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Kim J, Jung D, Chatterjee N, Clark B, Nacci D, Kim S, Choi J. Differential DNA methylation and metabolite profiling of Atlantic killifish (Fundulus heteroclitus) from the New Bedford Harbor Superfund site. ECOTOXICOLOGY (LONDON, ENGLAND) 2024; 33:22-33. [PMID: 38182934 PMCID: PMC10830762 DOI: 10.1007/s10646-023-02724-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/13/2023] [Indexed: 01/07/2024]
Abstract
Atlantic killifish (Fundulus heteroclitus) is a valuable model in evolutionary toxicology to study how the interactions between genetic and environmental factors serve the adaptive ability of organisms to resist chemical pollution. Killifish populations inhabiting environmental toxicant-contaminated New Bedford Harbor (NBH) show phenotypes tolerant to polychlorinated biphenyls (PCBs) and differences at the transcriptional and genomic levels. However, limited research has explored epigenetic alterations and metabolic effects in NBH killifish. To identify the involvement of epigenetic and metabolic regulation in the adaptive response of killifish, we investigated tissue- and sex-specific differences in global DNA methylation and metabolomic profiles of NBH killifish populations, compared to sensitive populations from a non-polluted site, Scorton Creek (SC). The results revealed that liver-specific global DNA hypomethylation and differential metabolites were evident in fish from NBH compared with those from SC. The sex-specific differences were not greater than the tissue-specific differences. We demonstrated liver-specific enriched metabolic pathways (e.g., amino acid metabolic pathways converged into the urea cycle and glutathione metabolism), suggesting possible crosstalk between differential metabolites and DNA hypomethylation in the livers of NBH killifish. Additional investigation of methylated gene regions is necessary to understand the functional role of DNA hypomethylation in the regulation of enzyme-encoding genes associated with metabolic processes and physiological changes in NBH populations.
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Affiliation(s)
- Jiwan Kim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Korea
| | - Dawoon Jung
- Korea Environment Institute, Division of Environmental Health, Sejong, 30147, Korea
| | - Nivedita Chatterjee
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Korea
- NanoSafety Group, International Iberian Nanotechnology Laboratory, Av. Mestre Jose Veiga s/n, 4715-330, Braga, Portugal
| | - Bryan Clark
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, RI, USA
| | - Diane Nacci
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, RI, USA
| | - Suhkmann Kim
- Department of Chemistry, Center for Proteome Biophysics and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Korea.
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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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3
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Assad J, Cho S, Dileo V, Gascoigne G, Hubberstey AV, Patterson D, Williams R. Contaminated sediment in the Detroit River provokes acclimated responses in wild brown bullhead (Ameiurus nebulosus) populations. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 265:106772. [PMID: 38039693 DOI: 10.1016/j.aquatox.2023.106772] [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: 06/26/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
In a previous study, adaptive responses to a single polycyclic aromatic hydrocarbon (PAH), benzo[a]pyrene (BaP), were identified in brown bullhead (Ameiurus nebulosus) captured from contaminated sites across the Great Lakes. The tumor suppressor p53 and phase I toxin metabolizing CYP1A genes showed a elevated and refractory response, respectively, up to the F1 generation (Williams and Hubberstey, 2014). As an extension to the first study, bullhead were exposed to sediment collected from sites along the Detroit River to see if these adaptive responses are attainable when fish from a contaminated site are exposed to a mixture of contaminants, instead of a single compound. p53 and CYP1A proteins were measured again with the addition of phase II glutathione-s-transferase (GST) activity in the present study. Three treatment groups were measured: acute (treated immediately), cleared (depurated for three months and subsequent treatment), and farm raised F1 offspring. All three treatment groups were exposed to clean and contaminated sediment for 24 and 96 h. Acute fish from contaminated sites exposed to contaminated sediment revealed an initial elevated p53 response that did not persist in fish after long-term contaminated sediment exposure. Acute fish from contaminated sites exposed to contaminated sediment revealed refractory CYP1A expression, which disappeared in cleared fish and whose F1 response overlapped with clean site F1 offspring. Decreasing GST activity was evident in both clean and contaminated fish over time, and only clean site fish responded to long-term contaminated sediment deliberately with increasing GST activity. Because p53 and CYP1A gene expression and GST activity responses did not overlap between contaminated fish treatment groups, our study suggests that contaminated fish have acclimated to the contaminants present in their environments and no evidence of adaptation could be detected within these biomarkers.
