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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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2
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Zhang WW, Weng ZY, Wang X, Yang Y, Li D, Wang L, Liu XC, Meng ZN. Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics. Zool Res 2024; 45:314-328. [PMID: 38485502 PMCID: PMC11017090 DOI: 10.24272/j.issn.2095-8137.2023.222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/05/2023] [Indexed: 03/19/2024] Open
Abstract
Animal body size variation is of particular interest in evolutionary biology, but the genetic basis remains largely unknown. Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size, providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates. Herein, we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea. Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size, respectively. A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups. Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups. These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks. Based on our results, we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection, leading to genetic variations in metabolic patterns, organ development, and lifespan, resulting in body size divergence between the two locally adapted populations. These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.
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Affiliation(s)
- Wei-Wei Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Zhuo-Ying Weng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong SAR 999077, China
| | - Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Duo Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Le Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, Singapore City 117604, Singapore
| | - Xiao-Chun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, Guangdong 519000, China
| | - Zi-Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, Guangdong 519000, China. E-mail:
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Scucchia F, Zaslansky P, Boote C, Doheny A, Mass T, Camp EF. The role and risks of selective adaptation in extreme coral habitats. Nat Commun 2023; 14:4475. [PMID: 37507378 PMCID: PMC10382478 DOI: 10.1038/s41467-023-39651-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The alarming rate of climate change demands new management strategies to protect coral reefs. Environments such as mangrove lagoons, characterized by extreme variations in multiple abiotic factors, are viewed as potential sources of stress-tolerant corals for strategies such as assisted evolution and coral propagation. However, biological trade-offs for adaptation to such extremes are poorly known. Here, we investigate the reef-building coral Porites lutea thriving in both mangrove and reef sites and show that stress-tolerance comes with compromises in genetic and energetic mechanisms and skeletal characteristics. We observe reduced genetic diversity and gene expression variability in mangrove corals, a disadvantage under future harsher selective pressure. We find reduced density, thickness and higher porosity in coral skeletons from mangroves, symptoms of metabolic energy redirection to stress response functions. These findings demonstrate the need for caution when utilizing stress-tolerant corals in human interventions, as current survival in extremes may compromise future competitive fitness.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H, Charney school of Marine Sciences, University of Haifa, Haifa, Israel.
| | - Paul Zaslansky
- Department for Operative, Preventive and Pediatric Dentistry, Charité-Universitätsmedizin, Berlin, Germany
| | - Chloë Boote
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Annabelle Doheny
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Tali Mass
- Department of Marine Biology, Leon H, Charney school of Marine Sciences, University of Haifa, Haifa, Israel
| | - Emma F Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia.
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Sheridan NE, Seyoum S, Sharp WC, Titus BM, Daly M, Richards CL, Schrey AW. Conservation genomics of an exploited, popular aquarium trade species: the giant Caribbean sea anemone Condylactis gigantea (Anthozoa: Actiniidae). CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01511-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Alvarado-Cerón V, Muñiz-Castillo AI, León-Pech MG, Prada C, Arias-González JE. A decade of population genetics studies of scleractinian corals: A systematic review. MARINE ENVIRONMENTAL RESEARCH 2023; 183:105781. [PMID: 36371949 DOI: 10.1016/j.marenvres.2022.105781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Coral reefs are the most diverse marine ecosystems. However, coral cover has decreased worldwide due to natural disturbances, climate change, and local anthropogenic drivers. In recent decades, various genetic methods and molecular markers have been developed to assess genetic diversity, structure, and connectivity in different coral species to determine the vulnerability of their populations. This review aims to identify population genetic studies of scleractinian corals in the last decade (2010-2020), and the techniques and molecular markers used. Bibliometric analysis was conducted to identify journals and authors working in this field. We then calculated the number of genetic studies by species and ecoregion based on data obtained from 178 studies found in Scopus and Web of Science. Coral Reefs and Molecular Ecology were the main journals published population genetics studies, and microsatellites are the most widely used molecular markers. The Caribbean, Australian Barrier Reef, and South Kuroshio in Japan are among the ecoregions with the most population genetics data. In contrast, we found limited information about the Coral Triangle, a region with the highest biodiversity and key to coral reef conservation. Notably, only 117 (out of 1500 described) scleractinian coral species have genetic studies. This review emphasizes which coral species have been studied and highlights remaining gaps and locations where such data is critical for coral conservation.
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Affiliation(s)
- Viridiana Alvarado-Cerón
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del I.P.N., Unidad Mérida. Km. 6 Antigua carretera a Progreso, Cordemex, 97310, Mérida, Yucatán, Mexico.
| | - Aarón Israel Muñiz-Castillo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del I.P.N., Unidad Mérida. Km. 6 Antigua carretera a Progreso, Cordemex, 97310, Mérida, Yucatán, Mexico.
| | - María Geovana León-Pech
- Department of Biological Science, University of Rhode Island, 120 Flag Road, Kingston, RI, 02881, USA.
| | - Carlos Prada
- Department of Biological Science, University of Rhode Island, 120 Flag Road, Kingston, RI, 02881, USA.
| | - Jesús Ernesto Arias-González
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del I.P.N., Unidad Mérida. Km. 6 Antigua carretera a Progreso, Cordemex, 97310, Mérida, Yucatán, Mexico.
