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Grupstra CGB, Gómez-Corrales M, Fifer JE, Aichelman HE, Meyer-Kaiser KS, Prada C, Davies SW. Integrating cryptic diversity into coral evolution, symbiosis and conservation. Nat Ecol Evol 2024; 8:622-636. [PMID: 38351091 DOI: 10.1038/s41559-023-02319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 04/13/2024]
Abstract
Understanding how diversity evolves and is maintained is critical to predicting the future trajectories of ecosystems under climate change; however, our understanding of these processes is limited in marine systems. Corals, which engineer reef ecosystems, are critically threatened by climate change, and global efforts are underway to conserve and restore populations as attempts to mitigate ocean warming continue. Recently, sequencing efforts have uncovered widespread undescribed coral diversity, including 'cryptic lineages'-genetically distinct but morphologically similar coral taxa. Such cryptic lineages have been identified in at least 24 coral genera spanning the anthozoan phylogeny and across ocean basins. These cryptic lineages co-occur in many reef systems, but their distributions often differ among habitats. Research suggests that cryptic lineages are ecologically specialized and several examples demonstrate differences in thermal tolerance, highlighting the critical implications of this diversity for predicting coral responses to future warming. Here, we draw attention to recent discoveries, discuss how cryptic diversity affects the study of coral adaptation and acclimation to future environments, explore how it shapes symbiotic partnerships, and highlight challenges and opportunities for conservation and restoration efforts.
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Affiliation(s)
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA.
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2
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Vaga CF, Seiblitz IGL, Stolarski J, Capel KCC, Quattrini AM, Cairns SD, Huang D, Quek RZB, Kitahara MV. 300 million years apart: the extreme case of macromorphological skeletal convergence between deltocyathids and a turbinoliid coral (Anthozoa, Scleractinia). INVERTEBR SYST 2024; 38:IS23053. [PMID: 38744500 DOI: 10.1071/is23053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus , molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. ZooBank: urn:lsid:zoobank.org:pub:5F1C0E25-3CC6-4D1F-B1F0-CD9D0014678E.
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Affiliation(s)
- C F Vaga
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - I G L Seiblitz
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, PL-00-818 Warsaw, Poland
| | - K C C Capel
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Invertebrate Department, National Museum of Rio de Janeiro, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, Brazil
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - D Huang
- Lee Kong Chian Natural History Museum, National University of Singapore, Conservatory Drive, Singapore 117377, Singapore; and Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - R Z B Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; and Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
| | - M V Kitahara
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
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3
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Chukaew T, Isomura N, Mezaki T, Matsumoto H, Kitano YF, Nozawa Y, Tachikawa H, Fukami H. Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species. Zoolog Sci 2023; 40:326-340. [PMID: 37522604 DOI: 10.2108/zs230009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/16/2023] [Indexed: 08/01/2023]
Abstract
The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.
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Affiliation(s)
- Thanapat Chukaew
- Graduate School of Agriculture, University of Miyazaki, Miyazaki 889-2155, Japan
| | - Naoko Isomura
- Bioresources Engineering, Institute of Technology, Okinawa College, Nago-city, Okinawa 905-2192, Japan
| | - Takuma Mezaki
- Kuroshio Biological Research Foundation, Otsuki, Kochi 788-0333, Japan
| | | | - Yuko F Kitano
- Japan Wildlife Research Center, Sumida-ku, Tokyo 130-8606, Japan
| | - Yoko Nozawa
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Hiroyuki Tachikawa
- Coastal Branch of Natural History Museum and Institute, Katsuura, Chiba 299-5242, Japan
| | - Hironobu Fukami
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, Miyazaki University, Miyazaki 889-2155, Japan,
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4
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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5
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Meziere Z, Rich WA, Carvalho S, Benzoni F, Morán XAG, Berumen ML. Stylophora under stress: A review of research trends and impacts of stressors on a model coral species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151639. [PMID: 34780827 DOI: 10.1016/j.scitotenv.2021.151639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/05/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Sometimes called the "lab rat" of coral research, Stylophora pistillata (Esper, 1797) has been extensively used in coral biology in studies ranging from reef ecology to coral metabolic processes, and has been used as a model for investigations into molecular and cellular biology. Previously thought to be a common species spanning a wide distribution through the Indo-Pacific region, "S. pistillata" is in fact four genetically distinct lineages (clades) with different evolutionary histories and geographical distributions. Here, we review the studies of stress responses of S. pistillatasensulato (clades 1-4) and highlight research trends and knowledge gaps. We identify 126 studies on stress responses including effects of temperature, acidification, eutrophication, pollutants and other local impacts. We find that most studies have focused on the effect of single stressors, especially increased temperature, and have neglected the combined effects of multiple stressors. Roughly 61% of studies on S. pistillata come from the northern Red Sea (clade 4), at the extreme limit of its current distribution; clades 2 and 3 are virtually unstudied. The overwhelming majority of studies were conducted in laboratory or mesocosm conditions, with field experiments constituting only 2% of studies. We also note that a variety of experimental designs and treatment conditions makes it difficult to draw general conclusions about the effects of particular stressors on S. pistillata. Given those knowledge gaps and limitations in the published research, we suggest a more standardized approach to compare responses across geographically disparate populations and more accurately anticipate responses to predicted future climate conditions.
