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Oury N, Magalon H. Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics. Sci Rep 2024; 14:6437. [PMID: 38499737 PMCID: PMC10948807 DOI: 10.1038/s41598-024-57136-5] [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: 10/03/2023] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). As the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection. Then, SNPs and genes variable within colonies were characterised. While most of the tested bioinformatics parameters did not significantly impact the detection of IGV, filtering on genotype depth of coverage strongly improved its detection by reducing genotyping errors. Mosaicism and chimerism, the two processes leading to IGV (the first through somatic mutations, the second through fusion of distinct organisms), were found in 7% and 12% of the colonies, respectively. Both processes led to several intra-colonial allelic differences, but most were non-coding or silent. However, 7% of the differences were non-silent and found in genes involved in a high diversity of biological processes, some of which were directly linked to responses to environmental stresses. IGV, therefore, appears as a source of genetic diversity and genetic plasticity, increasing the adaptive potential of colonies. Such benefits undoubtedly play an important role in the maintenance and the evolution of scleractinian populations and appear crucial for the future of coral reefs in the context of ongoing global changes.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France.
- Laboratoire Cogitamus, Paris, France.
- KAUST Red Sea Research Center and Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France
- Laboratoire Cogitamus, Paris, France
- Laboratoire d'Excellence CORAIL, Perpignan, France
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Guerrini G, Shefy D, Douek J, Shashar N, Goulet TL, Rinkevich B. Spatial distribution of conspecific genotypes within chimeras of the branching coral Stylophora pistillata. Sci Rep 2021; 11:22554. [PMID: 34799589 PMCID: PMC8604976 DOI: 10.1038/s41598-021-00981-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/18/2021] [Indexed: 01/27/2023] Open
Abstract
Chimerism is a coalescence of conspecific genotypes. Although common in nature, fundamental knowledge, such as the spatial distribution of the genotypes within chimeras, is lacking. Hence, we investigated the spatial distribution of conspecific genotypes within the brooding coral Stylophora pistillata, a common species throughout the Indo-Pacific and Red Sea. From eight gravid colonies, we collected planula larvae that settled in aggregates, forming 2–3 partner chimeras. Coral chimeras grew in situ for up to 25 months. Nine chimeras (8 kin, 1 non-related genotypes) were sectioned into 7–17 fragments (6–26 polyps/fragment), and genotyped using eight microsatellite loci. The discrimination power of each microsatellite-locus was evaluated with 330 ‘artificial chimeras,’ made by mixing DNA from three different S. pistillata genotypes in pairwise combinations. In 68% of ‘artificial chimeras,’ the second genotype was detected if it constituted 5–30% of the chimera. Analyses of S. pistillata chimeras revealed that: (a) chimerism is a long-term state; (b) conspecifics were intermixed (not separate from one another); (c) disproportionate distribution of the conspecifics occurred; (d) cryptic chimerism (chimerism not detected via a given microsatellite) existed, alluding to the underestimation of chimerism in nature. Mixed chimerism may affect ecological/physiological outcomes for a chimera, especially in clonal organisms, and challenges the concept of individuality, affecting our understanding of the unit of selection.
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Affiliation(s)
- Gabriele Guerrini
- Israel Oceanography and Limnological Research, National Institute, of Oceanography, Tel-Shikmona, P.O. Box 9753, 3109701, Haifa, Israel.,Department of Life Sciences, Eilat Campus, Ben Gurion University of the Negev, Eilat, Israel
| | - Dor Shefy
- Israel Oceanography and Limnological Research, National Institute, of Oceanography, Tel-Shikmona, P.O. Box 9753, 3109701, Haifa, Israel.,Department of Life Sciences, Eilat Campus, Ben Gurion University of the Negev, Eilat, Israel.,The Interuniversity Institute for Marine Science, 88000, Eilat, Israel
| | - Jacob Douek
- Israel Oceanography and Limnological Research, National Institute, of Oceanography, Tel-Shikmona, P.O. Box 9753, 3109701, Haifa, Israel
| | - Nadav Shashar
- Department of Life Sciences, Eilat Campus, Ben Gurion University of the Negev, Eilat, Israel
| | - Tamar L Goulet
- Department of Biology, University of Mississippi, P.O. Box 1848, University, MS, 38677-1848, USA.
