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Tan EYW, Neo ML, Huang D. Assessing taxonomic, functional and phylogenetic diversity of giant clams across the Indo‐Pacific for conservation prioritization. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Edwin Y. W. Tan
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Mei Lin Neo
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Tropical Marine Science Institute National University of Singapore Singapore Singapore
| | - Danwei Huang
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Tropical Marine Science Institute National University of Singapore Singapore Singapore
- Centre for Nature‐based Climate Solutions National University of Singapore Singapore Singapore
- Lee Kong Chian Natural History Museum National University of Singapore Singapore Singapore
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2
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Ng LWK, Chisholm C, Carrasco LR, Darling ES, Guilhaumon F, Mooers AØ, Tucker CM, Winter M, Huang D. Prioritizing phylogenetic diversity to protect functional diversity of reef corals. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Linus W. K. Ng
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | | | - Luis Roman Carrasco
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Centre for Nature‐based Climate Solutions National University of Singapore Singapore Singapore
| | | | | | - Arne Ø. Mooers
- Department of Biological Sciences Simon Fraser University Burnaby Canada
| | - Caroline M. Tucker
- Environment, Ecology and Energy Program University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - Marten Winter
- German Centre for Integrative Biodiversity Research Leipzig Germany
| | - Danwei Huang
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Centre for Nature‐based Climate Solutions National University of Singapore Singapore Singapore
- Lee Kong Chian Natural History Museum and Tropical Marine Science Institute National University of Singapore Singapore Singapore
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3
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Gault JA, Bentlage B, Huang D, Kerr AM. Lineage-specific variation in the evolutionary stability of coral photosymbiosis. SCIENCE ADVANCES 2021; 7:eabh4243. [PMID: 34550731 PMCID: PMC8457658 DOI: 10.1126/sciadv.abh4243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
More than half of reef-building corals (Scleractinia) participate in a nutritional symbiosis, known as photosymbiosis, with photosynthetic dinoflagellates that ranges from obligate to facultative dependence. Fitting hidden-rates models allowing among-lineage variation in the rate of trait evolution to supertree and molecular phylogenies of Scleractinia, we reconstruct the history of photosymbiosis within Scleractinia and characterize its evolutionary stability. We find that most lineages of scleractinians are extraordinarily stable for the trait, evincing no instances of loss, but that in some clades photosymbiosis is more labile, thus providing a framework for comparative studies to further our mechanistic understanding of the factors that shape the evolutionary fates of scleractinian photosymbiosis.
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Affiliation(s)
- Jordan A. Gault
- Marine Laboratory, University of Guam, 303 University Dr., Mangilao, GU 96913, USA
| | - Bastian Bentlage
- Marine Laboratory, University of Guam, 303 University Dr., Mangilao, GU 96913, USA
| | - Danwei Huang
- Department of Biological Sciences, Tropical Marine Science Institute, and Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore
| | - Alexander M. Kerr
- Marine Laboratory, University of Guam, 303 University Dr., Mangilao, GU 96913, USA
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4
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Wang X, Zoccola D, Liew YJ, Tambutte E, Cui G, Allemand D, Tambutte S, Aranda M. The Evolution of Calcification in Reef-Building Corals. Mol Biol Evol 2021; 38:3543-3555. [PMID: 33871620 PMCID: PMC8382919 DOI: 10.1093/molbev/msab103] [Citation(s) in RCA: 10] [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] [Indexed: 12/31/2022] Open
Abstract
Corals build the structural foundation of coral reefs, one of the most diverse and productive ecosystems on our planet. Although the process of coral calcification that allows corals to build these immense structures has been extensively investigated, we still know little about the evolutionary processes that allowed the soft-bodied ancestor of corals to become the ecosystem builders they are today. Using a combination of phylogenomics, proteomics, and immunohistochemistry, we show that scleractinian corals likely acquired the ability to calcify sometime between ∼308 and ∼265 Ma through a combination of lineage-specific gene duplications and the co-option of existing genes to the calcification process. Our results suggest that coral calcification did not require extensive evolutionary changes, but rather few coral-specific gene duplications and a series of small, gradual optimizations of ancestral proteins and their co-option to the calcification process.
