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Hamilton PB, Lockyer AE, Uren Webster TM, Studholme DJ, Paris JR, Baynes A, Nicol E, Dawson DA, Moore K, Farbos A, Jobling S, Stevens JR, Tyler CR. Investigation into Adaptation in Genes Associated with Response to Estrogenic Pollution in Populations of Roach ( Rutilus rutilus) Living in English Rivers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15935-15945. [PMID: 33227200 DOI: 10.1021/acs.est.0c00957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Exposure of male fish to estrogenic substances from wastewater treatment works (WwTWs) results in feminization and reduced reproductive fitness. Nevertheless, self-sustaining populations of roach (Rutilus rutilus) inhabit river stretches polluted with estrogenic WwTW effluents. In this study, we examine whether such roach populations have evolved adaptations to tolerate estrogenic pollution by comparing frequency differences in single-nucleotide polymorphisms (SNPs) between populations sampled from rivers receiving either high- or low-level WwTW discharges. SNPs within 36 "candidate" genes, selected for their involvement in estrogenic responses, and 120 SNPs in reference genes were genotyped in 465 roaches. There was no evidence for selection in highly estrogen-dependent candidate genes, including those for the estrogen receptors, aromatases, and vitellogenins. The androgen receptor (ar) and cytochrome P450 1A genes were associated with large shifts in allele frequencies between catchments and in individual populations, but there is no clear link to estrogen pollution. Selection at ar in the effluent-dominated River Lee may have resulted from historical contamination with endocrine-disrupting pesticides. Critically, although our results suggest population-specific selection including at genes related to endocrine disruption, there was no strong evidence that the selection resulted from exposure to estrogen pollution.
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Affiliation(s)
- Patrick B Hamilton
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
- College of Medicine and Health, University of Exeter, St Luke's Campus, Heavitree Road, Exeter EX1 2LU, U.K
| | - Anne E Lockyer
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Tamsyn M Uren Webster
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
- Biosciences, College of Science, Swansea University, Swansea SA2 8PP, U.K
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Josephine R Paris
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Alice Baynes
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Elizabeth Nicol
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, U.K
| | - Karen Moore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Audrey Farbos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Susan Jobling
- Institute of Environment, Health and Societies, Brunel University London, Uxbridge, Middlesex UB8 3PH, U.K
| | - Jamie R Stevens
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, U.K
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Crawford DL, Schulte PM, Whitehead A, Oleksiak MF. Evolutionary Physiology and Genomics in the Highly Adaptable Killifish (
Fundulus heteroclitus
). Compr Physiol 2020; 10:637-671. [DOI: 10.1002/cphy.c190004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Evolutionary Toxicogenomics of the Striped Killifish ( Fundulus majalis) in the New Bedford Harbor (Massachusetts, USA). Int J Mol Sci 2019; 20:ijms20051129. [PMID: 30841640 PMCID: PMC6429206 DOI: 10.3390/ijms20051129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 12/27/2022] Open
Abstract
In this paper, we used a Genotyping-by-Sequencing (GBS) approach to find and genotype more than 4000 genome-wide SNPs (Single Nucleotide Polymorphisms) from striped killifish exposed to a variety of polychlorinated biphenyls (PCBs) and other aromatic pollutants in New Bedford Harbor (NBH, Massachusetts, USA). The aims of this study were to identify the genetic consequences of exposure to aquatic pollutants and detect genes that may be under selection. Low genetic diversity (HE and π) was found in the site exposed to the highest pollution level, but the pattern of genetic diversity did not match the pollution levels. Extensive connectivity was detected among sampling sites, which suggests that balanced gene flow may explain the lack of genetic variation in response to pollution levels. Tests for selection identified 539 candidate outliers, but many of the candidate outliers were not shared among tests. Differences among test results likely reflect different test assumptions and the complex pollutant mixture. Potentially, selectively important loci are associated with 151 SNPs, and enrichment analysis suggests a likely involvement of these genes with pollutants that occur in NBH. This result suggests that selective processes at genes targeted by pollutants may be occurring, even at a small geographical scale, and may allow the local striped killifish to resist the high pollution levels.
