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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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Oury N, Noël C, Mona S, Aurelle D, Magalon H. From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 2023; 184:107803. [PMID: 37120114 DOI: 10.1016/j.ympev.2023.107803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France.
| | - Cyril Noël
- IFREMER - IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; EPHE, PSL Research University, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Didier Aurelle
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
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3
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Stephens TG, Lee J, Jeong Y, Yoon HS, Putnam HM, Majerová E, Bhattacharya D. High-quality genome assembles from key Hawaiian coral species. Gigascience 2022; 11:6815755. [PMID: 36352542 PMCID: PMC9646523 DOI: 10.1093/gigascience/giac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022] Open
Abstract
Background Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies. Results We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal. Conclusions These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawaiʻi but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.
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Affiliation(s)
- Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - YuJin Jeong
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University , Suwon 16419, Korea
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island , Kingston, RI 02881, USA
| | - Eva Majerová
- Hawaiʻi Institute of Marine Biology , Kāneʻohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
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4
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Drury C, Bean NK, Harris CI, Hancock JR, Huckeba J, H CM, Roach TNF, Quinn RA, Gates RD. Intrapopulation adaptive variance supports thermal tolerance in a reef-building coral. Commun Biol 2022; 5:486. [PMID: 35589814 PMCID: PMC9120509 DOI: 10.1038/s42003-022-03428-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 04/28/2022] [Indexed: 01/05/2023] Open
Abstract
Coral holobionts are multi-species assemblages, which adds significant complexity to genotype-phenotype connections underlying ecologically important traits like coral bleaching. Small scale heterogeneity in bleaching is ubiquitous in the absence of strong environmental gradients, which provides adaptive variance needed for the long-term persistence of coral reefs. We used RAD-seq, qPCR and LC-MS/MS metabolomics to characterize host genomic variation, symbiont community and biochemical correlates in two bleaching phenotypes of the vertically transmitting coral Montipora capitata. Phenotype was driven by symbiosis state and host genetic variance. We documented 5 gene ontologies that were significantly associated with both the binary bleaching phenotype and symbiont composition, representing functions that confer a phenotype via host-symbiont interactions. We bred these corals and show that symbiont communities were broadly conserved in bulk-crosses, resulting in significantly higher survivorship under temperature stress in juveniles, but not larvae, from tolerant parents. Using a select and re-sequence approach, we document numerous gene ontologies selected by heat stress, some of which (cell signaling, antioxidant activity, pH regulation) have unique selection dynamics in larvae from thermally tolerant parents. These data show that vertically transmitting corals may have an adaptive advantage under climate change if host and symbiont variance interact to influence bleaching phenotype. Selective breeding of corals with different bleaching phenotypes demonstrates the potential for climate adaptation in vertically transmitting species.
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Affiliation(s)
- Crawford Drury
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI, USA.
| | - Nina K Bean
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI, USA
| | - Casey I Harris
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI, USA
| | - Joshua R Hancock
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI, USA
| | - Joel Huckeba
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI, USA.,University of Amsterdam, Amsterdam, Netherlands
| | - Christian Martin H
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Ty N F Roach
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, HI, USA
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5
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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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6
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Henley EM, Quinn M, Bouwmeester J, Daly J, Zuchowicz N, Lager C, Bailey DW, Hagedorn M. Reproductive plasticity of Hawaiian Montipora corals following thermal stress. Sci Rep 2021; 11:12525. [PMID: 34108494 PMCID: PMC8190081 DOI: 10.1038/s41598-021-91030-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/09/2021] [Indexed: 11/08/2022] Open
Abstract
Ocean warming, fueled by climate change, is the primary cause of coral bleaching events which are predicted to increase in frequency. Bleaching is generally damaging to coral reproduction, can be exacerbated by concomitant stressors like ultraviolet radiation (UVR), and can have lasting impacts to successful reproduction and potential adaptation. We compared morphological and physiological reproductive metrics (e.g., sperm motility, mitochondrial membrane integrity, egg volume, gametes per bundle, and fertilization and settlement success) of two Hawaiian Montipora corals after consecutive bleaching events in 2014 and 2015. Between the species, sperm motility and mitochondrial membrane potential had the most disparate results. Percent sperm motility in M. capitata, which declined to ~ 40% during bleaching from a normal range of 70-90%, was still less than 50% motile in 2017 and 2018 and had not fully recovered in 2019 (63% motile). By contrast, percent sperm motility in Montipora spp. was 86% and 74% in 2018 and 2019, respectively. This reduction in motility was correlated with damage to mitochondria in M. capitata but not Montipora spp. A major difference between these species is the physiological foundation of their UVR protection, and we hypothesize that UVR protective mechanisms inherent in Montipora spp. mitigate this reproductive damage.
