastric cavity of the adult polyps is shared among Telestula and Pseudotelestula gen. nov. However, Pseudotelestula gen. nov. has sclerites arranged in a collaret and points below the tentacles, the sclerites of the calyx wall and the stolon are plump warty spindles, and the intrusion tissue has long sticks and spindles with cone-like spines.
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31
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Núñez-Flores M, Gomez-Uchida D, López-González PJ. Molecular systematics of Thouarella (Octocorallia:Primnoidae) with the description of three new species from the Southern Ocean based on combined molecular and morphological evidence. INVERTEBR SYST 2021. [DOI: 10.1071/is20078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria:Octocorallia:Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were integrated with species delimitation approaches as well as morphological colonial and polyps features and skeletal SEM examinations to describe and illustrate three new species within Thouarella, from the Weddell Sea, Southern Ocean: T. amundseni sp. nov., T. dolichoespinosa sp. nov. and T. pseudoislai sp. nov. Our species delimitation results suggest, for the first time, the potential presence of Antarctic and sub-Antarctic cryptic species of primnoids, based on the likely presence of sibling species within T. undulata and T. crenelata. With the three new species here described, the global diversity of Thouarella has increased to 41 species, 15 of which are endemic to the Antarctic and sub-Antarctic waters. Consequently, our results provide new steps for uncovering the shelf benthonic macrofauna’s hidden diversity in the Southern Ocean. Finally, we recommend using an integrative taxonomic framework in this group of organisms and species delimitation approaches because the distinctions between some Thouarella species based only on a superficial examination of their macro- and micromorphological features is, in many cases, limited.
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32
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Cowman PF, Quattrini AM, Bridge TC, Watkins-Colwell GJ, Fadli N, Grinblat M, Roberts TE, McFadden CS, Miller DJ, Baird AH. An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Mol Phylogenet Evol 2020; 153:106944. [DOI: 10.1016/j.ympev.2020.106944] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022]
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33
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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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34
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Lendvay B, Cartier LE, Gysi M, Meyer JB, Krzemnicki MS, Kratzer A, Morf NV. DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry. Sci Rep 2020; 10:8287. [PMID: 32427854 PMCID: PMC7237452 DOI: 10.1038/s41598-020-64582-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 04/17/2020] [Indexed: 11/09/2022] Open
Abstract
Precious coral species have been used to produce jewelry and ornaments since antiquity. Due to the high value and demand for corals, some coral beds have been heavily fished over past centuries. Fishing and international trade regulations were put in place to regulate fishing practices in recent decades. To this date, the control of precious coral exploitation and enforcement of trade rules have been somewhat impaired by the fact that different species of worked coral samples can be extremely difficult to distinguish, even for trained experts. Here, we developed methods to use DNA recovered from precious coral samples worked for jewelry to identify their species. We evaluated purity and quantity of DNA extracted using five different techniques. Then, a minimally invasive sampling protocol was tested, which allowed genetic analysis without compromising the value of the worked coral objects.The best performing DNA extraction technique applies decalcification of the skeletal material with EDTA in the presence of laurylsarcosyl and proteinase, and purification of the DNA with a commercial silica membrane. This method yielded pure DNA in all cases using 100 mg coral material and in over half of the cases when using "quasi non-destructive" sampling with sampled material amounts as low as 2.3 mg. Sequence data of the recovered DNA gave an indication that the range of precious coral species present in the trade is broader than previously anticipated.
