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Venney CJ, Cayuela H, Rougeux C, Laporte M, Mérot C, Normandeau E, Leitwein M, Dorant Y, Præbel K, Kenchington E, Clément M, Sirois P, Bernatchez L. Genome-wide DNA methylation predicts environmentally driven life history variation in a marine fish. Evolution 2023; 77:186-198. [PMID: 36622671 DOI: 10.1093/evolut/qpac028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/21/2022] [Accepted: 11/16/2022] [Indexed: 01/10/2023]
Abstract
Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g., lifespan, reproduction) are still scarce, likely due to the recent application of methylome resequencing methods to non-model species. In this study, we examined associations between whole genome DNA methylation and environmentally driven life history variation in 2 lineages of a marine fish, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbor 2 contrasting life history tactics (demersal vs. beach-spawning). Performing whole genome and methylome sequencing, we showed that life history tactics are associated with epigenetic changes in both lineages, though the effect was stronger in European capelin. Genetic differentiation between the capelin harboring different life history tactics was negligible, but we found genome-wide methylation changes in both lineages. We identified 9,125 European and 199 North American differentially methylated regions (DMRs) due to life history. Gene ontology (GO) enrichment analysis for both lineages revealed an excess of terms related to neural function. Our results suggest that environmental variation causes important epigenetic changes that are associated with contrasting life history tactics in lineages with divergent genetic backgrounds, with variable importance of genetic variation in driving epigenetic variation. Our study emphasizes the potential role of genome-wide epigenetic variation in adaptation to environmental variation.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,University of Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Clément Rougeux
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Maëva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Kim Præbel
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ellen Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial University of Newfoundland, St. John's, NL, Canada.,Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Pascal Sirois
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
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Cayuela H, Dorant Y, Mérot C, Laporte M, Normandeau E, Gagnon-Harvey S, Clément M, Sirois P, Bernatchez L. Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. Mol Ecol 2021; 30:1624-1641. [PMID: 33565147 DOI: 10.1111/mec.15835] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two types of genomic variation in population genomics studies.
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Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphane Gagnon-Harvey
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Marie Clément
- Center for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, NL, Canada.,Labrador Institute of Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Pascal Sirois
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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Carrier E, Ferchaud AL, Normandeau E, Sirois P, Bernatchez L. Estimating the contribution of Greenland Halibut ( Reinhardtius hippoglossoides) stocks to nurseries by means of genotyping-by-sequencing: Sex and time matter. Evol Appl 2020; 13:2155-2167. [PMID: 33005216 PMCID: PMC7513701 DOI: 10.1111/eva.12979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/19/2020] [Accepted: 04/01/2020] [Indexed: 12/14/2022] Open
Abstract
Identification of stocks and quantification of their relative contribution to recruitment are major objectives toward improving the management and conservation of marine exploited species. Next-generation sequencing allows for thousands of genomic markers to be analyzed, which provides the resolution needed to address these questions in marine species with weakly differentiated populations. Greenland Halibut (Reinhardtius hippoglossoides) is one of the most important exploited demersal species throughout the North Atlantic, in particular in the Gulf of St. Lawrence, Canada. There, two nurseries are known, the St. Lawrence Estuary and the northern Anticosti Island, but their contribution to the renewal of stocks remains unknown. The goals of this study were (a) to document the genetic structure and (b) to estimate the contribution of the different identified breeding stocks to nurseries. We sampled 100 juveniles per nursery and 50 adults from seven sites ranging from Saguenay Fjord to offshore Newfoundland, with some sites sampled over two consecutive years in order to evaluate the temporal stability of the contribution. Our results show that after removing sex-linked markers, the Estuary/Gulf of St. Lawrence represents a single stock which is genetically distinct from the Atlantic around Newfoundland (F ST = 0.00146, p-value = .001). Population assignment showed that recruitment in both nurseries is predominantly associated with the St. Lawrence stock. However, we found that the relative contribution of both stocks to the nurseries is temporally variable with 1% contribution of the Newfoundland stock one year but up to 33% for the second year, which may be caused by year-to-year variation in larval transport into the Gulf of St. Lawrence. This study serves as a model for the identification of stocks for fisheries resources in a context where few barriers to dispersal occur, in addition to demonstrating the importance of considering sex-linked markers and temporal replicates in studies of population genomics.
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Affiliation(s)
- Emilie Carrier
- Institut de biologie intégrative et des systèmes (IBIS) Université Laval Québec City QC Canada
| | - Anne-Laure Ferchaud
- Institut de biologie intégrative et des systèmes (IBIS) Université Laval Québec City QC Canada
| | - Eric Normandeau
- Institut de biologie intégrative et des systèmes (IBIS) Université Laval Québec City QC Canada
| | - Pascal Sirois
- Département des sciences fondamentales Université du Québec à Chicoutimi Chicoutimi QC Canada
| | - Louis Bernatchez
- Institut de biologie intégrative et des systèmes (IBIS) Université Laval Québec City QC Canada
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Bone B, Davoren GK. Egg cannibalism in capelin Mallotus villosus at beach and deep-water spawning habitats in the north-west Atlantic Ocean. JOURNAL OF FISH BIOLOGY 2018; 93:641-648. [PMID: 29962094 DOI: 10.1111/jfb.13740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
We investigated egg cannibalism in spawning capelin Mallotus villosus on the north-east Newfoundland coast during July 2012-2014, specifically whether sex, spawning condition (i.e., spawning or spent) and spawning habitat influenced egg cannibalism. Capelin spawning in deep-water were 4.5-14 times more likely to be cannibals than those at the beach, probably due to the higher spatial overlap of spawners and conspecific eggs within this habitat relative to beaches. Males were 2.1-3.7 times more likely to be cannibals than females, but female cannibals had more eggs per stomach. Spawning fish were 1.6-1.9 times more likely to be cannibals than spent fish, but spent female cannibals had more eggs per stomach relative to spawning males and females in either habitat. Findings suggest that cannibalism may be an important foraging strategy, especially at deep-water spawning habitat, possibly extending the spawning season for males or increasing the probability of post-spawning survival for females. Although 44% of sampled females and 50% of males were cannibals, the estimated mortality due to egg cannibalism was low (0.49-2.97% of eggs produced annually), suggesting that egg cannibalism does not influence recruitment to a great extent in Newfoundland capelin.
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Affiliation(s)
- Bryden Bone
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gail K Davoren
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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