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Urban L, Perlas A, Francino O, Martí‐Carreras J, Muga BA, Mwangi JW, Boykin Okalebo L, Stanton JL, Black A, Waipara N, Fontsere C, Eccles D, Urel H, Reska T, Morales HE, Palmada‐Flores M, Marques‐Bonet T, Watsa M, Libke Z, Erkenswick G, van Oosterhout C. Real-time genomics for One Health. Mol Syst Biol 2023; 19:e11686. [PMID: 37325891 PMCID: PMC10407731 DOI: 10.15252/msb.202311686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
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Affiliation(s)
- Lara Urban
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Albert Perlas
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
| | - Olga Francino
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Joan Martí‐Carreras
- Nano1Health SL, Parc de Recerca UABCampus Universitat Autònoma de BarcelonaBarcelonaSpain
| | - Brenda A Muga
- Department of AnatomyUniversity of OtagoDunedinNew Zealand
| | | | | | | | - Amanda Black
- Bioprotection AotearoaLincoln UniversityLincolnNew Zealand
| | | | - Claudia Fontsere
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
| | - David Eccles
- Hugh Green Cytometry CentreMalaghan Institute of Medical ResearchWellingtonNew Zealand
| | - Harika Urel
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Tim Reska
- Helmholtz AI, Helmholtz Zentrum MuenchenNeuherbergGermany
- Helmholtz Pioneer Campus, Helmholtz Zentrum MuenchenNeuherbergGermany
- School of Life Sciences, Technical University of MunichFreisingGermany
| | - Hernán E Morales
- Center for Evolutionary HologenomicsThe Globe Institute, University of CopenhagenCopenhagenDenmark
- Department of Biology, Ecology BuildingLund UniversityLundSweden
| | - Marc Palmada‐Flores
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
| | - Tomas Marques‐Bonet
- Institute of Evolutionary BiologyUniversitat Pompeu Fabra‐CSIC, PRBBBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAGCentre of Genomic AnalysisBarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | | | - Zane Libke
- Instituto Nacional de BiodiversidadQuitoEcuador
- Fundación Sumak Kawsay In SituCantón MeraEcuador
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Wirgin I, Chambers RC, Waldman JR, Roy NK, Witting DA, Mattson MT. Effects of Hudson River Stressors on Atlantic Tomcod: Contaminants and a Warming Environment. REVIEWS IN FISHERIES SCIENCE & AQUACULTURE 2023; 31:342-371. [PMID: 37621745 PMCID: PMC10446889 DOI: 10.1080/23308249.2023.2189483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The Hudson River (HR) Estuary has a long history of pollution with a variety of contaminants including PCBs, and dioxins. In fact, 200 miles of the mainstem HR is designated a U.S. federal Superfund site, the largest in the nation, because of PCB contamination. The tidal HR hosts the southernmost spawning population of Atlantic tomcod, and studies revealed a correlation between exposure of juveniles to warm water temperature during summer to abundance of spawning adults of the same cohort in the following winter. Further, a battery of mechanistically linked biomarkers, ranging from the molecular to the population levels, were significantly impacted from contaminant exposures of the HR tomcod population. In response to xenobiotic insult, the HR tomcod population developed resistance to PCB sand TCDD toxicity resulting from a deletion in the aryl hydrocarbon receptor2 (AHR2) gene. Furthermore, RNA-Seq analysis of global gene expression demonstrated that effects of the AHR2 polymorphism were far more pervasive than anticipated. The most highly PCB-contaminated sediments in the upper HR were dredged between 2009 and 2015 with the objective of lowering PCB concentrations in fishes in the lower HR. Success of the remediation project has been controversial. These observations suggest that tomcod provides an informative model to evaluate the efficacy of HR PCB remediation efforts on downriver fish populations and possible interactive effects between contaminant exposure and a warming environment.
