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Cortés-Miranda J, Rojas-Hernández N, Muñoz G, Copaja S, Quezada-Romegialli C, Veliz D, Vega-Retter C. Biomarker selection depends on gene function and organ: the case of the cytochrome P450 family genes in freshwater fish exposed to chronic pollution. PeerJ 2024; 12:e16925. [PMID: 38371375 PMCID: PMC10874176 DOI: 10.7717/peerj.16925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024] Open
Abstract
Pollution and its effects have been of major concern in recent decades. Many strategies and markers have been developed to assess their effects on biota. Cytochrome P450 (CYP) genes have received significant attention in this context because of their relationship with detoxification and activation of exogenous compounds. While their expression has been identified as a pollution exposure biomarker, in most cases, it has been tested only after acute exposures and for CYP genes associated with exogenous compounds. To elucidate CYP gene expression patterns under chronic pollution exposure, we have used the silverside Basilichthys microlepidotus as a model, which inhabits the Maipo River Basin, a freshwater system with different pollution levels. We performed next-generation RNA sequencing of liver and gill tissues from polluted and non-polluted populations. We found most CYP genes were not dysregulated by pollution, and the seven genes that were present and differentially expressed in liver and gill were mainly downregulated. Three CYP genes associated with exogenous compounds showed differential expression in the gill, while four CYP genes associated with endogenous compounds showed differential expression in the liver. The findings presented here highlight the importance of CYP genes, his family, tissues and his interaction in the context of pollution biomarkers use.
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Affiliation(s)
- Jorge Cortés-Miranda
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Noemí Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
| | - Gigliola Muñoz
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Region Metropolitana, Chile
| | - Sylvia Copaja
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Region Metropolitana, Chile
| | - Claudio Quezada-Romegialli
- Laboratorio de Genómica y ADN ambiental, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Arica y Parinacota, Chile
| | - David Veliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
- Centro de Ecología y Manejo Sustentable de Islas Oceánicas., Coquimbo, Coquimbo, Chile
| | - Caren Vega-Retter
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Región Metropolitana, Chile
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Andersen LW, Jacobsen MW, Frydenberg J, Møller JD, Jensen TS. Phylogeography using mitogenomes: A rare Dipodidae,
Sicista betulina
, in North‐western Europe. Ecol Evol 2022; 12:e8865. [PMID: 35475180 PMCID: PMC9022092 DOI: 10.1002/ece3.8865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/11/2022] Open
Abstract
Repeated climatic and vegetation changes during the Pleistocene have shaped biodiversity in Northern Europe including Denmark. The Northern Birch Mouse (Sicista betulina) was one of the first small rodent species to colonize Denmark after the Late Glacial Maximum. This study analyses complete mitochondrial genomes and two nuclear genes of the Northern Birch Mouse to investigate the phylogeographical pattern in North‐western Europe and test whether the species colonized Denmark through several colonization events. The latter was prompt by (i) the present‐day distinct northern and southern Danish distribution and (ii) the subfossil record of Northern Birch Mouse, supporting early Weichselian colonization. Samples from Denmark, Norway, Sweden, Russia, Latvia, Estonia, and Slovakia were included. Mitogenomes were obtained from 54 individuals, all representing unique mitogenomes supporting high genetic variation. Bayesian phylogenetic analysis identified two distinct evolutionary linages in Northern Europe diverging within the Elster glaciation period. The results of the two nuclear genomes showed lower genetic differentiation but supported the same evolutionary history. This suggests an allopatric origin of the clades followed by secondary contact. Individuals from southern Denmark were only found in one clade, while individuals from other areas, including northern Denmark, were represented in both clades. Nevertheless, we found no evidence for repeated colonization's explaining the observed fragmented distribution of the species today. The results indicated that the mitogenome pattern of the Northern Birch Mouse population in southern Denmark was either (i) due to the population being founded from northern Denmark, (ii) a result of climatic and anthropogenic effects reducing population size increasing genetic drift or (iii) caused by sampling bias.
