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King RA, Ellis CD, Bekkevold D, Ensing D, Lecointre T, Osmond DR, Piper A, Roberts DE, Launey S, Stevens JR. Leveraging the genetic diversity of trout in the rivers of the British Isles and northern France to understand the movements of sea trout ( Salmo trutta L.) around the English Channel. Evol Appl 2024; 17:e13759. [PMID: 39040811 PMCID: PMC11261213 DOI: 10.1111/eva.13759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed high-confidence assignment of known-origin individuals to region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.
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Affiliation(s)
- R. Andrew King
- Department of Biosciences, Faculty of Health and Life SciencesHatherly LaboratoriesExeterUK
| | - Charlie D. Ellis
- Department of Biosciences, Faculty of Health and Life SciencesHatherly LaboratoriesExeterUK
| | - Dorte Bekkevold
- National Institute for Aquatic ResearchTechnical University of DenmarkSilkeborgDenmark
| | - Dennis Ensing
- Environment, Marine and Fisheries GroupDepartment of Agriculture, Environment and Rural AffairsLisburnUK
| | - Thomas Lecointre
- Salmon and Trout Research Centre, The River LaboratoryGame and Wildlife Conservation TrustDorsetUK
| | - Daniel R. Osmond
- Department of Biosciences, Faculty of Health and Life SciencesHatherly LaboratoriesExeterUK
| | - Adam Piper
- Institute of ZoologyZoological Society of LondonLondonUK
| | - Dylan E. Roberts
- Salmon and Trout Research Centre, The River LaboratoryGame and Wildlife Conservation TrustDorsetUK
| | - Sophie Launey
- DECOD (Ecosystem Dynamics and Sustainability)INRAE, Institut Agro, IFREMERRennesFrance
| | - Jamie R. Stevens
- Department of Biosciences, Faculty of Health and Life SciencesHatherly LaboratoriesExeterUK
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2
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Osmond DR, King RA, Stockley B, Launey S, Stevens JR. A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales. JOURNAL OF FISH BIOLOGY 2023; 102:258-270. [PMID: 36281821 DOI: 10.1111/jfb.15258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.
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Affiliation(s)
- Daniel R Osmond
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - R Andrew King
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - Bruce Stockley
- Westcountry Rivers Trust, Rain-Charm House, Cornwall, UK
| | - Sophie Launey
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRAe, Rennes, France
| | - Jamie R Stevens
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
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3
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Hamilton PB, Baynes A, Nicol E, Harris G, Uren Webster TM, Beresford N, Straszkiewicz M, Jobling S, Tyler CR. Feminizing effects of ethinylestradiol in roach (Rutilus rutilus) populations with different estrogenic pollution exposure histories. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 249:106229. [PMID: 35753216 DOI: 10.1016/j.aquatox.2022.106229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 05/06/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Experimental exposures aimed at assessing the risks posed by estrogens in waste-water treatment work (WwTW) effluents to fish populations have rarely considered whether populations differ in their sensitivity to estrogenic compounds. This is despite evidence that selection at genes involved in the estrogen response has occurred in wild populations, and evidence that genotype can influence estrogen-response. In this study we compare the effects of a two-year exposure to a low measured concentration (1.3 ng/L) of ethinylestradiol (EE2) on the sexual development of roach (Rutilus rutilus) whose parental generation was sampled from two river stretches heavily contaminated with WwTW effluent and from two without any known WwTW effluent contamination. Exposure to EE2 significantly reduced the proportion of genetic males and induced a range of feminized phenotypes in males. Significantly, exposure also increased the proportion of genetic females with vitellogenic oocytes from 51 to 96%, raising the possibility that estrogen pollution could impact populations of annually spawning fish species through advancing female reproduction by at least a year. However, there was no evidence that river origin affected sensitivity to estrogens in either sex. Thus, we conclude that chronic exposure to low level EE2 has reproductive health outcomes for both male and female roach, but we find no evidence that the nature or magnitude of the response is affected by the population origin.
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Affiliation(s)
- Patrick B Hamilton
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK; College of Medicine and Health, St Luke's Campus, Heavitree Road, Exeter, EX1 2LU.
| | - Alice Baynes
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK
| | - Elizabeth Nicol
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK
| | - Graham Harris
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK
| | - Tamsyn M Uren Webster
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK; Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Nicola Beresford
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK
| | - Marta Straszkiewicz
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK
| | - Susan Jobling
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
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4
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Andrew King R, Miller AL, Stevens JR. Has stocking contributed to an increase in the rod catch of anadromous trout (Salmo trutta L.) in the Shetland Islands, UK? JOURNAL OF FISH BIOLOGY 2021; 99:980-989. [PMID: 33991118 DOI: 10.1111/jfb.14784] [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: 04/01/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
The stocking of hatchery-origin fish into rivers and lakes has long been used in fisheries management to try to enhance catches, especially for trout and salmon species. Frequently, however, the long-term impacts of stocking programmes have not been evaluated. In this study, the authors investigate the contribution of a stocking programme undertaken to support the rod catch of sea trout in the Shetland Islands, UK. Once a highly productive recreational fishery, Shetland sea trout catches crashed in the mid-1990s. Around the time that stocking began, increases in rod catches were also reported, with advocates of the stocking highlighting the apparent success of the programme. Using a suite of genetic markers (microsatellites), this study explores the contribution of the stocking programme to the Shetland sea trout population. The authors found that the domesticated broodstock and wild spawned brown trout from seven streams were genetically distinct. Despite extensive stocking, wild spawned brown trout dominated, even in those streams with a long history of supplementation. The majority of sea trout caught and analysed were of wild origin - only a single individual was of pure stocked origin, with a small number of fish being of wild × stocked origins. This study suggests that stocking with a domesticated strain of brown trout has made only a very limited contribution to the Shetland Islands rod catch, and that the revival of sea trout numbers appears to be driven almost exclusively by recovery of trout spawned in the wild.