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Affiliation(s)
- J Assad
- The College of Wooster 1189 Beall Ave., Wooster, Ohio 44691, United States
| | - S Cho
- Department of Biology, University of Windsor, Windsor, ON N9B3P4, Canada
| | - V Dileo
- The College of Wooster 1189 Beall Ave., Wooster, Ohio 44691, United States
| | - G Gascoigne
- The College of Wooster 1189 Beall Ave., Wooster, Ohio 44691, United States
| | - A V Hubberstey
- Department of Biolomedical Sciences, University of Windsor, Windsor, ON N9B3P4, Canada
| | - D Patterson
- The College of Wooster 1189 Beall Ave., Wooster, Ohio 44691, United States
| | - R Williams
- Department of Biology, University of Windsor, Windsor, ON N9B3P4, Canada.
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4
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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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5
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Rackliffe DR, Hoverman JT. Population-level variation in pesticide tolerance predicts survival under field conditions in mayflies. ECOTOXICOLOGY (LONDON, ENGLAND) 2022; 31:1477-1484. [PMID: 36352273 DOI: 10.1007/s10646-022-02603-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
An increasing number of studies have found tolerance variation in populations consistently exposed to contaminants, but few studies have examined whether these laboratory-derived estimates of tolerance have survival implications in field conditions. We examined four populations of the mayfly Stenacron interpunctatum for variation in tolerance to the common agricultural insecticide clothianidin. Using laboratory bioassays, we found a 2.3× range in 96 h EC50 tolerance values to clothianidin between our four populations. We then conducted a common-garden experiment with nymphs from each population placed into the collection stream most heavily impacted by upstream agricultural activities to assess whether our laboratory tolerance estimates predict survival under field conditions. We monitored survival and growth in situ for three weeks during the spring planting season, when clothianidin is applied to croplands upstream of our study site. While growth was similar across all groups, the most tolerant population, which was native to the impacted stream, had higher survival than the more sensitive populations. This suggests that population-level variation in contaminant tolerance as measured in laboratory bioassays could have real-world survival implications for sensitive aquatic macroinvertebrates in contaminated streams.
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Affiliation(s)
- D Riley Rackliffe
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA.
| | - Jason T Hoverman
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
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6
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Burraco P, Orizaola G. Ionizing radiation and melanism in Chornobyl tree frogs. Evol Appl 2022; 15:1469-1479. [PMID: 36187188 PMCID: PMC9488684 DOI: 10.1111/eva.13476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
Human actions are altering ecosystems worldwide. Among human‐released pollutants, ionizing radiation arises as a rare but potentially devastating threat to natural systems. The Chornobyl accident (1986) represents the largest release of radioactive material to the environment. Our aim was to examine how exposure to radiation from the Chornobyl accident influences dorsal skin coloration of Eastern tree frog (Hyla orientalis) males sampled across a wide gradient of radioactive contamination in northern Ukraine. We assessed the relationship between skin frog coloration (which can act as a protective mechanism against ionizing radiation), radiation conditions and oxidative stress levels. Skin coloration was darker in localities closest to areas with high radiation levels at the time of the accident, whereas current radiation levels seemed not to influence skin coloration in Chornobyl tree frogs. Tree frogs living within the Chornobyl Exclusion Zone had a remarkably darker dorsal skin coloration than frogs from outside the Zone. The maintenance of dark skin coloration was not linked to physiological costs in terms of frog body condition or oxidative status, and we did not detect short‐term changes in frog coloration. Dark coloration is known to protect against different sources of radiation by neutralizing free radicals and reducing DNA damage, and, particularly melanin pigmentation has been proposed as a buffering mechanism against ionizing radiation. Our results suggest that exposure to high levels of ionizing radiation, likely at the time of the accident, may have been selected for darker coloration in Chornobyl tree frogs. Further studies are needed to determine the underlying mechanisms and evolutionary consequences of the patterns found here.