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Affiliation(s)
- E Michael Henley
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA.
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA.
| | - Mariko Quinn
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Jessica Bouwmeester
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Jonathan Daly
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Nikolas Zuchowicz
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Claire Lager
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Daniel W Bailey
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Mary Hagedorn
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
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7
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Brown T, Sonett D, Zaneveld JR, Padilla-Gamiño JL. Characterization of the microbiome and immune response in corals with chronic Montipora white syndrome. Mol Ecol 2021; 30:2591-2606. [PMID: 33763924 DOI: 10.1111/mec.15899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 01/15/2021] [Accepted: 03/15/2021] [Indexed: 01/04/2023]
Abstract
Coral diseases have increased in frequency and intensity around the tropics worldwide. However, in many cases, little is known about their etiology. Montipora white syndrome (MWS) is a common disease affecting the coral Montipora capitata, a major reef builder in Hawai'i. Chronic Montipora white syndrome (cMWS) is a slow-moving form of the disease that affects M. capitata throughout the year. The effects of this chronic disease on coral immunology and microbiology are currently unknown. In this study, we use prophenoloxidase immune assays and 16S rRNA gene amplicon sequencing to characterize the microbiome and immunological response associated with cMWS. Our results show that immunological and microbiological responses are highly localized. Relative to diseased samples, apparently healthy portions of cMWS corals differed in immune activity and in the relative abundance of microbial taxa. Coral tissues with cMWS showed decreased tyrosinase-type catecholase and tyrosinase-type cresolase activity and increased laccase-type activity. Catecholase and cresolase activity were negatively correlated across all tissue types with microbiome richness. The localized effect of cMWS on coral microbiology and immunology is probably an important reason for the slow progression of the disease. This local confinement may facilitate interventions that focus on localized treatments on tissue types. This study provides an important baseline to understand the interplay between the microbiome and immune system and the mechanisms used by corals to manage chronic microbial perturbations associated with white syndrome.
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Affiliation(s)
- Tanya Brown
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, Washington, USA
| | - Dylan Sonett
- Division of Biological Sciences, University of Washington, Bothell, Washington, USA
| | - Jesse R Zaneveld
- Division of Biological Sciences, University of Washington, Bothell, Washington, USA
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8
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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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: 10] [Impact Index Per Article: 2.5] [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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10
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Cunha AF, Collins AG, Marques AC. When morphometry meets taxonomy: morphological variation and species boundaries in Proboscoida (Cnidaria: Hydrozoa). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract
Species delimitation in marine taxa is often problematic given large intraspecific variation. Based on extensive, recently published genetic sampling from specimens of the hydrozoan families Campanulariidae, Clytiidae and Obeliidae, we evaluate morphological variation in this group, correlating morphometric and phylogenetic patterns for species delimitation. Several species of Campanulariidae are confidently delimited based on differences in size (e.g. Bonneviella species, Tulpa tulipifera and Rhizocaulus verticillatus), while others are re-identified and corroborated based on differences in perisarc thickness (e.g. Silicularia rosea, Orthopyxis and Campanularia species). In Clytiidae, the length and diameter of hydrothecae, height of hydrothecal cusps and perisarc thickness delimit the species Clytia linearis, C. elsaeoswaldae and C. noliformis from others. However, few characters reliably differentiate the clades associated with the nominal species C. gracilis and C. hemisphaerica. In Obeliidae, Obelia geniculata is distinctive in its higher perisarc thickness, and corroborated as a widely distributed species. Obelia longissima and clades refered to O. dichotoma are subtly distinguished, showing a few differences in size and branching of colonies. The taxonomic implications of these results are discussed. With a few exceptions, species can be delimited based on morphometric patterns, once morphological variation is compared.