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Affiliation(s)
- R Andrew King
- College of Life and Environmental Sciences, Hatherly Building, University of Exeter, Exeter, UK
| | - Andrew L Miller
- Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR
- North Atlantic Fisheries College Marine Centre, University of the Highlands and Islands, Scalloway, Shetland, UK
| | - Jamie R Stevens
- College of Life and Environmental Sciences, Hatherly Building, University of Exeter, Exeter, UK
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5
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Arregui G, Hipólito P, Pallol B, Lara-Dampier V, García-Rodríguez D, Varela HP, Tavakoli Zaniani P, Balomenos D, Paape T, Coba de la Peña T, Lucas MM, Pueyo JJ. Mercury-Tolerant Ensifer medicae Strains Display High Mercuric Reductase Activity and a Protective Effect on Nitrogen Fixation in Medicago truncatula Nodules Under Mercury Stress. FRONTIERS IN PLANT SCIENCE 2021; 11:560768. [PMID: 33519831 PMCID: PMC7840509 DOI: 10.3389/fpls.2020.560768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 12/22/2020] [Indexed: 05/27/2023]
Abstract
Mercury (Hg) is extremely toxic for all living organisms. Hg-tolerant symbiotic rhizobia have the potential to increase legume tolerance, and to our knowledge, the mechanisms underlying Hg tolerance in rhizobia have not been investigated to date. Rhizobial strains of Ensifer medicae, Rhizobium leguminosarum bv. trifolii and Bradyrhizobium canariense previously isolated from severely Hg-contaminated soils showed different levels of Hg tolerance. The ability of the strains to reduce mercury Hg2+ to Hg0, a volatile and less toxic form of mercury, was assessed using a Hg volatilization assay. In general, tolerant strains displayed high mercuric reductase activity, which appeared to be inducible in some strains when grown at a sub-lethal HgCl2 concentration. A strong correlation between Hg tolerance and mercuric reductase activity was observed for E. medicae strains, whereas this was not the case for the B. canariense strains, suggesting that additional Hg tolerance mechanisms could be playing a role in B. canariense. Transcript abundance from merA, the gene that encodes mercuric reductase, was quantified in tolerant and sensitive E. medicae and R. leguminosarum strains. Tolerant strains presented higher merA expression than sensitive ones, and an increase in transcript abundance was observed for some strains when bacteria were grown in the presence of a sub-lethal HgCl2 concentration. These results suggest a regulation of mercuric reductase in rhizobia. Expression of merA genes and mercuric reductase activity were confirmed in Medicago truncatula nodules formed by a sensitive or a tolerant E. medicae strain. Transcript accumulation in nodules formed by the tolerant strain increased when Hg stress was applied, while a significant decrease in expression occurred upon stress application in nodules formed by the Hg-sensitive strain. The effect of Hg stress on nitrogen fixation was evaluated, and in our experimental conditions, nitrogenase activity was not affected in nodules formed by the tolerant strain, while a significant decrease in activity was observed in nodules elicited by the Hg-sensitive bacteria. Our results suggest that the combination of tolerant legumes with tolerant rhizobia constitutes a potentially powerful tool in the bioremediation of Hg-contaminated soils.
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Affiliation(s)
- Gabriela Arregui
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Pablo Hipólito
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Beatriz Pallol
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Victoria Lara-Dampier
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Diego García-Rodríguez
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Higinio P. Varela
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | | | | | - Timothy Paape
- Brookhaven National Laboratory, Upton, NY, United States
| | | | - M. Mercedes Lucas
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - José J. Pueyo
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
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6
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King RA, Stockley B, Stevens JR. Small coastal streams-Critical reservoirs of genetic diversity for trout ( Salmo trutta L.) in the face of increasing anthropogenic stressors. Ecol Evol 2020; 10:5651-5669. [PMID: 32607181 PMCID: PMC7319166 DOI: 10.1002/ece3.6306] [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: 01/10/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/05/2022] Open
Abstract
We used microsatellite markers to investigate levels and structuring of genetic diversity in trout (Salmo trutta L.) sampled from 16 rivers along the south coast of Cornwall in southwest England. This region is characterized by many small coastal streams with a few larger catchments. At a regional level, genetic structuring of contemporary populations has been influenced by a combination of events, including the last Ice Age and also more recent human activities over the last millennium. All populations are shown to have gone through strong genetic bottlenecks, coinciding with increased exploitation of mineral resources within catchments, beginning during the Medieval period. At more local levels, contemporary human-induced habitat fragmentation, such as weir and culvert construction, has disproportionally affected trout populations in the smaller catchments within the study area. However, where small catchments are relatively unaffected by such activities, they can host trout populations with diversity levels comparable to those found in larger rivers in the region. We also predict significant future loses of diversity and heterozygosity in the trout populations inhabiting small, isolated catchments. Our study highlights how multiple factors, especially the activity of humans, have and continue to affect the levels and structuring of genetic diversity in trout over long timescales.