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Affiliation(s)
- Xin Wang
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Didier Zoccola
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Yi Jin Liew
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Eric Tambutte
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Guoxin Cui
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Denis Allemand
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Sylvie Tambutte
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Manuel Aranda
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
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5
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Vega Thurber R, Mydlarz LD, Brandt M, Harvell D, Weil E, Raymundo L, Willis BL, Langevin S, Tracy AM, Littman R, Kemp KM, Dawkins P, Prager KC, Garren M, Lamb J. Deciphering Coral Disease Dynamics: Integrating Host, Microbiome, and the Changing Environment. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.575927] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Diseases of tropical reef organisms is an intensive area of study, but despite significant advances in methodology and the global knowledge base, identifying the proximate causes of disease outbreaks remains difficult. The dynamics of infectious wildlife diseases are known to be influenced by shifting interactions among the host, pathogen, and other members of the microbiome, and a collective body of work clearly demonstrates that this is also the case for the main foundation species on reefs, corals. Yet, among wildlife, outbreaks of coral diseases stand out as being driven largely by a changing environment. These outbreaks contributed not only to significant losses of coral species but also to whole ecosystem regime shifts. Here we suggest that to better decipher the disease dynamics of corals, we must integrate more holistic and modern paradigms that consider multiple and variable interactions among the three major players in epizootics: the host, its associated microbiome, and the environment. In this perspective, we discuss how expanding the pathogen component of the classic host-pathogen-environment disease triad to incorporate shifts in the microbiome leading to dysbiosis provides a better model for understanding coral disease dynamics. We outline and discuss issues arising when evaluating each component of this trio and make suggestions for bridging gaps between them. We further suggest that to best tackle these challenges, researchers must adjust standard paradigms, like the classic one pathogen-one disease model, that, to date, have been ineffectual at uncovering many of the emergent properties of coral reef disease dynamics. Lastly, we make recommendations for ways forward in the fields of marine disease ecology and the future of coral reef conservation and restoration given these observations.
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6
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Kim SW, Sampayo EM, Sommer B, Sims CA, Gómez-Cabrera MDC, Dalton SJ, Beger M, Malcolm HA, Ferrari R, Fraser N, Figueira WF, Smith SDA, Heron SF, Baird AH, Byrne M, Eakin CM, Edgar R, Hughes TP, Kyriacou N, Liu G, Matis PA, Skirving WJ, Pandolfi JM. Refugia under threat: Mass bleaching of coral assemblages in high-latitude eastern Australia. GLOBAL CHANGE BIOLOGY 2019; 25:3918-3931. [PMID: 31472029 DOI: 10.1111/gcb.14772] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/31/2019] [Accepted: 07/04/2019] [Indexed: 05/21/2023]
Abstract
Environmental anomalies that trigger adverse physiological responses and mortality are occurring with increasing frequency due to climate change. At species' range peripheries, environmental anomalies are particularly concerning because species often exist at their environmental tolerance limits and may not be able to migrate to escape unfavourable conditions. Here, we investigated the bleaching response and mortality of 14 coral genera across high-latitude eastern Australia during a global heat stress event in 2016. We evaluated whether the severity of assemblage-scale and genus-level bleaching responses was associated with cumulative heat stress and/or local environmental history, including long-term mean temperatures during the hottest month of each year (SSTLTMAX ), and annual fluctuations in water temperature (SSTVAR ) and solar irradiance (PARZVAR ). The most severely-bleached genera included species that were either endemic to the region (Pocillopora aliciae) or rare in the tropics (e.g. Porites heronensis). Pocillopora spp., in particular, showed high rates of immediate mortality. Bleaching severity of Pocillopora was high where SSTLTMAX was low or PARZVAR was high, whereas bleaching severity of Porites was directly associated with cumulative heat stress. While many tropical Acropora species are extremely vulnerable to bleaching, the Acropora species common at high latitudes, such as A. glauca and A. solitaryensis, showed little incidence of bleaching and immediate mortality. Two other regionally-abundant genera, Goniastrea and Turbinaria, were also largely unaffected by the thermal anomaly. The severity of assemblage-scale bleaching responses was poorly explained by the environmental parameters we examined. Instead, the severity of assemblage-scale bleaching was associated with local differences in species abundance and taxon-specific bleaching responses. The marked taxonomic disparity in bleaching severity, coupled with high mortality of high-latitude endemics, point to climate-driven simplification of assemblage structures and progressive homogenisation of reef functions at these high-latitude locations.