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Affiliation(s)
- Zoe Meziere
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955-6900, Saudi Arabia; School of Biological Sciences, University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Walter A Rich
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955-6900, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955-6900, Saudi Arabia
| | - Francesca Benzoni
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955-6900, Saudi Arabia
| | - Xosé Anxelu G Morán
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955-6900, Saudi Arabia; Instituto Español de Oceanografía (IEO), Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Spain
| | - Michael L Berumen
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955-6900, Saudi Arabia
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6
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Juszkiewicz DJ, White NE, Stolarski J, Benzoni F, Arrigoni R, Baird AH, Hoeksema BW, Wilson NG, Bunce M, Richards ZT. Full Title: Phylogeography of recent Plesiastrea (Scleractinia: Plesiastreidae) based on an integrated taxonomic approach. Mol Phylogenet Evol 2022; 172:107469. [DOI: 10.1016/j.ympev.2022.107469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
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7
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Buitrago-López C, Mariappan KG, Cárdenas A, Gegner HM, Voolstra CR. The Genome of the Cauliflower Coral Pocillopora verrucosa. Genome Biol Evol 2021; 12:1911-1917. [PMID: 32857844 PMCID: PMC7594246 DOI: 10.1093/gbe/evaa184] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here, we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) comprised repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.
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Affiliation(s)
- Carol Buitrago-López
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Germany
| | - Hagen M Gegner
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Centre for Organismal Studies (COS), University of Heidelberg, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Germany
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8
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Morphological stasis masks ecologically divergent coral species on tropical reefs. Curr Biol 2021; 31:2286-2298.e8. [PMID: 33811819 DOI: 10.1016/j.cub.2021.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/13/2021] [Accepted: 03/09/2021] [Indexed: 01/07/2023]
Abstract
Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa) and uncover, through a comprehensive genomic and phenotypic assessment, that it comprises morphologically indistinguishable but ecologically divergent lineages. Demographic modeling based on whole-genome resequencing indicated that morphological crypsis (across micro- and macromorphological traits) was due to ancient morphological stasis rather than recent divergence. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid molecular assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate the presence of ecologically and phenotypically divergent coral species without substantial morphological differentiation and provide new leads into the potential mechanisms facilitating such divergence. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.
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9
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Inclusivity is key to progressing coral biodiversity research: Reply to comment by Bonito et al. (2021). Mol Phylogenet Evol 2021; 162:107135. [PMID: 33684528 DOI: 10.1016/j.ympev.2021.107135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 11/23/2022]
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10
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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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11
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Forsman ZH, Ritson-Williams R, Tisthammer KH, Knapp ISS, Toonen RJ. Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae). Sci Rep 2020; 10:16995. [PMID: 33046719 PMCID: PMC7550562 DOI: 10.1038/s41598-020-73501-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/14/2020] [Indexed: 11/09/2022] Open
Abstract
The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāne'ohe Bay Hawai'i during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.
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Affiliation(s)
- Z H Forsman
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, USA.
| | | | - K H Tisthammer
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - I S S Knapp
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, USA
| | - R J Toonen
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, USA
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12
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Wepfer PH, Nakajima Y, Sutthacheep M, Radice VZ, Richards Z, Ang P, Terraneo T, Sudek M, Fujimura A, Toonen RJ, Mikheyev AS, Economo EP, Mitarai S. Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean. Mol Phylogenet Evol 2020; 151:106905. [DOI: 10.1016/j.ympev.2020.106905] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022]
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13
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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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14
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Leveque S, Afiq-Rosli L, Ip YCA, Jain SS, Huang D. Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals. PeerJ 2019; 7:e7669. [PMID: 31565579 PMCID: PMC6746223 DOI: 10.7717/peerj.7669] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/13/2019] [Indexed: 11/20/2022] Open
Abstract
Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.
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Affiliation(s)
- Sébastien Leveque
- National University of Singapore, Singapore, Singapore.,Université de La Rochelle, La Rochelle, Singapore
| | | | | | | | - Danwei Huang
- National University of Singapore, Singapore, Singapore
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15
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Porro B, Mallien C, Hume BCC, Pey A, Aubin E, Christen R, Voolstra CR, Furla P, Forcioli D. The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs. Heredity (Edinb) 2019; 124:351-366. [PMID: 31527783 DOI: 10.1038/s41437-019-0266-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 07/30/2019] [Accepted: 08/15/2019] [Indexed: 11/09/2022] Open
Abstract
How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.
