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Fortuna M, Varella ACC, Siqueira L, Soares SM, Freddo N, Nardi J, Barletto ÍP, Bertuol MZ, Barcellos LJG. Transgenerational effects of the levonorgestrel-based birth control pill in zebrafish offspring. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 110:104540. [PMID: 39173986 DOI: 10.1016/j.etap.2024.104540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
The consumption of hormone-derived medicines, such as levonorgestrel (LNG), is increasing worldwide, and its discharge into the environment reaches non-target organisms. In our previous study, we exposed the parental generation of zebrafish to environmentally relevant concentrations of LNG during the developmental phase. Subsequently, they had grown in a tank with clean water until adulthood. Now, we allowed this parental generation to reproduce to obtain F1 progeny unexposed to LGN, in order to analyze the transgenerational effects of parental LNG exposure on the survival and hatching of unexposed F1 embryos and the stress and behavior of F1 larvae. Here, we found decreased survival rates with higher LNG concentrations, providing a transgenerational effect. This highlights the environmental impact of exposure to LNG, causing damage at the individual and population level and affecting the next generation at the beginning of development, impacting qualities in the survival of the species.
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Affiliation(s)
- Milena Fortuna
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | | | - Lisiane Siqueira
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Suelen Mendonça Soares
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Natália Freddo
- Graduate Programa in Bioexperimentation, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Jéssica Nardi
- Graduate Programa in Bioexperimentation, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Ísis Piasson Barletto
- Undergraduate Course of Veterinary Medicine, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Milena Zanoello Bertuol
- Undergraduate Course of Veterinary Medicine, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Leonardo José Gil Barcellos
- Graduate Program in Pharmacology, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil; Graduate Programa in Bioexperimentation, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil; Undergraduate Course of Veterinary Medicine, University of Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil.
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2
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Yu T, Ma Z, Zhang Y. How does parental rearing patterns of children in upper primary school impact social withdrawal? A mediating effect of emotional regulation. Front Psychol 2024; 15:1382104. [PMID: 39035090 PMCID: PMC11258026 DOI: 10.3389/fpsyg.2024.1382104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024] Open
Abstract
Introduction The present study endeavors to elucidate the impact of emotional regulation and parental rearing patterns on the social development of children in the upper grades of primary school. A burgeoning body of literature suggests that these factors significantly influence children's social adaptation and emotional well-being, yet a comprehensive examination of these relationships is warranted. Methods Employing a cross-sectional design, this investigation utilized the Egna Minnen Beträffande Uppfostran (EMBU), Emotional Regulation Questionnaire for Children (ERQC), and Child Behavioural Issues Scale (CBCL) to assess a sample of 276 pupils across grades 4-6. The selection of these instruments allowed for a multifaceted evaluation of the constructs of interest. Results A pronounced disparity in parental rearing practices, emotional regulation capabilities, and levels of social withdrawal was observed among the different grades, with grade 5 exhibiting the most pronounced effects. Parental emotional warmth demonstrated a significant positive correlation with children's emotional regulation abilities, while punitive, rejecting, and preferential behaviors were inversely correlated. The study established that parental rearing practices indirectly influence social withdrawal through the mediating role of children's emotional regulation, underscoring the complexity of this relationship. Conclusion The results underscore the salient role of parental rearing and emotional regulation in the social development of children. The study contributes to the existing literature by providing a nuanced understanding of the mechanisms through which parenting styles and emotional competencies interplay to affect social withdrawal. Implications for educational practices and future research directions are discussed.
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Affiliation(s)
- Tao Yu
- School of Educational Science, Shenyang Normal University, Shenyang, China
| | - Zhengyu Ma
- Shenyang Seventh Middle School, Shenyang, China
| | - Yu Zhang
- School of Art and Information Engineering, Dalian University of Technology, Dalian, China
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3
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Anka IZ, Uren Webster TM, Berbel-Filho WM, Hitchings M, Overland B, Weller S, Garcia de Leaniz C, Consuegra S. Microbiome and epigenetic variation in wild fish with low genetic diversity. Nat Commun 2024; 15:4725. [PMID: 38830879 PMCID: PMC11148108 DOI: 10.1038/s41467-024-49162-8] [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: 05/11/2023] [Accepted: 05/23/2024] [Indexed: 06/05/2024] Open
Abstract
Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.