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Affiliation(s)
- Pablo Burraco
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre Uppsala University Uppsala Sweden
- Doñana Biological Station (CSIC), 41092 Seville Spain
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences University of Glasgow Glasgow UK
| | - Germán Orizaola
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre Uppsala University Uppsala Sweden
- IMIB‐Biodiversity Research Institute (Univ. Oviedo‐CSIC‐Princip. Asturias) University of Oviedo Mieres ‐Asturias Spain
- Zoology Unit, Department of Biology of Organisms and Systems University of Oviedo Oviedo ‐Asturias Spain
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7
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Cheek RG, Forester BR, Salerno PE, Trumbo DR, Chen N, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species. Mol Ecol 2022; 31:2830-2846. [PMID: 35315161 PMCID: PMC9325526 DOI: 10.1111/mec.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
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Affiliation(s)
- Rebecca G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20013, USA
| | | | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
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8
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Zhang W, Xie HQ, Li Y, Zhou M, Zhou Z, Wang R, Hahn ME, Zhao B. The aryl hydrocarbon receptor: A predominant mediator for the toxicity of emerging dioxin-like compounds. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128084. [PMID: 34952507 PMCID: PMC9039345 DOI: 10.1016/j.jhazmat.2021.128084] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/29/2021] [Accepted: 12/12/2021] [Indexed: 06/01/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a member of the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcription factors and has broad biological functions. Early after the identification of the AHR, most studies focused on its roles in regulating the expression of drug-metabolizing enzymes and mediating the toxicity of dioxins and dioxin-like compounds (DLCs). Currently, more diverse functions of AHR have been identified, indicating that AHR is not just a dioxin receptor. Dioxins and DLCs occur ubiquitously and have diverse health/ecological risks. Additional research is required to identify both shared and compound-specific mechanisms, especially for emerging DLCs such as polyhalogenated carbazoles (PHCZs), polychlorinated diphenyl sulfides (PCDPSs), and others, of which only a few investigations have been performed at present. Many of the toxic effects of emerging DLCs were observed to be predominantly mediated by the AHR because of their structural similarity as dioxins, and the in vitro TCDD-relative potencies of certain emerging DLC congeners are comparable to or even greater than the WHO-TEFs of OctaCDD, OctaCDF, and most coplanar PCBs. Due to the close relationship between AHR biology and environmental science, this review begins by providing novel insights into AHR signaling (canonical and non-canonical), AHR's biochemical properties (AHR structure, AHR-ligand interaction, AHR-DNA binding), and the variations during AHR transactivation. Then, AHR ligand classification and the corresponding mechanisms are discussed, especially the shared and compound-specific, AHR-mediated effects and mechanisms of emerging DLCs. Accordingly, a series of in vivo and in vitro toxicity evaluation methods based on the AHR signaling pathway are reviewed. In light of current advances, future research on traditional and emerging DLCs will enhance our understanding of their mechanisms, toxicity, potency, and ecological impacts.
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Affiliation(s)
- Wanglong Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Heidi Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunping Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingxi Zhou
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Zhiguang Zhou
- State Environmental Protection Key Laboratory of Dioxin Pollution Control, National Research Center for Environmental Analysis and Measurement, Beijing 100029, China
| | - Renjun Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA; Boston University Superfund Research Program, Boston University, Boston, MA 02118, USA
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Wild Zebrafish Sentinels: Biological Monitoring of Site Differences Using Behavior and Morphology. TOXICS 2021; 9:toxics9070165. [PMID: 34357908 PMCID: PMC8309768 DOI: 10.3390/toxics9070165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/03/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022]
Abstract
Environmental change poses a devastating risk to human and environmental health. Rapid assessment of water conditions is necessary for monitoring, evaluating, and addressing this global health danger. Sentinels or biological monitors can be deployed in the field using minimal resources to detect water quality changes in real time, quickly and cheaply. Zebrafish (Danio rerio) are ideal sentinels for detecting environmental changes due to their biomedical tool kit, widespread geographic distribution, and well-characterized phenotypic responses to environmental disturbances. Here, we demonstrate the utility of zebrafish sentinels by characterizing phenotypic differences in wild zebrafish between two field sites in India. Site 1 was a rural environment with flowing water, low-hypoxic conditions, minimal human-made debris, and high iron and lead concentrations. Site 2 was an urban environment with still water, hypoxic conditions, plastic pollution, and high arsenic, iron, and chromium concentrations. We found that zebrafish from Site 2 were smaller, more cohesive, and less active than Site 1 fish. We also found sexually dimorphic body shapes within the Site 2, but not the Site 1, population. Advancing zebrafish sentinel research and development will enable rapid detection, evaluation, and response to emerging global health threats.
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10
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Celander MC, Goldstone JV, Brun NR, Clark B, Jayaraman S, Nacci D, Stegeman JJ. Resistance to Cyp3a induction by polychlorinated biphenyls, including non-dioxin-like PCB153, in gills of killifish (Fundulus heteroclitus) from New Bedford Harbor. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 83:103580. [PMID: 33429071 PMCID: PMC8374885 DOI: 10.1016/j.etap.2020.103580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/19/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Previous reports suggested that non-dioxin-like (NDL) PCB153 effects on cytochrome P450 3A (Cyp3a) expression in Atlantic killifish (Fundulus heteroclitus) gills differed between F0 generation fish from a PCB site (New Bedford Harbor; NBH) and a reference site (Scorton Creek; SC). Here, we examined effects of PCB153, dioxin-like (DL) PCB126, or a mixture of both, on Cyp3a56 mRNA in killifish generations removed from the wild, without environmental PCB exposures. PCB126 effects in liver and gills differed between populations, as expected. Gill Cyp3a56 was not affected by either congener in NBH F2 generation fish, but was induced by PCB153 in SC F1 fish, with females showing a greater response. PCB153 did not affect Cyp3a56 in liver of either population. Results suggest a heritable resistance to NDL-PCBs in killifish from NBH, in addition to that reported for DL PCBs. Induction of Cyp3a56 in gills may be a biomarker of exposure to NDL PCBs in fish populations that are not resistant to PCBs.