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Affiliation(s)
- Bertalan Lendvay
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland. .,Swiss Gemmological Institute SSEF, Aeschengraben 26, CH-4051, Basel, Switzerland.
| | - Laurent E Cartier
- Swiss Gemmological Institute SSEF, Aeschengraben 26, CH-4051, Basel, Switzerland.,Institute of Earth Sciences, University of Lausanne, Géopolis, CH-1015, Lausanne, Switzerland
| | - Mario Gysi
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland
| | - Joana B Meyer
- Federal Office for the Environment FOEN, Worblentalstrasse 68, CH-3063, Ittigen, Switzerland
| | - Michael S Krzemnicki
- Swiss Gemmological Institute SSEF, Aeschengraben 26, CH-4051, Basel, Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland
| | - Nadja V Morf
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland
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35
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Maloney KN, Botts RT, Davis TS, Okada BK, Maloney EM, Leber CA, Alvarado O, Brayton C, Caraballo-Rodríguez AM, Chari JV, Chicoine B, Crompton JC, Davis SR, Gromek SM, Kurnianda V, Quach K, Samples RM, Shieh V, Sultana CM, Tanaka J, Dorrestein PC, Balunas MJ, McFadden CS. Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau. JOURNAL OF NATURAL PRODUCTS 2020; 83:693-705. [PMID: 31971803 DOI: 10.1021/acs.jnatprod.9b01128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sarcophyton glaucum is one of the most abundant and chemically studied soft corals with over 100 natural products reported in the literature, primarily cembrane diterpenoids. Yet, wide variation in the chemistry observed from S. glaucum over the past 50 years has led to its reputation as a capricious producer of bioactive metabolites. Recent molecular phylogenetic analysis revealed that S. glaucum is not a single species but a complex of at least seven genetically distinct species not distinguishable using traditional taxonomic criteria. We hypothesized that perceived intraspecific chemical variation observed in S. glaucum was actually due to differences between cryptic species (interspecific variation). To test this hypothesis, we collected Sarcophyton samples in Palau, performed molecular phylogenetic analysis, and prepared chemical profiles of sample extracts using gas chromatography-flame ionization detection. Both unsupervised (principal component analysis) and supervised (linear discriminant analysis) statistical analyses of these profiles revealed a strong relationship between cryptic species membership and chemical profiles. Liquid chromatography with tandem mass spectrometry-based analysis using feature-based molecular networking permitted identification of the chemical drivers of this difference between clades, including cembranoid diterpenes (2R,11R,12R)-isosarcophytoxide (5), (2S,11R,12R)-isosarcophytoxide (6), and isosarcophine (7). Our results suggest that early chemical studies of Sarcophyton may have unknowingly conflated different cryptic species of S. glaucum, leading to apparently idiosyncratic chemical variation.
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Affiliation(s)
- Katherine N Maloney
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Ryan T Botts
- Department of Mathematical, Information, and Computer Sciences, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - Taylor S Davis
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - Bethany K Okada
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Elizabeth M Maloney
- Department of Mathematical, Information, and Computer Sciences, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - Christopher A Leber
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Oscar Alvarado
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - Charlie Brayton
- Department of Biology, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jason V Chari
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - Brent Chicoine
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - J Chance Crompton
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Sydney R Davis
- Department of Chemistry, Point Loma Nazarene University, 3900 Lomaland Drive, San Diego, California 92106, United States
| | - Samantha M Gromek
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Viqqi Kurnianda
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Kim Quach
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Robert M Samples
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Vincent Shieh
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Camille M Sultana
- Department of Chemistry, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Marcy J Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Catherine S McFadden
- Department of Biology, Harvey Mudd College, 301 Platt Boulevard, Claremont, California 91711, United States
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Xu Y, Zhan Z, Xu K. Morphology and molecular phylogeny of three new deep-sea species of Chrysogorgia (Cnidaria, Octocorallia) from seamounts in the tropical Western Pacific Ocean. PeerJ 2020; 8:e8832. [PMID: 32257645 PMCID: PMC7102507 DOI: 10.7717/peerj.8832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/02/2020] [Indexed: 11/20/2022] Open