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Affiliation(s)
- Ishrat Z Anka
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Department of Aquaculture, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Tamsyn M Uren Webster
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Waldir M Berbel-Filho
- Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Biology, University of West Florida, Pensacola, FL, USA
| | - Matthew Hitchings
- Institute of Life Science, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Benjamin Overland
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Sarah Weller
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Carlos Garcia de Leaniz
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Marine Research Centre (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Sofia Consuegra
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK.
- Grupo de Biotecnología Acuática, Departamento de Biotecnología y Acuicultura, Instituto de Investigacións Mariñas, IIM-CSIC, Vigo, Spain.
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4
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Venney CJ, Mérot C, Normandeau E, Rougeux C, Laporte M, Bernatchez L. Epigenetic and Genetic Differentiation Between Coregonus Species Pairs. Genome Biol Evol 2024; 16:evae013. [PMID: 38271269 PMCID: PMC10849188 DOI: 10.1093/gbe/evae013] [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: 07/06/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental conditions for many generations, though there has been minimal empirical research on epigenetically induced mutagenesis in diversification and speciation. Whitefish, freshwater members of the salmonid family, are excellent systems to study phenotypic diversification and speciation due to the repeated divergence of benthic-limnetic species pairs serving as natural replicates. Here we investigate whole genome genetic and epigenetic differentiation between sympatric benthic-limnetic species pairs in lake and European whitefish (Coregonus clupeaformis and Coregonus lavaretus) from four lakes (N = 64). We found considerable, albeit variable, genetic and epigenetic differences between species pairs. All SNP types were enriched at CpG sites supporting the mutagenic nature of DNA methylation, though C>T SNPs were most common. We also found an enrichment of overlaps between outlier SNPs with the 5% highest FST between species and differentially methylated loci. This could possibly represent differentially methylated sites that have caused divergent genetic mutations between species, or divergent selection leading to both genetic and epigenetic variation at these sites. Our results support the hypothesis that DNA methylation contributes to phenotypic divergence and mutagenesis during whitefish speciation.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Clément Rougeux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Ministère des Forêts, de la Faune et des Parcs (MFFP), Québec, Québec, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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Clark FE, Greggor AL, Montgomery SH, Plotnik JM. The endangered brain: actively preserving ex-situ animal behaviour and cognition will benefit in-situ conservation. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230707. [PMID: 37650055 PMCID: PMC10465207 DOI: 10.1098/rsos.230707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Endangered species have small, unsustainable population sizes that are geographically or genetically restricted. Ex-situ conservation programmes are therefore faced with the challenge of breeding sufficiently sized, genetically diverse populations earmarked for reintroduction that have the behavioural skills to survive and breed in the wild. Yet, maintaining historically beneficial behaviours may be insufficient, as research continues to suggest that certain cognitive-behavioural skills and flexibility are necessary to cope with human-induced rapid environmental change (HIREC). This paper begins by reviewing interdisciplinary studies on the 'captivity effect' in laboratory, farmed, domesticated and feral vertebrates and finds that captivity imposes rapid yet often reversible changes to the brain, cognition and behaviour. However, research on this effect in ex-situ conservation sites is lacking. This paper reveals an apparent mismatch between ex-situ enrichment aims and the cognitive-behavioural skills possessed by animals currently coping with HIREC. After synthesizing literature across neuroscience, behavioural biology, comparative cognition and field conservation, it seems that ex-situ endangered species deemed for reintroduction may have better chances of coping with HIREC if their natural cognition and behavioural repertoires are actively preserved. Evaluating the effects of environmental challenges rather than captivity per se is recommended, in addition to using targeted cognitive enrichment.