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Affiliation(s)
- Sun W Kim
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Eugenia M Sampayo
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Brigitte Sommer
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Carrie A Sims
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Maria Del C Gómez-Cabrera
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Steve J Dalton
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- School of Biological Sciences, Centre for Biodiversity and Conservation Science, The University of Queensland, St. Lucia, QLD, Australia
| | - Hamish A Malcolm
- Fisheries Research, New South Wales Department of Primary Industries, Coffs Harbour, NSW, Australia
| | - Renata Ferrari
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Institute of Marine Sciences, Townsville, QLD, Australia
| | - Nicola Fraser
- Solitary Islands Underwater Research Group, Coffs Harbour, NSW, Australia
| | - Will F Figueira
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Stephen D A Smith
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia
| | - Scott F Heron
- Marine Geophysical Laboratory, Physics Department, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Coral Reef Watch, U.S. National Oceanic and Atmospheric Administration, College Park, MD, USA
| | - Andrew H Baird
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Maria Byrne
- Anatomy and Histology, Bosch Institute, The University of Sydney, Sydney, NSW, Australia
| | - C Mark Eakin
- Coral Reef Watch, U.S. National Oceanic and Atmospheric Administration, College Park, MD, USA
| | - Robert Edgar
- Solitary Islands Underwater Research Group, Coffs Harbour, NSW, Australia
| | - Terry P Hughes
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Nicole Kyriacou
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Gang Liu
- Coral Reef Watch, U.S. National Oceanic and Atmospheric Administration, College Park, MD, USA
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, USA
| | - Paloma A Matis
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - William J Skirving
- Coral Reef Watch, U.S. National Oceanic and Atmospheric Administration, College Park, MD, USA
| | - John M Pandolfi
- Australian Research Council Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
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7
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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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8
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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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9
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Huang D, Goldberg EE, Chou LM, Roy K. The origin and evolution of coral species richness in a marine biodiversity hotspot. Evolution 2017; 72:288-302. [PMID: 29178128 DOI: 10.1111/evo.13402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 10/30/2017] [Accepted: 11/12/2017] [Indexed: 12/25/2022]
Abstract
The Coral Triangle (CT) region of the Indo-Pacific realm harbors an extraordinary number of species, with richness decreasing away from this biodiversity hotspot. Despite multiple competing hypotheses, the dynamics underlying this regional diversity pattern remain poorly understood. Here, we use a time-calibrated evolutionary tree of living reef coral species, their current geographic ranges, and model-based estimates of regional rates of speciation, extinction, and geographic range shifts to show that origination rates within the CT are lower than in surrounding regions, a result inconsistent with the long-standing center of origin hypothesis. Furthermore, endemism of coral species in the CT is low, and the CT endemics are older than relatives found outside this region. Overall, our model results suggest that the high diversity of reef corals in the CT is largely due to range expansions into this region of species that evolved elsewhere. These findings strongly support the notion that geographic range shifts play a critical role in generating species diversity gradients. They also show that preserving the processes that gave rise to the striking diversity of corals in the CT requires protecting not just reefs within the hotspot, but also those in the surrounding areas.