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6
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García-Urueña R, Kitchen SA, Schizas NV. Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean. PeerJ 2022; 10:e13854. [PMID: 36061746 PMCID: PMC9438773 DOI: 10.7717/peerj.13854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/16/2022] [Indexed: 01/18/2023] Open
Abstract
Using a standardized SNP array, we identified two populations of Acropora cervicornis and one population of A. palmata in the Caribbean coast of Colombia. San Andrés was the most genetically differentiated location for both species. An average pairwise FST value of 0.131 and 0.050 between San Andrés and neighboring collection sites was estimated, for A. cervicornis and A. palmata, respectively. Based on population patterns of both acroporid species, we inferred that Magdalena River is not a barrier of genetic connectivity among Colombian populations. Genetic comparisons between the Colombian coast of Caribbean with other Caribbean locations agree with previous studies for both species, where four populations were identified in A. cervicornis and three in A. palmata. Our results support published bio-physical model predictions and highlight the Panama-Colombia gyre as a possible isolating mechanism within the western Caribbean. However, the genetic diversity in both species was about half (mean HE per site = 0.321 in A. palmata and 0.369 in A. cervicornis) than previous estimates in acroporid populations in the Caribbean. The lower genetic diversity as well their relative isolation and high levels of reef degradation may be of particular conservation concern that may require species-specific management coupled with science-based restoration efforts.
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Affiliation(s)
- Rocio García-Urueña
- Facultad de Ciencias Básicas, Universidad del Magdalena, Santa Marta, Magdalena, Colombia
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States of America
| | - Nikolaos V. Schizas
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, PR, United States of America
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7
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Li M, Huang W, Wu Q, Feng Y, Chen Y, Yu K, Chen B, Yang E, Meng L, Huang X, Wang X. High genetic differentiation and moderate genetic diversity of the degenerative branching coral Pocillopora verrucosa in the tropical South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:153076. [PMID: 35038534 DOI: 10.1016/j.scitotenv.2022.153076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Global warming is causing rapid degradation of coral reefs, among which branching corals are degrading the fastest. An assessment of coral genetic diversity and adaptive potential provides a basis for coral reef protection. In this study, we selected the branching coral Pocillopora verrucosa, a widely distributed species in the tropical South China Sea (SCS), to carry out population genetic studies. To analyze the genetic diversity and structure of 319 P. verrucosa samples from 10 populations in 4 SCS regions, twelve pairs of microsatellite primers and two nuclear markers, ITS and β-tub, were selected. Microsatellite marker results showed moderate genetic diversity for P. verrucosa in the SCS, but relatively low diversity in Dazhou Island and Yongxing Island. The haplotype network showed that P. verrucosa in the SCS was derived from two ancestors, which may be linked to geographical isolation in the Pleistocene glacial period. AMOVA (ΦST = 0.3375) and FST pairwise analysis results based on β-tub showed that the populations were highly differentiated, with most FST values (21/45) > 0.25. Yongxing and Qilianyu Islands populations were significantly different from those in the Xisha area. Mantel test results showed that genetic differentiation among P. verrucosa populations was significantly and positively correlated with both mean sea surface temperature (SST) and SST variance, and was not correlated with distance, chlorophyll-a, or turbidity. The reproductive mode of brooding planulae was an important factor contributing to high genetic differentiation among populations. The moderate genetic diversity of SCS P. verrucosa indicates that this population has a certain genetic potential in the context of global changes, but the high genetic differentiation between populations increases the risk of local degradation or extinction. This study provides a theoretical basis for the protection and restoration of SCS coral reefs.
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Affiliation(s)
- Ming Li
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China; Forestry College, Guangxi University, Nanning 530004, China
| | - Wen Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China.
| | - Qian Wu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Yi Feng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Yinmin Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519080, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Enguang Yang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Linqing Meng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Xueyong Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Xin Wang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning 530004, China; Gunagxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai 536000, China
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8
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Thomas L, Underwood JN, Rose NH, Fuller ZL, Richards ZT, Dugal L, Grimaldi CM, Cooke IR, Palumbi SR, Gilmour JP. Spatially varying selection between habitats drives physiological shifts and local adaptation in a broadcast spawning coral on a remote atoll in Western Australia. SCIENCE ADVANCES 2022; 8:eabl9185. [PMID: 35476443 PMCID: PMC9045720 DOI: 10.1126/sciadv.abl9185] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterizing the mechanisms of coral resilience to climate change. To explore these mechanisms in the reef coral Acropora tenuis, we collected samples from lagoon and reef slope habitats and combined whole-genome sequencing, ITS2 metabarcoding, experimental heat stress, and transcriptomics. Despite high gene flow across the atoll, we identified clear shifts in allele frequencies between habitats at relatively small linked genomic islands. Common garden heat stress assays showed corals from the lagoon to be more resistant to bleaching, and RNA sequencing revealed marked differences in baseline levels of gene expression between habitats. Our results provide new insight into the complex mechanisms of coral resilience to climate change and highlight the potential for spatially varying selection across complex coral reef seascapes to drive pronounced ecological divergence in climate-related traits.