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Affiliation(s)
- Barbara Porro
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
| | - Cédric Mallien
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Benjamin C C Hume
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Alexis Pey
- THALASSA Marine research & Environmental awareness, 17 rue Gutenberg, 06000, Nice, France
| | - Emilie Aubin
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Laboratoire Génome et Développement des Plantes-UMR CNRS/UPVD 5096, Université de Perpignan, 66860, Perpignan, France
| | - Richard Christen
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paola Furla
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France
| | - Didier Forcioli
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
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16
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Darras H, Kuhn A, Aron S. Evolution of hybridogenetic lineages in
Cataglyphis
ants. Mol Ecol 2019; 28:3073-3088. [DOI: 10.1111/mec.15116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Hugo Darras
- Evolutionary Biology & Ecology Université Libre de Bruxelles Brussels Belgium
- Department of Ecology and Evolution Université de Lausanne Lausanne Switzerland
| | - Alexandre Kuhn
- Evolutionary Biology & Ecology Université Libre de Bruxelles Brussels Belgium
| | - Serge Aron
- Evolutionary Biology & Ecology Université Libre de Bruxelles Brussels Belgium
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17
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Montgomery AD, Fenner D, Toonen RJ. Annotated checklist for stony corals of American Sāmoa with reference to mesophotic depth records. Zookeys 2019; 849:1-170. [PMID: 31171897 PMCID: PMC6538593 DOI: 10.3897/zookeys.849.34763] [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: 03/22/2019] [Accepted: 04/20/2019] [Indexed: 11/12/2022] Open
Abstract
An annotated checklist of the stony corals (Scleractinia, Milleporidae, Stylasteridae, and Helioporidae) of American Sāmoa is presented. A total of 377 valid species has been reported from American Sāmoa with 342 species considered either present (251) or possibly present (91). Of these 342 species, 66 have a recorded geographical range extension and 90 have been reported from mesophotic depths (30–150 m). Additionally, four new species records (Acanthastreasubechinata Veron, 2000, Favitesparaflexuosus Veron, 2000, Echinophylliaechinoporoides Veron & Pichon, 1980, Turbinariairregularis Bernard, 1896) are presented. Coral species of concern include species listed under the US Endangered Species Act (ESA) and the International Union for Conservation of Nature’s (IUCN) Red List of threatened species. Approximately 17.5% of the species present or possibly present are categorized as threatened by IUCN compared to 27% of the species globally. American Sāmoa has seven ESA-listed or ESA candidate species, including Acroporaglobiceps (Dana, 1846), Acroporajacquelineae Wallace, 1994, Acroporaretusa (Dana, 1846), Acroporaspeciosa (Quelch, 1886), Fimbriaphylliaparadivisa (Veron, 1990), Isoporacrateriformis (Gardiner, 1898), and Pocilloporameandrina Dana, 1846. There are two additional species possibly present, i.e., Pavonadiffluens (Lamarck, 1816) and Poritesnapopora Veron, 2000.
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Affiliation(s)
- Anthony D Montgomery
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA University of Hawai'i at Mānoa Kāne'ohe United States of America.,U.S. Fish and Wildlife Service, Pacific Islands Fish and Wildlife Office, 300 Ala Moana Blvd. Honolulu, HI 96850, USA U.S. Fish and Wildlife Service Honolulu United States of America
| | - Douglas Fenner
- Ocean Associates, Inc., NOAA Fisheries Service, Pacific Islands Regional Office, Pago Pago, AS, USA NOAA Fisheries Service, Pacific Islands Regional Office Pago Pago American Samoa
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA University of Hawai'i at Mānoa Kāne'ohe United States of America
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18
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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Phylogenet Evol 2019; 134:12-23. [DOI: 10.1016/j.ympev.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/28/2023]
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19
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Banguera-Hinestroza E, Ferrada E, Sawall Y, Flot JF. Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. Genes (Basel) 2019; 10:E324. [PMID: 31035578 PMCID: PMC6562464 DOI: 10.3390/genes10050324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/15/2023] Open
Abstract
More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.
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Affiliation(s)
- Eulalia Banguera-Hinestroza
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
| | - Evandro Ferrada
- Center for Genomics and Bioinformatics, Universidad Mayor, Santiago, Chile.
| | - Yvonne Sawall
- Coral Reef Ecology, Bermuda Institute of Ocean Sciences (BIOS), St.George's GE 01, Bermuda.
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
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20
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21
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Nakajima Y, Chuang PS, Ueda N, Mitarai S. First evidence of asexual recruitment of Pocillopora acuta in Okinawa Island using genotypic identification. PeerJ 2018; 6:e5915. [PMID: 30473933 PMCID: PMC6237110 DOI: 10.7717/peerj.5915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
Okinawa Island is located near the center of the Nansei Islands (∼24–31°N), at a relatively high latitude for coral reefs. Nevertheless, more than 80 coral genera (over 400 species) are abundant in the Nansei Islands. Since March, 2017, scleractinian corals have been held in an outdoor tank at the OIST Marine Science Station at Seragaki, Onna with natural sea water flow-through in order to be used in molecular biological and physiological studies. In January, 2018, we found small pocilloporid-like colonies suspected to have originated asexually. We collected 25 small colonies and measured their sizes and weights. Also, we validated the classification and clonality of the colonies using a mitochondrial locus and nine microsatellite loci. Almost all of the small colonies collected in the outdoor tank were ≤1 cm in both width and height. The weight of dried skeletons ranged from 0.0287 to 0.1807 g. Genetic analysis determined that they were, in fact, Pocillopora acuta. Only one mitochondrial haplotype was shared and two microsatellite multilocus genotypes were detected (20 colonies of one and four colonies of the other). The mitochondrial haplotype and one microsatellite multilocus genotype for 20 colonies corresponded to those of one P. acuta colony being kept in the tank. One small colony matched both multilocus genotypes. This may have been a chimeric colony resulting from allogenic fusion. These small colonies were not produced sexually, because the only potential parent in the tank was the aforementioned P. acuta colony. Instead, they were more likely derived from asexual planula release or polyp bail-out. Corals as Pocillopora acuta have the capacity to produce clonal offspring rapidly and to adapt readily to local environments. This is the first report of asexual reproduction by planulae or expelled polyps in P. acuta at Okinawa Island.