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Affiliation(s)
- Amanda F Cunha
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Allen G Collins
- National Systematics Laboratory, National Marine Fisheries Service (NMFS), National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA
| | - Antonio C Marques
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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11
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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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12
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Cunha RL, Forsman ZH, Belderok R, Knapp ISS, Castilho R, Toonen RJ. Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora. BMC Evol Biol 2019; 19:153. [PMID: 31340762 PMCID: PMC6657087 DOI: 10.1186/s12862-019-1476-2] [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: 02/06/2019] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. Results All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05–2.6] Myr) or assuming rate homogeneity (0.4 [0.14–0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. Conclusions Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms. Electronic supplementary material The online version of this article (10.1186/s12862-019-1476-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Regina L Cunha
- University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Roy Belderok
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Ingrid S S Knapp
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Rita Castilho
- University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
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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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Quattrini AM, Wu T, Soong K, Jeng MS, Benayahu Y, McFadden CS. A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals. BMC Evol Biol 2019; 19:116. [PMID: 31170912 PMCID: PMC6555025 DOI: 10.1186/s12862-019-1427-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. RESULTS Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. CONCLUSIONS A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life.
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Affiliation(s)
- Andrea M. Quattrini
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
| | - Tiana Wu
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
| | - Keryea Soong
- Institute of Marine Biology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ming-Shiou Jeng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yehuda Benayahu
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Catherine S. McFadden
- Biology Department, Harvey Mudd College, 1250 N. Dartmouth Ave, Claremont, CA 91711 USA
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Couch CS, Burns JHR, Liu G, Steward K, Gutlay TN, Kenyon J, Eakin CM, Kosaki RK. Mass coral bleaching due to unprecedented marine heatwave in Papahānaumokuākea Marine National Monument (Northwestern Hawaiian Islands). PLoS One 2017; 12:e0185121. [PMID: 28953909 PMCID: PMC5617177 DOI: 10.1371/journal.pone.0185121] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/06/2017] [Indexed: 11/19/2022] Open
Abstract
2014 marked the sixth and most widespread mass bleaching event reported in the Northwestern Hawaiian Islands, home to the Papahānaumokuākea Marine National Monument (PMNM), the world’s second largest marine reserve. This event was associated with an unusual basin-scale warming in the North Pacific Ocean, with an unprecedented peak intensity of around 20°C-weeks of cumulative heat stress at Lisianksi Island. In situ bleaching surveys and satellite data were used to evaluate the relative importance of potential drivers of bleaching patterns in 2014, assess the subsequent morality and its effects on coral communities and 3D complexity, test for signs of regional acclimation, and investigate long-term change in heat stress in PMNM. Surveys conducted at four island/atoll (French Frigate Shoals, Lisianski Island, Pearl and Hermes Atoll, and Midway Atoll) showed that in 2014, percent bleaching varied considerably between islands/atolls and habitats (back reef/fore reef and depth), and was up to 91% in shallow habitats at Lisianski. The percent bleaching during the 2014 event was best explained by a combination of duration of heat stress measured by Coral Reef Watch’s satellite Degree Heating Week, relative community susceptibility (bleaching susceptibility score of each taxon * the taxon’s abundance relative to the total number of colonies), depth and region. Mean coral cover at permanent Lisianski monitoring sites decreased by 68% due to severe losses of Montipora dilatata complex, resulting in rapid reductions in habitat complexity. Spatial distribution of the 2014 bleaching was significantly different from the 2002 and 2004 bleaching events likely due to a combination of differences in heat stress and local acclimatization. Historical satellite data demonstrated heat stress in 2014 was unlike any previous event and that the exposure of corals to the bleaching-level heat stress has increased significantly in the northern PMNM since 1982, highlighting the increasing threat of climate change to reefs.