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Affiliation(s)
- Danwei Huang
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Loke Ming Chou
- Department of Biological Sciences and Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, California 92093
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10
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Sol D, Bartomeus I, González-Lagos C, Pavoine S. Urbanisation and the loss of phylogenetic diversity in birds. Ecol Lett 2017; 20:721-729. [DOI: 10.1111/ele.12769] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/29/2016] [Accepted: 03/11/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Sol
- CREAF; Cerdanyola del Vallès; Catalonia 08193 Spain
- CSIC; Cerdanyola del Vallès; Catalonia 08193 Spain
| | | | - César González-Lagos
- Departamento de Ecología; Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
- Center of Applied Ecology & Sustainability; Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Santiago Chile
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation; Sorbonne Universités; Paris France
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11
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Baird AH, Hoogenboom MO, Huang D. Cyphastrea salae, a new species of hard coral from Lord Howe Island, Australia (Scleractinia, Merulinidae). Zookeys 2017; 662:49-66. [PMID: 28769608 PMCID: PMC5539699 DOI: 10.3897/zookeys.662.11454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 02/16/2017] [Indexed: 11/19/2022] Open
Abstract
A new zooxanthellate reef-dwelling scleractinian coral species, Cyphastrea salaesp. n. (Scleractinia, Merulinidae), is described from Lord Howe Island Australia. The new species can be distinguished morphologically from the only other congeneric species on Lord Howe Island, C. microphthalma, by the number of primary septa (12 vs. 10) and the much taller corallites (mean ± SE: 1.0 ± 0.07 mm v 0.4 ± 0.04 mm). The relationship of C. salae to four of the other eleven currently accepted species in the genus was explored through analyses of nuclear (28S rDNA) and mitochondrial (noncoding intergenic region) gene sequences. Cyphastrea salaesp. n. forms a strongly supported clade that is distinct from a clade containing three species found commonly in Australia, C. chalcidicum, C. serailia, and C. microphthalma. One specimen was also found in the Solitary Islands, another high latitude location in south-eastern Australia. The discovery of a new species in the genus Cyphastrea on high latitude reefs in south-eastern Australia suggests that other new species might be found among more diverse genera represented here and that the scleractinian fauna of these isolated locations is more distinct than previously recognised.
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Affiliation(s)
- Andrew H. Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Mia O. Hoogenboom
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Danwei Huang
- Department of Biological Sciences & Tropical Marine Science Institute, National University of Singapore, Singapore 117543, Singapore
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12
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Huang D, Arrigoni R, Benzoni F, Fukami H, Knowlton N, Smith ND, Stolarski J, Chou LM, Budd AF. Taxonomic classification of the reef coral family Lobophylliidae (Cnidaria: Anthozoa: Scleractinia). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12391] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Danwei Huang
- Department of Biological Sciences and Tropical Marine Science Institute; National University of Singapore; Singapore 117543 Singapore
| | - 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
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Francesca Benzoni
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Hironobu Fukami
- Department of Marine Biology and Environmental Science; University of Miyazaki; Miyazaki 889-2192 Japan
| | - Nancy Knowlton
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; Washington DC 20013 USA
| | - Nathan D. Smith
- The Dinosaur Institute; Natural History Museum of Los Angeles County; 900 Exposition Boulevard Los Angeles CA 90007 USA
| | - Jarosław Stolarski
- Institute of Paleobiology; Polish Academy of Sciences; Twarda 51/55 PL-00-818 Warsaw Poland
| | - Loke Ming Chou
- Department of Biological Sciences and Tropical Marine Science Institute; 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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13
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Bellwood DR, Goatley CHR, Bellwood O. The evolution of fishes and corals on reefs: form, function and interdependence. Biol Rev Camb Philos Soc 2016; 92:878-901. [PMID: 26970292 DOI: 10.1111/brv.12259] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Abstract
Coral reefs are renowned for their spectacular biodiversity and the close links between fishes and corals. Despite extensive fossil records and common biogeographic histories, the evolution of these two key groups has rarely been considered together. We therefore examine recent advances in molecular phylogenetics and palaeoecology, and place the evolution of fishes and corals in a functional context. In critically reviewing the available fossil and phylogenetic evidence, we reveal a marked congruence in the evolution of the two groups. Despite one group consisting of swimming vertebrates and the other colonial symbiotic invertebrates, fishes and corals have remarkably similar evolutionary histories. In the Paleocene and Eocene [66-34 million years ago (Ma)] most modern fish and coral families were present, and both were represented by a wide range of functional morphotypes. However, there is little evidence of diversification at this time. By contrast, in the Oligocene and Miocene (34-5.3 Ma), both groups exhibited rapid lineage diversification. There is also evidence of increasing reef area, occupation of new habitats, increasing coral cover, and potentially, increasing fish abundance. Functionally, the Oligocene-Miocene is marked by the appearance of new fish and coral taxa associated with high-turnover fast-growth ecosystems and the colonization of reef flats. It is in this period that the functional characteristics of modern coral reefs were established. Most species, however, only arose in the last 5.3 million years (Myr; Plio-Pleistocene), with the average age of fish species being 5.3 Myr, and corals just 1.9 Myr. While these species are genetically distinct, phenotypic differences are often limited to variation in colour or minor morphological features. This suggests that the rapid increase in biodiversity during the last 5.3 Myr was not matched by changes in ecosystem function. For reef fishes, colour appears to be central to recent diversification. However, the presence of pigment patterns in the Eocene suggests that colour may not have driven recent diversification. Furthermore, the lack of functional changes in fishes or corals over the last 5 Myr raises questions over the role and importance of biodiversity in shaping the future of coral reefs.