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Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Po-Shun Chuang
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Nobuo Ueda
- Okinawa Marine Science Support Section, OIST Marine Science Station, Onna, Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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22
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Arrigoni R, Berumen ML, Stolarski J, Terraneo TI, Benzoni F. Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean. Cladistics 2018; 35:301-328. [DOI: 10.1111/cla.12346] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- Roberto Arrigoni
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
| | - Michael L. Berumen
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
| | - Jaroslaw Stolarski
- Institute of Paleobiology Polish Academy of Sciences Twarda 51/55 Warsaw PL‐00‐818 Poland
| | - Tullia I. Terraneo
- Red Sea Research Center Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Saudi Arabia
- College of Marine and Environmental Science James Cook University Townsville QLD 4811 Australia
| | - Francesca Benzoni
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Piazza della Scienza 2 Milano 20126 Italy
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS) Laboratoire d'excellence‐CORAIL Centre IRD de Nouméa 101 Promenade Roger Laroque, BP A5 Noumea Cedex 98848 New Caledonia
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23
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Gélin P, Fauvelot C, Bigot L, Baly J, Magalon H. From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals. Ecol Evol 2018; 8:1411-1426. [PMID: 29375807 PMCID: PMC5773318 DOI: 10.1002/ece3.3747] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
Here, we examined the genetic variability in the coral genus Pocillopora, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods [also named Pocillopora eydouxi/meandrina complex sensu, Schmidt-Roach, Miller, Lundgren, & Andreakis (2014)] and which was found to split into three secondary species hypotheses (SSH09a, SSH09b, and SSH09c) according to assignment tests using multi-locus genotypes (13 microsatellites). From a large sampling (2,507 colonies) achieved in three marine provinces [Western Indian Ocean (WIO), Tropical Southwestern Pacific (TSP), and Southeast Polynesia (SEP)], genetic structuring analysis conducted with two clustering analyses (structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels (PSH > SSH > cluster), each level hiding highly differentiated genetic groups. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. The issue is now to understand which hierarchical level (SSH, cluster, or even below) corresponds to the species one. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.
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Affiliation(s)
- Pauline Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
| | - Cécile Fauvelot
- Laboratoire d'excellence‐CORAILPerpignanFrance
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS)Centre IRD de NouméaNoumeaNew Caledonia
- Present address:
Université Côte d'AzurCNRSNiceFrance
| | - Lionel Bigot
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
| | - Joseph Baly
- Laboratoire d'excellence‐CORAILPerpignanFrance
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS)Centre IRD de NouméaNoumeaNew Caledonia
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt DenisLa Réunion
- Laboratoire d'excellence‐CORAILPerpignanFrance
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24
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Dimond JL, Gamblewood SK, Roberts SB. Genetic and epigenetic insight into morphospecies in a reef coral. Mol Ecol 2017; 26:5031-5042. [DOI: 10.1111/mec.14252] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 12/27/2022]
Affiliation(s)
- James L. Dimond
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
- Shannon Point Marine Center Western Washington University Anacortes WA USA
| | | | - Steven B. Roberts
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
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25
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Johnston EC, Forsman ZH, Flot JF, Schmidt-Roach S, Pinzón JH, Knapp ISS, Toonen RJ. A genomic glance through the fog of plasticity and diversification in Pocillopora. Sci Rep 2017; 7:5991. [PMID: 28729652 PMCID: PMC5519588 DOI: 10.1038/s41598-017-06085-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/07/2017] [Indexed: 01/01/2023] Open
Abstract
Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset. These datasets also show strong concordance with previously published clustering of the mitochondrial clades based on the mtDNA open reading frame (ORF). We resolve seven clear monophyletic groups, with no evidence for introgressive hybridization among any but the most recently derived sister species. In contrast, ribosomal and histone datasets, which are most commonly used in coral phylogenies to date, were less informative and contradictory to these other datasets. These data indicate that extant Pocillopora species diversified from a common ancestral lineage within the last ~3 million years. Key to this evolutionary success story may be the high phenotypic plasticity exhibited by Pocillopora species.
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Affiliation(s)
- Erika C Johnston
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA.
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Avenue F.D. Roosevelt 50, B-1050, Bruxelles, Belgium
| | - Sebastian Schmidt-Roach
- Australian Institute of Marine Science, 4810, Townsville, Australia
- Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Jorge H Pinzón
- Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ingrid S S Knapp
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
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26
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Genetic structure of coral-Symbiodinium symbioses on the world's warmest reefs. PLoS One 2017; 12:e0180169. [PMID: 28666005 PMCID: PMC5493405 DOI: 10.1371/journal.pone.0180169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/12/2017] [Indexed: 12/02/2022] Open
Abstract
Corals in the Arabian/Persian Gulf (PAG) survive extreme sea temperatures (summer mean: >34°C), and it is unclear whether these corals have genetically adapted or physiologically acclimated to these conditions. In order to elucidate the processes involved in the thermal tolerance of PAG corals, it is essential to understand the connectivity between reefs within and outside of the PAG. To this end, this study set out to investigate the genetic structure of the coral, Platygyra daedalea, and its symbiotic algae in the PAG and neighbouring Gulf of Oman. Using nuclear markers (the ITS region and an intron of the Pax-C gene), this study demonstrates genetic divergence of P. daedalea on reefs within the thermally extreme PAG compared with those in the neighbouring Gulf of Oman. Isolation by distance of P. daedalea was supported by the ITS dataset but not the Pax-C intron. In addition, the symbiont community within the PAG was dominated by C3 symbionts, while the purportedly thermotolerant clade D was extremely rare and was common only at sites outside of the PAG. Analysis of the psbAncr indicates that the C3 variant hosted by P. daedalea in the PAG belongs to the newly described species, Symbiodinium thermophilum. The structuring of the coral and symbiont populations suggests that both partners of the symbiosis may contribute to the high bleaching thresholds of PAG corals. While limited gene flow has likely played a role in local adaptation within the PAG, it also indicates limited potential for natural export of thermal tolerance traits to reefs elsewhere in the Indian Ocean threatened by climate change.