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Affiliation(s)
| | - Magnus W. Jacobsen
- Department of Ecoscience Aarhus University Aarhus C Denmark
- Section for Marine Living Resources National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
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Iannello M, Mezzelani M, Dalla Rovere G, Smits M, Patarnello T, Ciofi C, Carraro L, Boffo L, Ferraresso S, Babbucci M, Mazzariol S, Centelleghe C, Cardazzo B, Carrer C, Varagnolo M, Nardi A, Pittura L, Benedetti M, Fattorini D, Regoli F, Ghiselli F, Gorbi S, Bargelloni L, Milan M. Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam. Evol Appl 2021; 14:2864-2880. [PMID: 34950234 PMCID: PMC8674894 DOI: 10.1111/eva.13319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Marica Mezzelani
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Morgan Smits
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceSesto FiorentinoItaly
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Luciano Boffo
- Associazione “Vongola Verace di Chioggia”ChioggiaItaly
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Sandro Mazzariol
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Cinzia Centelleghe
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Carrer
- c/o Magistrato alle Acque di Venezia Ufficio Tecnico Antinquinamento Laboratorio CSMOPadovaItaly
| | | | - Alessandro Nardi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Lucia Pittura
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Maura Benedetti
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Daniele Fattorini
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Francesco Regoli
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Stefania Gorbi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimo Milan
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
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Quina AS, Durão AF, Mathias MDL. Evidence of micro-evolution in Crocidura russula from two abandoned heavy metal mines: potential use of Cytb, CYP1A1, and p53 as gene biomarkers. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1969-1982. [PMID: 34505200 DOI: 10.1007/s10646-021-02472-9] [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: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Heavy metals accumulated in the environment due to the mining industry may impact on the health of exposed wild animals with consequences at the population level via survival and selection of the most resistant individuals. The detection and quantification of shifts in gene frequencies or in the genetic structure in populations inhabiting polluted sites may be used as early indicators of environmental stress and reveal potential 'candidate gene biomarkers' for environmental health assessment. We had previously observed that specimens of the Greater white-toothed shrew (Crocidura russula) from two heavy metal mines in Southern Portugal (the Aljustrel and the Preguiça mines) carried physiological alterations compared to shrews from an unpolluted site. Here, we further investigated whether these populations showed genetic differences in genes relevant for physiological homeostasis and/or that are associated with pathways altered in animals living under chronic exposure to pollution, and which could be used as biomarkers. We analysed the mitochondrial cytochrome b (Cytb) gene and intronic and/or exonic regions of four nuclear genes: CYP1A1, LCAT, PRPF31, and p53. We observed (1) population differences in allele frequencies, types of variation, and diversity parameters in the Cytb, CYP1A1, and p53 genes; (2) purifying selection of Cytb in the mine populations; (3) genetic differentiation of the two mine populations from the reference by the p53 gene. Adding to our previous observations with Mus spretus, we provide unequivocal evidence of a population effect exerted by the contaminated environment of the mines on the local species of small mammals.
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Affiliation(s)
- Ana Sofia Quina
- CESAM - Centro de Estudos do Ambiente e do Mar, Departamento de Biologia Universidade de Aveiro Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
- CESAM - Centro de Estudos do Ambiente e do Mar, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
| | - Ana Filipa Durão
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, Spain
| | - Maria da Luz Mathias
- CESAM - Centro de Estudos do Ambiente e do Mar, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
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Petitjean Q, Jacquin L, Riem L, Pitout M, Perrault A, Cousseau M, Laffaille P, Jean S. Intraspecific variability of responses to combined metal contamination and immune challenge among wild fish populations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 272:116042. [PMID: 33190983 DOI: 10.1016/j.envpol.2020.116042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/26/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Wild organisms are increasingly exposed to multiple anthropogenic and natural stressors that can interact in complex ways and lead to unexpected effects. In aquatic ecosystems, contamination by trace metals has deleterious effects on fish health and commonly co-occurs with pathogens, which affect similar physiological and behavioral traits. However, the combined effects of metal contamination and parasitism are still poorly known. In addition, the sensitivity to multiple stressors could be highly variable among different fish populations depending on their evolutionary history, but this intraspecific variability is rarely taken into account in existing ecotoxicological studies. Here, we investigated i) the interactive effects of metal contamination (i.e., realistic mixture of Cd, Cu and Zn) and immune challenge mimicking a parasite attack on fish health across biological levels. In addition, we compared ii) the physiological and behavioral responses among five populations of gudgeon fish (Gobio occitaniae) having evolved along a gradient of metal contamination. Results show that single stressors exposure resulted in an increase of immune defenses and oxidative stress at the expense of body mass (contamination) or fish swimming activity (immune challenge). Multiple stressors had fewer interactive effects than expected, especially on physiological traits, but mainly resulted in antagonistic effects on fish swimming activity. Indeed, the immune challenge modified or inhibited the effects of contamination on fish behavior in most populations, suggesting that multiple stressors could reduce behavioral plasticity. Interestingly, the effects of stressors were highly variable among populations, with lower deleterious effects of metal contamination in populations from highly contaminated environments, although the underlying evolutionary mechanisms remain to be investigated. This study highlights the importance of considering multiple stressors effects and intraspecific variability of sensitivity to refine our ability to predict the effects of environmental contaminants on aquatic wildlife.
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Affiliation(s)
- Quentin Petitjean
- Laboratoire Écologie Fonctionnelle et Environnement, UMR5245, Université de Toulouse, CNRS, 118 Route de Narbonne, 31062, Toulouse, France; EDB, Laboratoire Évolution et Diversité Biologique, UMR5174 EDB, Université de Toulouse, CNRS, IRD, 118 Route de Narbonne, 31062, Toulouse, France; LTSER France, Zone Atelier PYGAR « Pyrénées-Garonne », Auzeville-Tolosane, France.