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Affiliation(s)
- Luke Thomas
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
- UWA Oceans Institute, Oceans Graduate School, The University of Western Australia, Crawley, Australia
- Corresponding author.
| | - Jim N. Underwood
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
| | - Noah H. Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Zachary L. Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Zoe T. Richards
- Coral Conservation and Research Group, School of Molecular and Life Sciences, Curtin University, Perth, Australia
- Collections and Research, Western Australian Museum, Welshpool, Australia
| | - Laurence Dugal
- UWA Oceans Institute, Oceans Graduate School, The University of Western Australia, Crawley, Australia
| | - Camille M. Grimaldi
- UWA Oceans Institute, Oceans Graduate School, The University of Western Australia, Crawley, Australia
| | - Ira R. Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Stephen R. Palumbi
- Hopkins Marine Station, Biology Department, Stanford University, Pacific Grove, CA, USA
| | - James P. Gilmour
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, Crawley, Australia
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Reich HG, Kitchen SA, Stankiewicz KH, Devlin-Durante M, Fogarty ND, Baums IB. Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts. Mol Ecol 2021; 30:3500-3514. [PMID: 33964051 DOI: 10.1111/mec.15952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022]
Abstract
Mutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef-building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids (Acropora palmata, A. cervicornis and their F1 hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellate Symbiodinium 'fitti'. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whether S. 'fitti' populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) among S. 'fitti' strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600-Mb draft assembly of the S. 'fitti' genome (from the CFL14120 A. cervicornis metagenome). Phylogenomic and multivariate analyses revealed that genomic variation among S. 'fitti' strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation of S. 'fitti' strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting among S. 'fitti' strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.
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Affiliation(s)
- Hannah G Reich
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sheila A Kitchen
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Nicole D Fogarty
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
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10
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Abstract
Climate-driven reef decline has prompted the development of next-generation coral conservation strategies, many of which hinge on the movement of adaptive variation across genetic and environmental gradients. This process is limited by our understanding of how genetic and genotypic drivers of coral bleaching will manifest in different environmental conditions. We reciprocally transplanted 10 genotypes of Acropora cervicornis across eight sites along a 60 km span of the Florida Reef Tract and documented significant genotype × environment interactions in bleaching response during the severe 2015 bleaching event. Performance relative to site mean was significantly different between genotypes and can be mostly explained by ensemble models of correlations with genetic markers. The high explanatory power was driven by significant enrichment of loci associated DNA repair, cell signalling and apoptosis. No genotypes performed above (or below) bleaching average at all sites, so genomic predictors can provide practitioners with 'confidence intervals' about the chance of success in novel habitats. These data have important implications for assisted gene flow and managed relocation, and their integration with traditional active restoration.
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Affiliation(s)
- Crawford Drury
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Diego Lirman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
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11
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Goodall J, Westfall KM, Magnúsdóttir H, Pálsson S, Örnólfsdóttir EB, Jónsson ZO. RAD sequencing of common whelk, Buccinum undatum, reveals fine-scale population structuring in Europe and cryptic speciation within the North Atlantic. Ecol Evol 2021; 11:2616-2629. [PMID: 33767824 PMCID: PMC7981227 DOI: 10.1002/ece3.7219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 01/01/2023] Open
Abstract
Buccinum undatum is a subtidal gastropod that exhibits clear spatial variation in several phenotypic shell traits (color, shape, and thickness) across its North Atlantic distribution. Studies of spatial phenotypic variation exist for the species; however, population genetic studies have thus far relied on a limited set of mitochondrial and microsatellite markers. Here, we greatly expand on previous work by characterizing population genetic structure in B. undatum across the North Atlantic from SNP variation obtained by RAD sequencing. There was a high degree of genetic differentiation between Canadian and European populations (Iceland, Faroe Islands, and England) consistent with the divergence of populations in allopatry (F ST > 0.57 for all pairwise comparisons). In addition, B. undatum populations within Iceland, the Faroe Islands, and England are typified by weak but significant genetic structuring following an isolation-by-distance model. Finally, we established a significant correlation between genetic structuring in Iceland and two phenotypic traits: shell shape and color frequency. The works detailed here enhance our understanding of genetic structuring in B. undatum and establish the species as an intriguing model for future genome-wide association studies.
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Affiliation(s)
- Jake Goodall
- Faculty of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókurIceland
| | - Kristen Marie Westfall
- Vör – Marine Research Center in BreiðafjörðurÓlafsvíkIceland
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Hildur Magnúsdóttir
- Faculty of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Department of Aquaculture and Fish BiologyHólar UniversitySauðárkrókurIceland
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
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12
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Population genetic structure of the great star coral, Montastraea cavernosa, across the Cuban archipelago with comparisons between microsatellite and SNP markers. Sci Rep 2020; 10:15432. [PMID: 32963271 PMCID: PMC7508986 DOI: 10.1038/s41598-020-72112-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/17/2020] [Indexed: 11/25/2022] Open
Abstract
Coral reef habitats surrounding Cuba include relatively healthy, well-developed shallow and mesophotic (30–150 m) scleractinian communities at the cross-currents of the Tropical Western Atlantic (TWA). However, Cuba’s coral communities are not immune to the declines observed throughout the TWA, and there is limited information available regarding genetic connectivity, diversity, and structure among these populations. This represents an immense gap in our understanding of coral ecology and population dynamics at both local and regional scales. To address this gap, we evaluated the population genetic structure of the coral Montastraea cavernosa across eight reef sites surrounding Cuba. Colonies were genotyped using nine microsatellite markers and > 9,000 single nucleotide polymorphism (SNP) markers generated using the 2bRAD approach to assess fine-scale genetic structure across these sites. Both the microsatellite and SNP analyses identified patterns of genetic differentiation among sample populations. While the microsatellite analyses did not identify significant genetic structure across the seven shallow M. cavernosa sampling sites, the SNP analyses revealed significant pairwise population differentiation, suggesting that differentiation is greater between eastern and western sites. This study provides insight into methodological differences between microsatellite and SNP markers including potential trade-offs between marker-specific biases, sample size, sequencing costs, and the ability to resolve subtle patterns of population genetic structure. Furthermore, this study suggests that locations in western Cuba may play important roles in this species’ regional metapopulation dynamics and therefore may merit incorporation into developing international management efforts in addition to the local management the sites receive.