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27
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Wagner F, Härtl S, Vogt R, Oberprieler C. "Fix Me Another Marguerite!": Species delimitation in a group of intensively hybridizing lineages of ox-eye daisies (Leucanthemum Mill., Compositae-Anthemideae). Mol Ecol 2017; 26:4260-4283. [PMID: 28502098 DOI: 10.1111/mec.14180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/28/2017] [Accepted: 05/05/2017] [Indexed: 01/26/2023]
Abstract
Delineating species boundaries in the framework of the multi-species coalescent (MSC) proves to be a reliable, objective, and reproducible method in an increasing number of studies. However, the underlying model assumes the lack of gene flow after speciation; an assumption which may be frequently violated in plant evolution. This study evaluates the robustness of currently available species delimitation methods implemented in beast (BFD, BFD*, and dissect) in the closely-knit ox-eye daisy group around Leucanthemum ageratifolium Pau. Comprising five taxa being allopatrically distributed between northern Spain and southern Italy this study group shows signs of hybridization with the widespread and codistributed species Leucanthemum vulgare (Vaill.) Lam. to various extent. As expected, our empirical analyses based on both AFLP fingerprinting and sequence data demonstrate that the robustness of species delimitation results is considerably influenced by the intensity of hybridization among species and the number of hybrid individuals included. Therefore, we set up a methodological pipeline with a first step of identification and subsequent removal of individuals showing admixed genetic patterns caused by actual interbreeding using AFLP-fingerprint and morphometric data, followed by application of different Bayesian MSC species delimitation methods based on the remnant individuals using both AFLP-fingerprint and sequence data (four nuclear markers, five concatenated intergenic spacer regions of the plastid genome). The results argue for acknowledgement of Leucanthemum laciniatum, L. legraeanum, and L. ligusticum as independent species, show the close relationship of L. ageratifolium, L. monspeliense, and L. vulgare, and give rise to the description of three nothospecies new to science.
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Affiliation(s)
- Florian Wagner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - Sabine Härtl
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - Robert Vogt
- Botanic Garden & Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
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28
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The c-Jun N-terminal kinase prevents oxidative stress induced by UV and thermal stresses in corals and human cells. Sci Rep 2017; 7:45713. [PMID: 28374828 PMCID: PMC5379690 DOI: 10.1038/srep45713] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Coral reefs are of major ecological and socio-economic interest. They are threatened by global warming and natural pressures such as solar ultraviolet radiation. While great efforts have been made to understand the physiological response of corals to these stresses, the signalling pathways involved in the immediate cellular response exhibited by corals remain largely unknown. Here, we demonstrate that c-Jun N-terminal kinase (JNK) activation is involved in the early response of corals to thermal and UV stress. Furthermore, we found that JNK activity is required to repress stress-induced reactive oxygen species (ROS) accumulation in both the coral Stylophora pistillata and human skin cells. We also show that inhibiting JNK activation under stress conditions leads to ROS accumulation, subsequent coral bleaching and cell death. Taken together, our results suggest that an ancestral response, involving the JNK pathway, is remarkably conserved from corals to human, protecting cells from the adverse environmental effects.
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Gélin P, Postaire B, Fauvelot C, Magalon H. Reevaluating species number, distribution and endemism of the coral genus Pocillopora Lamarck, 1816 using species delimitation methods and microsatellites. Mol Phylogenet Evol 2017; 109:430-446. [PMID: 28219759 DOI: 10.1016/j.ympev.2017.01.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 01/25/2017] [Accepted: 01/30/2017] [Indexed: 01/06/2023]
Abstract
Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson Tree Processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2). Then, we confronted identified PSHs to the results of clustering analyses using 13 microsatellites to determine Secondary Species Hypotheses (SSH). Based on the congruence of all methods used and adding sequences from the literature, we defined at least 18 Secondary Species Hypotheses among 14 morphotypes, confirming the high phenotypic plasticity in Pocillopora species and the presence of cryptic lineages. We also identified three new genetic lineages never found to date, which could represent three new putative species. Moreover, the biogeographical ranges of several SSHs were re-assessed in the light of genetic data, which may have direct implications in conservation policies. Indeed, the cryptic diversity within this genus should be taken into account seriously, as neglecting its importance is source of confusion in our understanding of ecosystem functioning. Next generation sequencing, combined with other parameters (i.e. microstructure, zooxanthellae identification, ecology even at a micro-scale, resistance and resilience ability to bleaching) will be the next step towards an integrative framework of Pocillopora taxonomy, which will have profound implications for ecological studies, such as studying biodiversity, response to global warming and symbiosis.
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Affiliation(s)
- P Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France
| | - B Postaire
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France
| | - C Fauvelot
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d'excellence-CORAIL, Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Nouméa cedex, New Caledonia
| | - H Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS), Laboratoire d'excellence-CORAIL, Faculté des Sciences et Technologies, 15 Bd René Cassin, CS 92003, 97744 St Denis Cedex 09, La Réunion, France.
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Rosser NL, Thomas L, Stankowski S, Richards ZT, Kennington WJ, Johnson MS. Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora. Proc Biol Sci 2017; 284:20162182. [PMID: 28077772 PMCID: PMC5247495 DOI: 10.1098/rspb.2016.2182] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora, including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC, provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.