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Expression Procedure Optimization of Carassius aurantus CYP1A in Shewanella Using Plasmid Construction Strategy. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-017-0330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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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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Robertson M, Schrey A, Shayter A, Moss CJ, Richards C. Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill. Evol Appl 2017; 10:792-801. [PMID: 29151871 PMCID: PMC5680422 DOI: 10.1111/eva.12482] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/13/2017] [Indexed: 12/13/2022] Open
Abstract
Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation sensitive fragment length polymorphism (MS‐AFLP) to test the hypothesis that response to oil exposure in S. alterniflora resulted in genetically and epigenetically based population differentiation. We found high genetic and epigenetic variation within and among sites and found significant genetic differentiation between contaminated and uncontaminated sites, which may reflect nonrandom mortality in response to oil exposure. Additionally, despite a lack of genomewide patterns in DNA methylation between contaminated and uncontaminated sites, we found five MS‐AFLP loci (12% of polymorphic MS‐AFLP loci) that were correlated with oil exposure. Overall, our findings support genetically based differentiation correlated with exposure to the oil spill in this system, but also suggest a potential role for epigenetic mechanisms in population differentiation.
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Affiliation(s)
- Marta Robertson
- Department of Integrative BiologyUniversity of South FloridaTampaFLUSA
| | - Aaron Schrey
- Department of BiologyArmstrong State UniversitySavannahGAUSA
| | - Ashley Shayter
- Rehabilitation InstituteSouthern Illinois UniversityCarbondaleILUSA
| | - Christina J Moss
- Department of Cell BiologyMicrobiology and Molecular BiologyUniversity of South FloridaTampaFLUSA
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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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Baris TZ, Crawford DL, Oleksiak MF. Acclimation and acute temperature effects on population differences in oxidative phosphorylation. Am J Physiol Regul Integr Comp Physiol 2015; 310:R185-96. [PMID: 26582639 DOI: 10.1152/ajpregu.00421.2015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/12/2015] [Indexed: 11/22/2022]
Abstract
Temperature changes affect metabolism on acute, acclamatory, and evolutionary time scales. To better understand temperature's affect on metabolism at these different time scales, we quantified cardiac oxidative phosphorylation (OxPhos) in three Fundulus taxa acclimated to 12 and 28°C and measured at three acute temperatures (12, 20, and 28°C). The Fundulus taxa (northern Maine and southern Georgia F. heteroclitus, and a sister taxa, F. grandis) were used to identify evolved changes in OxPhos. Cardiac OxPhos metabolism was quantified by measuring six traits: state 3 (ADP and substrate-dependent mitochondrial respiration); E state (uncoupled mitochondrial activity); complex I, II, and IV activities; and LEAK ratio. Acute temperature affected all OxPhos traits. Acclimation only significantly affected state 3 and LEAK ratio. Populations were significantly different for state 3. In addition to direct effects, there were significant interactions between acclimation and population for complex I and between population and acute temperature for state 3. Further analyses suggest that acclimation alters the acute temperature response for state 3, E state, and complexes I and II: at the low acclimation temperature, the acute response was dampened at low assay temperatures, and at the high acclimation temperature, the acute response was dampened at high assay temperatures. Closer examination of the data also suggests that differences in state 3 respiration and complex I activity between populations were greatest between fish acclimated to low temperatures when assayed at high temperatures, suggesting that differences between the populations become more apparent at the edges of their thermal range.
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Affiliation(s)
- Tara Z Baris
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida
| | - Douglas L Crawford
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida
| | - Marjorie F Oleksiak
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida
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9
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Nunez JCB, Seale TP, Fraser MA, Burton TL, Fortson TN, Hoover D, Travis J, Oleksiak MF, Crawford DL. Population Genomics of the Euryhaline Teleost Poecilia latipinna. PLoS One 2015; 10:e0137077. [PMID: 26335684 PMCID: PMC4559437 DOI: 10.1371/journal.pone.0137077] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/11/2015] [Indexed: 01/09/2023] Open
Abstract
Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence.