Abstract
Three new species of Chrysogorgia were discovered from seamounts in the tropical Western Pacific Ocean. Chrysogorgia dendritica sp. nov. and Chrysogorgia fragilis sp. nov. were collected from the Kocebu Guyot of the Magellan Seamount chain with the water depth of 1,821 m and 1,279-1,321 m, respectively, and Chrysogorgia gracilis sp. nov. was collected from a seamount adjacent to the Mariana Trench with the water depth of 298 m. They all belong to the Chrysogorgia "group A, Spiculosae" with rods distributed in body wall and tentacles, and differ from all congeners except C. abludo Pante & Watling, 2012 by having a tree-shaped colony (vs. bottlebrush-shaped, planar or biflabellate). Chrysogorgia dendritica sp. nov. is unique in having a monopodial stem, the 1/3L branching sequence and the amoeba-shaped sclerites (sclerites branched toward to many directions) at the body bases of polyps. Chrysogorgia fragilis sp. nov. is most similar to C. abludo, but differs by the regular 1/3L branching sequence and elongate flat scales in coenenchyme. Chrysogorgia gracilis sp. nov. is easily separated from congeners by the 1/4L branching sequence, the absence of sclerites in the basal body wall, and the very sparse scales in coenenchyme. Based on the phylogenetic and genetic distance analyses of mtMutS gene, all the available Chrysogorgia species were separated into two main groups: one includes C. binata, C. cf. stellata and C. chryseis, which have two or more fans emerging from a short main stem (bi- or multi-flabellate colony); the other one includes all the species with the branching patterns as a single ascending spiral (clockwise or counterclockwise, bottlebrush-shaped colony), a fan (planar colony) and a bush of branches perched on top of a long straight stem (tree-shaped colony). Additionally, the tree-shaped colony represents a new branching pattern in Chrysogorgia, and therefore we extend the generic diagnosis.
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Affiliation(s)
- Yu Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
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37
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Bogantes VE, Whelan NV, Webster K, Mahon AR, Halanych KM. Unrecognized diversity of a scale worm,Polyeunoa laevis(Annelida: Polynoidae), that feeds on soft coral. ZOOL SCR 2019. [DOI: 10.1111/zsc.12400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Viktoria E. Bogantes
- Department of Biological Sciences Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University Auburn AL USA
| | - Nathan V. Whelan
- Southeast Conservation Genetics Lab Warm Springs Fish Technology Center United States Fish and Wildlife Service Auburn AL USA
- School of Fisheries, Aquaculture, and Aquatic Sciences Auburn University Auburn AL USA
| | - Katelynn Webster
- Department of Biological Sciences Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University Auburn AL USA
| | - Andrew R. Mahon
- Department of Biology Central Michigan University Mount Pleasant MI USA
| | - Kenneth M. Halanych
- Department of Biological Sciences Molette Biology Laboratory for Environmental and Climate Change Studies Auburn University Auburn AL USA
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Xiao M, Brugler MR, Broe MB, Gusmão LC, Daly M, Rodríguez E. Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria. Sci Rep 2019; 9:18182. [PMID: 31796816 PMCID: PMC6890759 DOI: 10.1038/s41598-019-54637-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
Relicanthus daphneae (formerly Boloceroides daphneae) was first described in 2006 as a giant sea anemone based on morphology. In 2014, its classification was challenged based on molecular data: using five genes, Relicanthus was resolved sister to zoanthideans, but with mixed support. To better understand the evolutionary relationship of Relicanthus with other early-branching metazoans, we present 15 newly-sequenced sea anemone mitochondrial genomes and a mitogenome-based phylogeny including all major cnidarian groups, sponges, and placozoans. Our phylogenetic reconstruction reveals a moderately supported sister relationship between Relicanthus and the Actiniaria. Morphologically, the cnidae of Relicanthus has apical flaps, the only existing synapomorphy for sea anemones. Based on both molecular and morphological results, we propose a third suborder (Helenmonae) within the Actiniaria to accommodate Relicanthus. Although Relicanthus shares the same gene order and content with other available actiniarian mitogenomes, it is clearly distinct at the nucleotide level from anemones within the existing suborders. The phylogenetic position of Relicanthus could reflect its association with the periphery of isolated hydrothermal vents, which, although patchy and ephemeral, harbor unique chemosynthetic communities that provide a relatively stable food source to higher trophic levels over long evolutionary timescales. The ability to colonize the deep sea and the periphery of new vent systems may be facilitated by Relicanthus’ large and extremely yolky eggs.