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Affiliation(s)
- Isaac Wirgin
- Department of Environmental Medicine, New York University School of Medicine, New York, New York
| | | | | | - Nirmal K Roy
- Department of Environmental Medicine, New York University School of Medicine, New York, New York
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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4
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [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: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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5
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Scharsack JP, Franke F. Temperature effects on teleost immunity in the light of climate change. JOURNAL OF FISH BIOLOGY 2022; 101:780-796. [PMID: 35833710 DOI: 10.1111/jfb.15163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Temperature is an important environmental modulator of teleost immune activity. Susceptibility of teleosts to temperature variation depends on the species-specific adaptive temperature range, and the activity of the teleost immune system is generally temperature-dependent. Similar to many physiological and metabolic traits of ectotherms, temperature modulates the activity of immune traits. At low temperatures, acquired immunity of many teleost species is down-modulated, and their immuno-competence mainly depends on innate immunity. At intermediate temperatures, both innate and acquired immunity are fully active and provide optimal protection, including long-lasting immunological memory. When temperatures increase and reach the upper permissive range, teleost immunity is compromised. Moreover, temperature shifts may have negative effects on teleost immune functions, in particular if shifts occur rapidly with high amplitudes. On the contrary, short-term temperature increase may help teleost immunity to fight against pathogens transiently. A major challenge to teleosts therefore is to maintain immuno-competence throughout the temperature range they are exposed to. Climate change coincides with rising temperatures, and more frequent and more extreme temperature shifts. Both are likely to influence the immuno-competence of teleosts. Nonetheless, teleosts exist in habitats that differ substantially in temperature, ranging from below zero in the Arctic's to above 40°C in warm springs, illustrating their enormous potential to adapt to different temperature regimes. The present review seeks to discuss how changes in temperature variation, induced by climate change, might influence teleost immunity.
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Affiliation(s)
- Jörn Peter Scharsack
- Department for Fish Diseases, Thuenen-Institute of Fisheries Ecology, Bremerhaven, Germany
| | - Frederik Franke
- Bavarian State Institute of Forestry, Department of Biodiversity, Nature Protection & Wildlife Management, Freising, Germany
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6
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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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7
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Asseng S, Spänkuch D, Hernandez-Ochoa IM, Laporta J. The upper temperature thresholds of life. Lancet Planet Health 2021; 5:e378-e385. [PMID: 34119012 DOI: 10.1016/s2542-5196(21)00079-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/21/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Temperature affects many life processes, but its effect might be expected to differ among eukaryotic organisms inhabiting similar environments. We reviewed literature on temperature thresholds of humans, livestock, poultry, agricultural crops, and sparse examples of fisheries. We found that preferable and harmful temperatures are similar for humans, cattle, pigs, poultry, fish, and agricultural crops. Preferable temperatures range from 17°C to 24°C. Stress temperature thresholds are lower when humidity is higher. However, extended exposure to temperatures above 25°C with high humidity can cause heat stress in many organisms. Short exposures to temperatures above 35°C with high humidity, or above 40°C with low humidity, can be lethal. Increases in exposure, frequency, and duration of stressful and lethal temperatures increase the physiological stress and bodily damage suffered by humans, livestock, poultry, fish, and agricultural crops.
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Affiliation(s)
- Senthold Asseng
- Department of Life Science Engineering, Technical University of Munich, Freising, Germany.
| | | | - Ixchel M Hernandez-Ochoa
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Jimena Laporta
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
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8
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Ocampo Daza D, Bergqvist CA, Larhammar D. The Evolution of Oxytocin and Vasotocin Receptor Genes in Jawed Vertebrates: A Clear Case for Gene Duplications Through Ancestral Whole-Genome Duplications. Front Endocrinol (Lausanne) 2021; 12:792644. [PMID: 35185783 PMCID: PMC8851675 DOI: 10.3389/fendo.2021.792644] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/22/2021] [Indexed: 12/02/2022] Open
Abstract
The neuronal and neuroendocrine peptides oxytocin (OT) and vasotocin (VT), including vasopressins, have six cognate receptors encoded by six receptor subtype genes in jawed vertebrates. The peptides elicit a broad range of responses that are specifically mediated by the receptor subtypes including neuronal functions regulating behavior and hormonal actions on reproduction and water/electrolyte balance. Previously, we have demonstrated that these six receptor subtype genes, which we designated VTR1A, VTR1B, OTR, VTR2A, VTR2B and VTR2C, arose from a syntenic ancestral gene pair, one VTR1/OTR ancestor and one VTR2 ancestor, through the early vertebrate whole-genome duplications (WGD) called 1R and 2R. This was supported by both phylogenetic and chromosomal conserved synteny data. More recently, other studies have focused on confounding factors, such as the OTR/VTR orthologs in cyclostomes, to question this scenario for the origin of the OTR/VTR gene family; proposing instead less parsimonious interpretations involving only one WGD followed by complex series of chromosomal or segmental duplications. Here, we have updated the phylogeny of the OTR/VTR gene family, including a larger number of vertebrate species, and revisited seven representative neighboring gene families from our previous conserved synteny analyses, adding chromosomal information from newer high-coverage genome assemblies from species that occupy key phylogenetic positions: the polypteriform fish reedfish (Erpetoichthys calabaricus), the cartilaginous fish thorny skate (Amblyraja radiata) and a more recent high-quality assembly of the Western clawed frog (Xenopus tropicalis) genome. Our analyses once again add strong support for four-fold symmetry, i.e., chromosome quadruplication in the same time window as the WGD events early in vertebrate evolution, prior to the jawed vertebrate radiation. Thus, the evolution of the OTR/VTR gene family can be most parsimoniously explained by two WGD events giving rise to the six ancestral genes, followed by differential gene losses of VTR2 genes in different lineages. We also argue for more coherence and clarity in the nomenclature of OT/VT receptors, based on the most parsimonious scenario.