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Affiliation(s)
- J. C. B. Nunez
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - T. P. Seale
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - M. A. Fraser
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - T. L. Burton
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - T. N. Fortson
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - D. Hoover
- Department of Biology, Florida State University, Tallahassee, FL 32306, United States of America
| | - J. Travis
- Department of Biology, Florida State University, Tallahassee, FL 32306, United States of America
| | - M. F. Oleksiak
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - D. L. Crawford
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
- * E-mail:
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Du X, Crawford DL, Oleksiak MF. Effects of Anthropogenic Pollution on the Oxidative Phosphorylation Pathway of Hepatocytes from Natural Populations of Fundulus heteroclitus. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 165:231-40. [PMID: 26122720 DOI: 10.1016/j.aquatox.2015.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/11/2015] [Accepted: 06/12/2015] [Indexed: 05/24/2023]
Abstract
Persistent organic pollutants (POPs), including polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), potentially target mitochondria and cause toxicity. We compared the effects of POPs on mitochondrial respiration by measuring oxidative phosphorylation (OxPhos) metabolism in hepatocytes isolated from lab-depurated Fundulus heteroclitus from a Superfund site contaminated with PAHs (Elizabeth River VA, USA) relative to OxPhos metabolism in individuals from a relatively clean, reference population (King's Creek VA, USA). In individuals from the polluted Elizabeth River population, OxPhos metabolism displayed lower LEAK and lower activities in complex III, complex IV, and E State, but higher activity in complex I compared to individuals from the reference King's Creek population. To test the supposition that these differences were due to or related to the chronic PAH contamination history of the Elizabeth River population, we compared the OxPhos functions of undosed individuals from the polluted and reference populations to individuals from these populations dosed with a PAH {benzo [α] pyrene (BaP)} or a PCB {PCB126 (3,3',4,4',5-pentachlorobiphenyl)}, respectively. Exposure to PAH or PCB affected OxPhos in the reference King's Creek population but had no detectable effects on the polluted Elizabeth River population. Thus, PAH exposure significantly increased LEAK, and exposure to PCB126 significantly decreased State 3, E state and complex I activity in the reference King's Creek population. These data strongly implicate an evolved tolerance in the Elizabeth River fish where dosed fish are not affected by PAH exposure and undosed fish show decreased LEAK and increased State 3 and E state.
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Affiliation(s)
- Xiao Du
- Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, University of Miami, Miami, FL 33149, USA
| | - Douglas L Crawford
- Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, University of Miami, Miami, FL 33149, USA
| | - Marjorie F Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, University of Miami, Miami, FL 33149, USA.
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Souche EL, Hellemans B, Babbucci M, MacAoidh E, Guinand B, Bargelloni L, Chistiakov DA, Patarnello T, Bonhomme F, Martinsohn JT, Volckaert FAM. Range-wide population structure of European sea bassDicentrarchus labrax. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12572] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Erika L. Souche
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Center of Human Genetics; University of Leuven; O&N I Herestraat 49 - PO Box 602 B-3000 Leuven Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
| | - Massimiliano Babbucci
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - Eoin MacAoidh
- Joint Research Centre; Institute for the Protection and Security of the Citizen; European Commission; Maritime Affairs Unit (G.03) - TP051 (Bldg. 51), Via Enrico Fermi nr. 2749 I-21027 Ispra Italy
| | - Bruno Guinand
- Institut des Sciences de l'Evolution de Montpellier; Université de Montpellier; UMR CNRS 5554, Place Eugène Bataillon - cc63 F-34095 Montpellier Cedex 5 France
| | - Luca Bargelloni
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - Dimitry A. Chistiakov
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Department of Medical Nanobiotechnology; Pirogov Russian State Medical University Research Center; Ulitsa Ostrovityanova 1 117997 Moscow Russia
| | - Tomaso Patarnello
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - François Bonhomme
- Institut des Sciences de l'Evolution de Montpellier; Université de Montpellier; UMR CNRS 5554, Place Eugène Bataillon - cc63 F-34095 Montpellier Cedex 5 France
| | - Jann T. Martinsohn
- Joint Research Centre; Institute for the Protection and Security of the Citizen; European Commission; Maritime Affairs Unit (G.03) - TP051 (Bldg. 51), Via Enrico Fermi nr. 2749 I-21027 Ispra Italy
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Department of Biological and Environmental Sciences; CeMEB; University of Gothenburg; Box 463 SE-405 30 Gothenburg Sweden
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12
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Reitzel AM, Karchner SI, Franks DG, Evans BR, Nacci D, Champlin D, Vieira VM, Hahn ME. Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats. BMC Evol Biol 2014; 14:6. [PMID: 24422594 PMCID: PMC3899389 DOI: 10.1186/1471-2148-14-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/18/2013] [Indexed: 11/27/2022] Open