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Affiliation(s)
- Madelyne Xiao
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Mercer R Brugler
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.,Biological Sciences Department, NYC College of Technology (CUNY), 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Michael B Broe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA
| | - Luciana C Gusmão
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 300 Aronoff Laboratory, Columbus, OH, 43210, USA.
| | - Estefanía Rodríguez
- Department of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
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Silvestri S, Figueroa DF, Hicks D, Figueroa NJ. Mitogenomic phylogenetic analyses of Leptogorgia virgulata and Leptogorgia hebes (Anthozoa: Octocorallia) from the Gulf of Mexico provides insight on Gorgoniidae divergence between Pacific and Atlantic lineages. Ecol Evol 2019; 9:14114-14129. [PMID: 31938507 PMCID: PMC6953674 DOI: 10.1002/ece3.5847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022] Open
Abstract
The use of genetics in recent years has brought to light the need to reevaluate the classification of many gorgonian octocorals. This study focuses on two Leptogorgia species-Leptogorgia virgulata and Leptogorgia hebes-from the northwestern Gulf of Mexico (GOM). We target complete mitochondrial genomes and mtMutS sequences, and integrate this data with previous genetic research of gorgonian corals to resolve phylogenetic relationships and estimate divergence times. This study contributes the first complete mitochondrial genomes for L. ptogorgia virgulata and L. hebes. Our resulting phylogenies stress the need to redefine the taxonomy of the genus Leptogorgia in its entirety. The fossil-calibrated divergence times for Eastern Pacific and Western Atlantic Leptogorgia species based on complete mitochondrial genomes shows that the use of multiple genes results in estimates of more recent speciation events than previous research based on single genes. These more recent divergence times are in agreement with geologic data pertaining to the formation of the Isthmus of Panama.
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Affiliation(s)
- Samantha Silvestri
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - Diego F. Figueroa
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - David Hicks
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
| | - Nicole J. Figueroa
- School of Earth, Environmental, and Marine SciencesUniversity of Texas Rio Grande ValleyBrownsvilleTXUSA
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Gąsiorek P, Blagden B, Michalczyk Ł. Towards a better understanding of echiniscid intraspecific variability: A redescription of Nebularmis reticulatus (Murray, 1905) (Heterotardigrada: Echiniscoidea). ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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41
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Wang M, Cheng F. The complete mitochondrial genome of the Ctenophore Beroe cucumis, a mitochondrial genome showing rapid evolutionary rates. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3774-3775. [PMID: 33366185 PMCID: PMC7687593 DOI: 10.1080/23802359.2019.1580165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We described the complete mitochondrial genome of the Ctenophore Beroe cucumis, which is a circular molecule of 10,487 bp in length. The new mitochondrial genome comprised only 12 genes, making it one of the smallest animals' mtDNA. Both nucleotide substitution and gene order rearrangements exhibited extreme high evolutionary rate in mitogenomes of Ctenophore. The phylogenetic analysis based on mitogenomics failed to reveal the basal position of Ctenophore within metazoan, owing to the extreme evolutionary rate. Based on the available Ctenophora mitogenomes, we found the optimized primers designed by Geller et al. for DNA barcoding suited for the taxon.
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Affiliation(s)
- Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences and Centre of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Fangping Cheng
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences and Centre of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Centre for Research on the Ecological Security of Ports and Shipping, Shanghai, China
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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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43
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Takata K, Taninaka H, Nonaka M, Iwase F, Kikuchi T, Suyama Y, Nagai S, Yasuda N. Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype. PeerJ 2019; 7:e7769. [PMID: 31598424 PMCID: PMC6779117 DOI: 10.7717/peerj.7769] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/27/2019] [Indexed: 11/20/2022] Open
Abstract
Background Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation. Methodology We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared. Results P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs. Conclusion This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).