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Affiliation(s)
- Daniel Ocampo Daza
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA, United States
| | - Christina A. Bergqvist
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- *Correspondence: Dan Larhammar,
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9
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Smith CH, Johnson NA, Havlik K, Doyle RD, Randklev CR. Resolving species boundaries in the critically imperiled freshwater mussel species,
Fusconaia mitchelli
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department Baylor University Waco TX USA
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
- Department of Integrative Biology University of Texas Austin TX USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville FL USA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
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10
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Fé-Gonçalves LM, Araújo JDA, Santos CHDAD, Val AL, Almeida-Val VMFD. How will farmed populations of freshwater fish deal with the extreme climate scenario in 2100? Transcriptional responses of Colossoma macropomum from two Brazilian climate regions. J Therm Biol 2020; 89:102487. [PMID: 32364997 DOI: 10.1016/j.jtherbio.2019.102487] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/29/2019] [Accepted: 12/22/2019] [Indexed: 12/27/2022]
Abstract
Tambaqui (Colossoma macropomum Cuvier, 1818) is an endemic fish of the Amazon and Orinoco basins, and it is the most economically important native species in Brazil being raised in five climatically distinct regions. In the face of current global warming, environmental variations in farm ponds represent additional challenges that may drive new adaptive regional genetic variations among broodstocks of tambaqui. In an experimental context based on the high-emission scenario of the 5th Intergovernmental Panel on Climate Change (IPCC) report, we used two farmed tambaqui populations to test this hypothesis. RNA-seq transcriptome analysis was performed in the liver of juvenile tambaqui from northern (Balbina Experimental Station, Balbina, AM) and southeastern (Brumado Fish Farming, Mogi Mirim, SP) Brazilian regions kept for 30 days in artificial environmental rooms mimicking the current and extreme climate scenarios. Three Illumina MiSeq runs produced close to 120 million 500 bp paired-end reads; 191,139 contigs were assembled with N50 = 1595. 355 genes were differentially expressed for both populations in response to the extreme scenario. After enrichment analysis, each population presented a core set of genes to cope with climate change. Northern fish induced genes related to the cellular response to stress, activation of MAPK activity, response to unfolded protein, protein metabolism and cellular response to DNA damage stimuli. Genes biologically involved in regulating cell proliferation, protein stabilisation and protein ubiquitination for degradation through the ubiquitin-proteasome system were downregulated. Genes associated with biological processes, including the cellular response to stress, MAPK cascade activation, homeostatic processes and positive regulation of immune responses were upregulated in southeastern fish. The downregulated genes were related to cytoskeleton organisation, energy metabolism, and the regulation of transcription and biological rhythms. Our findings reveal the signatures of promising candidate genes involved in the regional plasticity of each population of tambaqui in dealing with upcoming climate changes.