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Affiliation(s)
- R. Andrew King
- Department of BiosciencesCollege of Life and Environmental SciencesUniversity of Exeter, Hatherly LaboratoriesExeterUK
| | | | - Jamie R. Stevens
- Department of BiosciencesCollege of Life and Environmental SciencesUniversity of Exeter, Hatherly LaboratoriesExeterUK
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7
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Finlay R, Poole R, Coughlan J, Phillips KP, Prodöhl P, Cotter D, McGinnity P, Reed TE. Telemetry and genetics reveal asymmetric dispersal of a lake-feeding salmonid between inflow and outflow spawning streams at a microgeographic scale. Ecol Evol 2020; 10:1762-1783. [PMID: 32128115 PMCID: PMC7042748 DOI: 10.1002/ece3.5937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/01/2022] Open
Abstract
The degree of natal philopatry relative to natal dispersal in animal populations has important demographic and genetic consequences and often varies substantially within species. In salmonid fishes, lakes have been shown to have a strong influence on dispersal and gene flow within catchments; for example, populations spawning in inflow streams are often reproductively isolated and genetically distinct from those spawning in relatively distant outflow streams. Less is known, however, regarding the level of philopatry and genetic differentiation occurring at microgeographic scales, for example, where inflow and outflow streams are separated by very small expanses of lake habitat. Here, we investigated the interplay between genetic differentiation and fine-scale spawning movements of brown trout between their lake-feeding habitat and two spawning streams (one inflow, one outflow, separated by <100 m of lake habitat). Most (69.2%) of the lake-tagged trout subsequently detected during the spawning period were recorded in just one of the two streams, consistent with natal fidelity, while the remainder were detected in both streams, creating an opportunity for these individuals to spawn in both natal and non-natal streams. The latter behavior was supported by genetic sibship analysis, which revealed several half-sibling dyads containing one individual that was sampled as a fry in the outflow and another that was sampled as fry in the inflow. Genetic clustering analyses in conjunction with telemetry data suggested that asymmetrical dispersal patterns were occurring, with natal fidelity being more common among individuals originating from the outflow than the inflow stream. This was corroborated by Bayesian analysis of gene flow, which indicated significantly higher rates of gene flow from the inflow into the outflow than vice versa. Collectively, these results reveal how a combination of telemetry and genetics can identify distinct reproductive behaviors and associated asymmetries in natal dispersal that produce subtle, but nonetheless biologically relevant, population structuring at microgeographic scales.
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Affiliation(s)
- Ross Finlay
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | | | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Karl P. Phillips
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | - Paulo Prodöhl
- Institute for Global Food SecuritySchool of Biological SciencesQueen's University BelfastBelfastIreland
| | | | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
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8
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Jones JI, Murphy JF, Collins AL, Spencer KL, Rainbow PS, Arnold A, Pretty JL, Moorhouse AML, Aguilera V, Edwards P, Parsonage F, Potter H, Whitehouse P. The Impact of Metal-Rich Sediments Derived from Mining on Freshwater Stream Life. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 248:111-189. [PMID: 30671689 DOI: 10.1007/398_2018_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Metal-rich sediments have the potential to impair life in freshwater streams and rivers and, thereby, to inhibit recovery of ecological conditions after any remediation of mine water discharges. Sediments remain metal-rich over long time periods and have long-term potential ecotoxicological interactions with local biota, unless the sediments themselves are physically removed or replaced by less metal-rich sediment. Laboratory-derived environmental quality standards are difficult to apply to the field situation, as many complicating factors exist in the real world. Therefore, there is a strong case to consider other, field-relevant, measures of toxic effects as alternatives to laboratory-derived standards and to seek better biological tools to detect, diagnose and ideally predict community-level ecotoxicological impairment. Hence, this review concentrated on field measures of toxic effects of metal-rich sediment in freshwater streams, with less emphasis on laboratory-based toxicity testing approaches. To this end, this review provides an overview of the impact of metal-rich sediments on freshwater stream life, focusing on biological impacts linked to metal contamination.