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Affiliation(s)
- Courtney S. Couch
- Hawaiʻi Institute of Marine Biology, Kāne‘ohe, Hawaiʻi, United States of America
- Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, NOAA, Honolulu, Hawaiʻi, United States of America
- * E-mail:
| | - John H. R. Burns
- Hawaiʻi Institute of Marine Biology, Kāne‘ohe, Hawaiʻi, United States of America
| | - Gang Liu
- Coral Reef Watch, NOAA/NESDIS/STAR, College Park, Maryland, United States of America
- Global Science & Technology Inc., Greenbelt, Maryland, United States of America
| | - Kanoelani Steward
- Marine Science Program University of Hawaiʻi at Hilo, Hilo Hawaiʻi, United States of America
| | | | - Jean Kenyon
- U.S. Fish and Wildlife Service, Honolulu, Hawaiʻi, United States of America
| | - C. Mark Eakin
- Coral Reef Watch, NOAA/NESDIS/STAR, College Park, Maryland, United States of America
| | - Randall K. Kosaki
- NOAA Papahānaumokuākea Marine National Monument, Honolulu, Hawaiʻi, United States of America
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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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McFadden CS, Haverkort-Yeh R, Reynolds AM, Halàsz A, Quattrini AM, Forsman ZH, Benayahu Y, Toonen RJ. Species boundaries in the absence of morphological, ecological or geographical differentiation in the Red Sea octocoral genus Ovabunda (Alcyonacea: Xeniidae). Mol Phylogenet Evol 2017; 112:174-184. [DOI: 10.1016/j.ympev.2017.04.025] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 01/05/2023]
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18
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Uriz MJ, Garate L, Agell G. Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida). PeerJ 2017; 5:e2958. [PMID: 28286707 PMCID: PMC5344016 DOI: 10.7717/peerj.2958] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 01/04/2017] [Indexed: 01/22/2023] Open
Abstract
Background Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Bayesian inference (BI), and maximum likelihood (ML) criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope. Results The several phylogenetic reconstructions retrieved both Crella and Hemimycale polyphyletic. Strong differences in COI sequences indicated that C. cyathophora from the Red Sea might belong in a different genus, closer to Hemimycale arabica than to the Atlanto-Mediterranean Crella spp. Molecular and external morphological differences between Hemimycale arabica and the Atlanto-Mediterranean Hemimycale also suggest that Hemimycale arabica fit in a separate genus. On the other hand, the Atlanto-Mediterranean Crellidae appeared in 18S and 28S phylogenies as a sister group of the Atlanto-Mediterranean Hemimycale. Moreover, what was known up to now as Hemimycale columella, is formed by two cryptic species with contrasting bathymetric distributions. Some small but consistent morphological differences allow species distinction. Conclusions A new family (Hemimycalidae) including the genus Hemimycale and the two purported new genera receiving C. cyathophora and Hemimycale arabica might be proposed according to our phylogenetic results. However, the inclusion of additional Operational Taxonomic Unit (OTUs) appears convenient before taking definite taxonomical decisions. A new cryptic species (Hemimycale mediterranea sp. nov.) is described. Morphologically undifferentiated species with contrasting biological traits, as those here reported, confirm that unidentified cryptic species may confound ecological studies.
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Affiliation(s)
- Maria J Uriz
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes, Girona , Spain
| | - Leire Garate
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes, Girona , Spain
| | - Gemma Agell
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes, Girona , Spain
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19
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Ju YM, Hsiao ST, Kuo FW, Wu JH. The complete mitochondrial genome of Montipora aequituberculata (Scleractinia, Acroporidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:62-63. [PMID: 33473718 PMCID: PMC7800442 DOI: 10.1080/23802359.2016.1186508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The complete mitogenome of the hexacorallia, Montipora aequituberculata has been amplified and sequenced. The mitogenome consists of 17,886 bp, with 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a control region. It has been observed that ND5 gene is split into two parts by a large fragment of genes, which commonly presented in scleractinian coral. The overall base composition of the H-strand was A, 24.91%; G, 24.1%; C, 14.2%; and T, 36.8%, with a slight AT bias of 61.7%. The control region was 627 bp in length and located between 12S rRNA and COIII gene. Based on the neighbour-joining (NJ) tree, M. aequituberculata was grouped with M. cactus, Anacropora matthai and Acropora tenuis, and formed a clade of Acroporidae. In conclusion, the complete mitogenome of M. aequituberculata data may provide more informative for phylogenetic approach for corals phylogeny.