Abstract
Background The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other “dioxin-like compounds” (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and evidence for positive selection at three AHR-related loci (AHR1, AHR2, AHRR) in F. heteroclitus by comparing alleles from seven locations ranging over 600 km along the northeastern US, including extremely polluted and reference estuaries, with a focus on New Bedford Harbor (MA, USA), a PCB Superfund site, and nearby reference sites. Results We identified 98 single nucleotide polymorphisms within three AHR-related loci among all populations, including synonymous and nonsynonymous substitutions. Haplotype distributions were spatially segregated and F-statistics suggested strong population genetic structure at these loci, consistent with previous studies showing strong population genetic structure at other F. heteroclitus loci. Genetic diversity at these three loci was not significantly different in contaminated sites as compared to reference sites. However, for AHR2 the New Bedford Harbor population had significant FST values in comparison to the nearest reference populations. Tests for positive selection revealed ten nonsynonymous polymorphisms in AHR1 and four in AHR2. Four nonsynonymous SNPs in AHR1 and three in AHR2 showed large differences in base frequency between New Bedford Harbor and its reference site. Tests for isolation-by-distance revealed evidence for non-neutral change at the AHR2 locus. Conclusion Together, these data suggest that F. heteroclitus populations in reference and polluted sites have similar genetic diversity, providing no evidence for strong genetic bottlenecks for populations in polluted locations. However, the data provide evidence for genetic differentiation among sites, selection at specific nucleotides in AHR1 and AHR2, and specific AHR2 SNPs and haplotypes that are associated with the PCB-resistant phenotype in the New Bedford Harbor population. The results suggest that AHRs, and especially AHR2, may be important, recurring targets for selection in local adaptation to dioxin-like aromatic hydrocarbon contaminants.
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Affiliation(s)
| | | | | | | | | | | | | | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02568, USA.
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13
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Proestou DA, Flight P, Champlin D, Nacci D. Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic killifish (Fundulus heteroclitus). BMC Evol Biol 2014; 14:7. [PMID: 24422627 PMCID: PMC4029433 DOI: 10.1186/1471-2148-14-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed. Results Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs. Conclusions The observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance.
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Affiliation(s)
- Dina A Proestou
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882, USA.
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Bozinovic G, Sit TL, Di Giulio R, Wills LF, Oleksiak MF. Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences. BMC Genomics 2013; 14:779. [PMID: 24215130 PMCID: PMC3835409 DOI: 10.1186/1471-2164-14-779] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/26/2013] [Indexed: 12/31/2022] Open
Abstract
Background Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explain these phenotypic changes. Embryos from a population of the teleost fish, Fundulus heteroclitus, inhabiting a clean estuary do not survive when exposed to sediment extract from a site highly contaminated with polycyclic aromatic hydrocarbons (PAHs) while embryos derived from a population inhabiting a PAH polluted estuary are remarkably resistant to the polluted sediment extract. We exposed embryos from these two populations to surrogate model PAHs and analyzed changes in gene expression, morphology, and cardiac physiology in order to better understand sensitivity and adaptive resistance mechanisms mediating PAH exposure during development. Results The synergistic effects of two model PAHs, an aryl hydrocarbon receptor (AHR) agonist (β-naphthoflavone) and a cytochrome P4501A (CYP1A) inhibitor (α-naphthoflavone), caused significant developmental delays, impaired cardiac function, severe morphological alterations and failure to hatch, leading to the deaths of reference embryos; resistant embryos were mostly unaffected. Unexpectedly, patterns of gene expression among normal and moderately deformed embryos were similar, and only severely deformed embryos showed a contrasting pattern of gene expression. Given the drastic morphological differences between reference and resistant embryos, a surprisingly low percentage of genes, 2.24% of 6,754 analyzed, show statistically significant differences in transcript levels during late organogenesis between the two embryo populations. Conclusions Our study demonstrates important contrasts in responses between reference and resistant natural embryo populations to synergistic effects of surrogate model PAHs that may be important in adaptive mechanisms mediating PAH effects during fish embryo development. These results suggest that statistically significant changes in gene expression of relatively few genes contribute to the phenotypic changes and large morphological differences exhibited by reference and resistant populations upon exposure to PAH pollutants. By correlating cardiac physiology and morphology with changes in gene expression patterns of reference and resistant embryos, we provide additional evidence for acquired resistance among embryos whose parents live at heavily contaminated sites.