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9
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Harding HR, Gordon TAC, Eastcott E, Simpson SD, Radford AN. Causes and consequences of intraspecific variation in animal responses to anthropogenic noise. Behav Ecol 2019; 30:1501-1511. [PMID: 31723315 PMCID: PMC6838653 DOI: 10.1093/beheco/arz114] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/07/2019] [Accepted: 06/16/2019] [Indexed: 12/24/2022] Open
Abstract
Anthropogenic noise is a recognized global pollutant, affecting a wide range of nonhuman animals. However, most research considers only whether noise pollution has an impact, ignoring that individuals within a species or population exhibit substantial variation in responses to stress. Here, we first outline how intrinsic characteristics (e.g., body size, condition, sex, and personality) and extrinsic factors (e.g., environmental context, repeated exposure, prior experience, and multiple stressors) can affect responses to environmental stressors. We then present the results of a systematic search of the anthropogenic-noise literature, identifying articles that investigated intraspecific variation in the responses of nonhuman animals to noise. This reveals that fewer than 10% of articles (51 of 589) examining impacts of noise test experimentally for intraspecific variation in responses; of those that do, more than 75% report significant effects. We assess these existing studies to determine the current scope of research and findings to-date, and to provide suggestions for good practice in the design, implementation, and reporting of robust experiments in this field. We close by explaining how understanding intraspecific variation in responses to anthropogenic noise is crucial for improving how we manage captive animals, monitor wild populations, model species responses, and mitigate effects of noise pollution on wildlife. Our aim is to stimulate greater knowledge and more effective management of the harmful consequences of this global pollutant.
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Affiliation(s)
- Harry R Harding
- School of Biological Sciences, University of Bristol, Bristol, UK
- Marine Scotland Science, Aberdeen, UK
| | - Timothy A C Gordon
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
- Australian Institute of Marine Science, Perth, WA, Australia
| | - Emma Eastcott
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Stephen D Simpson
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew N Radford
- School of Biological Sciences, University of Bristol, Bristol, UK
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10
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Paris JR, Usher J. Functional genomic characterization of metallothioneins in brown trout (Salmo trutta L.). using synthetic genetic analysis. Sci Rep 2019; 9:11827. [PMID: 31413359 PMCID: PMC6694099 DOI: 10.1038/s41598-019-48303-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 08/02/2019] [Indexed: 11/25/2022] Open
Abstract
Metal pollution has made a significant impact on the earth's ecosystems and tolerance to metals in a wide variety of species has evolved. Metallothioneins, a group of cysteine-rich metal-ion binding proteins, are known to be a key physiological mechanism in regulating protection against metal toxicity. Many rivers across the southwest of England are detrimentally affected by metal pollution, but brown trout (Salmo trutta L.) populations are known to reside within them. In this body of work, two isoforms of metallothionein (MetA and MetB) isolated from trout occupying a polluted and a control river are examined. Using synthetic genetic array (SGA) analyses in the model yeast, Saccharomyces cerevisiae, functional genomics is used to explore the role of metallothionein isoforms in driving metal tolerance. By harnessing this experimental system, S. cerevisiae is used to (i) determine the genetic interaction maps of MetA and MetB isoforms; (ii) identify differences between the genetic interactions in both isoforms and (iii) demonstrate that pre-exposure to metals in metal-tolerant trout influences these interactions. By using a functional genomics approach leveraged from the model yeast Saccharomyces cerevisiae, we demonstrate how such approaches could be used in understanding the ecology and evolution of a non-model species.
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Affiliation(s)
- Josephine R Paris
- School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Jane Usher
- School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
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11
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Lemopoulos A, Prokkola JM, Uusi‐Heikkilä S, Vasemägi A, Huusko A, Hyvärinen P, Koljonen M, Koskiniemi J, Vainikka A. Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation. Ecol Evol 2019; 9:2106-2120. [PMID: 30847096 PMCID: PMC6392366 DOI: 10.1002/ece3.4905] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022] Open
Abstract
The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.
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Affiliation(s)
- Alexandre Lemopoulos
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Jenni M. Prokkola
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Silva Uusi‐Heikkilä
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anti Vasemägi
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
- Estonian University of Life SciencesInstitute of Veterinary Medicine and Animal SciencesTartuEstonia
| | - Ari Huusko
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | - Pekka Hyvärinen
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | | | - Jarmo Koskiniemi
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Anssi Vainikka
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
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12
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Nadukkalam Ravindran P, Bentzen P, Bradbury IR, Beiko RG. RADProc: A computationally efficient de novo locus assembler for population studies using RADseq data. Mol Ecol Resour 2018; 19:272-282. [PMID: 30312001 DOI: 10.1111/1755-0998.12954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/09/2018] [Accepted: 09/26/2018] [Indexed: 11/30/2022]
Abstract
Restriction site-associated DNA sequencing (RADseq) is a powerful tool for genotyping of individuals, but the identification of loci and assignment of sequence reads is a crucial and often challenging step. The optimal parameter settings for a given de novo RADseq assembly vary between data sets and can be difficult and computationally expensive to determine. Here, we introduce RADProc, a software package that uses a graph data structure to represent all sequence reads and their similarity relationships. Storing sequence-comparison results in a graph eliminates unnecessary and redundant sequence similarity calculations. De novo locus formation for a given parameter set can be performed on the precomputed graph, making parameter sweeps far more efficient. RADProc also uses a clustering approach for faster nucleotide-distance calculation. The performance of RADProc compares favourably with that of the widely used Stacks software. The run-time comparisons between RADProc and Stacks for 32 different parameter settings using 20 green-crab (Carcinus maenas) samples showed that RADProc took as little as 2 hr 40 min compared to 78 hr by Stacks, while 16 brown trout (Salmo trutta L.) samples were processed by RADProc and Stacks in 23 and 263 hr, respectively. Comparisons of the de novo loci formed, and catalog built using both the methods demonstrate that the improvement in processing speeds achieved by RADProc does not affect much the actual loci formed and the results of downstream analyses based on those loci.
