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Johnston EC, Burgess SC. Pocillopora tuahiniensis: a new species of scleractinian coral (Scleractinia, Pocilloporidae) from French Polynesia. Zootaxa 2023; 5369:117-124. [PMID: 38220724 DOI: 10.11646/zootaxa.5369.1.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Indexed: 01/16/2024]
Abstract
Pocillopora tuahiniensis sp. nov. is described based on mitochondrial and nuclear genomic data, algal symbiont genetic data, geographic isolation, and its distribution pattern within reefs that is distinct from other sympatric Pocillopora species (Johnston et al. 2022a, b). Mitochondrial and nuclear genomic data reveal that P. tuahiniensis sp. nov. is a unique species, sister to P. verrucosa, and in a clade different from that of P. meandrina (Johnston et al. 2022a). However, the gross in situ colony appearance of P. tuahiniensis sp. nov. cannot easily be differentiated from that of P. verrucosa or P. meandrina at Moorea. By sequencing the mtORF region, P. tuahiniensis sp. nov. can be easily distinguished from other Pocillopora species. Pocillopora tuahiniensis sp. nov. has so far been sampled in French Polynesia, Ducie Island, and Rapa Nui (Armstrong et al. 2023; Edmunds et al. 2016; Forsman et al. 2013; Glin et al. 2017; Mayfield et al. 2015; Oury et al. 2021; Voolstra et al. 2023). On the fore reefs of Moorea, P. tuahiniensis sp. nov. is very abundant 10 m and is one of the most common Pocillopora species at these depths (Johnston et al. 2022b). It can also be found at a much lower abundance at shallow depths on the fore reef and back reef lagoon. The holotype is deposited at the Smithsonian Institution as USNM-SI 1522390 and the mtORF Genbank accession number is OP418359.
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Affiliation(s)
- Erika C Johnston
- Department of Biological Science; Florida State University; 319 Stadium Drive; Tallahassee; FL; 32306-4296; USA. Hawaii Institute of Marine Biology; 46-007 Lilipuna Rd; Kneohe; HI; 96744; USA.
| | - Scott C Burgess
- Department of Biological Science; Florida State University; 319 Stadium Drive; Tallahassee; FL; 32306-4296; USA.
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Hayes JM, Abdul-Rahman NH, Gerdes MJ, Musah RA. Coral Genus Differentiation Based on Direct Analysis in Real Time-High Resolution Mass Spectrometry-Derived Chemical Fingerprints. Anal Chem 2021; 93:15306-15314. [PMID: 34761917 DOI: 10.1021/acs.analchem.1c02519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coral reefs are one of the most biologically diverse ecosystems, and the accurate identification of the species is essential for diversity assessment and conservation. Current genus determination approaches are time-consuming and resource-intensive and can be highly subjective. To explore the hypothesis that the small-molecule profiles of coral are genus-specific and can be used as a rapid tool to catalogue and distinguish between coral genera, the small-molecule chemical fingerprints of the species Acanthastrea echinata, Catalaphyllia jardinei, Duncanopsammia axifuga, Echinopora lamellosa, Euphyllia divisa, Euphyllia paraancora, Euphyllia paradivisa, Galaxea fascicularis, Herpolitha limax, Montipora confusa, Monitpora digitata, Montipora setosa, Pachyseris rugosa, Pavona cactus, Plerogyra sinuosa, Pocillopora acuta, Seriatopora hystrix, Sinularia dura, Turbinaria peltata, Turbinaria reniformis, Xenia elongata, and Xenia umbellata were generated using direct analysis in real time-high resolution mass spectrometry (DART-HRMS). It is demonstrated here that the mass spectrum-derived small-molecule profiles for coral of different genera are distinct. Multivariate statistical analysis processing of the DART-HRMS data enabled rapid genus-level differentiation based on the chemical composition of the coral. Coral samples were analyzed with no sample preparation required, making the approach rapid and efficient. The resulting spectra were subjected to kernel discriminant analysis (KDA), which furnished accurate genus differentiation of the coral. Leave-one-out cross-validation (LOOCV) was carried out to determine the classification accuracy of each model and confirm that this approach can be used for coral genus attribution with prediction accuracies ranging from 86.67 to 97.33%. The advantages and application of the statistical analysis to DART-HRMS-derived coral chemical signatures for genus-level differentiation are discussed.