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Affiliation(s)
- Luciana Mara Fé-Gonçalves
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil.
| | - José Deney Alves Araújo
- Computational Systems Biology Laboratory, University of São Paulo, Professor Lúcio Martins Rodrigues Avenue, 370, 05508020, Butantã, São Paulo, SP, Brazil
| | - Carlos Henrique Dos Anjos Dos Santos
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil
| | - Adalberto Luis Val
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil
| | - Vera Maria Fonseca de Almeida-Val
- Laboratory of Ecophysiology and Molecular Evolution, Brazilian National Institute for Research of the Amazon, André Araújo Avenue, 2936, 69067-375, Petrópolis, Manaus, AM, Brazil
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11
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Jeremias G, Gonçalves FJM, Pereira JL, Asselman J. Prospects for incorporation of epigenetic biomarkers in human health and environmental risk assessment of chemicals. Biol Rev Camb Philos Soc 2020; 95:822-846. [PMID: 32045110 DOI: 10.1111/brv.12589] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic mechanisms have gained relevance in human health and environmental studies, due to their pivotal role in disease, gene × environment interactions and adaptation to environmental change and/or contamination. Epigenetic mechanisms are highly responsive to external stimuli and a wide range of chemicals has been shown to determine specific epigenetic patterns in several organisms. Furthermore, the mitotic/meiotic inheritance of such epigenetic marks as well as the resulting changes in gene expression and cell/organismal phenotypes has now been demonstrated. Therefore, epigenetic signatures are interesting candidates for linking environmental exposures to disease as well as informing on past exposures to stressors. Accordingly, epigenetic biomarkers could be useful tools in both prospective and retrospective risk assessment but epigenetic endpoints are currently not yet incorporated into risk assessments. Achieving a better understanding on this apparent impasse, as well as identifying routes to promote the application of epigenetic biomarkers within environmental risk assessment frameworks are the objectives of this review. We first compile evidence from human health studies supporting the use of epigenetic exposure-associated changes as reliable biomarkers of exposure. Then, specifically focusing on environmental science, we examine the potential and challenges of developing epigenetic biomarkers for environmental fields, and discuss useful organisms and appropriate sequencing techniques to foster their development in this context. Finally, we discuss the practical incorporation of epigenetic biomarkers in the environmental risk assessment of chemicals, highlighting critical data gaps and making key recommendations for future research within a regulatory context.
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Affiliation(s)
- Guilherme Jeremias
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Fernando J M Gonçalves
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Joana L Pereira
- Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.,CESAM - Centre for Environmental and Marine Studies, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jana Asselman
- Laboratory of Environmental Toxicology and Aquatic Ecology, Environmental Toxicology Unit - GhEnToxLab, Ghent University, 9000, Gent, Belgium
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12
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Sandoval-Castillo J. Conservation genetics of elasmobranchs of the Mexican Pacific Coast, trends and perspectives. ADVANCES IN MARINE BIOLOGY 2019; 83:115-157. [PMID: 31606069 DOI: 10.1016/bs.amb.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the most critical threats to biodiversity is the high extinction rate driven by human activities. Reducing extinction rates requires the implementation of conservation programmes based on robust scientific data. Elasmobranchs are important ecological components of the ocean, and several species sustain substantial economic activities. Unfortunately, elasmobranchs are one of the most threatened and understudied animal taxa. The Mexican Pacific Coast (MPC) is a region with high elasmobranch diversity and is the seat of major elasmobranch fisheries. But it is also a developing region with several conservation and management challenges which require national and international attention. Here, we review the conservation genetics literature of elasmobranchs from the MPC. We present a synthesis of the works using samples from the region and emphasize the main gaps and biases in these data. In addition, we discuss the benefits and challenges of generating genomic information to improve the management and conservation of an elasmobranch biodiversity hotspot in a developing country. We found 47 elasmobranch genetic articles that cover <30% of the elasmobranch diversity in the region. These studies mainly used mitochondrial DNA sequences to analyse the genetic structure of commercially important and abundant species of the order Carcharhiniformes. Some of these papers also assessed mating systems, demographic parameters, and taxonomic uncertainties, all of which are important topics for efficient management decisions. In terms of conservation genetics, elasmobranchs from the MPC remain understudied. However, high-throughput sequencing technologies have increased the power and accessibility of genomic tools, even in developing countries such as Mexico. The tools described here provide information relevant for biodiversity conservation. Therefore, we strongly suggest that investment in genomic research will assist implementation of efficient management strategies. In time, this will reduce the extinction risk of the unique elasmobranch biodiversity from the MPC.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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13
