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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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Guo W, He S, Liang X, Tian C, Dou Y, Lv L. A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using 2.3K genotyping-by-sequencing SNPs. Anim Genet 2021; 52:311-320. [PMID: 33598959 DOI: 10.1111/age.13046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2021] [Indexed: 11/27/2022]
Abstract
Chinese perch, Siniperca chuatsi (Basilewsky), is one of the most commercially important cultured fishes in China. In the present study, a high-density genetic linkage map of Chinese perch was constructed by genotyping-by-sequencing technique with an F1 mapping panel containing 190 progenies. A total of 2328 SNPs were assigned to 24 linkage groups (LGs), agreeing with the chromosome haploid number in this species (n = 24). The sex-averaged map covered 97.9% of the Chinese perch genome, with the length of 1694.3 cM and a marker density of 0.7 cM/locus. The number of markers per LG ranged from 57 to 222, with a mean of 97. The length of LGs varied from 43.2 to 108.2 cM, with a mean size of 70.6 cM. The recombination rate of females was 1.5:1, which was higher than that of males. To better understand the distribution pattern of segregation distortion between the two sexes of Chinese perch, the skewed markers were retained and used to reconstruct the sex-specific maps. The 16 segregation distortion regions were identified on 10 LGs of the female map, while 12 segregation distortion regions on eight LGs of the male map. Among these LGs, six LGs matched between the sex-specific maps. This high-density linkage map could provide a solid basis for identifying QTL associated with economically important traits, and for implementing marker-assisted selection breeding of Chinese perch.
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Affiliation(s)
- Wenjie Guo
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shan He
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xufang Liang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Changxu Tian
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yaqi Dou
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Liyuan Lv
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, China
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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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Barts N, Greenway R, Passow CN, Arias-Rodriguez L, Kelley JL, Tobler M. Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs. Genome 2018; 61:273-286. [DOI: 10.1139/gen-2017-0051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.
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Affiliation(s)
- Nicholas Barts
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Courtney N. Passow
- Ecology, Evolution and Behavior, University of Minnesota St. Paul, 205 Cargill Building, St. Paul, MN 55108, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México
| | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, 431 Heald Hall, Pullman, WA 99164, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
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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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Nacci D, Proestou D, Champlin D, Martinson J, Waits ER. Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species. Mol Ecol 2016; 25:5467-5482. [DOI: 10.1111/mec.13848] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 08/22/2016] [Accepted: 08/30/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Diane Nacci
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Dina Proestou
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Denise Champlin
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - John Martinson
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
| | - Eric R. Waits
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
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