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13
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Kitchen SA, Von Kuster G, Kuntz KLV, Reich HG, Miller W, Griffin S, Fogarty ND, Baums IB. STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts. Sci Rep 2020; 10:12488. [PMID: 32719467 PMCID: PMC7385180 DOI: 10.1038/s41598-020-69101-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/22/2020] [Indexed: 11/26/2022] Open
Abstract
Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium ‘fitti’. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.
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Affiliation(s)
- S A Kitchen
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - G Von Kuster
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - K L Vasquez Kuntz
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - H G Reich
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - W Miller
- Centre for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - S Griffin
- NOAA Restoration Center, 260 Guard Rd., Aguadilla, PR, 00603, USA
| | - Nicole D Fogarty
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | - I B Baums
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
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14
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Ware M, Garfield EN, Nedimyer K, Levy J, Kaufman L, Precht W, Winters RS, Miller SL. Survivorship and growth in staghorn coral (Acropora cervicornis) outplanting projects in the Florida Keys National Marine Sanctuary. PLoS One 2020; 15:e0231817. [PMID: 32374734 PMCID: PMC7202597 DOI: 10.1371/journal.pone.0231817] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 04/01/2020] [Indexed: 12/29/2022] Open
Abstract
Significant population declines in Acropora cervicornis and A. palmata began in the 1970s and now exceed over 90%. The losses were caused by a combination of coral disease and bleaching, with possible contributions from other stressors, including pollution and predation. Reproduction in the wild by fragment regeneration and sexual recruitment is inadequate to offset population declines. Starting in 2007, the Coral Restoration Foundation™ evaluated the feasibility of outplanting A. cervicornis colonies to reefs in the Florida Keys to restore populations at sites where the species was previously abundant. Reported here are the results of 20 coral outplanting projects with each project defined as a cohort of colonies outplanted at the same time and location. Photogrammetric analysis and in situ monitoring (2007 to 2015) measured survivorship, growth, and condition of 2419 colonies. Survivorship was initially high but generally decreased after two years. Survivorship among projects based on colony counts ranged from 4% to 89% for seven cohorts monitored at least five years. Weibull survival models were used to estimate survivorship beyond the duration of the projects and ranged from approximately 0% to over 35% after five years and 0% to 10% after seven years. Growth rate averaged 10 cm/year during the first two years then plateaued in subsequent years. After four years, approximately one-third of surviving colonies were ≥ 50 cm in maximum diameter. Projects used three to sixteen different genotypes and significant differences did not occur in survivorship, condition, or growth. Restoration times for three reefs were calculated based on NOAA Recovery Plan (NRP) metrics (colony abundance and size) and the findings from projects reported here. Results support NRP conclusions that reducing stressors is required before significant population growth and recovery will occur. Until then, outplanting protects against local extinction and helps to maintain genetic diversity in the wild.
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Affiliation(s)
- Matthew Ware
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, United States of America
| | - Eliza N. Garfield
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Ken Nedimyer
- Reef Renewal, LLC, Tavernier, FL, United States of America
| | - Jessica Levy
- Coral Restoration Foundation, Key Largo, FL, United States of America
| | - Les Kaufman
- Marine Program and Pardee Center for the Study of the Longer-Range Future, Boston University, Boston, MA, United States of America
| | - William Precht
- Marine and Coastal Programs, Dial Cordy and Associates, Miami, FL, United States of America
| | - R. Scott Winters
- Coral Restoration Foundation, Key Largo, FL, United States of America
| | - Steven L. Miller
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, United States of America
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15
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Drury C. Resilience in reef-building corals: The ecological and evolutionary importance of the host response to thermal stress. Mol Ecol 2020; 29:448-465. [PMID: 31845413 DOI: 10.1111/mec.15337] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023]
Abstract
Coral reefs are under extreme threat due to a number of stressors, but temperature increases due to changing climate are the most severe. Rising ocean temperatures coupled with local extremes lead to extensive bleaching, where the coral-algal symbiosis breaks down and corals may die, compromising the structure and function of reefs. Although the symbiotic nature of the coral colony has historically been a focus of research on coral resilience, the host itself is a foundational component in the response to thermal stress. Fixed effects in the coral host set trait baselines through evolutionary processes, acting on many loci of small effect to create mosaics of thermal tolerance across latitudes and individual coral reefs. These genomic differences can be strongly heritable, producing wide variation among clones of different genotypes or families of a specific larval cross. Phenotypic plasticity is overlaid on these baselines and a growing body of knowledge demonstrates the potential for acclimatization of reef-building corals through a variety of mechanisms that promote resilience and stress tolerance. The long-term persistence of coral reefs will require many of these mechanisms to adjust to warmer temperatures within a generation, bridging the gap to reproductive events that allow recombination of standing diversity and adaptive change. Business-as-usual climate scenarios will probably lead to the loss of some coral populations or species in the future, so the interaction between intragenerational effects and evolutionary pressure is critical for the survival of reefs.