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Affiliation(s)
- Fay E. Clark
- School of Psychological Science, University of Bristol, Bristol, UK
| | | | | | - Joshua M. Plotnik
- Department of Psychology, Hunter College, City University of New York, New York, NY, USA
- Department of Psychology, The Graduate Center, City University of New York, New York, NY, USA
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6
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van Oers K, van den Heuvel K, Sepers B. The Epigenetics of Animal Personality. Neurosci Biobehav Rev 2023; 150:105194. [PMID: 37094740 DOI: 10.1016/j.neubiorev.2023.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
Animal personality, consistent individual differences in behaviour, is an important concept for understanding how individuals vary in how they cope with environmental challenges. In order to understand the evolutionary significance of animal personality, it is crucial to understand the underlying regulatory mechanisms. Epigenetic marks such as DNA methylation are hypothesised to play a major role in explaining variation in phenotypic changes in response to environmental alterations. Several characteristics of DNA methylation also align well with the concept of animal personality. In this review paper, we summarise the current literature on the role that molecular epigenetic mechanisms may have in explaining personality variation. We elaborate on the potential for epigenetic mechanisms to explain behavioural variation, behavioural development and temporal consistency in behaviour. We then suggest future routes for this emerging field and point to potential pitfalls that may be encountered. We conclude that a more inclusive approach is needed for studying the epigenetics of animal personality and that epigenetic mechanisms cannot be studied without considering the genetic background.
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Affiliation(s)
- Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands.
| | - Krista van den Heuvel
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
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7
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Venney CJ, Bouchard R, April J, Normandeau E, Lecomte L, Côté G, Bernatchez L. Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: Sex-specificity and intergenerational stability. Mol Ecol Resour 2023. [PMID: 36760032 DOI: 10.1111/1755-0998.13766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/20/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning and potential for transmission to future generations. Here we performed whole genome methylation sequencing of fin tissue for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec, Canada. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing can be minimal in F0 . There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are rather complex and the field would benefit from further research on minimizing the epigenetic effects of captive rearing in conservation efforts.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Raphaël Bouchard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Julien April
- Direction de l'expertise sur la faune aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Quebec, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Laurie Lecomte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Guillaume Côté
- Direction de l'expertise sur la faune aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Quebec, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
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8
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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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9
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Green MR, Swaney WT. Interacting effects of environmental enrichment across multiple generations on early life phenotypes in zebrafish. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B: MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022. [DOI: 10.1002/jez.b.23184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Michael R. Green
- School of Biological and Environmental Sciences Liverpool John Moores University Liverpool UK
- Chester Medical School University of Chester Chester UK
| | - William T. Swaney
- School of Biological and Environmental Sciences Liverpool John Moores University Liverpool UK
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10
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Lattin CR, Kelly TR, Kelly MW, Johnson KM. Constitutive gene expression differs in three brain regions important for cognition in neophobic and non-neophobic house sparrows (Passer domesticus). PLoS One 2022; 17:e0267180. [PMID: 35536842 PMCID: PMC9089922 DOI: 10.1371/journal.pone.0267180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Neophobia (aversion to new objects, food, and environments) is a personality trait that affects the ability of wildlife to adapt to new challenges and opportunities. Despite the ubiquity and importance of this trait, the molecular mechanisms underlying repeatable individual differences in neophobia in wild animals are poorly understood. We evaluated wild-caught house sparrows (Passer domesticus) for neophobia in the lab using novel object tests. We then selected a subset of neophobic and non-neophobic individuals (n = 3 of each, all females) and extracted RNA from four brain regions involved in learning, memory, threat perception, and executive function: striatum, caudal dorsomedial hippocampus, medial ventral arcopallium, and caudolateral nidopallium (NCL). Our analysis of differentially expressed genes (DEGs) used 11,889 gene regions annotated in the house sparrow reference genome for which we had an average of 25.7 million mapped reads/sample. PERMANOVA identified significant effects of brain region, phenotype (neophobic vs. non-neophobic), and a brain region by phenotype interaction. Comparing neophobic and non-neophobic birds revealed constitutive differences in DEGs in three of the four brain regions examined: hippocampus (12% of the transcriptome significantly differentially expressed), striatum (4%) and NCL (3%). DEGs included important known neuroendocrine mediators of learning, memory, executive function, and anxiety behavior, including serotonin receptor 5A, dopamine receptors 1, 2 and 5 (downregulated in neophobic birds), and estrogen receptor beta (upregulated in neophobic birds). These results suggest that some of the behavioral differences between phenotypes may be due to underlying gene expression differences in the brain. The large number of DEGs in neophobic and non-neophobic birds also implies that there are major differences in neural function between the two phenotypes that could affect a wide variety of behavioral traits beyond neophobia.