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Affiliation(s)
- Natalie L Rosser
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Luke Thomas
- School of Plant Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Sean Stankowski
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Zoe T Richards
- Department of Aquatic Zoology, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, Australia
| | - W Jason Kennington
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Michael S Johnson
- School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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Arrigoni R, Berumen ML, Huang D, Terraneo TI, Benzoni F. Cyphastrea (Cnidaria : Scleractinia : Merulinidae) in the Red Sea: phylogeny and a new reef coral species. INVERTEBR SYST 2017. [DOI: 10.1071/is16035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The scleractinian coral Cyphastrea is a common and widespread genus throughout the coral reefs of the Indo-Pacific. Little is known about the phylogenetic relationships within this taxon and species identification is based mainly on traditional skeletal characters, such as the number of septa, septa cycles, growth form and corallite dimensions. Here we present the first focussed reconstruction of phylogenetic relationships among Cyphastrea species, analysing 57 colonies from the Red Sea, where five morphospecies live in sympatry. Analyses based on three loci (nuclear histone H3, 28S rDNA and a mitochondrial intergenic region) reveal the existence of three well-supported molecular lineages. None of the five previously defined morphospecies are monophyletic and they cluster into two clades, suggesting the need of a systematic revision in Cyphastrea. The third lineage is described as C. magna Benzoni & Arrigoni, sp. nov., a new reef coral species collected from the northern and central Red Sea. Cyphastrea magna Benzoni & Arrigoni, sp. nov. is characterised by the largest corallite diameter among known Cyphastrea species, a wide trabecular columella >1/4 of calice width, and 12 equal primary septa. This study suggests that morphology-based taxonomy in Cyphastrea may not identify monophyletic units and strengthens the application of genetics in coral systematics.
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Recent origin and semi-permeable species boundaries in the scleractinian coral genus Stylophora from the Red Sea. Sci Rep 2016; 6:34612. [PMID: 27713475 PMCID: PMC5054360 DOI: 10.1038/srep34612] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 09/08/2016] [Indexed: 11/08/2022] Open
Abstract
Reticulate evolution, introgressive hybridisation, and phenotypic plasticity have been documented in scleractinian corals and have challenged our ability to interpret speciation processes. Stylophora is a key model system in coral biology and physiology, but genetic analyses have revealed that cryptic lineages concealed by morphological stasis exist in the Stylophora pistillata species complex. The Red Sea represents a hotspot for Stylophora biodiversity with six morphospecies described, two of which are regionally endemic. We investigated Stylophora species boundaries from the Red Sea and the associated Symbiodinium by sequencing seven DNA loci. Stylophora morphospecies from the Red Sea were not resolved based on mitochondrial phylogenies and showed nuclear allele sharing. Low genetic differentiation, weak isolation, and strong gene flow were found among morphospecies although no signals of genetic recombination were evident among them. Stylophora mamillata harboured Symbiodinium clade C whereas the other two Stylophora morphospecies hosted either Symbiodinium clade A or C. These evolutionary patterns suggest that either gene exchange occurs through reticulate evolution or that multiple ecomorphs of a phenotypically plastic species occur in the Red Sea. The recent origin of the lineage leading to the Red Sea Stylophora may indicate an ongoing speciation driven by environmental changes and incomplete lineage sorting.
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Terraneo TI, Benzoni F, Arrigoni R, Berumen ML. Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea. Mol Phylogenet Evol 2016; 102:278-94. [DOI: 10.1016/j.ympev.2016.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 06/15/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022]
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Arrigoni R, Berumen ML, Chen CA, Terraneo TI, Baird AH, Payri C, Benzoni F. Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species. Mol Phylogenet Evol 2016; 105:146-159. [PMID: 27593164 DOI: 10.1016/j.ympev.2016.08.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.
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Affiliation(s)
- Roberto Arrigoni
- Red Sea Research Center, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Chaolun Allen Chen
- Biodiversity Research Centre, Academia Sinica, Nangang, Taipei 115, Taiwan; Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Tullia I Terraneo
- Red Sea Research Center, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Andrew H Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, Australia
| | - Claude Payri
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d'excellence-CORAIL, centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Noumea Cedex, New Caledonia
| | - Francesca Benzoni
- UMR ENTROPIE (IRD, Université de La Réunion, CNRS), Laboratoire d'excellence-CORAIL, centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5, 98848 Noumea Cedex, New Caledonia; Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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35
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Nicotra AB, Chong C, Bragg JG, Ong CR, Aitken NC, Chuah A, Lepschi B, Borevitz JO. Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium. Mol Ecol 2016; 25:2000-14. [PMID: 26864117 DOI: 10.1111/mec.13584] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 01/21/2016] [Accepted: 01/26/2016] [Indexed: 02/05/2023]
Abstract
Species delimitation has seen a paradigm shift as increasing accessibility of genomic-scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogenomic and population genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the eight currently described species but provided little evidence for differences in genetic structure within the most widely distributed group that containing P. australe. In contrast, morphometric analysis detected three deep lineages within Australian Pelargonium; with P. australe consisting of five previously unrecognized entities occupying separate geographic ranges. The genomic approach enabled elucidation of parallel evolution in some traits formerly used to delineate species, as well as identification of ecotypic morphological differentiation within recognized species. Highly variable morphology and trait convergence each contribute to the discordance between phylogenomic relationships and morphological taxonomy. Data suggest that genetic divergence among species within the Australian Pelargonium may result from allopatric speciation while morphological differentiation within and among species may be more strongly driven by environmental differences.