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16
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Baums IB, Baker AC, Davies SW, Grottoli AG, Kenkel CD, Kitchen SA, Kuffner IB, LaJeunesse TC, Matz MV, Miller MW, Parkinson JE, Shantz AA. Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01978. [PMID: 31332879 PMCID: PMC6916196 DOI: 10.1002/eap.1978] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 05/06/2023]
Abstract
Active coral restoration typically involves two interventions: crossing gametes to facilitate sexual larval propagation; and fragmenting, growing, and outplanting adult colonies to enhance asexual propagation. From an evolutionary perspective, the goal of these efforts is to establish self-sustaining, sexually reproducing coral populations that have sufficient genetic and phenotypic variation to adapt to changing environments. Here, we provide concrete guidelines to help restoration practitioners meet this goal for most Caribbean species of interest. To enable the persistence of coral populations exposed to severe selection pressure from many stressors, a mixed provenance strategy is suggested: genetically unique colonies (genets) should be sourced both locally as well as from more distant, environmentally distinct sites. Sourcing three to four genets per reef along environmental gradients should be sufficient to capture a majority of intraspecies genetic diversity. It is best for practitioners to propagate genets with one or more phenotypic traits that are predicted to be valuable in the future, such as low partial mortality, high wound healing rate, high skeletal growth rate, bleaching resilience, infectious disease resilience, and high sexual reproductive output. Some effort should also be reserved for underperforming genets because colonies that grow poorly in nurseries sometimes thrive once returned to the reef and may harbor genetic variants with as yet unrecognized value. Outplants should be clustered in groups of four to six genets to enable successful fertilization upon maturation. Current evidence indicates that translocating genets among distant reefs is unlikely to be problematic from a population genetic perspective but will likely provide substantial adaptive benefits. Similarly, inbreeding depression is not a concern given that current practices only raise first-generation offspring. Thus, proceeding with the proposed management strategies even in the absence of a detailed population genetic analysis of the focal species at sites targeted for restoration is the best course of action. These basic guidelines should help maximize the adaptive potential of reef-building corals facing a rapidly changing environment.
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Affiliation(s)
- Iliana B. Baums
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
| | - Andrew C. Baker
- Department of Marine Biology and EcologyRosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida33149USA
| | - Sarah W. Davies
- Department of BiologyBoston UniversityBostonMassachusetts02215USA
| | | | - Carly D. Kenkel
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCalifornia90007USA
| | - Sheila A. Kitchen
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
| | - Ilsa B. Kuffner
- U.S. Geological Survey600 4th Street S.St. PetersburgFlorida33701USA
| | - Todd C. LaJeunesse
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
| | - Mikhail V. Matz
- Department of Integrative BiologyThe University of Texas at AustinAustinTexas78712USA
| | | | - John E. Parkinson
- SECORE InternationalMiamiFlorida33145USA
- Department of Integrative BiologyUniversity of South FloridaTampaFlorida33620USA
| | - Andrew A. Shantz
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania16803USA
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17
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Afiq-Rosli L, Huang D, Toh TC, Taira D, Ng CSL, Song T, Chou LM. Maximising genetic diversity during coral transplantation from a highly impacted source reef. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01164-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Abstract
Genomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genus Acropora We generated genomic sequence data from multiple samples of the Caribbean A. cervicornis (staghorn coral) and A. palmata (elkhorn coral), and predicted millions of nucleotide variants among these two species and the Pacific A. digitifera A subset of predicted nucleotide variants were verified using restriction length polymorphism assays and proved useful in distinguishing the two Caribbean acroporids and the hybrid they form ("A. prolifera"). Nucleotide variants are freely available from the Galaxy server (usegalaxy.org), and can be analyzed there with computational tools and stored workflows that require only an internet browser. We describe these data and some of the analysis tools, concentrating on fixed differences between A. cervicornis and A. palmata In particular, we found that fixed amino acid differences between these two species were enriched in proteins associated with development, cellular stress response, and the host's interactions with associated microbes, for instance in the ABC transporters and superoxide dismutase. Identified candidate genes may underlie functional differences in how these threatened species respond to changing environments. Users can expand the presented analyses easily by adding genomic data from additional species, as they become available.
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19
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Drury C, Greer JB, Baums I, Gintert B, Lirman D. Clonal diversity impacts coral cover in Acropora cervicornisthickets: Potential relationships between density, growth, and polymorphisms. Ecol Evol 2019; 9:4518-4531. [PMID: 31031924 PMCID: PMC6476746 DOI: 10.1002/ece3.5035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/25/2022] Open
Abstract
As coral reefs decline, cryptic sources of resistance and resilience to stress may be increasingly important for the persistence of these communities. Among these sources, inter- and intraspecific diversity remain understudied on coral reefs but extensively impact a variety of traits in other ecosystems. We use a combination of field and sequencing data at two sites in Florida and two in the Dominican Republic to examine clonal diversity and genetic differentiation of high- and low-density aggregations of the threatened coral Acropora cervicornisin the Caribbean. We find that high-density aggregations called thickets are composed of up to 30 genotypes at a single site, but 47% of genotypes are also found as isolated, discrete colonies outside these aggregations. Genet-ramet ratios are comparable for thickets (0.636) and isolated colonies after rarefaction (0.569), suggesting the composition of each aggregation is not substantially different and highlighting interactions between colonies as a potential influence on structure. There are no differences in growth rate, but a significant positive correlation between genotypic diversity and coral cover, which may be due to the influence of interactions between colonies on survivorship or fragment retention during asexual reproduction. Many polymorphisms distinguish isolated colonies from thickets despite the shared genotypes found here, including putative nonsynonymous mutations that change amino acid sequence in 25 loci. These results highlight intraspecific diversity as a density-dependent factor that may impact traits important for the structure and function of coral reefs.