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Affiliation(s)
- Christine R. Lattin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
- * E-mail:
| | - Tosha R. Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Morgan W. Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Kevin M. Johnson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
- Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, United States of America
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Venney CJ, Wellband KW, Normandeau E, Houle C, Garant D, Audet C, Bernatchez L. Thermal regime during parental sexual maturation, but not during offspring rearing, modulates DNA methylation in brook charr ( Salvelinus fontinalis). Proc Biol Sci 2022; 289:20220670. [PMID: 35506232 PMCID: PMC9065957 DOI: 10.1098/rspb.2022.0670] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 01/04/2023] Open
Abstract
Epigenetic inheritance can result in plastic responses to changing environments being faithfully transmitted to offspring. However, it remains unclear how epigenetic mechanisms such as DNA methylation can contribute to multigenerational acclimation and adaptation to environmental stressors. Brook charr (Salvelinus fontinalis), an economically important salmonid, is highly sensitive to thermal stress and is of conservation concern in the context of climate change. We studied the effects of temperature during parental sexual maturation and offspring rearing on whole-genome DNA methylation in brook charr juveniles (fry). Parents were split between warm and cold temperatures during sexual maturation, mated in controlled breeding designs, then offspring from each family were split between warm (8°C) and cold (5°C) rearing environments. Using whole-genome bisulfite sequencing, we found 188 differentially methylated regions (DMRs) due to parental maturation temperature after controlling for family structure. By contrast, offspring rearing temperature had a negligible effect on offspring methylation. Stable intergenerational inheritance of DNA methylation and minimal plasticity in progeny could result in the transmission of acclimatory epigenetic states to offspring, priming them for a warming environment. Our findings have implications pertaining to the role of intergenerational epigenetic inheritance in response to ongoing climate change.
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Affiliation(s)
- Clare J. Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
| | - Kyle W. Wellband
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
| | - Carolyne Houle
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1 K 2R1
| | - Dany Garant
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1 K 2R1
| | - Céline Audet
- Institut des sciences de la mer de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Rimouski, QC, Canada G5 L 2Z9
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada G1 V 0A6
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12
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Robaire B, Delbes G, Head JA, Marlatt VL, Martyniuk CJ, Reynaud S, Trudeau VL, Mennigen JA. A cross-species comparative approach to assessing multi- and transgenerational effects of endocrine disrupting chemicals. ENVIRONMENTAL RESEARCH 2022; 204:112063. [PMID: 34562476 DOI: 10.1016/j.envres.2021.112063] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
A wide range of chemicals have been identified as endocrine disrupting chemicals (EDCs) in vertebrate species. Most studies of EDCs have focused on exposure of both male and female adults to these chemicals; however, there is clear evidence that EDCs have dramatic effects when mature or developing gametes are exposed, and consequently are associated with in multigenerational and transgenerational effects. Several publications have reviewed such actions of EDCs in subgroups of species, e.g., fish or rodents. In this review, we take a holistic approach synthesizing knowledge of the effects of EDCs across vertebrate species, including fish, anurans, birds, and mammals, and discuss the potential mechanism(s) mediating such multi- and transgenerational effects. We also propose a series of recommendations aimed at moving the field forward in a structured and coherent manner.
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Affiliation(s)
- Bernard Robaire
- Department of Pharmacology and Therapeutics and of Obstetrics and Gynecology, McGill University, Montreal, Canada.