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Affiliation(s)
- Adrienne B Nicotra
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Caroline Chong
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Jason G Bragg
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Chong Ren Ong
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Nicola C Aitken
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Aaron Chuah
- Genome Discovery Unit, Australian National University, Canberra, ACT, 0200, Australia
| | - Brendan Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia.,Centre of Excellence in Plant Energy Biology, Australian National University, ACT, 2601, Australia
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36
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Papakostas S, Michaloudi E, Proios K, Brehm M, Verhage L, Rota J, Peña C, Stamou G, Pritchard VL, Fontaneto D, Declerck SAJ. Integrative Taxonomy Recognizes Evolutionary Units Despite Widespread Mitonuclear Discordance: Evidence from a Rotifer Cryptic Species Complex. Syst Biol 2016; 65:508-24. [DOI: 10.1093/sysbio/syw016] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 02/09/2016] [Indexed: 01/23/2023] Open
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37
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Affiliation(s)
- Jean-François Flot
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom
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38
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Rosser NL. Asynchronous spawning in sympatric populations of a hard coral reveals cryptic species and ancient genetic lineages. Mol Ecol 2015; 24:5006-19. [DOI: 10.1111/mec.13372] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Natalie L. Rosser
- School of Animal Biology (M092); University of Western Australia; Crawley WA 6009 Australia
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39
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Nakajima Y, Shinzato C, Satoh N, Mitarai S. Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis. PLoS One 2015; 10:e0130176. [PMID: 26147677 PMCID: PMC4492964 DOI: 10.1371/journal.pone.0130176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/18/2015] [Indexed: 11/30/2022] Open
Abstract
The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (NMLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.
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Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- * E-mail: ,
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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Combosch DJ, Vollmer SV. Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals. Mol Phylogenet Evol 2015; 88:154-62. [DOI: 10.1016/j.ympev.2015.03.022] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/23/2015] [Accepted: 03/26/2015] [Indexed: 01/30/2023]
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41
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Warner PA, van Oppen MJH, Willis BL. Unexpected cryptic species diversity in the widespread coralSeriatopora hystrixmasks spatial-genetic patterns of connectivity. Mol Ecol 2015; 24:2993-3008. [DOI: 10.1111/mec.13225] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/25/2015] [Accepted: 04/29/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Patricia A. Warner
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld 4811 Australia
| | - Madeleine J. H. van Oppen
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- Australian Institute of Marine Science; PMB3, Townsville MC; Townsville Qld 4810 Australia
| | - Bette L. Willis
- AIMS@JCU; Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
- College of Marine and Environmental Sciences; James Cook University; Townsville Qld 4811 Australia
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Dellicour S, Flot JF. Delimiting Species-Poor Data Sets using Single Molecular Markers: A Study of Barcode Gaps, Haplowebs and GMYC. Syst Biol 2015; 64:900-8. [PMID: 25601944 DOI: 10.1093/sysbio/syu130] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/18/2014] [Indexed: 01/14/2023] Open
Abstract
Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.
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Affiliation(s)
- Simon Dellicour
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK and
| | - Jean-François Flot
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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Arrigoni R, Berumen ML, Terraneo TI, Caragnano A, Bouwmeester J, Benzoni F. Forgotten in the taxonomic literature: resurrection of the scleractinian coral genusSclerophyllia(Scleractinia, Lobophylliidae) from the Arabian Peninsula and its phylogenetic relationships. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.978915] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Terraneo TI, Berumen ML, Arrigoni R, Waheed Z, Bouwmeester J, Caragnano A, Stefani F, Benzoni F. Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): a new reef coral species from the Red Sea and its phylogenetic relationships. Zookeys 2014:1-30. [PMID: 25152672 PMCID: PMC4141178 DOI: 10.3897/zookeys.433.8036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 07/24/2014] [Indexed: 11/12/2022] Open
Abstract
A new scleractinian coral species, Pachyseris inattesa sp. n., is described from the Red Sea. Despite a superficial resemblance with some species in the agariciid genus Leptoseris with which it has been previously confused, P. inattesa sp. n. has micro-morphological characters typical of the genus Pachyseris. This genus, once part of the Agariciidae, is comprised of five extant species and is widely distributed throughout the tropical Indo-Pacific. It is currently incertae sedis as a result of recent molecular analysis and appears to be closely related to the Euphylliidae. A molecular phylogenetic reconstruction including P. inattesa sp. n., the genus type species P. rugosa, and P. speciosa, all present in the Red Sea, was performed using the mitochondrial intergenic spacer between COI and 16S-rRNA. The results confirm that P. inattesa sp. n. is a monophyletic lineage closely related to the other Pachyseris species examined.