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Affiliation(s)
- David R Bellwood
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Christopher H R Goatley
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Orpha Bellwood
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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14
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Veron S, Davies TJ, Cadotte MW, Clergeau P, Pavoine S. Predicting loss of evolutionary history: Where are we? Biol Rev Camb Philos Soc 2015; 92:271-291. [PMID: 26467982 DOI: 10.1111/brv.12228] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 01/29/2023]
Abstract
The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.
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Affiliation(s)
- Simon Veron
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - T Jonathan Davies
- Department of Biology, McGill University, 1205 ave Docteur Penfield, Montreal, Quebec H3A 1B1, Canada.,African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Marc W Cadotte
- Department of Biology, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Philippe Clergeau
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France.,Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, U.K
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15
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Huang D, Roy K. The future of evolutionary diversity in reef corals. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140010. [PMID: 25561671 DOI: 10.1098/rstb.2014.0010] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One-third of the world's reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures-phylogenetic diversity and phylogenetic species variability-we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.
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Affiliation(s)
- Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, CA 92093, USA
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16
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Fukami H. Regional specific approach is a next step for setting evolutionary-based conservation priorities in the scleractinian corals. Anim Conserv 2015. [DOI: 10.1111/acv.12224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- H. Fukami
- Department of Marine Biology and Environmental Science; Faculty of Agriculture; University of Miyazaki; Miyazaki Japan
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17
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Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions. Proc Natl Acad Sci U S A 2015; 112:4909-14. [PMID: 25901313 DOI: 10.1073/pnas.1409886112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic impacts are endangering many long-lived species and lineages, possibly leading to a disproportionate loss of existing evolutionary history (EH) in the future. However, surprisingly little is known about the loss of EH during major extinctions in the geological past, and thus we do not know whether human impacts are pruning the tree of life in a manner that is unique in the history of life. A major impediment to comparing the loss of EH during past and current extinctions is the conceptual difference in how ages are estimated from paleontological data versus molecular phylogenies. In the former case the age of a taxon is its entire stratigraphic range, regardless of how many daughter taxa it may have produced; for the latter it is the time to the most recent common ancestor shared with another extant taxon. To explore this issue, we use simulations to understand how the loss of EH is manifested in the two data types. We also present empirical analyses of the marine bivalve clade Pectinidae (scallops) during a major Plio-Pleistocene extinction in California that involved a preferential loss of younger species. Overall, our results show that the conceptual difference in how ages are estimated from the stratigraphic record versus molecular phylogenies does not preclude comparisons of age selectivities of past and present extinctions. Such comparisons not only provide fundamental insights into the nature of the extinction process but should also help improve evolutionarily informed models of conservation prioritization.