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Affiliation(s)
- Malin C Celander
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE 405 30, Gothenburg, Sweden; Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
| | - Jared V Goldstone
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Nadja R Brun
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Bryan Clark
- United States Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI, 02882, USA
| | - Saro Jayaraman
- United States Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI, 02882, USA
| | - Diane Nacci
- United States Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI, 02882, USA
| | - John J Stegeman
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
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11
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Adaptive Evolution in Cities: Progress and Misconceptions. Trends Ecol Evol 2020; 36:239-257. [PMID: 33342595 DOI: 10.1016/j.tree.2020.11.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022]
Abstract
Current narratives suggest that urban adaptation - the adaptive evolution of organisms to cities - is pervasive across taxa and cities. However, in reviewing hundreds of studies, we find only six comprehensive examples of species adaptively evolving to urbanization. We discuss the utility and shortcomings of methods for studying urban adaptation. We then review diverse systems offering preliminary evidence for urban adaptation and outline a research program for advancing its study. Urban environments constitute diverse, interacting selective agents that test the limits of adaptation. Understanding urban adaptation therefore offers unique opportunities for addressing fundamental questions in evolutionary biology and for better conserving biodiversity in cities. However, capitalizing on these opportunities requires appropriate research methods and dissemination of accurate narratives.
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12
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Emami-Khoyi A, Parbhu SP, Ross JG, Murphy EC, Bothwell J, Monsanto DM, Vuuren BJV, Teske PR, Paterson AM. De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums ( Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control. Genes (Basel) 2020; 11:genes11040436. [PMID: 32316496 PMCID: PMC7230921 DOI: 10.3390/genes11040436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
The common brushtail possum (Trichosurus vulpecula), introduced from Australia in the mid-nineteenth century, is an invasive species in New Zealand where it is widespread and forms the largest self-sustained reservoir of bovine tuberculosis (Mycobacterium bovis) among wild populations. Conservation and agricultural authorities regularly apply a series of population control measures to suppress brushtail possum populations. The evolutionary consequence of more than half a century of intensive population control operations on the species’ genomic diversity and population structure is hindered by a paucity of available genomic resources. This study is the first to characterise the functional content and diversity of brushtail possum liver and brain cerebral cortex transcriptomes. Raw sequences from hepatic cells and cerebral cortex were assembled into 58,001 and 64,735 transcripts respectively. Functional annotation and polymorphism assignment of the assembled transcripts demonstrated a considerable level of variation in the core metabolic pathways that represent potential targets for selection pressure exerted by chemical toxicants. This study suggests that the brushtail possum population in New Zealand harbours considerable variation in metabolic pathways that could potentially promote the development of tolerance against chemical toxicants.
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Affiliation(s)
- Arsalan Emami-Khoyi
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Shilpa Pradeep Parbhu
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - James G Ross
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Elaine C Murphy
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jennifer Bothwell
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Daniela M Monsanto
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Bettine Jansen van Vuuren
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Peter R Teske
- Center for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa
| | - Adrian M Paterson
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
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13
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Oziolor EM, DeSchamphelaere K, Lyon D, Nacci D, Poynton H. Evolutionary Toxicology-An Informational Tool for Chemical Regulation? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2020; 39:257-268. [PMID: 31978273 PMCID: PMC7885860 DOI: 10.1002/etc.4611] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Elias M Oziolor
- Department of Environmental Toxicology, University of California at Davis, Davis, CA, USA
| | - Karel DeSchamphelaere
- Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab Unit, Ghent University, Gent, Belgium
| | - Delina Lyon
- Shell Health, Shell Oil Company, Houston, TX, USA
| | - Diane Nacci
- Atlantic Coastal Environmental Sciences Division, Center for Environmental Measurements and Modeling, Office of Research and Development, US Environmental Protection Agency, Narragansett, RI, USA
| | - Helen Poynton
- School for the Environment, University of Massachusetts Boston, Boston, MA, USA
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14
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Abstract
Quantitative trait loci (QTL) are genetic regions that influence phenotypic variation of a complex trait, often through genetic interactions with each other and the environment. These are commonly identified through a statistical genetic analysis known as QTL mapping. Here, I present a step-by-step, practical approach to QTL mapping along with a sample data file. I focus on methods commonly used and discoveries that have been made in fishes, and utilize a multiple QTL mapping (MQM) approach in the free software package R/qtl.
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Affiliation(s)
- Kara E Powder
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.