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Affiliation(s)
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ian R Bradbury
- Salmonids Section, Science Branch, Department of Fisheries and Oceans Canada, St. John's, Newfoundland, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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13
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Low population genetic differentiation in two Tamarix species (Tamarix austromongolica and Tamarix chinensis) along the Yellow River. Genetica 2018; 147:13-22. [DOI: 10.1007/s10709-018-0047-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/16/2018] [Indexed: 10/27/2022]
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14
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Rose NL, Turner SD, Yang H, Yang C, Hall C, Harrad S. Palaeotoxicity: reconstructing the risk of multiple sedimentary pollutants to freshwater organisms. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2018; 40:1667-1682. [PMID: 29500539 PMCID: PMC6061110 DOI: 10.1007/s10653-018-0080-5] [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: 09/22/2017] [Accepted: 02/21/2018] [Indexed: 05/06/2023]
Abstract
'Real-world' contaminant exposure of sediment-dwelling biota is typically long-term, low-level and to multiple pollutants. However, sediment quality guidelines, designed to protect these organisms, relate only to single contaminants. This study uses radiometrically dated sediment cores from 7 English lakes with varying contamination histories to reconstruct temporal changes in likely risk to biota (herein termed 'palaeotoxicity'). The Probable Effects Concentration Quotient (PEC-Q) approach was used to combine sediment concentrations from multiple contaminants (trace metals; PCBs; PBDEs) to determine risk allocated to metals and persistent organic pollutants (POPs) separately as well as combined (PEC-Q Mean-All). Urban-influenced lakes were considerably more contaminated, exceeding PEC-Q thresholds of 0.5 and 2.0 over long durations (some since the nineteenth century). This has been mainly due to metals (principally lead) and by factors of up to 10 for individual metals and by > 2 for PEC-Q Mean-Metals. In 6 out of 7 lakes, considerable reductions in risk associated with trace metals are observed since emissions reductions in the 1970s. However, at all lakes, PEC-Q Mean-POPs has increased sharply since the 1950s and at 5 out of 7 lakes now exceeds PEC-Q Mean-Metals. These organic pollutants are therefore now the dominant driver behind elevated contaminant risk to sediment-dwelling biota and recent temporal trends in PEC-Q Mean-All remain above threshold values as a result. Finally, PEC-Q Mean-All values were compared to standard biological toxicity tests for surface sediments at each site. While chironomid growth and daphniid reproduction were significantly reduced compared to controls at 5 out of 7, and all lakes, respectively, the scale of these reductions showed only limited quantitative agreement with predicted risk.
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Affiliation(s)
- Neil L Rose
- Environmental Change Research Centre, Department of Geography, University College London, Gower St, London, WC1E 6BT, UK.
| | - Simon D Turner
- Environmental Change Research Centre, Department of Geography, University College London, Gower St, London, WC1E 6BT, UK
| | - Handong Yang
- Environmental Change Research Centre, Department of Geography, University College London, Gower St, London, WC1E 6BT, UK
| | - Congqiao Yang
- Department of Earth Sciences, University of Toronto, Toronto, ON, M5S 3B1, Canada
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Charlotte Hall
- Environmental Change Research Centre, Department of Geography, University College London, Gower St, London, WC1E 6BT, UK
| | - Stuart Harrad
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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15
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Vittecoq M, Giraudeau M, Sepp T, Marcogliese DJ, Klaassen M, Renaud F, Ujvari B, Thomas F. Turning natural adaptations to oncogenic factors into an ally in the war against cancer. Evol Appl 2018; 11:836-844. [PMID: 29928293 PMCID: PMC5999213 DOI: 10.1111/eva.12608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/25/2018] [Indexed: 12/14/2022] Open
Abstract
Both field and experimental evolution studies have demonstrated that organisms naturally or artificially exposed to environmental oncogenic factors can, sometimes rapidly, evolve specific adaptations to cope with pollutants and their adverse effects on fitness. Although numerous pollutants are mutagenic and carcinogenic, little attention has been given to exploring the extent to which adaptations displayed by organisms living in oncogenic environments could inspire novel cancer treatments, through mimicking the processes allowing these organisms to prevent or limit malignant progression. Building on a substantial knowledge base from the literature, we here present and discuss this progressive and promising research direction, advocating closer collaboration between the fields of medicine, ecology, and evolution in the war against cancer.
