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Miller JT, Clark BW, Reid NM, Karchner SI, Roach JL, Hahn ME, Nacci D, Whitehead A. Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect. Evol Appl 2024; 17:e13648. [PMID: 38293268 PMCID: PMC10824703 DOI: 10.1111/eva.13648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD-seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that one to two large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.
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Affiliation(s)
- Jeffrey T. Miller
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences InstituteUniversity of California, DavisDavisCaliforniaUSA
- Present address:
Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Bryan W. Clark
- Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences DivisionUS Environmental Protection AgencyNarragansettRhode IslandUSA
| | - Noah M. Reid
- Department of Molecular & Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Sibel I. Karchner
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Jennifer L. Roach
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences InstituteUniversity of California, DavisDavisCaliforniaUSA
| | - Mark E. Hahn
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Diane Nacci
- Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences DivisionUS Environmental Protection AgencyNarragansettRhode IslandUSA
| | - Andrew Whitehead
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences InstituteUniversity of California, DavisDavisCaliforniaUSA
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Sepp T, Baines C, Kreitsberg R, Scharsack JP, Nogueira P, Lang T, Fort J, Sild E, Clarke JT, Tuvikene A, Meitern R. Differences on the level of hepatic transcriptome between two flatfish species in response to liver cancer and environmental pollution levels. Comp Biochem Physiol C Toxicol Pharmacol 2024; 275:109781. [PMID: 37923151 DOI: 10.1016/j.cbpc.2023.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Environmental factors can cause cancer in both wild animals and humans. In ecological settings, genetic variation and natural selection can sometimes produce resilience to the negative impacts of environmental change. An increase in oncogenic substances in natural habitats has therefore, unintentionally, created opportunities for using polluted habitats to study cancer defence mechanisms. The Baltic and North Sea are among the most contaminated marine areas, with a long history of pollution. Two flatfish species (flounder, Platichthys flesus and dab, Limanda limanda) are used as ecotoxicological indicator species due to pollution-induced liver cancer. Cancer is more prevalent in dab, suggesting species-specific differences in vulnerability and/or defence mechanisms. We conducted gene expression analyses for 30 flatfishes. We characterize between- and within-species patterns in potential cancer-related mechanisms. By comparing cancerous and healthy fishes, and non-cancerous fishes from clean and polluted sites, we suggest also genes and related physiological mechanisms that could contribute to a higher resistance to pollution-induced cancer in flounders. We discovered changes in transcriptome related to elevated pollutant metabolism, alongside greater tumour suppression mechanisms in the liver tissue of flounders compared to dabs. This suggests either hormetic upregulation of tumour suppression or a stronger natural selection pressure for higher cancer resistance for flounders in polluted environment. Based on gene expression patterns seen in cancerous and healthy fish, for liver cancer to develop in flounders, genetic defence mechanisms need to be suppressed, while in dabs, analogous process is weak or absent. We conclude that wild species could offer novel insights and ideas for understanding the nature and evolution of natural cancer defence mechanisms.
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Affiliation(s)
- Tuul Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia. https://twitter.com/@TuulSeppLab
| | - Ciara Baines
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia; Estonian Marine Institute, University of Tartu, Mäealuse 14, 12618 Tallinn, Harju County, Estonia
| | - Randel Kreitsberg
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Jörn Peter Scharsack
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572 Bremerhaven, Germany
| | - Pedro Nogueira
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572 Bremerhaven, Germany
| | - Thomas Lang
- Thünen Institute of Fisheries Ecology, Herwigstraße 31, 27572 Bremerhaven, Germany
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR7266 CNRS - La Rochelle University, 2 rue Olympe de Gouges, 17000 La Rochelle, France
| | - Elin Sild
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - John T Clarke
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia; GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany; Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany; Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Arvo Tuvikene
- Estonian University of Life Sciences, Friedrich Reinhold Kreutzwaldi 1a, 51014 Tartu, Estonia
| | - Richard Meitern
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
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Miller JT, Clark BW, Reid NM, Karchner SI, Roach JL, Hahn ME, Nacci D, Whitehead A. Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536079. [PMID: 37066319 PMCID: PMC10104127 DOI: 10.1101/2023.04.07.536079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts the influence of few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that a few large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling, where some (but not all) of these QTL loci were shared across all populations, and some (but not all) of these loci showed signatures of recent natural selection in the corresponding wild population. Some strong candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.
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Affiliation(s)
- Jeffrey T Miller
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
| | - Bryan W Clark
- US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, RI
| | - Noah M Reid
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - Jennifer L Roach
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - Diane Nacci
- US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, RI
| | - Andrew Whitehead
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
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Chen C, Luo J, Shu X, Dai W, Guan M, Ma L. Spatio-temporal variations and ecological risks of organochlorine pesticides in surface waters of a plateau lake in China. CHEMOSPHERE 2022; 303:135029. [PMID: 35605728 DOI: 10.1016/j.chemosphere.2022.135029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Qilu Lake is one of the 9 plateau lakes in Yunnan, China, with a lake surface altitude of 1796.62 m above sea level. In spite of the importance and agriculturally-intensive phenomenon in Qilu Lake Basin, few studies have provided a modern evaluation of pesticide residues and potential effects to local aquatic organisms. The primary goal of this study was to determine the spatio-temporal variations of organochlorine pesticides (OCPs) in this area, and to further assess the related ecological risks. Of the 25 OCPs analyzed, 14 were detected, and the concentrations of ∑25OCPs were highest in the upstream of rivers, followed by regions close to the lake shore, and the lowest concentrations were found in Qilu Lake in every season except winter. The concentrations of ∑25OCPs were the highest in summer, and the lowest in winter. OCP concentrations in spring and in autumn were similar. 4,4'-DDD, γ-HCH, HCB, trans-chlordane, and cis-chlordane were 5 OCPs with relatively high risk in Qilu Lake Basin. Interestingly, higher OCP concentrations do not necessarily correspond to higher ecological risk levels. Low predicted no-effect concentration (PNEC) values and relatively high toxicity of these OCPs led to their high risk quotient (RQ) values. This work further illustrated that although OCPs have been banned for many years, they were still frequently detected in surface waters, and caused risks to aquatic animals.
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Affiliation(s)
- Chong Chen
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Jiahong Luo
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Xingquan Shu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China; Yunnan Construction and Investment Holding Group Co., Ltd., Kunming, 650501, PR China
| | - Wenshao Dai
- Yunnan Construction and Investment Holding Group Co., Ltd., Kunming, 650501, PR China
| | - Mengsha Guan
- Yunnan Construction and Investment Holding Group Co., Ltd., Kunming, 650501, PR China
| | - Limin Ma
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China.
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