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15
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Developing a High-Quality Linkage Map for the Atlantic Killifish Fundulus heteroclitus. G3-GENES GENOMES GENETICS 2019; 9:2851-2862. [PMID: 31289021 PMCID: PMC6723127 DOI: 10.1534/g3.119.400262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Killifish (Fundulus heteroclitus) are widely distributed among different aquatic environments where they demonstrate an impressive range of highly-plastic and locally adaptive phenotypes. High-throughput sequencing has begun to unravel the mechanisms and evolutionary history of these interesting features by establishing relationships in the genotype-phenotype map. However, some genotype-phenotype analyses require a higher order of contiguity than what initial scaffolded (fragmented genome assembly where contigs have been assemble into scaffolds) genome assemblies can provide. Here, we used 5,685 high-quality RAD-Seq markers from a single mapping family to order 84% of the scaffolded genome assembly to 24 chromosomes. This serves to: 1) expand the killifish genomic toolkit, 2) estimate genome-wide recombination rates, and 3) compare genome synteny to humans and other fishes. After initially building our map, we found that the selection of thresholds for sequence data filtration highly impacted scaffold placement in the map. We outline each step of the approach that dramatically improved our map to help guide others toward more effective linkage mapping for genome assembly. Our final map supports strong conservation of genomic synteny among closely related fish species and reveals previously described chromosomal rearrangements between more distantly related clades. However, we also commonly found minor scaffold misorientations in F. heteroclitus and in other assemblies, suggesting that further mapping (such as optical mapping) is necessary for finer scale resolution of genome structure. Lastly, we discuss the problems that would be expected from misoriented/unplaced scaffolds and stress the importance of a quality mapped genome as a key feature for further investigating population and comparative genomic questions with F. heteroclitus and other taxa.
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16
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Demin KA, Lakstygal AM, Alekseeva PA, Sysoev M, de Abreu MS, Alpyshov ET, Serikuly N, Wang D, Wang M, Tang Z, Yan D, Strekalova TV, Volgin AD, Amstislavskaya TG, Wang J, Song C, Kalueff AV. The role of intraspecies variation in fish neurobehavioral and neuropharmacological phenotypes in aquatic models. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 210:44-55. [PMID: 30822702 DOI: 10.1016/j.aquatox.2019.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Intraspecies variation is common in both clinical and animal research of various brain disorders. Relatively well-studied in mammals, intraspecies variation in aquatic fish models and its role in their behavioral and pharmacological responses remain poorly understood. Like humans and mammals, fishes show high variance of behavioral and drug-evoked responses, modulated both genetically and environmentally. The zebrafish (Danio rerio) has emerged as a particularly useful model organism tool to access neurobehavioral and drug-evoked responses. Here, we discuss recent findings and the role of the intraspecies variance in neurobehavioral, pharmacological and toxicological studies utilizing zebrafish and other fish models. We also critically evaluate common sources of intraspecies variation and outline potential strategies to improve data reproducibility and translatability.
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Affiliation(s)
- Konstantin A Demin
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton M Lakstygal
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Polina A Alekseeva
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Maxim Sysoev
- Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Murilo S de Abreu
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Bioscience Institute, University of Passo Fundo, Passo Fundo, RS, Brazil
| | | | - Nazar Serikuly
- School of Pharmacy, Southwest University, Chongqing, China
| | - DongMei Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - MengYao Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - ZhiChong Tang
- School of Pharmacy, Southwest University, Chongqing, China
| | - DongNi Yan
- School of Pharmacy, Southwest University, Chongqing, China
| | - Tatyana V Strekalova
- Department of Neuroscience, Maastricht University, Maastricht, Netherlands; Laboratory of Psychiatric Neurobiology and Department of Normal Physiology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Andrey D Volgin
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia
| | | | - JiaJia Wang
- Research Institute of Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Cai Song
- Research Institute of Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China; Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Ural Federal University, Ekaterinburg, Russia; ZENEREI Research Center, Slidell, LA, USA; Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia.
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17
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Huang W, Bencic DC, Flick RL, Nacci DE, Clark BW, Burkhard L, Lahren T, Biales AD. Characterization of the Fundulus heteroclitus embryo transcriptional response and development of a gene expression-based fingerprint of exposure for the alternative flame retardant, TBPH (bis (2-ethylhexyl)-tetrabromophthalate). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:696-705. [PMID: 30721860 PMCID: PMC7495336 DOI: 10.1016/j.envpol.2019.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 05/07/2023]
Abstract
Although alternative Flame Retardant (FR) chemicals are expected to be safer than the legacy FRs they replace, their risks to human health and the environment are often poorly characterized. This study used a small volume, fish embryo system to reveal potential mechanisms of action and diagnostic exposure patterns for TBPH (bis (2-ethylhexyl)-tetrabromophthalate), a component of several widely-used commercial products. Two different concentration of TBPH were applied to sensitive early life stages of an ecologically important test species, Fundulus heteroclitus (Atlantic killifish), with a well-annotated genome. Exposed fish embryos were sampled for transcriptomics or chemical analysis of parent compound and primary metabolite or observed for development and survival through larval stage. Global transcript profiling using RNA-seq was conducted (n = 16 per treatment) to provide a non-targeted and statistically robust approach to characterize TBPH gene expression patterns. Transcriptomic analysis revealed a dose-response in the expression of genes associated with a surprisingly limited number of biological pathways, but included the aryl hydrocarbon receptor signal transduction pathway, which is known to respond to several toxicologically-important chemical classes. A transcriptional fingerprint using Random Forests was developed that was able to perfectly discriminate exposed vs. non-exposed individuals in test sets. These results suggest that TBPH has a relatively low potential for developmental toxicity (at least in fishes), despite concerns related to its structural similarities to endocrine disrupting chemicals and that the early life stage Fundulus system may provide a convenient test system for exposure characterization. More broadly, this study advances the usefulness of a biological testing and analysis system utilizing non-targeted transcriptomics profiling and early developmental endpoints that complements current screening methods to characterize chemicals of ecological and human health concern.