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Affiliation(s)
- Goran Bozinovic
- Department of Environmental and Molecular Toxicology, North Carolina State University, Box 7633, Raleigh, NC 27695-7633, USA.
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15
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Bélanger-Deschênes S, Couture P, Campbell PGC, Bernatchez L. Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens). ECOTOXICOLOGY (LONDON, ENGLAND) 2013; 22:938-957. [PMID: 23722603 DOI: 10.1007/s10646-013-1083-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/30/2013] [Indexed: 06/02/2023]
Abstract
Pollution can drive rapid evolutionary change in wild populations. This study targets functional polymorphisms of chronically metal-contaminated wild yellow perch (Perca flavescens). A de novo transcriptome scan contrasted subsets of individuals from clean (n = 16) and contaminated (n = 16) lakes to identify 87 candidate annotated coding SNPs. Candidate genotypes and liver [metal] were obtained in 10 populations (n = 1,052) and a genome scan distinguished outliers: one nuclear (cyclin G1 gene) and two mitochondrial (cytochrome b and NADH dehydrogenase subunit 2 genes) also displaying allelic correlation to mean population [cadmium]. Whole mtDNA and 17 kb surrounding cyclin G1 were characterised through 454 sequencing thus revealing two non-synonymous substitutions involving dissimilar amino acids. Based on associated functions and inter-population differentiation, contaminated perch may have been selected for fast life cycle completion (p53 pathway) and memorization impairment mitigation (long-term potentiation pathway). In accordance with predicted evolutionary trajectory for stressed and energy deprived organisms, adapted perch would not compensate for repair mechanism inhibition, instead reallocating energy towards growth and favouring inexpensive impairment mitigation adaptations over costly detoxification. Overall, 85 years of selection could have driven rapid, potentially adaptive evolution by selecting alleles increasing perch fitness in polluted environments.
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Affiliation(s)
- Sébastien Bélanger-Deschênes
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.
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16
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Abstract
In the presence of environmental change, natural selection can shape the transcriptome. Under a scenario of environmental change, genotypes that are better able to modulate gene expression to maximize fitness will tend to be favoured. Therefore, it is important to examine gene expression at the population level to distinguish random or neutral gene expression variation from the pattern produced by natural selection. This study investigates the natural variation in transcriptional response to a cactus host shift utilizing the mainland Sonora population of Drosophila mojavensis. Drosophila mojavensis is a cactophilic species composed of four cactus host populations endemic to the deserts of North America. Overall, the change in cactus host was associated with a significant reduction in larval viability as well as the differential expression of 21% of the genome (3109 genes). Among the genes identified were a set of genes previously known to be involved in xenobiotic metabolism, as well as genes involved in cellular energy production, oxidoreductase/carbohydrate metabolism, structural components and mRNA binding. Interestingly, of the 3109 genes whose expression was affected by host use, there was a significant overrepresentation of genes that lacked an orthologous call to the D. melanogaster genome, suggesting the possibility of an accelerated rate of evolution in these genes. Of the genes with a significant cactus effect, the majority, 2264 genes, did not exhibit a significant cactus-by-line interaction. This population-level approach facilitated the identification of genes involved in past cactus host shifts.
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Affiliation(s)
- Luciano M Matzkin
- Department of Biological Sciences, Huntsville, University of Alabama in Huntsville, AL 35899, USA.
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