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Affiliation(s)
- Crawford Drury
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
| | - Justin B. Greer
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
| | - Iliana Baums
- Department of BiologyPennsylvania State UniversityUniversity ParkPennsylvania
| | - Brooke Gintert
- Department of Marine Geoscience, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
| | - Diego Lirman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric ScienceUniversity of MiamiMiamiFlorida
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20
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Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity. Genetics 2018; 210:1429-1452. [PMID: 30315068 DOI: 10.1534/genetics.118.301502] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 10/08/2018] [Indexed: 11/18/2022] Open
Abstract
Positive natural selection can lead to a decrease in genomic diversity at the selected site and at linked sites, producing a characteristic signature of elevated expected haplotype homozygosity. These selective sweeps can be hard or soft. In the case of a hard selective sweep, a single adaptive haplotype rises to high population frequency, whereas multiple adaptive haplotypes sweep through the population simultaneously in a soft sweep, producing distinct patterns of genetic variation in the vicinity of the selected site. Measures of expected haplotype homozygosity have previously been used to detect sweeps in multiple study systems. However, these methods are formulated for phased haplotype data, typically unavailable for nonmodel organisms, and some may have reduced power to detect soft sweeps due to their increased genetic diversity relative to hard sweeps. To address these limitations, we applied the H12 and H2/H1 statistics proposed in 2015 by Garud et al., which have power to detect both hard and soft sweeps, to unphased multilocus genotypes, denoting them as G12 and G2/G1. G12 (and the more direct expected homozygosity analog to H12, denoted G123) has comparable power to H12 for detecting both hard and soft sweeps. G2/G1 can be used to classify hard and soft sweeps analogously to H2/H1, conditional on a genomic region having high G12 or G123 values. The reason for this power is that, under random mating, the most frequent haplotypes will yield the most frequent multilocus genotypes. Simulations based on parameters compatible with our recent understanding of human demographic history suggest that expected homozygosity methods are best suited for detecting recent sweeps, and increase in power under recent population expansions. Finally, we find candidates for selective sweeps within the 1000 Genomes CEU, YRI, GIH, and CHB populations, which corroborate and complement existing studies.
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21
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [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: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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22
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Muller EM, Bartels E, Baums IB. Bleaching causes loss of disease resistance within the threatened coral species Acropora cervicornis. eLife 2018; 7:35066. [PMID: 30203745 PMCID: PMC6133546 DOI: 10.7554/elife.35066] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 07/30/2018] [Indexed: 12/24/2022] Open
Abstract
Determining the adaptive potential of foundation species, such as reef-building corals, is urgent as the oceans warm and coral populations decline. Theory predicts that corals may adapt to climate change via selection on standing genetic variation. Yet, corals face not only rising temperatures but also novel diseases. We studied the interaction between two major stressors affecting colonies of the threatened coral, Acropora cervicornis: white-band disease and high water temperature. We determined that 27% of A. cervicornis were disease resistant prior to a thermal anomaly. However, disease resistance was largely lost during a bleaching event because of more compromised coral hosts or increased pathogenic dose/virulence. There was no tradeoff between disease resistance and temperature tolerance; disease susceptibility was independent of Symbiodinium strain. The present study shows that susceptibility to temperature stress creates an increased risk in disease-associated mortality, and only rare genets may maintain or gain infectious disease resistance under high temperature. We conclude that A. cervicornis populations in the lower Florida Keys harbor few existing genotypes that are resistant to both warming and disease. The staghorn coral was once prevalent throughout the Florida Reef Tract. However, the last few decades have seen a substantial reduction in the coral population because of disease outbreaks and increasing ocean temperatures. The staghorn coral shows no evidence of natural recovery, and so has been the focus of restoration efforts throughout much of the Florida region. Why put the time and effort into growing corals that are unlikely to survive within environmental conditions that continue to deteriorate? One reason is that the genetic make-up – the genotype – of some corals makes them more resilient to certain threats. However, there could be tradeoffs associated with these resilient traits. For example, a coral may be able to tolerate heat, but may easily succumb to disease. Previous studies have identified some staghorn coral genotypes that are resistant to an infection called white-band disease. The influence of high water temperatures on the ability of the coral to resist this disease was not known. There also remained the possibility that more varieties of coral might show similar disease resistance. To investigate Muller et al. conducted two experiments exposing staghorn coral genotypes to white-band diseased tissue before and during a coral bleaching event. Approximately 25% of the population of staghorn tested was resistant to white-band disease before the bleaching event. When the corals were exposed to white-band disease during bleaching, twice as much of the coral died. Two out of the 15, or 13%, of the coral genotypes tested were resistant to the disease even while bleached. Additionally, the level of bleaching within the coral genotypes was not related to how easily they developed white-band disease, suggesting that there are no direct tradeoffs between heat tolerance and disease resistance. These results suggest that there are very hardy corals, created by nature, already in existence. Incorporating these traits thoughtfully into coral restoration plans may increase the likelihood of population-based recovery. The Florida Reef Tract is estimated to be worth over six billion dollars to the state economy, providing over 70,000 jobs and attracting millions of tourists into Florida each year. However, much of these ecosystem services will be lost if living coral is not restored within the reef tract. The results presented by Muller et al. emphasize the need for maintaining high genetic diversity while increasing resiliency when restoring coral. They also emphasize that disease resistant corals, even when bleached, already exist and may be an integral part of the recovery of Florida’s reef tract.