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18
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Curnick DJ, Head CEI, Huang D, Crabbe MJC, Gollock M, Hoeksema BW, Johnson KG, Jones R, Koldewey HJ, Obura DO, Rosen BR, Smith DJ, Taylor ML, Turner JR, Wren S, Redding DW. Setting evolutionary-based conservation priorities for a phylogenetically data-poor taxonomic group (Scleractinia). Anim Conserv 2015. [DOI: 10.1111/acv.12185] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. J. Curnick
- Centre for Biodiversity and Environment Research; Department of Genetics, Evolution and Environment; University College London; London UK
- Zoological Society of London; London UK
| | - C. E. I. Head
- Zoological Society of London; London UK
- Department of Zoology; University of Oxford; Oxford UK
| | - D. Huang
- Department of Biological Sciences; National University of Singapore; Singapore
| | - M. J. C. Crabbe
- Department of Zoology; University of Oxford; Oxford UK
- Institute of Biomedical and Environmental Science and Technology; Faculty of Creative Arts, Technologies and Science; University of Bedfordshire; Luton UK
| | | | - B. W. Hoeksema
- Department of Marine Zoology; Naturalis Biodiversity Center; Leiden The Netherlands
| | - K. G. Johnson
- Department of Earth Sciences; Natural History Museum; London UK
| | - R. Jones
- Zoological Society of London; London UK
| | | | - D. O. Obura
- Coastal Oceans Research and Development in the Indian Ocean (CORDIO) East Africa; Mombasa Kenya
| | - B. R. Rosen
- Department of Earth Sciences; Natural History Museum; London UK
| | - D. J. Smith
- Coral Reef Research Unit; University of Essex; Colchester UK
| | - M. L. Taylor
- Department of Zoology; University of Oxford; Oxford UK
| | - J. R. Turner
- School of Ocean Sciences; Bangor University; Anglesey UK
| | - S. Wren
- Zoological Society of London; London UK
- Department of Zoology; University of Otago; Dunedin New Zealand
| | - D. W. Redding
- Centre for Biodiversity and Environment Research; Department of Genetics, Evolution and Environment; University College London; London UK
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19
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Eiserhardt WL, Borchsenius F, Plum CM, Ordonez A, Svenning JC. Climate-driven extinctions shape the phylogenetic structure of temperate tree floras. Ecol Lett 2015; 18:263-72. [PMID: 25604755 DOI: 10.1111/ele.12409] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/04/2014] [Accepted: 12/15/2014] [Indexed: 11/26/2022]
Abstract
When taxa go extinct, unique evolutionary history is lost. If extinction is selective, and the intrinsic vulnerabilities of taxa show phylogenetic signal, more evolutionary history may be lost than expected under random extinction. Under what conditions this occurs is insufficiently known. We show that late Cenozoic climate change induced phylogenetically selective regional extinction of northern temperate trees because of phylogenetic signal in cold tolerance, leading to significantly and substantially larger than random losses of phylogenetic diversity (PD). The surviving floras in regions that experienced stronger extinction are phylogenetically more clustered, indicating that non-random losses of PD are of increasing concern with increasing extinction severity. Using simulations, we show that a simple threshold model of survival given a physiological trait with phylogenetic signal reproduces our findings. Our results send a strong warning that we may expect future assemblages to be phylogenetically and possibly functionally depauperate if anthropogenic climate change affects taxa similarly.
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Affiliation(s)
- Wolf L Eiserhardt
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark; Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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20
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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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21
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Huang D, Benzoni F, Fukami H, Knowlton N, Smith ND, Budd AF. Taxonomic classification of the reef coral families Merulinidae, Montastraeidae, and Diploastraeidae (Cnidaria: Anthozoa: Scleractinia). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12140] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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
| | - Hironobu Fukami
- Department of Marine Biology and Environmental Science; University of Miyazaki; Miyazaki 889-2192 Japan
| | - Nancy Knowlton
- Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093 USA
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; Washington, DC 20013 USA
| | - Nathan D. Smith
- Department of Biology; Howard University; Washington, DC 20059 USA
- Department of Paleobiology; National Museum of Natural History; Smithsonian Institution; Washington, DC 20013 USA
| | - Ann F. Budd
- Department of Earth and Environmental Sciences; University of Iowa; Iowa City IA 52242 USA
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