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Affiliation(s)
- Tullia I Terraneo
- Dept. of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy ; Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Roberto Arrigoni
- Dept. of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Zarinah Waheed
- Department of Marine Zoology, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands ; Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Jessica Bouwmeester
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Annalisa Caragnano
- Dept. of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Fabrizio Stefani
- Water Research Institute-National Research Council (IRSA-CNR), Via del Mulino 19, I-20861 Brugherio, Italy
| | - Francesca Benzoni
- Dept. of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy ; Institut de Recherche pour le Développement, UMR227 Coreus2, 101 Promenade Roger Laroque, BP A5, 98848 Noumea Cedex, New Caledonia
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45
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Bongaerts P, Frade PR, Ogier JJ, Hay KB, van Bleijswijk J, Englebert N, Vermeij MJA, Bak RPM, Visser PM, Hoegh-Guldberg O. Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef. BMC Evol Biol 2013; 13:205. [PMID: 24059868 PMCID: PMC3849765 DOI: 10.1186/1471-2148-13-205] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/14/2013] [Indexed: 11/30/2022] Open
Abstract
Background Scleractinian corals and their algal endosymbionts (genus Symbiodinium) exhibit distinct bathymetric distributions on coral reefs. Yet, few studies have assessed the evolutionary context of these ecological distributions by exploring the genetic diversity of closely related coral species and their associated Symbiodinium over large depth ranges. Here we assess the distribution and genetic diversity of five agariciid coral species (Agaricia humilis, A. agaricites, A. lamarcki, A. grahamae, and Helioseris cucullata) and their algal endosymbionts (Symbiodinium) across a large depth gradient (2-60 m) covering shallow to mesophotic depths on a Caribbean reef. Results The five agariciid species exhibited distinct depth distributions, and dominant Symbiodinium associations were found to be species-specific, with each of the agariciid species harbouring a distinct ITS2-DGGE profile (except for a shared profile between A. lamarcki and A. grahamae). Only A. lamarcki harboured different Symbiodinium types across its depth distribution (i.e. exhibited symbiont zonation). Phylogenetic analysis (atp6) of the coral hosts demonstrated a division of the Agaricia genus into two major lineages that correspond to their bathymetric distribution (“shallow”: A. humilis / A. agaricites and “deep”: A. lamarcki / A. grahamae), highlighting the role of depth-related factors in the diversification of these congeneric agariciid species. The divergence between “shallow” and “deep” host species was reflected in the relatedness of the associated Symbiodinium (with A. lamarcki and A. grahamae sharing an identical Symbiodinium profile, and A. humilis and A. agaricites harbouring a related ITS2 sequence in their Symbiodinium profiles), corroborating the notion that brooding corals and their Symbiodinium are engaged in coevolutionary processes. Conclusions Our findings support the hypothesis that the depth-related environmental gradient on reefs has played an important role in the diversification of the genus Agaricia and their associated Symbiodinium, resulting in a genetic segregation between coral host-symbiont communities at shallow and mesophotic depths.
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Affiliation(s)
- Pim Bongaerts
- School of Biological Sciences, The University of Queensland, 4072 St Lucia, QLD, Australia.
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Flot JF, Bauermeister J, Brad T, Hillebrand-Voiculescu A, Sarbu SM, Dattagupta S. Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania. Mol Ecol 2013; 23:1405-1417. [PMID: 24044653 PMCID: PMC4282457 DOI: 10.1111/mec.12461] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/06/2013] [Accepted: 07/13/2013] [Indexed: 12/03/2022]
Abstract
Niphargus is a speciose amphipod genus found in groundwater habitats across Europe. Three Niphargus species living in the sulphidic Frasassi caves in Italy harbour sulphur-oxidizing Thiothrix bacterial ectosymbionts. These three species are distantly related, implying that the ability to form ectosymbioses with Thiothrix may be common among Niphargus. Therefore, Niphargus–Thiothrix associations may also be found in sulphidic aquifers other than Frasassi. In this study, we examined this possibility by analysing niphargids of the genera Niphargus and Pontoniphargus collected from the partly sulphidic aquifers of the Southern Dobrogea region of Romania, which are accessible through springs, wells and Movile Cave. Molecular and morphological analyses revealed seven niphargid species in this region. Five of these species occurred occasionally or exclusively in sulphidic locations, whereas the remaining two were restricted to nonsulphidic areas. Thiothrix were detected by PCR on all seven Dobrogean niphargid species and observed using microscopy to be predominantly attached to their hosts' appendages. 16S rRNA gene sequences of the Thiothrix epibionts fell into two main clades, one of which (herein named T4) occurred solely on niphargids collected in sulphidic locations. The other Thiothrix clade was present on niphargids from both sulphidic and nonsulphidic areas and indistinguishable from the T3 ectosymbiont clade previously identified on Frasassi-dwelling Niphargus. Although niphargids from Frasassi and Southern Dobrogea are not closely related, the patterns of their association with Thiothrix are remarkably alike. The finding of similar Niphargus–Thiothrix associations in aquifers located 1200 km apart suggests that they may be widespread in European groundwater ecosystems.
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Affiliation(s)
- Jean-François Flot
- Courant Research Center Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077, Göttingen, Germany; Max Planck Institute for Dynamics and Self-Organization, Biological Physics and Evolutionary Dynamics, Bunsenstraße 10, 37073, Göttingen, Germany
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DNA barcoding reveals the coral "laboratory-rat", Stylophora pistillata encompasses multiple identities. Sci Rep 2013; 3:1520. [PMID: 23519209 PMCID: PMC3605610 DOI: 10.1038/srep01520] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation.
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Almaraz-Abarca N, Delgado-Alvarado EA, Torres-Morán MI, Herrera-Corral J, Ávila-Reyes JA, Naranjo-Jiménez N, Uribe-Soto JN. Genetic Variability in Natural Populations of Agave durangensis(Agavaceae) Revealed by Morphological and Molecular Traits. SOUTHWEST NAT 2013. [DOI: 10.1894/0038-4909-58.3.314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Miralles A, Vences M. New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS One 2013; 8:e68242. [PMID: 23874561 PMCID: PMC3710018 DOI: 10.1371/journal.pone.0068242] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/24/2013] [Indexed: 01/17/2023] Open
Abstract
Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence C tax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index R tax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist approaches). Quantifying excessive splitting is more difficult than quantifying excessive lumping, suggesting a priority for conservative taxonomies in which errors are more liable to be detected and corrected by subsequent studies.
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Affiliation(s)
- Aurélien Miralles
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
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Characterization of new microsatellite loci for population genetic studies in the Smooth Cauliflower Coral (Stylophora sp.). CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-012-9852-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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