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Affiliation(s)
- Erinn M Muller
- Coral Health and Disease Program, Mote Marine Laboratory, Sarasota, United States
| | - Erich Bartels
- Coral Reef Monitoring and Assessment Program, Mote Marine Laboratory, Florida, United States
| | - Iliana B Baums
- Department of Biology, Pennsylvania State University, Pennsylvania, United States
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23
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Chang ES, Orive ME, Cartwright P. Nonclonal coloniality: Genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan Ectopleura larynx. Evol Lett 2018; 2:442-455. [PMID: 30283694 PMCID: PMC6121865 DOI: 10.1002/evl3.68] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/18/2018] [Indexed: 12/20/2022] Open
Abstract
Hydrozoans typically develop colonies through asexual budding of polyps. Although colonies of Ectopleura are similar to other hydrozoans in that they consist of multiple polyps physically connected through continuous epithelia and shared gastrovascular cavity, Ectopleura larynx does not asexually bud polyps indeterminately. Instead, after an initial phase of limited budding in a young colony, E. larynx achieves its large colony size through the aggregation and fusion of sexually (nonclonally) produced polyps. The apparent chimerism within a physiologically integrated colony presents a potential source of conflict between distinct genetic lineages, which may vary in their ability to access the germline. To determine the extent to which the potential for genetic conflict exists, we characterized the types of genetic relationships between polyps within colonies, using a RAD‐Seq approach. Our results indicate that E. larynx colonies are indeed comprised of polyps that are clones and sexually reproduced siblings and offspring, consistent with their life history. In addition, we found that colonies also contain polyps that are genetically unrelated, and that estimates of genome‐wide relatedness suggests a potential for conflict within a colony. Taken together, our data suggest that there are distinct categories of relationships in colonies of E. larynx, likely achieved through a range of processes including budding, regeneration, and fusion of progeny and unrelated polyps, with the possibility for a genetic conflict resolution mechanism. Together these processes contribute to the reevolution of the ecologically important trait of coloniality in E. larynx.
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Affiliation(s)
- E Sally Chang
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
| | - Maria E Orive
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
| | - Paulyn Cartwright
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
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24
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Parkinson JE, Bartels E, Devlin‐Durante MK, Lustic C, Nedimyer K, Schopmeyer S, Lirman D, LaJeunesse TC, Baums IB. Extensive transcriptional variation poses a challenge to thermal stress biomarker development for endangered corals. Mol Ecol 2018; 27:1103-1119. [DOI: 10.1111/mec.14517] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/29/2017] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- John Everett Parkinson
- Department of Biology Pennsylvania State University State College PA USA
- Department of Integrative Biology Oregon State University Corvallis OR USA
| | - Erich Bartels
- Center for Coral Reef Research Mote Marine Laboratory Summerland Key FL USA
| | | | - Caitlin Lustic
- The Nature Conservancy Florida Keys Office Summerland Key FL USA
| | | | - Stephanie Schopmeyer
- Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Diego Lirman
- Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Todd C. LaJeunesse
- Department of Biology Pennsylvania State University State College PA USA
| | - Iliana B. Baums
- Department of Biology Pennsylvania State University State College PA USA
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Zayasu Y, Satoh N, Shinzato C. Genetic diversity of farmed and wild populations of the reef-building coral, Acropora tenuis. Restor Ecol 2018. [DOI: 10.1111/rec.12687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yuna Zayasu
- Marine Genomics Unit; Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
| | - Noriyuki Satoh
- Marine Genomics Unit; Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son, Okinawa, 904-0495 Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute; The University of Tokyo; Chiba, 277-8564 Japan
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26
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Adaptation Without Boundaries: Population Genomics in Marine Systems. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Devlin-Durante MK, Baums IB. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata. PeerJ 2017; 5:e4077. [PMID: 29181279 PMCID: PMC5701561 DOI: 10.7717/peerj.4077] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/31/2017] [Indexed: 12/18/2022] Open
Abstract
The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.
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Affiliation(s)
- Meghann K Devlin-Durante
- Department of Biology, Pennsylvania State University, University Park, PA, United States of America
| | - Iliana B Baums
- Department of Biology, Pennsylvania State University, University Park, PA, United States of America
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28
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Drury C, Schopmeyer S, Goergen E, Bartels E, Nedimyer K, Johnson M, Maxwell K, Galvan V, Manfrino C, Lirman D. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity. Ecol Evol 2017; 7:6188-6200. [PMID: 28861224 PMCID: PMC5574808 DOI: 10.1002/ece3.3184] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/08/2017] [Accepted: 05/21/2017] [Indexed: 12/21/2022] Open
Abstract
Threatened Caribbean coral communities can benefit from high‐resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis, across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis, including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.