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Affiliation(s)
- Yu-Min Ju
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, Republic of China
| | - Sheng-Tai Hsiao
- Marine Fisheries Division, Fisheries Research Institute, Keelung, Taiwan, Republic of China
| | - Fu-Wen Kuo
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, Republic of China
| | - Jui-Hsien Wu
- Eastern Marine Biology Research Center, Fisheries Research Institute, Council of Agriculture, Taitung, Taiwan, Republic of China
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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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Veazey LM, Franklin EC, Kelley C, Rooney J, Frazer LN, Toonen RJ. The implementation of rare events logistic regression to predict the distribution of mesophotic hard corals across the main Hawaiian Islands. PeerJ 2016; 4:e2189. [PMID: 27441122 PMCID: PMC4941748 DOI: 10.7717/peerj.2189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/08/2016] [Indexed: 11/26/2022] Open
Abstract
Predictive habitat suitability models are powerful tools for cost-effective, statistically robust assessment of the environmental drivers of species distributions. The aim of this study was to develop predictive habitat suitability models for two genera of scleractinian corals (Leptoserisand Montipora) found within the mesophotic zone across the main Hawaiian Islands. The mesophotic zone (30–180 m) is challenging to reach, and therefore historically understudied, because it falls between the maximum limit of SCUBA divers and the minimum typical working depth of submersible vehicles. Here, we implement a logistic regression with rare events corrections to account for the scarcity of presence observations within the dataset. These corrections reduced the coefficient error and improved overall prediction success (73.6% and 74.3%) for both original regression models. The final models included depth, rugosity, slope, mean current velocity, and wave height as the best environmental covariates for predicting the occurrence of the two genera in the mesophotic zone. Using an objectively selected theta (“presence”) threshold, the predicted presence probability values (average of 0.051 for Leptoseris and 0.040 for Montipora) were translated to spatially-explicit habitat suitability maps of the main Hawaiian Islands at 25 m grid cell resolution. Our maps are the first of their kind to use extant presence and absence data to examine the habitat preferences of these two dominant mesophotic coral genera across Hawai‘i.
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Affiliation(s)
- Lindsay M Veazey
- Department of Biology, University of Hawaii at Manoa , Honolulu , HI , United States
| | - Erik C Franklin
- School of Ocean and Earth Science and Technology, University of Hawaii, Hawaii Institute of Marine Biology , Kaneohe , HI , United States
| | - Christopher Kelley
- The Hawaii Undersea Research Lab, University of Hawaii at Manoa , Honolulu , HI , United States
| | - John Rooney
- Joint Institute for Marine and Atmospheric Research, University of Hawaii at Manoa , Honolulu , HI , United States
| | - L Neil Frazer
- Department of Geology and Geophysics, University of Hawaii at Manoa , Honolulu , HI , United States
| | - Robert J Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa , Kaneohe , HI , United States
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Aboal M, Werner O, García-Fernández ME, Palazón JA, Cristóbal JC, Williams W. Should ecomorphs be conserved? The case of Nostoc flagelliforme, an endangered extremophile cyanobacteria. J Nat Conserv 2016. [DOI: 10.1016/j.jnc.2016.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Knapp IS, Forsman ZH, Williams GJ, Toonen RJ, Bell JJ. Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella) caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific. PeerJ 2015; 3:e1170. [PMID: 26339548 PMCID: PMC4558080 DOI: 10.7717/peerj.1170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/20/2015] [Indexed: 11/30/2022] Open
Abstract
Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella) caerulea from the Caribbean to Palmyra Atoll via Hawai'i using morphological characteristics and genetic analyses based on one nuclear (18s rDNA) and three mitochondrial (COI, the barcoding COI extension (COI ext.) and rnl rDNA) markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68%) between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawai'i and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawai'i remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms.