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Affiliation(s)
- Weichun Huang
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - David C Bencic
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Robert L Flick
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Diane E Nacci
- U.S. EPA National Health and Environmental Effects Research Laboratory, 27 Tarzwell Drive Narragansett, RI, 02882, USA
| | - Bryan W Clark
- U.S. EPA National Health and Environmental Effects Research Laboratory, 27 Tarzwell Drive Narragansett, RI, 02882, USA
| | - Lawrence Burkhard
- U.S. EPA National Health and Environmental Effects Research Laboratory, 6201 Congdon Boulevard, Duluth, MN, 55804, USA
| | - Tylor Lahren
- U.S. EPA National Health and Environmental Effects Research Laboratory, 6201 Congdon Boulevard, Duluth, MN, 55804, USA
| | - Adam D Biales
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA.
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18
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Volkova PY, Geras'kin SA. 'Omic' technologies as a helpful tool in radioecological research. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 189:156-167. [PMID: 29677564 DOI: 10.1016/j.jenvrad.2018.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.
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Affiliation(s)
- Polina Yu Volkova
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia.
| | - Stanislav A Geras'kin
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia
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19
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Murphy CA, Nisbet RM, Antczak P, Garcia-Reyero N, Gergs A, Lika K, Mathews T, Muller EB, Nacci D, Peace A, Remien CH, Schultz IR, Stevenson LM, Watanabe KH. Incorporating Suborganismal Processes into Dynamic Energy Budget Models for Ecological Risk Assessment. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2018; 14:615-624. [PMID: 29870141 PMCID: PMC6643959 DOI: 10.1002/ieam.4063] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/27/2018] [Accepted: 05/31/2018] [Indexed: 05/19/2023]
Abstract
A working group at the National Institute for Mathematical and Biological Synthesis (NIMBioS) explored the feasibility of integrating 2 complementary approaches relevant to ecological risk assessment. Adverse outcome pathway (AOP) models provide "bottom-up" mechanisms to predict specific toxicological effects that could affect an individual's ability to grow, reproduce, and/or survive from a molecular initiating event. Dynamic energy budget (DEB) models offer a "top-down" approach that reverse engineers stressor effects on growth, reproduction, and/or survival into modular characterizations related to the acquisition and processing of energy resources. Thus, AOP models quantify linkages between measurable molecular, cellular, or organ-level events, but they do not offer an explicit route to integratively characterize stressor effects at higher levels of organization. While DEB models provide the inherent basis to link effects on individuals to those at the population and ecosystem levels, their use of abstract variables obscures mechanistic connections to suborganismal biology. To take advantage of both approaches, we developed a conceptual model to link DEB and AOP models by interpreting AOP key events as measures of damage-inducing processes affecting DEB variables and rates. We report on the type and structure of data that are generated for AOP models that may also be useful for DEB models. We also report on case studies under development that merge information collected for AOPs with DEB models and highlight some of the challenges. Finally, we discuss how the linkage of these 2 approaches can improve ecological risk assessment, with possibilities for progress in predicting population responses to toxicant exposures within realistic environments. Integr Environ Assess Manag 2018;14:615-624. © 2018 SETAC.