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Affiliation(s)
- Marion Vittecoq
- Institut de Recherche de la Tour du Valat Arles France.,CREEC/MIVEGEC IRD CNRS University of Montpellier Montpellier France
| | - Mathieu Giraudeau
- School of Life Sciences Arizona State University Tempe AZ USA.,Centre for Ecology & Conservation College of Life and Environmental Sciences University of Exeter Penryn UK
| | - Tuul Sepp
- School of Life Sciences Arizona State University Tempe AZ USA.,Department of Zoology University of Tartu Tartu Estonia
| | - David J Marcogliese
- Aquatic Contaminants Research Division Water Science and Technology Directorate Environment and Climate Change Canada St. Lawrence Centre Montreal QC Canada.,Fisheries and Oceans Canada St. Andrews Biological Station St. Andrews NB Canada
| | - Marcel Klaassen
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Deakin Vic. Australia
| | - François Renaud
- CREEC/MIVEGEC IRD CNRS University of Montpellier Montpellier France
| | - Beata Ujvari
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Deakin Vic. Australia.,School of Biological Sciences University of Tasmania Hobart TAS Australia
| | - Frédéric Thomas
- CREEC/MIVEGEC IRD CNRS University of Montpellier Montpellier France
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16
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Hamilton PB, Rolshausen G, Uren Webster TM, Tyler CR. Adaptive capabilities and fitness consequences associated with pollution exposure in fish. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0042. [PMID: 27920387 PMCID: PMC5182438 DOI: 10.1098/rstb.2016.0042] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2016] [Indexed: 12/22/2022] Open
Abstract
Many fish populations are exposed to harmful levels of chemical pollution and selection pressures associated with these exposures have led to the evolution of tolerance. Our understanding of the physiological basis for these adaptations is limited, but they are likely to include processes involved with the absorption, distribution, metabolism and/or excretion of the target chemical. Other potential adaptive mechanisms include enhancements in antioxidant responses, an increased capacity for DNA and/or tissue repair and alterations to the life cycle of fish that enable earlier reproduction. Analysis of single-nucleotide polymorphism frequencies has shown that tolerance to hydrocarbon pollutants in both marine and estuarine fish species involves alteration in the expression of the xenobiotic metabolism enzyme CYP1A. In this review, we present novel data showing also that variants of the CYP1A gene have been under selection in guppies living in Trinidadian rivers heavily polluted with crude oil. Potential costs associated with these adaptations could reduce fitness in unpolluted water conditions. Integrating knowledge of local adaptation to pollution is an important future consideration in conservation practices such as for successful restocking, and improving connectivity within river systems.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Patrick B Hamilton
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Tamsyn M Uren Webster
- Department of Biosciences, Swansea University, Wallace Building, Swansea SA2 8PP, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
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17
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Pedrosa JAM, Cocchiararo B, Verdelhos T, Soares AMVM, Pestana JLT, Nowak C. Population genetic structure and hybridization patterns in the cryptic sister species Chironomus riparius and Chironomus piger across differentially polluted freshwater systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 141:280-289. [PMID: 28359994 DOI: 10.1016/j.ecoenv.2017.03.004] [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] [Received: 11/05/2016] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
Chironomids are an integral and functionally important part of many freshwater ecosystems. Yet, to date, there is limited understanding of their microevolutionary processes under chemically polluted natural environments. In this study, we investigated the genetic variation within populations of the ecotoxicological model species Chironomus riparius and its cryptic sister species Chironomus piger at 18 metal-contaminated and reference sites in northwestern Portugal. Microsatellite analysis was conducted on 909 samples to answer if metal contamination affects genetic variation in natural chironomid populations as previously suggested from controlled laboratory experiments. Similarly high levels of genetic diversity and significant but weak genetic substructuring were found across all sites and temporal replicates, with no effects of metal contamination on the genetic variation or species' abundance, although C. piger tended to be less frequent at highly contaminated sites. Our results indicate that high levels of gene flow and population dynamic processes may overlay potential pollutant effects. At least for our study species, we conclude that the "genetic erosion hypothesis", which suggests that chemical pollution will reduce genome-wide genetic variability in affected populations, does not hold under natural conditions. Interestingly, our study provides evidence of successful hybridization between the two sister species under natural conditions.
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Affiliation(s)
- João A M Pedrosa
- Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal; Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571 Gelnhausen, Germany.
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571 Gelnhausen, Germany
| | - Tiago Verdelhos
- MARE - Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Amadeu M V M Soares
- Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - João L T Pestana
- Department of Biology & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571 Gelnhausen, Germany
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18
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Pedrosa J, Campos D, Cocchiararo B, Nowak C, Soares AMVM, Barata C, L T Pestana J. Evolutionary consequences of historical metal contamination for natural populations of Chironomus riparius (Diptera: Chironomidae). ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:534-546. [PMID: 28353160 DOI: 10.1007/s10646-017-1784-5] [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] [Accepted: 02/15/2017] [Indexed: 06/06/2023]
Abstract
Populations inhabiting metal-impacted freshwater systems located nearby industrial and urban areas may be under intense selection. The present study aims to address two fundamental microevolutionary aspects of metal contamination in the midge Chironomus riparius (Meigen): Are populations inhabiting historically metal contaminated sites genetically adapted to metals? And, are populations from these sites genetically eroded? To answer these questions, C. riparius populations were sampled from three sites with well-known histories of metal contamination and three nearby-located references. Genetic adaptation to metals was investigated through acute and chronic exposures to cadmium (Cd), after rearing all populations for at least six generations under laboratory clean conditions. Genetic diversity was estimated based on the allelic variation of seven microsatellite markers. Results showed higher acute tolerance to Cd in populations originating from metal contaminated sites compared to their respective references and significant differences in two out of three pairwise comparisons. However, there was a mismatch between acute and chronic tolerance to Cd with results of the partial life-cycle tests suggesting fitness costs under control clean conditions in two metal-adapted populations. Despite no evidences of genetic erosion in populations sampled from metal contaminated sites, our results suggest genetically inherited tolerance to Cd in populations inhabiting historically contaminated sites. These findings lend support to the use of C. riparius as a model organism in evolutionary toxicology and highlight the importance of coupling measures of neutral genetic diversity with assessments of chemical tolerance of populations for a better understanding of contaminant-induced adaptation and evolutionary processes.