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Affiliation(s)
- Ingrid S. Knapp
- School of Ocean and Earth Science and Technology, Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Manoa, Kāneʻohe, HI, USA
| | - Zac H. Forsman
- School of Ocean and Earth Science and Technology, Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Manoa, Kāneʻohe, HI, USA
| | - Gareth J. Williams
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, CA, USA
| | - Robert J. Toonen
- School of Ocean and Earth Science and Technology, Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Manoa, Kāneʻohe, HI, USA
| | - James J. Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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DeBiasse MB, Hellberg ME. Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia. Ecol Evol 2015; 5:663-75. [PMID: 25691989 PMCID: PMC4328770 DOI: 10.1002/ece3.1381] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/03/2014] [Indexed: 01/29/2023] Open
Abstract
Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.
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Affiliation(s)
- Melissa B DeBiasse
- Department of Biological Sciences, Louisiana State University202 Life Sciences Building, Baton Rouge, Louisiana, 70803
- Correspondence Melissa B DeBiasse, Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803., Tel: 225 578 4284; Fax: 225 578 2597; E-mail:
| | - Michael E Hellberg
- Department of Biological Sciences, Louisiana State University202 Life Sciences Building, Baton Rouge, Louisiana, 70803
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Huang D, Benzoni F, Arrigoni R, Baird AH, Berumen ML, Bouwmeester J, Chou LM, Fukami H, Licuanan WY, Lovell ER, Meier R, Todd PA, Budd AF. Towards a phylogenetic classification of reef corals: the Indo-Pacific generaMerulina,GoniastreaandScapophyllia(Scleractinia, Merulinidae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12061] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Danwei Huang
- Department of Earth and Environmental Sciences; University of Iowa; Iowa City IA 52242 USA
- Scripps Institution of Oceanography; University of California; San Diego La Jolla CA 92093 USA
- Department of Biological Sciences; National University of Singapore; Singapore 117543 Singapore
| | - Francesca Benzoni
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Roberto Arrigoni
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Andrew H. Baird
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld 4811 Australia
| | - Michael L. Berumen
- Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal Jeddah 23955 Kingdom of Saudi Arabia
| | - Jessica Bouwmeester
- Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal Jeddah 23955 Kingdom of Saudi Arabia
| | - Loke Ming Chou
- Department of Biological Sciences; National University of Singapore; Singapore 117543 Singapore
| | - Hironobu Fukami
- Department of Marine Biology and Environmental Science; University of Miyazaki; Miyazaki 889-2192 Japan
| | - Wilfredo Y. Licuanan
- Br. Alfred Shields FSC Ocean Research Center and Biology Department; De La Salle University; Manila 1004 The Philippines
| | - Edward R. Lovell
- School of Marine Studies; University of the South Pacific; Laucala Campus Suva Fiji
| | - Rudolf Meier
- Department of Biological Sciences; National University of Singapore; Singapore 117543 Singapore
| | - Peter A. Todd
- Department of Biological Sciences; National University of Singapore; Singapore 117543 Singapore
| | - Ann F. Budd
- Department of Earth and Environmental Sciences; University of Iowa; Iowa City IA 52242 USA
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Brainard RE, Weijerman M, Eakin CM, McElhany P, Miller MW, Patterson M, Piniak GA, Dunlap MJ, Birkeland C. Incorporating climate and ocean change into extinction risk assessments for 82 coral species. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2013; 27:1169-1178. [PMID: 24299083 DOI: 10.1111/cobi.12171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 06/29/2013] [Indexed: 06/02/2023]
Abstract
Many marine invertebrate species facing potential extinction have uncertain taxonomies and poorly known demographic and ecological traits. Uncertainties are compounded when potential extinction drivers are climate and ocean changes whose effects on even widespread and abundant species are only partially understood. The U.S. Endangered Species Act mandates conservation management decisions founded on the extinction risk to species based on the best available science at the time of consideration-requiring prompt action rather than awaiting better information. We developed an expert-opinion threat-based approach that entails a structured voting system to assess extinction risk from climate and ocean changes and other threats to 82 coral species for which population status and threat response information was limited. Such methods are urgently needed because constrained budgets and manpower will continue to hinder the availability of desired data for many potentially vulnerable marine species. Significant species-specific information gaps and uncertainties precluded quantitative assessments of habitat loss or population declines and necessitated increased reliance on demographic characteristics and threat vulnerabilities at genus or family levels. Adapting some methods (e.g., a structured voting system) used during other assessments and developing some new approaches (e.g., integrated assessment of threats and demographic characteristics), we rated the importance of threats contributing to coral extinction risk and assessed those threats against population status and trend information to evaluate each species' extinction risk over the 21st century. This qualitative assessment resulted in a ranking with an uncertainty range for each species according to their estimated likelihood of extinction. We offer guidance on approaches for future biological extinction risk assessments, especially in cases of data-limited species likely to be affected by global-scale threats. Incorporación del Cambio Climático y Oceánico en Estudios de Riesgo de Extinción para 82 Especies de Coral.