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Affiliation(s)
- Kenji Takata
- Graduate School of Agriculture, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Hiroki Taninaka
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masanori Nonaka
- Okinawa Churashima Foundation Reseach Center, Motobu, Okinawa, Japan
| | | | - Taisei Kikuchi
- Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Nina Yasuda
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan
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Zooxanthellate, Sclerite-Free, and Pseudopinnuled Octocoral Hadaka nudidomus gen. nov. et sp. nov. (Anthozoa, Octocorallia) from Mesophotic Reefs of the Southern Ryukyus Islands. DIVERSITY 2019. [DOI: 10.3390/d11100176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Shallow water coral reefs are the most diverse marine ecosystems, but there is an immense gap in knowledge when it comes to understanding the diversity of the vast majority of marine biota in these ecosystems. This is especially true when it comes to understudied small and cryptic coral reef taxa in understudied ecosystems, such as mesophotic coral reef ecosystems (MCEs). MCEs were reported in Japan almost fifty years ago, although only in recent years has there been an increase in research concerning the diversity of these reefs. In this study we describe the first stoloniferous octocoral from MCEs, Hadaka nudidomus gen. nov. et sp. nov., from Iriomote and Okinawa Islands in the southern Ryukyus Islands. The species is zooxanthellate; both specimens host Cladocopium LaJeunesse & H.J.Jeong, 2018 (formerly Symbiodinium ‘Clade C’) and were collected from depths of ~33 to 40 m. Additionally, H. nudidomus gen. nov. et sp. nov. is both sclerite-free and lacks free pinnules, and both of these characteristics are typically diagnostic for octocorals. The discovery and morphology of H. nudidomus gen. nov. et sp. nov. indicate that we still know very little about stoloniferous octocoral diversity in MCEs, their genetic relationships with shallower reef species, and octocoral–symbiont associations. Continued research on these subjects will improve our understanding of octocoral diversity in both shallow and deeper reefs.
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Lau YW, Reimer JD. A first phylogenetic study on stoloniferous octocorals off the coast of Kota Kinabalu, Sabah, Malaysia, with the description of two new genera and five new species. Zookeys 2019; 872:127-158. [PMID: 31528119 PMCID: PMC6718372 DOI: 10.3897/zookeys.872.36288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/12/2019] [Indexed: 11/12/2022] Open
Abstract
Sabah, Malaysia, is well known for its extensive and diverse coral reefs. It is located on the northwestern edge of the Coral Triangle, the region with the highest marine biodiversity. Much of the marine fauna here is still unknown, especially inconspicuous animals, such as small stoloniferous octocorals, which are common on coral reefs. Here, we describe two new monospecific genera of the family Arulidae found off the coast of Kota Kinabalu, Sabah, East Malaysia; Bunga payung gen. nov. et sp. nov. and Laeta waheedae gen. nov. et sp. nov. As well, the stoloniferan genus Phenganax Alderslade & McFadden, 2011 belonging to the family Clavulariidae is expanded with three new species, P. marumi sp. nov., P. subtilis sp. nov., and P. stokvisi sp. nov., which are all sclerite-free. Additionally, we report a possibly undescribed species, closely related to the clavulariid genera Azoriella Lopez-Gonzalez & Gili, 2001 and Cervera Lopez-Gonzalez et al., 1995. As this and other recent studies have shown, discoveries of small stoloniferous octocorals are helping to fill gaps in our knowledge of the overall systematics of Octocorallia.
