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Aurelle D, Thomas S, Albert C, Bally M, Bondeau A, Boudouresque C, Cahill AE, Carlotti F, Chenuil A, Cramer W, Davi H, De Jode A, Ereskovsky A, Farnet A, Fernandez C, Gauquelin T, Mirleau P, Monnet A, Prévosto B, Rossi V, Sartoretto S, Van Wambeke F, Fady B. Biodiversity, climate change, and adaptation in the Mediterranean. Ecosphere 2022. [DOI: 10.1002/ecs2.3915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS Sorbonne Université, EPHE Paris France
| | - Séverine Thomas
- Aix Marseille Université, Labex‐OT‐Med Aix‐en‐Provence France
| | - Cécile Albert
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Marc Bally
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Alberte Bondeau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - François Carlotti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Wolfgang Cramer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Hendrik Davi
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
| | - Aurélien De Jode
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Department of Marine Sciences‐Tjärnö University of Gothenburg, Tjärnö Marine Laboratory Gothenburg Sweden
| | - Alexander Ereskovsky
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Saint‐Petersburg State University St. Petersburg Russia
| | - Anne‐Marie Farnet
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | - Thierry Gauquelin
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Pascal Mirleau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - Vincent Rossi
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | | | - France Van Wambeke
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Bruno Fady
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
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Thia JA, McGuigan K, Liggins L, Figueira WF, Bird CE, Mather A, Evans JL, Riginos C. Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation. Mol Ecol 2021; 30:4392-4414. [PMID: 33544414 DOI: 10.1111/mec.15829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/12/2021] [Accepted: 01/28/2021] [Indexed: 11/28/2022]
Abstract
Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.
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Affiliation(s)
- Joshua A Thia
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia.,School of BioSciences, The University of Melbourne, Melbourne, VIC., Australia
| | - Katrina McGuigan
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Libby Liggins
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Will F Figueira
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Christopher E Bird
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, USA
| | - Andrew Mather
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Jennifer L Evans
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
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Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper ( Epinephelus tukula). BIOLOGY 2021; 10:biology10010036. [PMID: 33430356 PMCID: PMC7825770 DOI: 10.3390/biology10010036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary The potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits. Abstract The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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