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Affiliation(s)
- Russell E Brainard
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 1125B Ala Moana Boulevard, Honolulu, HI, 96814, U.S.A
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27
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Suzuki G, Nomura K. Species boundaries of Astreopora corals (Scleractinia, Acroporidae) inferred by mitochondrial and nuclear molecular markers. Zoolog Sci 2013; 30:626-32. [PMID: 23915155 DOI: 10.2108/zsj.30.626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The genus Astreopora is a small but ancestral group in Acroporidae, which is one of the most diverse and dominant families of scleractinian coral in Indo-Pacific reefs. We estimated the species boundaries of Astreopora corals using two molecular markers: a mitochondrial non-coding region and a nuclear ribosomal 5.8S region. Seven species (59 specimens) commonly observed around Japan (Astreopora expansa, A. gracilis, A. incrustans, A. listeri, A. myriophthalma, A. cf. suggesta, and Astreopora sp.1) were investigated, and we observed no genetic divergence in the mitochondrial marker, suggesting that these species are closely related, consistent with a species complex or recent divergence, although genotyping by the marker is not so sensitive. In the nuclear 5.8S region, 121 clones consisted of six species were divided into the four major genetic groups. Although there were no monophyletic clades, the two dominant species A. myriophthalma and A. gracilis rarely shared the same haplotypes, suggesting that gene flow is limited between them. However, A. incrustans frequently shared the same haplotypes with A. gracilis although the distributions do not overlap. We found that the ancestral genus Astreopora in Acroporidae shows less genetic variation than traditionally identified morphospecies. Although further research on fertilization rate among these species is required to determine if there are reproductive barriers, the low level of genetic diversification in this genus hints that some ecological differences among acroporid corals play a role in the evolution of scleractinian corals, considering that the other members of this family, Acropora and Montipora, are highly diversified.
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Affiliation(s)
- Go Suzuki
- Seikai National Fisheries Research Institute, Fisheries Agency, Fukai-ota, Ishigaki, Okinawa, Japan.
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28
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Meyer JB, Cartier LE, Pinto-Figueroa EA, Krzemnicki MS, Hänni HA, McDonald BA. DNA fingerprinting of pearls to determine their origins. PLoS One 2013; 8:e75606. [PMID: 24130725 PMCID: PMC3794040 DOI: 10.1371/journal.pone.0075606] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/16/2013] [Indexed: 11/18/2022] Open
Abstract
We report the first successful extraction of oyster DNA from a pearl and use it to identify the source oyster species for the three major pearl-producing oyster species Pinctada margaritifera, P. maxima and P. radiata. Both mitochondrial and nuclear gene fragments could be PCR-amplified and sequenced. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in the internal transcribed spacer (ITS) region was developed and used to identify 18 pearls of unknown origin. A micro-drilling technique was developed to obtain small amounts of DNA while maintaining the commercial value of the pearls. This DNA fingerprinting method could be used to document the source of historic pearls and will provide more transparency for traders and consumers within the pearl industry.