| | - Geraldine Delbes
- Centre Armand Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), Laval, QC, Canada
| | - Jessica A Head
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Vicki L Marlatt
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christopher J Martyniuk
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Stéphane Reynaud
- Univ. Grenoble-Alpes, Université. Savoie Mont Blanc, CNRS, LECA, Grenoble, 38000, France
| | - Vance L Trudeau
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
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13
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Monroe AA, Schunter C, Welch MJ, Munday PL, Ravasi T. Molecular basis of parental contributions to the behavioural tolerance of elevated pCO 2 in a coral reef fish. Proc Biol Sci 2021; 288:20211931. [PMID: 34875194 PMCID: PMC8651409 DOI: 10.1098/rspb.2021.1931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/15/2021] [Indexed: 12/27/2022] Open
Abstract
Knowledge of adaptive potential is crucial to predicting the impacts of ocean acidification (OA) on marine organisms. In the spiny damselfish, Acanthochromis polyacanthus, individual variation in behavioural tolerance to elevated pCO2 has been observed and is associated with offspring gene expression patterns in the brain. However, the maternal and paternal contributions of this variation are unknown. To investigate parental influence of behavioural pCO2 tolerance, we crossed pCO2-tolerant fathers with pCO2-sensitive mothers and vice versa, reared their offspring at control and elevated pCO2 levels, and compared the juveniles' brain transcriptional programme. We identified a large influence of parental phenotype on expression patterns of offspring, irrespective of environmental conditions. Circadian rhythm genes, associated with a tolerant parental phenotype, were uniquely expressed in tolerant mother offspring, while tolerant fathers had a greater role in expression of genes associated with histone binding. Expression changes in genes associated with neural plasticity were identified in both offspring types: the maternal line had a greater effect on genes related to neuron growth while paternal influence impacted the expression of synaptic development genes. Our results confirm cellular mechanisms involved in responses to varying lengths of OA exposure, while highlighting the parental phenotype's influence on offspring molecular phenotype.
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Affiliation(s)
- Alison A. Monroe
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX 78412, USA
| | - Celia Schunter
- Swire Institute of Marine Science, The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR
| | - Megan J. Welch
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Philip L. Munday
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Timothy Ravasi
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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14
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Wellband K, Roth D, Linnansaari T, Curry RA, Bernatchez L. Environment-driven reprogramming of gamete DNA methylation occurs during maturation and is transmitted intergenerationally in Atlantic Salmon. G3 (BETHESDA, MD.) 2021; 11:jkab353. [PMID: 34849830 PMCID: PMC8664423 DOI: 10.1093/g3journal/jkab353] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 02/06/2023]
Abstract
An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally induced intergenerational effects, but solely in the context of early life environmental differences. Using whole-genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Some genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.
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Affiliation(s)
- Kyle Wellband
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - David Roth
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Tommi Linnansaari
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - R Allen Curry
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
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Anastasiadi D, Venney CJ, Bernatchez L, Wellenreuther M. Epigenetic inheritance and reproductive mode in plants and animals. Trends Ecol Evol 2021; 36:1124-1140. [PMID: 34489118 DOI: 10.1016/j.tree.2021.08.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022]
Abstract
Epigenetic inheritance is another piece of the puzzle of nongenetic inheritance, although the prevalence, sources, persistence, and phenotypic consequences of heritable epigenetic marks across taxa remain unclear. We systematically reviewed over 500 studies from the past 5 years to identify trends in the frequency of epigenetic inheritance due to differences in reproductive mode and germline development. Genetic, intrinsic (e.g., disease), and extrinsic (e.g., environmental) factors were identified as sources of epigenetic inheritance, with impacts on phenotype and adaptation depending on environmental predictability. Our review shows that multigenerational persistence of epigenomic patterns is common in both plants and animals, but also highlights many knowledge gaps that remain to be filled. We provide a framework to guide future studies towards understanding the generational persistence and eco-evolutionary significance of epigenomic patterns.
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Affiliation(s)
- Dafni Anastasiadi
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, 293 Akersten St, Nelson 7010, New Zealand
| | - Clare J Venney
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Québec, QC, Canada
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, 293 Akersten St, Nelson 7010, New Zealand; School of Biological Sciences, The University of Auckland, 3A Symonds St, Auckland 1010, New Zealand.
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Layton KKS, Bradbury IR. Harnessing the power of multi-omics data for predicting climate change response. J Anim Ecol 2021; 91:1064-1072. [PMID: 34679193 DOI: 10.1111/1365-2656.13619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/11/2021] [Indexed: 01/19/2023]
Abstract
Predicting how species will respond to future climate change is of central importance in the midst of the global biodiversity crisis, and recent work has demonstrated the utility of population genomics for improving these predictions. Here, we suggest a broadening of the approach to include other types of genomic variants that play an important role in adaptation, like structural (e.g. copy number variants) and epigenetic variants (e.g. DNA methylation). These data could provide additional power for forecasting response, especially in weakly structured or panmictic species. Incorporating structural and epigenetic variation into estimates of climate change vulnerability, or maladaptation, may not only improve prediction power but also provide insight into the molecular mechanisms underpinning species' response to climate change.