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Swain DP, Benoît HP, Hammill MO, Sulikowski JA. Risk of extinction of a unique skate population due to predation by a recovering marine mammal. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01921. [PMID: 31059188 DOI: 10.1002/eap.1921] [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: 05/22/2018] [Revised: 01/02/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Benefitting from reduced harvesting and an end to culling, many marine mammals are now recovering from past overexploitation. These recoveries represent important conservation successes but present a serious conservation problem when the recovering mammals are predators of species of conservation concern. Here, we examine the role of predation by recovering grey seals (Halichoerus grypus) in the near-extinction of a unique skate population in the southern Gulf of St. Lawrence (sGSL) in Atlantic Canada. Winter skate (Leucoraja ocellata) in the sGSL are distinct from winter skate elsewhere and may represent an endemic species. Their adult abundance has declined by 98% since 1980, and these skates are now detectable in only a small fraction of their former range. Population modeling indicates that the ongoing collapse of this population is due to increases in the natural mortality of adults. Based on model projections, this population would be extinct by mid-century if its current rate of productivity were to persist. A second population model incorporated predation by grey seals. Model estimates of skate consumption by seals were consistent with historical and recent estimates of the contribution of skates to grey seal diets. The estimated consumption accounted for the increases in the natural mortality of adult skates. A Type III functional response for grey seals preying on winter skate emerged from the model results. This indicates that, when skate abundance is very low, grey seals are expected to switch to alternate prey, resulting in declines in the mortality of skates due to predation. Consequently, contrary to projections at current productivity, winter skate are expected to be trapped at very low abundance in a "predator pit" instead of declining to extinction. Nonetheless, extinction risk would remain very high at the very small population size in the predator pit. Our results emphasize the need for an ecosystem-based approach to the management of living resources in this ecosystem.
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Affiliation(s)
- Douglas P Swain
- Gulf Fisheries Centre, Fisheries and Oceans Canada, P.O. Box 5030, Moncton, New Brunswick, E1C 9B6, Canada
| | - Hugues P Benoît
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, Mont-Joli, Quebec, G5H 3Z4, Canada
| | - Mike O Hammill
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, Mont-Joli, Quebec, G5H 3Z4, Canada
| | - James A Sulikowski
- Arthur P. Girard Marine Science Department, University of New England, 11 Hills Beach Road, Biddeford, Maine, 04005, USA
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O'Connell KA, Santo VD, Maldonado J, Molina E, Fujita MK. A Tale of Two Skates: Comparative Phylogeography of North American Skate Species with Implications for Conservation. COPEIA 2019. [DOI: 10.1643/cg-18-114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Kyle A. O'Connell
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Valentina Di Santo
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138
| | - Jose Maldonado
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Erika Molina
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
| | - Matthew K. Fujita
- Department of Biology and Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, Texas 76019; (KAO) ; (JM) ; and (MKF) . Send reprint request
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15
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Lyons K, Bigman JS, Kacev D, Mull CG, Carlisle AB, Imhoff JL, Anderson JM, Weng KC, Galloway AS, Cave E, Gunn TR, Lowe CG, Brill RW, Bedore CN. Bridging disciplines to advance elasmobranch conservation: applications of physiological ecology. CONSERVATION PHYSIOLOGY 2019; 7:coz011. [PMID: 31110763 PMCID: PMC6519003 DOI: 10.1093/conphys/coz011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/02/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
A strength of physiological ecology is its incorporation of aspects of both species' ecology and physiology; this holistic approach is needed to address current and future anthropogenic stressors affecting elasmobranch fishes that range from overexploitation to the effects of climate change. For example, physiology is one of several key determinants of an organism's ecological niche (along with evolutionary constraints and ecological interactions). The fundamental role of physiology in niche determination led to the development of the field of physiological ecology. This approach considers physiological mechanisms in the context of the environment to understand mechanistic variations that beget ecological trends. Physiological ecology, as an integrative discipline, has recently experienced a resurgence with respect to conservation applications, largely in conjunction with technological advances that extended physiological work from the lab into the natural world. This is of critical importance for species such as elasmobranchs (sharks, skates and rays), which are an especially understudied and threatened group of vertebrates. In 2017, at the American Elasmobranch Society meeting in Austin, Texas, the symposium entitled `Applications of Physiological Ecology in Elasmobranch Research' provided a platform for researchers to showcase work in which ecological questions were examined through a physiological lens. Here, we highlight the research presented at this symposium, which emphasized the strength of linking physiological tools with ecological questions. We also demonstrate the applicability of using physiological ecology research as a method to approach conservation issues, and advocate for a more available framework whereby results are more easily accessible for their implementation into management practices.