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Affiliation(s)
- Joana B. Meyer
- Department of Environmental System Science, Swiss Federal Institute of Technology, Zurich, Switzerland
- Swiss Gemmological Institute SSEF, Basel, Switzerland
- * E-mail: (JBM); (LEC)
| | - Laurent E. Cartier
- Swiss Gemmological Institute SSEF, Basel, Switzerland
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
- * E-mail: (JBM); (LEC)
| | | | | | | | - Bruce A. McDonald
- Department of Environmental System Science, Swiss Federal Institute of Technology, Zurich, Switzerland
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29
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Bowen BW, Rocha LA, Toonen RJ, Karl SA. The origins of tropical marine biodiversity. Trends Ecol Evol 2013; 28:359-66. [DOI: 10.1016/j.tree.2013.01.018] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 01/30/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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Morphological and genetic analyses of xeniid soft coral diversity (Octocorallia; Alcyonacea). ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0119-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Stat M, Baker AC, Bourne DG, Correa AMS, Forsman Z, Huggett MJ, Pochon X, Skillings D, Toonen RJ, van Oppen MJH, Gates RD. Molecular delineation of species in the coral holobiont. ADVANCES IN MARINE BIOLOGY 2012; 63:1-65. [PMID: 22877610 DOI: 10.1016/b978-0-12-394282-1.00001-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The coral holobiont is a complex assemblage of organisms spanning a diverse taxonomic range including a cnidarian host, as well as various dinoflagellate, prokaryotic and acellular symbionts. With the accumulating information on the molecular diversity of these groups, binomial species classification and a reassessment of species boundaries for the partners in the coral holobiont is a logical extension of this work and will help enhance the capacity for comparative research among studies. To aid in this endeavour, we review the current literature on species diversity for the three best studied partners of the coral holobiont (coral, Symbiodinium, prokaryotes) and provide suggestions for future work on systematics within these taxa. We advocate for an integrative approach to the delineation of species using both molecular genetics in combination with phenetic characters. We also suggest that an a priori set of criteria be developed for each taxonomic group as no one species concept or accompanying set of guidelines is appropriate for delineating all members of the coral holobiont.
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Affiliation(s)
- Michael Stat
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii, Kaneohe, HI, USA.
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Carlon DB, Budd AF, Lippé C, Andrew RL. The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs. Evolution 2011; 65:3428-47. [PMID: 22133216 DOI: 10.1111/j.1558-5646.2011.01389.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h(2) ) in a suite of measurements that define corallite architecture, and could partition additive and nonadditive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h(2) estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h(2) were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.
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Affiliation(s)
- David B Carlon
- Department of Zoology, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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Work TM, Forsman ZH, Szabó Z, Lewis TD, Aeby GS, Toonen RJ. Inter-specific coral chimerism: genetically distinct multicellular structures associated with tissue loss in Montipora capitata. PLoS One 2011; 6:e22869. [PMID: 21829541 PMCID: PMC3145771 DOI: 10.1371/journal.pone.0022869] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 07/03/2011] [Indexed: 12/04/2022] Open
Abstract
Montipora white syndrome (MWS) results in tissue-loss that is often lethal to Montipora capitata, a major reef building coral that is abundant and dominant in the Hawai'ian Archipelago. Within some MWS-affected colonies in Kane'ohe Bay, Oahu, Hawai'i, we saw unusual motile multicellular structures within gastrovascular canals (hereafter referred to as invasive gastrovascular multicellular structure-IGMS) that were associated with thinning and fragmentation of the basal body wall. IGMS were in significantly greater densities in coral fragments manifesting tissue-loss compared to paired normal fragments. Mesenterial filaments from these colonies yielded typical M. capitata mitochondrial haplotypes (CO1, CR), while IGMS from the same colony consistently yielded distinct haplotypes previously only found in a different Montipora species (Montipora flabellata). Protein profiles showed consistent differences between paired mesenterial filaments and IGMS from the same colonies as did seven microsatellite loci that also exhibited an excess of alleles per locus inconsistent with a single diploid organism. We hypothesize that IGMS are a parasitic cellular lineage resulting from the chimeric fusion between M. capitata and M. flabellata larvae followed by morphological reabsorption of M. flabellata and subsequent formation of cell-lineage parasites. We term this disease Montiporaiasis. Although intra-specific chimerism is common in colonial animals, this is the first suspected inter-specific example and the first associated with tissue loss.
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Affiliation(s)
- Thierry M Work
- Honolulu Field Station, National Wildlife Health Center, United States Geological Survey, Honolulu, Hawai'i, United States of America.
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