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Affiliation(s)
- João Pedrosa
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum of Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Diana Campos
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum of Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum of Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Amadeu M V M Soares
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Carlos Barata
- Department of Environmental Chemistry (IDAEA-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - João L T Pestana
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
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19
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Affiliation(s)
- Josephine R. Paris
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Jamie R. Stevens
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter UK
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois at Urbana–Champaign Urbana IL 61801 USA
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20
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Uren Webster TM, Williams TD, Katsiadaki I, Lange A, Lewis C, Shears JA, Tyler CR, Santos EM. Hepatic transcriptional responses to copper in the three-spined stickleback are affected by their pollution exposure history. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 184:26-36. [PMID: 28081447 DOI: 10.1016/j.aquatox.2016.12.023] [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] [Received: 09/01/2016] [Revised: 12/05/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
Some fish populations inhabiting contaminated environments show evidence of increased chemical tolerance, however the mechanisms contributing to this tolerance, and whether this is heritable, are poorly understood. We investigated the responses of two populations of wild three-spined stickleback (Gasterosteus aculeatus) with different histories of contaminant exposure to an oestrogen and copper, two widespread aquatic pollutants. Male stickleback originating from two sites, the River Aire, with a history of complex pollution discharges, and Siblyback Lake, with a history of metal contamination, were depurated and then exposed to copper (46μg/L) and the synthetic oestrogen ethinyloestradiol (22ng/L). The hepatic transcriptomic response was compared between the two populations and to a reference population with no known history of exposure (Houghton Springs, Dorset). Gene responses included those typical for both copper and oestrogen, with no discernable difference in response to oestrogen between populations. There was, however, some difference in the magnitude of response to copper between populations. Siblyback fish showed an elevated baseline transcription of genes encoding metallothioneins and a lower level of metallothionein induction following copper exposure, compared to those from the River Aire. Similarly, a further experiment with an F1 generation of Siblyback fish bred in the laboratory found evidence for elevated transcription of genes encoding metallothioneins in unexposed fish, together with an altered transcriptional response to 125μg/L copper, compared with F1 fish originating from the clean reference population exposed to the same copper concentration. These data suggest that the stickleback from Siblyback Lake have a differential response to copper, which is inherited by the F1 generation in laboratory conditions, and for which the underlying mechanism may include an elevation of baseline transcription of genes encoding metallothioneins. The genetic and/or epigenetic mechanisms contributing to this inherited alteration of metallothionein transcription have yet to be established.
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Affiliation(s)
- Tamsyn M Uren Webster
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Tim D Williams
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Ioanna Katsiadaki
- Centre for Environment, Fisheries and Aquaculture Science, Cefas Weymouth Laboratory, Weymouth DT4 8UB, UK
| | - Anke Lange
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Ceri Lewis
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Janice A Shears
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Eduarda M Santos
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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21
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Kemppainen P, Rønning B, Kvalnes T, Hagen IJ, Ringsby TH, Billing AM, Pärn H, Lien S, Husby A, Saether BE, Jensen H. Controlling for P
-value inflation in allele frequency change in experimental evolution and artificial selection experiments. Mol Ecol Resour 2016; 17:770-782. [DOI: 10.1111/1755-0998.12631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/23/2016] [Accepted: 10/28/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Petri Kemppainen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Bernt Rønning
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Ingerid J. Hagen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Thor Harald Ringsby
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Anna M. Billing
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Henrik Pärn
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Sigbjørn Lien
- CIGENE; Norwegian University of Life Sciences; P.O. Box 5003 NO-1432 Ås Norway
| | - Arild Husby
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
- Department of Biosciences; University of Helsinki; P.O. Box 65 (Viikinkaari 1) 00014 Helsinki Finland
| | - Bernt-Erik Saether
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics; Department of Biology; Norwegian University of Science and Technology; Høgskoleringen 5, Realfagbygget E1-126 NO-7491 Trondheim Norway
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22
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Di Paolo C, Groh KJ, Zennegg M, Vermeirssen ELM, Murk AJ, Eggen RIL, Hollert H, Werner I, Schirmer K. Early life exposure to PCB126 results in delayed mortality and growth impairment in the zebrafish larvae. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 169:168-178. [PMID: 26551687 DOI: 10.1016/j.aquatox.2015.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 10/18/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