| | - Baruch Rinkevich
- Israel Oceanography and Limnological Research, National Institute, of Oceanography, Tel-Shikmona, P.O. Box 9753, 3109701, Haifa, Israel
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Oury N, Gélin P, Magalon H. Together stronger: Intracolonial genetic variability occurrence in Pocillopora corals suggests potential benefits. Ecol Evol 2020; 10:5208-5218. [PMID: 32607144 PMCID: PMC7319244 DOI: 10.1002/ece3.5807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 01/18/2023] Open
Abstract
We investigated the occurrence of intracolonial genetic variability (IGV) in Pocillopora corals in the southwestern Indian Ocean. Ninety-six colonies were threefold-sampled from three sites in Reunion Island. Nubbins were genotyped using 13 microsatellite loci, and their multilocus genotypes compared. Over 50% of the colonies presented at least two different genotypes among their three nubbins, and IGV was found abundant in all sites (from 36.7% to 58.1%). To define the threshold distinguishing mosaicism from chimerism, we developed a new method based on different evolution models by computing the number of different alleles for the infinite allele model (IAM) and the Bruvo's distance for the stepwise mutation model (SMM). Colonies were considered as chimeras if their nubbins differed from more than four alleles and if the pairwise Bruvo's distance was higher than 0.12. Thus 80% of the IGV colonies were mosaics and 20% chimeras (representing almost 10% of the total sampling). IGV seems widespread in scleractinians and beyond the disabilities of this phenomenon reported in several studies, it should also bring benefits. Next steps are to identify these benefits and to understand processes leading to IGV, as well as factors influencing them.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt Denis, La RéunionFrance
| | - Pauline Gélin
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt Denis, La RéunionFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS)Université de La RéunionSt Denis, La RéunionFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
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Rugiu L, Manninen I, Rothäusler E, Jormalainen V. Tolerance to climate change of the clonally reproducing endemic Baltic seaweed, Fucus radicans: is phenotypic plasticity enough? JOURNAL OF PHYCOLOGY 2018; 54:888-898. [PMID: 30315649 DOI: 10.1111/jpy.12796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
To predict the effects of climate change, we first need information on both the current tolerance ranges of species and their future adaptive potential. Adaptive responses may originate either in genetic variation or in phenotypic plasticity, but the relative importance of these factors is poorly understood. Here, we tested the tolerance of Fucus radicans to the combination of hyposalinity and warming projected by climate models for 2070-2099. We measured the growth and survival responses of thalli in both current and future conditions, focusing on variations in tolerance among and within different clonal lineages. Survival was 32% lower in future than in current conditions, but the weight and length of the thalli which survived was respectively 267% and 178% higher when exposed to future conditions. The relatively high tolerance to the future conditions suggests that F. radicans is likely to persist in its current distributional range, which is limited to the Gulf of Bothia and Estonian coast in the Baltic Sea. Furthermore, this species may be able to expand its distribution southward and replace its congener F. vesiculosus, which, in previous studies, has not tolerated the future conditions as well. In addition, we discovered variation in tolerance to future conditions within one of the clonal lineages, which have been hitherto presumed to lack adaptive variation. The discovery of intra-clonal phenotypic plasticity means that this alga has the potential for adaptive responses to climate change, which may be the key to the future persistence of F. radicans in the Baltic Sea.
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Affiliation(s)
- Luca Rugiu
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
| | - Iita Manninen
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
| | - Eva Rothäusler
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
| | - Veijo Jormalainen
- Section of Ecology, Department of Biology, University of Turku, FIN-20014, Turku, Finland
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