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Affiliation(s)
- K Lyons
- Georgia Aquarium, Atlanta, GA, USA
| | - J S Bigman
- Simon Fraser University, Burnaby, Canada
| | - D Kacev
- Southwest Fisheries Science Center, La Jolla, CA, USA
| | - C G Mull
- Simon Fraser University, Burnaby, Canada
| | | | - J L Imhoff
- Florida State University Coastal and Marine Laboratory, St. Teresa, FL, USA
| | - J M Anderson
- University of Hawai`i at Mānoa, Honolulu, HI, USA
| | - K C Weng
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - A S Galloway
- South Carolina Department of Natural Resources, SC, USA
| | - E Cave
- Florida Atlantic University, Boca Raton, FL, USA
| | - T R Gunn
- Georgia Southern University, Statesboro, GA USA
| | - C G Lowe
- California State University Long Beach, Long Beach, CA, USA
| | - R W Brill
- Virginia Institute of Marine Science, Gloucester Point, VA, USA
| | - C N Bedore
- Georgia Southern University, Statesboro, GA USA
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16
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Redmond AK, Macqueen DJ, Dooley H. Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets. BMC Evol Biol 2018; 18:169. [PMID: 30442091 PMCID: PMC6238376 DOI: 10.1186/s12862-018-1290-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The cartilaginous fishes diverged from other jawed vertebrates ~ 450 million years ago (mya). Despite this key evolutionary position, the only high-quality cartilaginous fish genome available is for the elephant shark (Callorhinchus milii), a chimaera whose ancestors split from the elasmobranch lineage ~ 420 mya. Initial analysis of this resource led to proposals that key components of the cartilaginous fish adaptive immune system, most notably their array of T cell subsets, was primitive compared to mammals. This proposal is at odds with the robust, antigen-specific antibody responses reported in elasmobranchs following immunization. To explore this discrepancy, we generated a multi-tissue transcriptome for small-spotted catshark (Scyliorhinus canicula), a tractable elasmobranch model for functional studies. We searched this, and other newly available sequence datasets, for CD4+ T cell subset-defining genes, aiming to confirm the presence or absence of each subset in cartilaginous fishes. RESULTS We generated a new transcriptome based on a normalised, multi-tissue RNA pool, aiming to maximise representation of tissue-specific and lowly expressed genes. We utilized multiple transcriptomic datasets and assembly variants in phylogenetic reconstructions to unambiguously identify several T cell subset-specific molecules in cartilaginous fishes for the first time, including interleukins, interleukin receptors, and key transcription factors. Our results reveal the inability of standard phylogenetic reconstruction approaches to capture the site-specific evolutionary processes of fast-evolving immune genes but show that site-heterogeneous mixture models can adequately do so. CONCLUSIONS Our analyses reveal that cartilaginous fishes are capable of producing a range of CD4+ T cell subsets comparable to that of mammals. Further, that the key molecules required for the differentiation and functioning of these subsets existed in the jawed vertebrate ancestor. Additionally, we highlight the importance of considering phylogenetic diversity and, where possible, utilizing multiple datasets for individual species, to accurately infer gene presence or absence at higher taxonomic levels.
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Affiliation(s)
- Anthony K Redmond
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- Centre for Genome-Enabled Biology & Medicine, University of Aberdeen, Aberdeen, AB24 2TZ, UK
- Present address: Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Daniel J Macqueen
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Helen Dooley
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Institute of Marine & Environmental Technology, 701 E Pratt St, Baltimore, MD21202, USA.
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17
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Bernal MA, Donelson JM, Veilleux HD, Ryu T, Munday PL, Ravasi T. Phenotypic and molecular consequences of stepwise temperature increase across generations in a coral reef fish. Mol Ecol 2018; 27:4516-4528. [PMID: 30267545 DOI: 10.1111/mec.14884] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 09/04/2018] [Accepted: 09/14/2018] [Indexed: 12/12/2022]
Abstract
Global warming will have far-reaching consequences for marine species over coming decades, yet the magnitude of these effects may depend on the rate of warming across generations. Recent experiments show coral reef fishes can compensate the metabolic challenges of elevated temperature when warm conditions are maintained across generations. However, the effects of a gradual temperature increase across generations remain unknown. In the present study, we analysed metabolic and molecular traits in the damselfish Acanthochromis polyacanthus that were exposed to +1.5°C in the first generation and +3.0°C in the second (Step +3.0°C). This treatment of stepwise warming was compared to fish reared at current-day temperatures (Control), second-generation fish of control parents reared at +3.0°C (Developmental +3.0°C) and fish exposed to elevated temperatures for two generations (Transgenerational +1.5°C and Transgenerational +3.0°C). Hepatosomatic index, oxygen consumption and liver gene expression were compared in second-generation fish of the multiple treatments. Hepatosomatic index increased in fish that developed at +3.0°C, regardless of the parental temperature. Routine oxygen consumption of Step +3.0°C fish was significantly higher than Control; however, their aerobic scope recovered to the same level as Control fish. Step +3.0°C fish exhibited significant upregulation of genes related to mitochondrial activity and energy production, which could be associated with their increased metabolic rates. These results indicate that restoration of aerobic scope is possible when fish experience gradual thermal increase across multiple generations, but the metabolic and molecular responses are different from fish reared at the same elevated thermal conditions in successive generations.