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Affiliation(s)
- Yee Wah Lau
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, JapanUniversity of the RyukyusNishiharaJapan
| | - James D. Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, JapanUniversity of the RyukyusNishiharaJapan
- Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, JapanUniversity of the RyukyusNishiharaJapan
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Horvath EA. A review of gorgonian coral species (Cnidaria, Octocorallia, Alcyonacea) held in the Santa Barbara Museum of Natural History research collection: focus on species from Scleraxonia, Holaxonia, and Calcaxonia - Part I: Introduction, species of Scleraxonia and Holaxonia (Family Acanthogorgiidae). Zookeys 2019; 860:1-66. [PMID: 31327927 PMCID: PMC6624213 DOI: 10.3897/zookeys.860.19961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 03/25/2019] [Indexed: 11/12/2022] Open
Abstract
Gorgonian specimens collected from the California Bight (northeastern Pacific Ocean) and adjacent areas held in the collection of the Santa Barbara Museum of Natural History (SBMNH) were reviewed and evaluated for species identification; much of this material is of historic significance as a large percentage of the specimens were collected by the Allan Hancock Foundation (AHF) 'Velero' Expeditions of 1931-1941 and 1948-1985. Examination and reorganization of this collection began early in 2002; initially, it was estimated that at most, twelve to fifteen species of gorgonian could be found within the Bight. Following collection evaluation, it was determined that at a minimum, approximately twenty three genera, encompassing some forty-plus species, of gorgonian coral have been found living within the California Bight region, often extending some distance into adjacent geographical areas both north and south. All species from the California Bight in the collection are discussed to some degree (in three separate parts, this being Part I), with digital images of both colony form and sclerite composition provided for most. Collection specimens from the suborders and families covered in Part I are not extensive, but several genera are featured that have not been previously reported for the California Bight region. Additionally, a potential new species (genus Sibogagorgia Stiasny, 1937) from the Paragorgiidae is described in Part I. Overall, the collection displays an emphasis on species belonging to the Holaxonia, particularly the plexaurids. A brief discussion of a California Bight grouping, referred to as the "red whips," is presented in Part II; this grouping encompasses several species with very similar colony appearance across a number of genera. A new species (a whip or thread-like form) in the genus Eugorgia Verrill, 1868, belonging to the Gorgoniidae, is described in Part II. The genus Swiftia Duchassaing & Michelotti, 1864 is one of the most challenging taxon groups represented; those species in the genus Swiftia collected within the California Bight are discussed fully, based on SBMNH (and other) specimens in Part III. Scanning electron microscopy images for species of Swiftia from the California coast have rarely, if ever, been published and are included, with a discussion of the geographic range of the genus in the eastern Pacific, from the southern boundary of the California Bight to the Bering Sea, Alaska. Finally, specimens of the genus Thesea Duchassaing & Michelotti, 1860, displaying a whip or thread-like body form, are discussed at a preliminary level in Part III; they also presented challenges to a clear understanding of their taxonomy. While Part I focuses on species of Scleraxonia and those of the Holaxonia in the Acanthogorgiidae family held in the SBMNH collection, all three parts taken together represent the first comprehensive work that reviews the research collection of SBMNH, which focuses on species of gorgonian coral known to inhabit the California Bight.
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Affiliation(s)
- Elizabeth Anne Horvath
- Westmont College, 955 La Paz Road, Santa Barbara, California 93108 USAWestmont CollegeSanta BarbaraUnited States of America
- Invertebrate Laboratory, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Road, Santa Barbara, California 93105, USASanta Barbara Museum of Natural HistorySanta BarbaraUnited States of America
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Kellogg CA. Microbiomes of stony and soft deep-sea corals share rare core bacteria. MICROBIOME 2019; 7:90. [PMID: 31182168 PMCID: PMC6558771 DOI: 10.1186/s40168-019-0697-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/19/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis. RESULTS Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians. CONCLUSIONS Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts' phylogeny.
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Affiliation(s)
- Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, 600 4th Street South, St. Petersburg, FL, 33701, USA.