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Affiliation(s)
- Jessica M Hayes
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nana-Hawwa Abdul-Rahman
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Michael J Gerdes
- CapitalCorals Inc., 20 Colvin Avenue, Albany, New York 12206, United States
| | - Rabi A Musah
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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Soto D, De Palmas S, Ho M, Denis V, Allen Chen C. A molecular census of early-life stage scleractinian corals in shallow and mesophotic zones. Ecol Evol 2021; 11:14573-14584. [PMID: 34765126 PMCID: PMC8571570 DOI: 10.1002/ece3.8122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/06/2022] Open
Abstract
The decline of coral reefs has fueled interest in determining whether mesophotic reefs can shield against disturbances and help replenish deteriorated shallower reefs. In this study, we characterized spatial (horizontal and vertical) and seasonal patterns of diversity in coral recruits from Dabaisha and Guiwan reefs at Ludao, Taiwan. Concrete blocks supporting terra-cotta tiles were placed at shallow (15m) and mesophotic (40m) depths, during 2016-2018. Half of the tiles were retrieved and replaced biannually over three 6-month surveys (short-term); the remainder retrieved at the end of the 18-month (long-term) survey. 451 recruits were located using fluorescent censusing and identified by DNA barcoding. Barcoding the mitochondrial cytochrome oxidase I (COI) gene resulted in 17 molecular operational taxonomic units (MOTUs). To obtain taxonomic resolution to the generic level, Pocillopora were phylotyped using the mitochondrial open reading frame (ORF), resolving eight MOTUs. Acropora, Isopora, and Montipora recruits were identified by the nuclear PaxC intron, yielding ten MOTUs. Overall, 35 MOTUs were generated and were comprised primarily of Pocillopora and, in fewer numbers, Acropora, Isopora, Pavona, Montipora, Stylophora, among others. 40% of MOTUs recruited solely within mesophotic reefs while 20% were shared by both depth zones. MOTUs recruiting across a broad depth distribution appear consistent with the hypothesis of mesophotic reefs acting as a refuge for shallow-water coral reefs. In contrast, Acropora and Isopora MOTUs were structured across depth zones representing an exception to this hypothesis. This research provides an imperative assessment of coral recruitment in understudied mesophotic reefs and imparts insight into the refuge hypothesis.
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Affiliation(s)
- Derek Soto
- Biodiversity ProgramTaiwan International Graduate ProgramAcademia Sinica and National Taiwan Normal UniversityTaipeiTaiwan
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Stéphane De Palmas
- Biodiversity ProgramTaiwan International Graduate ProgramAcademia Sinica and National Taiwan Normal UniversityTaipeiTaiwan
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Ming‐Jay Ho
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Green Island Marine Research StationAcademia SinicaLudao, Taitung CountyTaiwan
| | - Vianney Denis
- Institute of OceanographyNational Taiwan UniversityTaipeiTaiwan
| | - Chaolun Allen Chen
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
- Department of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
- Department of Life ScienceTung Hai UniversityTaichungTaiwan
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de Palmas S, Soto D, Ho MJ, Denis V, Chen CA. Strong horizontal and vertical connectivity in the coral Pocillopora verrucosa from Ludao, Taiwan, a small oceanic island. PLoS One 2021; 16:e0258181. [PMID: 34634065 PMCID: PMC8504772 DOI: 10.1371/journal.pone.0258181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/22/2021] [Indexed: 12/01/2022] Open
Abstract
Mesophotic habitats could be sheltered from natural and anthropogenic disturbances and act as reproductive refuges, providing propagules to replenish shallower populations. Molecular markers can be used as proxies evaluating the connectivity and inferring population structure and larval dispersal. This study characterizes population structure as well as horizontal and vertical genetic connectivity of the broadcasting coral Pocillopora verrucosa from Ludao, a small oceanic island off the eastern coast of Taiwan. We genotyped 75 P. verrucosa specimens from three sites (Gongguan, Dabaisha, and Guiwan) at three depth ranges (Shallow: 7-15 m, Mid-depth: 23-30 m, and Deep: 38-45 m), spanning shallow to upper mesophotic coral reefs, with eight microsatellite markers. F-statistics