The occurrence of chronic or delayed toxicity resulting from the exposure to sublethal chemical concentrations is an increasing concern in environmental risk assessment. The Fish Embryo Toxicity (FET) test with zebrafish provides a reliable prediction of acute toxicity in adult fish, but it cannot yet be applied to predict the occurrence of chronic or delayed toxicity. Identification of sublethal FET endpoints that can assist in predicting the occurrence of chronic or delayed toxicity would be advantageous. The present study characterized the occurrence of delayed toxicity in zebrafish larvae following early exposure to PCB126, previously described to cause delayed effects in the common sole. The first aim was to investigate the occurrence and temporal profiles of delayed toxicity during zebrafish larval development and compare them to those previously described for sole to evaluate the suitability of zebrafish as a model fish species for delayed toxicity assessment. The second aim was to examine the correlation between the sublethal endpoints assessed during embryonal and early larval development and the delayed effects observed during later larval development. After exposure to PCB126 (3-3000ng/L) until 5 days post fertilization (dpf), larvae were reared in clean water until 14 or 28 dpf. Mortality and sublethal morphological and behavioural endpoints were recorded daily, and growth was assessed at 28 dpf. Early life exposure to PCB126 caused delayed mortality (300 ng/L and 3000 ng/L) as well as growth impairment and delayed development (100 ng/L) during the clean water period. Effects on swim bladder inflation and cartilaginous tissues within 5 dpf were the most promising for predicting delayed mortality and sublethal effects, such as decreased standard length, delayed metamorphosis, reduced inflation of swim bladder and column malformations. The EC50 value for swim bladder inflation at 5 dpf (169 ng/L) was similar to the LC50 value at 8 dpf (188 and 202 ng/L in two experiments). Interestingly, the patterns of delayed mortality and delayed effects on growth and development were similar between sole and zebrafish. This indicates the comparability of critical developmental stages across divergent fish species such as a cold water marine flatfish and a tropical freshwater cyprinid. Additionally, sublethal effects in early embryo-larval stages were found promising for predicting delayed lethal and sublethal effects of PCB126. Therefore, the proposed method with zebrafish is expected to provide valuable information on delayed mortality and delayed sublethal effects of chemicals and environmental samples that may be extrapolated to other species.
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Affiliation(s)
- Carolina Di Paolo
- Swiss Centre for Applied Ecotoxicology Eawag-EPFL, 8600, Dübendorf, Switzerland; Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, 52074, Aachen, Germany.
| | - Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600, Dübendorf, Switzerland; ETH Zürich, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Markus Zennegg
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, 8600, Dübendorf, Switzerland.
| | | | - Albertinka J Murk
- Wageningen University, Marine Animal Ecology Group, 6708WD, Wageningen, The Netherlands; IMARES, Institute for Marine Resources and Ecosystem Studies, Wageningen UR, 1780 AB, Den Helder, The Netherlands.
| | - Rik I L Eggen
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600, Dübendorf, Switzerland; ETH Zürich, Department of Environmental Systems Science, 8092 Zürich, Switzerland.
| | - Henner Hollert
- Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, 52074, Aachen, Germany.
| | - Inge Werner
- Swiss Centre for Applied Ecotoxicology Eawag-EPFL, 8600, Dübendorf, Switzerland.
| | - Kristin Schirmer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600, Dübendorf, Switzerland; ETH Zürich, Department of Environmental Systems Science, 8092 Zürich, Switzerland; EPF Lausanne, School of Architecture, Civil and Environmental Engineering, 1015 Lausanne, Switzerland.
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23
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Wirgin I, Maceda L, Waldman J, Mayack DT. Genetic variation and population structure of American mink Neovison vison from PCB-contaminated and non-contaminated locales in eastern North America. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1961-75. [PMID: 26374638 PMCID: PMC4662875 DOI: 10.1007/s10646-015-1533-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
American mink Neovison vison may be particularly vulnerable to toxicities of persistent contaminants such as PCBs because of their aquatic-based diet, position near the top of the food web, and small deme sizes. Furthermore, ranched mink are sensitive to reproductive toxicities of fish diets from PCB-polluted sites. The upper Hudson River is highly contaminated with PCBs and previous studies have shown elevated hepatic burdens of total and coplanar PCBs in mink collected near the river compared with those from more distant locales in New York and elsewhere. We hypothesized that bioaccumulation of PCBs in Hudson River mink has reduced their levels of genetic diversity or altered their genetic population structure. To address this, we conducted microsatellite DNA analysis on collections made in proximity to and from more distant locales in the Hudson River watershed, elsewhere in New York State, and at other sites in eastern North America including New Brunswick, four locales in Ontario, multiple drainages in Maine, and two ecoregions in Rhode Island. We did not find reduced genetic diversity at the individual or population levels in mink collected near (<6 km) to PCB hotspots in the Hudson River nor evidence of altered population structure. Consistent with their distribution in small localized and isolated demes, we did find significant genetic population structure among many mink collections in New York State and elsewhere. Depending on the analytical approach used, genetically distinct populations numbered between 16 when using STRUCTURE to 19-20 when using Exact G tests, F ST, or AMOVA analyses. Genetically distinct population units were found among major ecoregions and minor ecoregions in New York State, among different hydrologic subunits within the Hudson River watershed, among spatially separate locales in Ontario, and among most watersheds in Maine. However, despite this localization and potential heightened impact of stressors, genetic diversity and genetic population structure in mink does not seem to be affected by their bioaccumulation of high levels of PCBs of Hudson River origin.
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Affiliation(s)
- Isaac Wirgin
- Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY, 10987, USA.
| | - Lorraine Maceda
- Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY, 10987, USA
| | - John Waldman
- Biology Department, Queens College, 65-30 Kissena Boulevard, Flushing, NY, 11367, USA
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