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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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Morín JG, Venera-Pontón DE, Driskell AC, Sánchez JA, Lasker HR, Collin R. Reference DNA barcodes and other mitochondrial markers for identifying Caribbean Octocorals. Biodivers Data J 2019:e30970. [PMID: 30828253 PMCID: PMC6393399 DOI: 10.3897/bdj.7.e30970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/04/2019] [Indexed: 12/01/2022] Open
Abstract
DNA barcoding is a useful tool for documenting the diversity of metazoans. The most commonly used barcode markers, 16S and COI, are not considered suitable for species identification within some "basal" phyla of metazoans. Nevertheless metabarcoding studies of bulk mixed samples commonly use these markers and may obtain sequences for "basal" phyla. We sequenced mitochondrial DNA fragments of cytochrome oxidase c subunit I (COI), 16S ribosomal RNA (16S), NADH dehydrogenase subunits 2 (16S-ND2), 6 (ND6-ND3) and 4L (ND4L-MSH) for 27 species of Caribbean octocorals to create a reference barcode dataset and to compare the utility of COI and 16S to other markers more typically used for octocorals. The most common genera (Erythropodium, Ellisella, Briareum, Plexaurella, Muriceopsis and Pterogorgia) were effectively distinguished by small differences (5 or more substitutions or indels) in COI and 16S sequences. Gorgonia and Antillogorgia were effectively distinguished from each other by unique haplotypes, but the small genetic differences make distance approaches ineffective for these taxa. Plexaura, Pseudoplexaura and Eunicea were indistinguishable from each other but were generally effectively distinguished from other genera, further supporting the idea that these genera have undergone a rapid endemic radiation in the Caribbean.
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Affiliation(s)
- Jaime G Morín
- Laboratorio de Sistemática Molecular y Filogeografía, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru Laboratorio de Sistemática Molecular y Filogeografía, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos Lima Peru
| | - Dagoberto E Venera-Pontón
- Smithsonian Tropical Research Institute, Panama City, Panama Smithsonian Tropical Research Institute Panama City Panama
| | - Amy C Driskell
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution Washington, D.C. United States of America
| | - Juan A Sánchez
- Laboratorio de Biología Molecular Marina - BIOMMAR, Bogotá, Colombia Laboratorio de Biología Molecular Marina - BIOMMAR Bogotá Colombia
| | - Howard R Lasker
- Department of Geology, University at Buffalo, Buffalo, United States of America Department of Geology, University at Buffalo Buffalo United States of America
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Balboa, Panama Smithsonian Tropical Research Institute Balboa Panama
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Bryce M, Wilson NG. A new genus with two new capitate species of dimorphic soft corals (Octocorallia : Alcyoniidae) from north-western Australia. INVERTEBR SYST 2019. [DOI: 10.1071/is17051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Soft coral diversity in tropical northern Australia remains relatively understudied compared with other parts of the world. As a result of ongoing biodiversity surveys, we describe here a new genus of Octocorallia, Anastromvos, gen. nov., and two new species, A. aldersladei, sp. nov. and A. catherinae, sp. nov., collected from waters off the Pilbara, Kimberley and Darwin. To test the validity of the new genus, we used traditional morphological approaches combined with a molecular phylogeny using three mitochondrial genes (COI, mtMutS, ND2) and nuclear 28S. The markers did not amplify for the colony of A. catherinae, sp. nov., which was described on the basis of morphology only. The new genus, belonging to the family Alcyoniidae, is dimorphic, possessing autozooids and siphonozooids, and is characterised by its unique capitate growth form, stone-like colony consistency, heavy autozooid polyp armature and the possession of clubs, tuberculated spindles and/or oval-shaped sclerites and crosses. The molecular phylogeny shows the new genus as the sister group to Sarcophyton+Lobophytum, and forms a unique clade among other alcyoniid clades. The Sarcophyton–Lobophytum group of taxa can be ecologically dominant in shallow-water coral reef communities but there is still much taxonomic refinement needed for these and related genera.
http://zoobank.org/urn:lsid:zoobank.org:pub:71E96A7A-A24D-4485-AF3B-834CEF959578
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