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Affiliation(s)
- Cheryl A Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Roger M Nisbet
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Philipp Antczak
- Institute for Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, Mississippi
| | - Andre Gergs
- gaiac-Research Institute for Ecosystem Analysis and Assessment, Aachen, Germany
| | - Konstadia Lika
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Greece
| | - Teresa Mathews
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erik B Muller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Diane Nacci
- US Environmental Protection Agency, Office of Research and Development, Narragansett, Rhode Island
| | - Angela Peace
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, Texas, USA
| | | | - Irvin R Schultz
- Marine Sciences Lab, Pacific NW National Laboratory, Sequim, Washington, USA
- Present address: Lynker Technologies, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Louise M Stevenson
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USA
| | - Karen H Watanabe
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, Arizona, USA
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20
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Osterberg JS, Cammen KM, Schultz TF, Clark BW, Di Giulio RT. Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 200:73-82. [PMID: 29727773 PMCID: PMC6957077 DOI: 10.1016/j.aquatox.2018.04.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/21/2018] [Accepted: 04/24/2018] [Indexed: 05/09/2023]
Abstract
In many human-altered ecosystems, organisms are increasingly faced with more diverse and complex environmental stressors and pollutant mixtures, to which the adaptations necessary to survive exposure are likely to be numerous and varied. Improving our understanding of the molecular mechanisms that underlie complex polygenic adaptations in natural settings requires significant toxicological, biochemical, physiological, and genomic data rarely available for non-model organisms. Here, we build upon two decades of study of adaptation to anthropogenic pollutants in a population of Atlantic killifish (Fundulus heteroclitus) that inhabits the creosote-contaminated Atlantic Wood Industries Superfund (AW) site on the Elizabeth River, Virginia in the United States. To better understand the genotypes that underlie previously characterized resistance to PCBs and PAHs, we performed Restriction site-Associated DNA sequencing (RADseq) on killifish from AW and two relatively clean reference sites (King's Creek-KC, and Mains Creek-MC). Across the genome, we analyzed over 83,000 loci and 12,000 single nucleotide polymorphisms (SNPs). Shared across both comparisons of killifish from polluted (AW) and relatively unpolluted (KC and MC) sites, we found eight genomic regions with smoothed FST values significantly (p < 0.001) elevated above background. Using the recently published F. heteroclitus reference genome, we identified candidate genes in these significant regions involved in the AHR pathway (e.g. AIP, ARNT1c), as well as genes relating to cardiac structure and function. These genes represent both previously characterized and potentially novel molecular adaptations involved with various aspects of resistance to these environmental toxins.
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Affiliation(s)
- J S Osterberg
- Duke University, Nicholas School of the Environment, Duke Superfund Research Center, Durham, NC, 27708, USA; Duke University, Nicholas School of the Environment, Duke Marine Lab, Beaufort, NC, 28516, USA.
| | - K M Cammen
- Duke University, Nicholas School of the Environment, Duke Marine Lab, Beaufort, NC, 28516, USA
| | - T F Schultz
- Duke University, Nicholas School of the Environment, Duke Marine Lab, Beaufort, NC, 28516, USA
| | - B W Clark
- Duke University, Nicholas School of the Environment, Duke Superfund Research Center, Durham, NC, 27708, USA
| | - R T Di Giulio
- Duke University, Nicholas School of the Environment, Duke Superfund Research Center, Durham, NC, 27708, USA
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21
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Nunez JCB, Biancani LM, Flight PA, Nacci DE, Rand DM, Crawford DL, Oleksiak MF. Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171532. [PMID: 29892357 PMCID: PMC5990737 DOI: 10.1098/rsos.171532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/02/2018] [Indexed: 05/15/2023]
Abstract
Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.
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Affiliation(s)
- Joaquin C. B. Nunez
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Leann M. Biancani
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Patrick A. Flight
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Diane E. Nacci
- Population Ecology Branch, Atlantic Ecology Division, Office of Research and Development, US Environmental Protection Agency, 27 Tarzwell Drive, Narragansett, RI 02882, USA
| | - David M. Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI 02912, USA
| | - Douglas L. Crawford
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Marjorie F. Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
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22
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González-Pech RA, Ragan MA, Chan CX. Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Sci Rep 2017; 7:15021. [PMID: 29101370 PMCID: PMC5670126 DOI: 10.1038/s41598-017-15029-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/19/2017] [Indexed: 12/02/2022] Open
Abstract
Symbiodinium is best-known as the photosynthetic symbiont of corals, but some clades are symbiotic in other organisms or include free-living forms. Identifying similarities and differences among these clades can help us understand their relationship with corals, and thereby inform on measures to manage coral reefs in a changing environment. Here, using sequences from 24 publicly available transcriptomes and genomes of Symbiodinium, we assessed 78,389 gene families in Symbiodinium clades and the immediate outgroup Polarella glacialis, and identified putative overrepresented functions in gene families that (1) distinguish Symbiodinium from other members of Order Suessiales, (2) are shared by all of the Symbiodinium clades for which we have data, and (3) based on available information, are specific to each clade. Our findings indicate that transmembrane transport, mechanisms of response to reactive oxygen species, and protection against UV radiation are functions enriched in all Symbiodinium clades but not in P. glacialis. Enrichment of these functions indicates the capability of Symbiodinium to establish and maintain symbiosis, and to respond and adapt to its environment. The observed differences in lineage-specific gene families imply extensive genetic divergence among clades. Our results provide a platform for future investigation of lineage- or clade-specific adaptation of Symbiodinium to their environment.