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Affiliation(s)
- Kara K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Ian R Bradbury
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Canada
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Reiser S, Pohlmann DM, Blancke T, Koops U, Trautner J. Environmental enrichment during early rearing provokes epigenetic changes in the brain of a salmonid fish. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100838. [PMID: 33930773 DOI: 10.1016/j.cbd.2021.100838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Environmental enrichment is used to increase structural complexity of captive rearing systems and has been shown to provoke a wide range of effects in the kept animals. Here we studied the effects of enrichment on DNA methylation patterns at the whole-genome level in the brain of rainbow trout reared in an aquaculture setting. We investigated the epigenetic effects between different types of enrichment (natural substrate vs. artificial substrate vs. barren) in three developmental stages (egg vs. alevin vs. fry) and as enrichment was discontinued at the fingerling stage by means of the Methylation-Sensitive Amplified Polymorphism (MSAP) technique. While enrichment did not affect growth in body size, we found enrichment to affected global DNA methylation in the brain at the egg and alevin stage, i.e., the period during development where the animals are in close physical contact with the substrate. At these stages, trout reared on the two substrates differed more from the control than the substrates differed from each other. Only minor differences between rearing environments were detected following emergence at the fry stage. When enrichment was discontinued during the rearing of fingerlings, no differences in DNA methylation patterns were observed between the rearing environments. Our results provide further evidence on the effects of enrichment in the captive rearing of fish and show that enrichment can even modulate epigenetic patterns. The effect on the epigenome may be causal for the previously reported effects of enrichment on gene expression, behaviour and brain development.
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Affiliation(s)
- Stefan Reiser
- Thünen Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany.
| | | | - Tina Blancke
- Thünen Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany
| | - Udo Koops
- Thünen Institute of Fisheries Ecology, Wulfsdorfer Weg 204, 22926 Ahrensburg, Germany
| | - Jochen Trautner
- Thünen Institute of Fisheries Ecology, Palmaille 9, 22767 Hamburg, Germany
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Krick MV, Desmarais E, Samaras A, Guéret E, Dimitroglou A, Pavlidis M, Tsigenopoulos C, Guinand B. Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.). BMC Genomics 2021; 22:111. [PMID: 33563212 PMCID: PMC7871408 DOI: 10.1186/s12864-021-07420-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/31/2021] [Indexed: 12/13/2022] Open
Abstract
Abstract Background In fish, minimally invasive blood sampling is widely used to monitor physiological stress with blood plasma biomarkers. As fish blood cells are nucleated, they might be a source a potential new markers derived from ‘omics technologies. We modified the epiGBS (epiGenotyping By Sequencing) technique to explore changes in genome-wide cytosine methylation in the red blood cells (RBCs) of challenged European sea bass (Dicentrarchus labrax), a species widely studied in both natural and farmed environments. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Minor changes in RBC methylome appeared to manifest after the challenge test and a family-effect was detected. Only fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-challenge individuals. Thirty-seven of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. While further investigation remains necessary, few DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, appear relevant to integrate a centrally produced stress response in RBCs. Conclusion Our modified epiGBS protocol was powerful to analyze patterns of cytosine methylation in RBCs of D. labrax and to evaluate the impact of a challenge using minimally invasive blood samples. This study is the first approximation to identify epigenetic biomarkers of exposure to stress in fish. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07420-9.
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Affiliation(s)
- Madoka Vera Krick
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France
| | - Erick Desmarais
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France
| | | | - Elise Guéret
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.,Univ. Montpellier, CNRS, INSERM, Montpellier, France.,Montpellier GenomiX, France Génomique, Montpellier, France
| | | | - Michalis Pavlidis
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Costas Tsigenopoulos
- Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 715 00, Heraklion, Greece
| | - Bruno Guinand
- UMR UM CNRS IRD EPHE ISEM- Institut des Sciences de l'Evolution de Montpellier, Montpellier, France.
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