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Affiliation(s)
- Crawford Drury
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Stephanie Schopmeyer
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
| | - Elizabeth Goergen
- Department of Marine and Environmental Sciences Nova Southeastern University Dania Beach FL USA
| | - Erich Bartels
- Mote Marine Tropical Research Laboratory Summerland Key FL USA
| | | | | | - Kerry Maxwell
- Federal Fish and Wildlife Conservation Commission Marathon FL USA
| | - Victor Galvan
- Punta Cana Ecological Foundation Punta Cana Dominican Republic
| | - Carrie Manfrino
- Central Caribbean Marine Institute Princeton NJ USA.,Little Cayman Research Centre Little Cayman Cayman Islands
| | - Diego Lirman
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Science University of Miami Miami FL USA
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29
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Revisiting Adaptive Potential, Population Size, and Conservation. Trends Ecol Evol 2017; 32:506-517. [PMID: 28476215 DOI: 10.1016/j.tree.2017.03.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 11/24/2022]
Abstract
Additive genetic variance (VA) reflects the potential for evolutionary shifts and can be low for some traits or populations. High VA is critical for the conservation of threatened species under selection to facilitate adaptation. Theory predicts tight associations between population size and VA, but data from some experimental models, and managed and natural populations do not always support this prediction. However, VA comparisons often have low statistical power, are undertaken in highly controlled environments distinct from natural habitats, and focus on traits with limited ecological relevance. Moreover, investigations of VA typically fail to consider rare alleles, genetic load, or linkage disequilibrium, resulting in deleterious effects associated with favored alleles in small populations. Large population size remains essential for ensuring adaptation.
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30
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Genotype and local environment dynamically influence growth, disturbance response and survivorship in the threatened coral, Acropora cervicornis. PLoS One 2017; 12:e0174000. [PMID: 28319134 PMCID: PMC5358778 DOI: 10.1371/journal.pone.0174000] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 03/01/2017] [Indexed: 01/17/2023] Open
Abstract
The relationship between the coral genotype and the environment is an important area of research in degraded coral reef ecosystems. We used a reciprocal outplanting experiment with 930 corals representing ten genotypes on each of eight reefs to investigate the influence of genotype and the environment on growth and survivorship in the threatened Caribbean staghorn coral, Acropora cervicornis. Coral genotype and site were strong drivers of coral growth and individual genotypes exhibited flexible, non-conserved reaction norms, complemented by ten-fold differences in growth between specific G-E combinations. Growth plasticity may diminish the influence of local adaptation, where foreign corals grew faster than native corals at their home sites. Novel combinations of environment and genotype also significantly affected disturbance response during and after the 2015 bleaching event, where these factors acted synergistically to drive variation in bleaching and recovery. Importantly, small differences in temperature stress elicit variable patterns of survivorship based on genotype and illustrate the importance of novel combinations of coral genetics and small differences between sites representing habitat refugia. In this context, acclimatization and flexibility is especially important given the long lifespan of corals coping with complex environmental change. The combined influence of site and genotype creates short-term differences in growth and survivorship, contributing to the standing genetic variation needed for adaptation to occur over longer timescales and the recovery of degraded reefs through natural mechanisms.
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31
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Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis. Sci Rep 2017; 7:44559. [PMID: 28300177 PMCID: PMC5353582 DOI: 10.1038/srep44559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/09/2017] [Indexed: 12/15/2022] Open
Abstract
Marine benthic organisms inhabit a heterogeneous environment in which connectivity between populations occurs mainly through dispersive larval stages, while local selective pressures acting on early life history stages lead to non-random mortality, shaping adaptive genetic structure. In order to test the influence of local adaptation and neutral processes in a marine benthic species with low dispersal, in this study we used Genotyping by Sequencing technology to compare the neutral and putatively selected signals (neutral and outlier loci, respectively) in SNPs scattered throughout the genome in six local populations of the commercially exploited ascidian Pyura chilensis along the southeast Pacific coast (24°–42°S). This species is sessile as an adult, has a short-lived larval stage, and may also be dispersed by artificial transport as biofouling. We found that the main signal in neutral loci was a highly divergent lineage present at 39°S, and a subjacent signal that indicated a separation at 30°S (north/south), widely reported in the area. North/south separation was the main signal in outlier loci, and the linage divergence at 39°S was subjacent. We conclude that the geographic structure of the genetic diversity of outlier and neutral loci was established by different strengths of environmental, historical and anthropogenic factors.
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32
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Lirman D, Schopmeyer S. Ecological solutions to reef degradation: optimizing coral reef restoration in the Caribbean and Western Atlantic. PeerJ 2016; 4:e2597. [PMID: 27781176 PMCID: PMC5075686 DOI: 10.7717/peerj.2597] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/16/2016] [Indexed: 01/22/2023] Open
Abstract
Reef restoration activities have proliferated in response to the need to mitigate coral declines and recover lost reef structure, function, and ecosystem services. Here, we describe the recent shift from costly and complex engineering solutions to recover degraded reef structure to more economical and efficient ecological approaches that focus on recovering the living components of reef communities. We review the adoption and expansion of the coral gardening framework in the Caribbean and Western Atlantic where practitioners now grow and outplant 10,000’s of corals onto degraded reefs each year. We detail the steps for establishing a gardening program as well as long-term goals and direct and indirect benefits of this approach in our region. With a strong scientific basis, coral gardening activities now contribute significantly to reef and species recovery, provide important scientific, education, and outreach opportunities, and offer alternate livelihoods to local stakeholders. While challenges still remain, the transition from engineering to ecological solutions for reef degradation has opened the field of coral reef restoration to a wider audience poised to contribute to reef conservation and recovery in regions where coral losses and recruitment bottlenecks hinder natural recovery.
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Affiliation(s)
- Diego Lirman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, United States
| | - Stephanie Schopmeyer
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, United States
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33
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Crawford DL, Oleksiak MF. Ecological population genomics in the marine environment. Brief Funct Genomics 2016; 15:342-51. [DOI: 10.1093/bfgp/elw008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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