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Affiliation(s)
- Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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23
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Whitehead A, Clark BW, Reid NM, Hahn ME, Nacci D. When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish ( Fundulus heteroclitus) populations. Evol Appl 2017; 10:762-783. [PMID: 29151869 PMCID: PMC5680427 DOI: 10.1111/eva.12470] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022] Open
Abstract
For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human‐mediated environmental changes, including environmental pollution. Here we review how key features of populations, the characteristics of environmental pollution, and the genetic architecture underlying adaptive traits, may interact to shape the likelihood of evolutionary rescue from pollution. Large populations of Atlantic killifish (Fundulus heteroclitus) persist in some of the most contaminated estuaries of the United States, and killifish studies have provided some of the first insights into the types of genomic changes that enable rapid evolutionary rescue from complexly degraded environments. We describe how selection by industrial pollutants and other stressors has acted on multiple populations of killifish and posit that extreme nucleotide diversity uniquely positions this species for successful evolutionary adaptation. Mechanistic studies have identified some of the genetic underpinnings of adaptation to a well‐studied class of toxic pollutants; however, multiple genetic regions under selection in wild populations seem to reflect more complex responses to diverse native stressors and/or compensatory responses to primary adaptation. The discovery of these pollution‐adapted killifish populations suggests that the evolutionary influence of anthropogenic stressors as selective agents occurs widely. Yet adaptation to chemical pollution in terrestrial and aquatic vertebrate wildlife may rarely be a successful “solution to pollution” because potentially adaptive phenotypes may be complex and incur fitness costs, and therefore be unlikely to evolve quickly enough, especially in species with small population sizes.
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Affiliation(s)
- Andrew Whitehead
- Department of Environmental Toxicology University of California Davis Davis CA USA
| | - Bryan W Clark
- Atlantic Ecology Division National Health and Environmental Effects Research Laboratory Office of Research and Development Oak Ridge Institute for Science and Education US Environmental Protection Agency Narragansett RI USA
| | - Noah M Reid
- Department of Molecular and Cell Biology University of Connecticut Storrs CT USA
| | - Mark E Hahn
- Department of Biology Woods Hole Oceanographic Institution Woods Hole MA USA.,Superfund Research Program Boston University Boston MA USA
| | - Diane Nacci
- Atlantic Ecology Division National Health and Environmental Effects Research Laboratory Office of Research and Development US Environmental Protection Agency Narragansett RI USA
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Oziolor EM, Bickham JW, Matson CW. Evolutionary toxicology in an omics world. Evol Appl 2017; 10:752-761. [PMID: 29151868 PMCID: PMC5680431 DOI: 10.1111/eva.12462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
Evolutionary toxicology is a young field that has grown rapidly in the past two decades. The potential of this field comes from the ability to link chemical contamination to multigenerational and population-wide effects in various species. The advancements and rapidly decreasing costs of -omic tools are improving the power and resolution of evolutionary toxicology studies. In this manuscript, we aim to address the trajectories and perspectives for conducting evolutionary toxicology studies with -omic approaches. We discuss the complementarity of using multiple -omic tools (genomics, eDNA, transcriptomics, proteomics, and metabolomics) for utility in understanding the toxicological relevance of adaptive responses in populations. In addition, we discuss phenotypic plasticity and its relevance to transcriptomic studies in toxicology. As evolutionary toxicology grows and expands its capacity to link toxicology with population-wide end points, we emphasize the applications of such studies in answering questions about ecological and population health, as well as future applicability to regulation. Thus, we aim to emphasize the enormous potential for evolutionary toxicology in an -omics world and give perspectives on the directions of future investigations.
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Affiliation(s)
- Elias M Oziolor
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
| | - John W Bickham
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
| | - Cole W Matson
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
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25
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Reid NM, Proestou DA, Clark BW, Warren WC, Colbourne JK, Shaw JR, Karchner SI, Hahn ME, Nacci D, Oleksiak MF, Crawford DL, Whitehead A. The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 2016; 354:1305-1308. [PMID: 27940876 PMCID: PMC5206662 DOI: 10.1126/science.aah4993] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/31/2016] [Indexed: 01/20/2023]
Abstract
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor-based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.
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Affiliation(s)
- Noah M Reid
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA
| | - Dina A Proestou
- Agricultural Research Service, U.S. Department of Agriculture, Kingston, RI 02881, USA
| | - Bryan W Clark
- Oak Ridge Institute for Science and Education, Office of Research and Development, U.S. Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - John K Colbourne
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Joseph R Shaw
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, USA
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Boston University Superfund Research Program, Boston University, Boston, MA 02118, USA
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Boston University Superfund Research Program, Boston University, Boston, MA 02118, USA
| | - Diane Nacci
- Office of Research and Development, U.S. Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Marjorie F Oleksiak
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Douglas L Crawford
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA.
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