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Affiliation(s)
- Moisés A Bernal
- KAUST Environmental Epigenetics Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Jennifer M Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Heather D Veilleux
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Taewoo Ryu
- APEC Climate Center (APCC), Busan, Republic of Korea
| | - Philip L Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Timothy Ravasi
- KAUST Environmental Epigenetics Program (KEEP), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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18
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Jeremias G, Barbosa J, Marques SM, Asselman J, Gonçalves FJM, Pereira JL. Synthesizing the role of epigenetics in the response and adaptation of species to climate change in freshwater ecosystems. Mol Ecol 2018; 27:2790-2806. [DOI: 10.1111/mec.14727] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 12/23/2022]
Affiliation(s)
| | - João Barbosa
- Department of Biology; University of Aveiro; Aveiro Portugal
| | - Sérgio M. Marques
- Department of Biology; University of Aveiro; Aveiro Portugal
- CESAM - Centre for Environmental and Marine Studies; University of Aveiro; Aveiro Portugal
| | - Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology (GhEnToxLab); Ghent University; Ghent Belgium
| | - Fernando J. M. Gonçalves
- Department of Biology; University of Aveiro; Aveiro Portugal
- CESAM - Centre for Environmental and Marine Studies; University of Aveiro; Aveiro Portugal
| | - Joana L. Pereira
- Department of Biology; University of Aveiro; Aveiro Portugal
- CESAM - Centre for Environmental and Marine Studies; University of Aveiro; Aveiro Portugal
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19
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Mothersill C, Abend M, Bréchignac F, Iliakis G, Impens N, Kadhim M, Møller AP, Oughton D, Powathil G, Saenen E, Seymour C, Sutcliffe J, Tang FR, Schofield PN. When a duck is not a duck; a new interdisciplinary synthesis for environmental radiation protection. ENVIRONMENTAL RESEARCH 2018; 162:318-324. [PMID: 29407763 DOI: 10.1016/j.envres.2018.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
This consensus paper presents the results of a workshop held in Essen, Germany in September 2017, called to examine critically the current approach to radiological environmental protection. The meeting brought together participants from the field of low dose radiobiology and those working in radioecology. Both groups have a common aim of identifying radiation exposures and protecting populations and individuals from harmful effects of ionising radiation exposure, but rarely work closely together. A key question in radiobiology is to understand mechanisms triggered by low doses or dose rates, leading to adverse outcomes of individuals while in radioecology a key objective is to recognise when harm is occurring at the level of the ecosystem. The discussion provided a total of six strategic recommendations which would help to address these questions.
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Affiliation(s)
- Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Michael Abend
- Bundeswehr Institute of Radiobiology, Neuherbergstr. 11, 80937 Munich, Germany.
| | - François Bréchignac
- Institute for Radioprotection and Nuclear Safety (IRSN) & International Union of Radioecology (IUR), Centre du Cadarache, Bldg 229, St Paul-lez-Durance, France.
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen, Medical School, Hufeland Str. 55, 45122 Essen, Germany.
| | - Nathalie Impens
- Institute of Environment, Health and Safety, Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium.
| | - Munira Kadhim
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
| | - Anders Pape Møller
- Ecologie Systématique Evolution, Equipe Diversité, Ecologie et Evolution Microbiennes Université Paris-Sud, CNRS, and AgroParisTech, Université Paris-Saclay, F-91405 Orsay Cedex, France.
| | - Deborah Oughton
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Campus Ås, Universitetstunet 3, 1432 Ås, Norway.
| | - Gibin Powathil
- Department of Mathematics, College of Science, Swansea University, Singleton Park, Swansea Wales SA2 8PP, UK.
| | - Eline Saenen
- Institute of Environment, Health and Safety, Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium.