showed a moderate differentiation (FST = 0.106, p<0.05) between two adjacent locations (Dabaisha 23-30 and Dabaisha 38-45 m), but no differentiation elsewhere, suggesting high levels of connectivity among sites and depths. STRUCTURE analysis showed no genetic clustering among sites or depths, indicating that all Pocillopora individuals could be drawn from a single panmictic population. Simulations of recent migration assigned 30 individuals (40%) to a different location from where they were collected. Among them, 1/3 were assigned to deeper locations, 1/3 to shallower populations and 1/3 were assigned to the right depth but a different site. These results suggest high levels of vertical and horizontal connectivity, which could enhance the recovery of P. verrucosa following disturbances around Ludao, a feature that agrees with demographic studies portraying this species as an opportunistic scleractinian.
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Affiliation(s)
- Stéphane de Palmas
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Derek Soto
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Ming-Jay Ho
- Green Island Marine Research Station, Marine Science Thematic Centre, Biodiversity Research Center, Academia Sinica, Green Island, Taitung, Taiwan
| | - Vianney Denis
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Sciences, Tunghai University, Taichung, Taiwan
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Buitrago-López C, Mariappan KG, Cárdenas A, Gegner HM, Voolstra CR. The Genome of the Cauliflower Coral Pocillopora verrucosa. Genome Biol Evol 2021; 12:1911-1917. [PMID: 32857844 PMCID: PMC7594246 DOI: 10.1093/gbe/evaa184] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here, we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) comprised repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.
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Affiliation(s)
- Carol Buitrago-López
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Germany
| | - Hagen M Gegner
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Centre for Organismal Studies (COS), University of Heidelberg, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Germany
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Chow GSE, Chan YKS, Jain SS, Huang D. Light limitation selects for depth generalists in urbanised reef coral communities. MARINE ENVIRONMENTAL RESEARCH 2019; 147:101-112. [PMID: 31029435 DOI: 10.1016/j.marenvres.2019.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Depth range is an important species trait for coral reef organisms, yet it remains to be quantified and analysed adequately among tropical coral species. Filling this knowledge gap is crucial as the depth limits of corals are related to important environmental factors such as light and temperature. Furthermore, the health and survivorship of corals may be threatened due to warming-induced sea-level rise, particularly for colonies living at the deeper limits of species depth ranges. Here we collected benthic and environmental data along the reef profile to characterise the depth ranges of coral species, and analysed species diversity and community structure in relation to possible depth-related biophysical parameters on the sediment-stressed reefs of Singapore. The results reveal clear environmental covariations with depth, expectedly with light availability showing the most marked decline as depth increases. Live coral cover, species richness and diversity are associated positively and significantly with light, which also structures coral communities along the reef profile more strongly than temperature or sediment levels. Relatedly, we detect species-specific depth distributions with two main strategies observed among coral species: shallow specialists and depth generalists. We suggest that corals in Singapore are unlikely to be impacted by light limitation specifically as sea level rises due to the wider depth range of the deeper species. Our data will inform conservation efforts especially in the selection of sites and depths for coral transplantation.
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Affiliation(s)
- Gwendolyn S E Chow
- Department of Biological Sciences, National University of Singapore, 117558, Singapore
| | - Y K Samuel Chan
- Department of Biological Sciences, National University of Singapore, 117558, Singapore
| | | | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 117558, Singapore; Tropical Marine Science Institute, National University of Singapore, 119227, Singapore.
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