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Jill Sutcliffe
- Low Level Radiation and Health Group, Ingrams Farm Fittleworth Road, Wisborough Green RH14 0JA, West Sussex, UK.
| | - Fen-Ru Tang
- National University of Singapore, Radiobiology Research Laboratory, Singapore Nuclear, Research and Safety Initiative, Singapore.
| | - Paul N Schofield
- Dept of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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20
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Larson SE, Daly-Engel TS, Phillips NM. Review of Current Conservation Genetic Analyses of Northeast Pacific Sharks. ADVANCES IN MARINE BIOLOGY 2017; 77:79-110. [PMID: 28882215 DOI: 10.1016/bs.amb.2017.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Conservation genetics is an applied science that utilizes molecular tools to help solve problems in species conservation and management. It is an interdisciplinary specialty in which scientists apply the study of genetics in conjunction with traditional ecological fieldwork and other techniques to explore molecular variation, population boundaries, and evolutionary relationships with the goal of enabling resource managers to better protect biodiversity and identify unique populations. Several shark species in the northeast Pacific (NEP) have been studied using conservation genetics techniques, which are discussed here. The primary methods employed to study population genetics of sharks have historically been nuclear microsatellites and mitochondrial (mt) DNA. These markers have been used to assess genetic diversity, mating systems, parentage, relatedness, and genetically distinct populations to inform management decisions. Novel approaches in conservation genetics, including next-generation DNA and RNA sequencing, environmental DNA (eDNA), and epigenetics are just beginning to be applied to elasmobranch evolution, physiology, and ecology. Here, we review the methods and results of past studies, explore future directions for shark conservation genetics, and discuss the implications of molecular research and techniques for the long-term management of shark populations in the NEP.
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Affiliation(s)
| | | | - Nicole M Phillips
- The University of Southern Mississippi, Hattiesburg, MS, United States
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21
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Burgerhout E, Mommens M, Johnsen H, Aunsmo A, Santi N, Andersen Ø. Genetic background and embryonic temperature affect DNA methylation and expression of myogenin and muscle development in Atlantic salmon (Salmo salar). PLoS One 2017; 12:e0179918. [PMID: 28662198 PMCID: PMC5491062 DOI: 10.1371/journal.pone.0179918] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/06/2017] [Indexed: 12/13/2022] Open
Abstract
The development of ectothermic embryos is strongly affected by incubation temperature, and thermal imprinting of body growth and muscle phenotype has been reported in various teleost fishes. The complex epigenetic regulation of muscle development in vertebrates involves DNA methylation of the myogenin promoter. Body growth is a heritable and highly variable trait among fish populations that allows for local adaptations, but also for selective breeding. Here we studied the epigenetic effects of embryonic temperature and genetic background on body growth, muscle cellularity and myogenin expression in farmed Atlantic salmon (Salmo salar). Eggs from salmon families with either high or low estimated breeding values for body growth, referred to as Fast and Slow genotypes, were incubated at 8°C or 4°C until the embryonic 'eyed-stage' followed by rearing at the production temperature of 8°C. Rearing temperature strongly affected the growth rates, and the 8°C fish were about twice as heavy as the 4°C fish in the order Fast8>Slow8>Fast4>Slow4 prior to seawater transfer. Fast8 was the largest fish also at harvest despite strong growth compensation in the low temperature groups. Larval myogenin expression was approximately 4-6 fold higher in the Fast8 group than in the other groups and was associated with relative low DNA methylation levels, but was positively correlated with the expression levels of the DNA methyltransferase genes dnmt1, dnmt3a and dnmt3b. Juvenile Fast8 fish displayed thicker white muscle fibres than Fast4 fish, while Slow 8 and Slow 4 showed no difference in muscle cellularity. The impact of genetic background on the thermal imprinting of body growth and muscle development in Atlantic salmon suggests that epigenetic variation might play a significant role in the local adaptation to fluctuating temperatures over short evolutionary time.
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Affiliation(s)
| | | | | | | | | | - Øivind Andersen
- Nofima AS, Ås, Norway
- Department of Animal and Aquaculture Sciences, Norwegian University of Life Sciences, Ås, Norway
- * E-mail:
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