| | - Lisa Jacquin
- EDB, Laboratoire Évolution et Diversité Biologique, UMR5174 EDB, Université de Toulouse, CNRS, IRD, 118 Route de Narbonne, 31062, Toulouse, France; LTSER France, Zone Atelier PYGAR « Pyrénées-Garonne », Auzeville-Tolosane, France
| | - Louna Riem
- Laboratoire Écologie Fonctionnelle et Environnement, UMR5245, Université de Toulouse, CNRS, 118 Route de Narbonne, 31062, Toulouse, France; EDB, Laboratoire Évolution et Diversité Biologique, UMR5174 EDB, Université de Toulouse, CNRS, IRD, 118 Route de Narbonne, 31062, Toulouse, France
| | - Mathilde Pitout
- Laboratoire Écologie Fonctionnelle et Environnement, UMR5245, Université de Toulouse, CNRS, 118 Route de Narbonne, 31062, Toulouse, France
| | - Annie Perrault
- Laboratoire Écologie Fonctionnelle et Environnement, UMR5245, Université de Toulouse, CNRS, 118 Route de Narbonne, 31062, Toulouse, France
| | - Myriam Cousseau
- Laboratoire Écologie Fonctionnelle et Environnement, UMR5245, Université de Toulouse, CNRS, 118 Route de Narbonne, 31062, Toulouse, France
| | - Pascal Laffaille
- Laboratoire Écologie Fonctionnelle et Environnement, UMR5245, Université de Toulouse, CNRS, 118 Route de Narbonne, 31062, Toulouse, France; LTSER France, Zone Atelier PYGAR « Pyrénées-Garonne », Auzeville-Tolosane, France
| | - Séverine Jean
- Laboratoire Écologie Fonctionnelle et Environnement, UMR5245, Université de Toulouse, CNRS, 118 Route de Narbonne, 31062, Toulouse, France; LTSER France, Zone Atelier PYGAR « Pyrénées-Garonne », Auzeville-Tolosane, France
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6
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Li Y, Liu C, Lin L, Li Y, Xiao J, Loh KH. Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. Zookeys 2020; 969:137-154. [PMID: 33013170 PMCID: PMC7515929 DOI: 10.3897/zookeys.969.52069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/28/2020] [Indexed: 11/26/2022] Open
Abstract
The southern lesser pomfret (Pampusminor) is an economically important fish, and its numbers are declining because of overfishing and environmental pollution. In addition, owing to the similarities of its external morphological characteristics to other species in the genus Pampus, it is often mistaken for grey pomfret (P.cinereus) or silver pomfret (P.argenteus) juveniles. In this study, the genetic diversity and structure of 264 P.minor individuals from 11 populations in China and Malaysia coastal waters were evaluated for the first time, to the best of our knowledge, using mitochondrial cytochrome b fragments. The results showed that P.minor had moderate haplotype diversity and low nucleotide diversity. Furthermore, two divergent lineages were detected within the populations, but the phylogenetic structure corresponded imperfectly with geographical location; thus, the populations may have diverged in different glacial refugia during the Pleistocene low sea levels. Analysis of molecular variation (AMOVA) showed that genetic variation originated primarily from individuals within the population. Pairwise FST results showed significant differentiation between the Chinese and Malaysian populations. Except for the Xiamen population, which was classified as a marginal population, the genetic differentiation among the other Chinese populations was not significant. During the Late Pleistocene, P.minor experienced a population expansion event starting from the South China Sea refugium that expanded outward, and derivative populations quickly occupied and adapted to the new habitat. The results of this study will provide genetic information for the scientific conservation and management of P.minor resources.
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Affiliation(s)
- Yuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
| | - Cheng Liu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China.,College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China
| | - Longshan Lin
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China.,College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China Shanghai Ocean University Shanghai China
| | - Yuanyuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
| | - Jiaguang Xiao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China Ministry of Natural Resources Xiamen China
| | - Kar-Hoe Loh
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia University of Malaya Kuala Lumpur Malaysia
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7
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Jacquin L, Petitjean Q, Côte J, Laffaille P, Jean S. Effects of Pollution on Fish Behavior, Personality, and Cognition: Some Research Perspectives. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00086] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Asaduzzaman M, Igarashi Y, Wahab MA, Nahiduzzaman M, Rahman MJ, Phillips MJ, Huang S, Asakawa S, Rahman MM, Wong LL. Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation. Genes (Basel) 2019; 11:genes11010046. [PMID: 31905942 PMCID: PMC7017241 DOI: 10.3390/genes11010046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 11/23/2022] Open
Abstract
The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the FST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.
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Affiliation(s)
- Md Asaduzzaman
- Department of Marine Bioresource Science, Faculty of Fisheries, Chattogram Veterinary and Animal Sciences University, Khulsi, Chattogram 4225, Bangladesh
- Department of Aquatic Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.I.); (S.H.); (S.A.)
- Correspondence: (M.A.); (L.L.W.); Tel.: +880-1717-412049 (M.A.); +609-668-3671 (L.L.W.)
| | - Yoji Igarashi
- Department of Aquatic Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.I.); (S.H.); (S.A.)
| | - Md Abdul Wahab
- WorldFish, Bangladesh and South Asia Office, Banani, Dhaka 1213, Bangladesh; (M.A.W.); (M.N.); (M.J.R.)
| | - Md Nahiduzzaman
- WorldFish, Bangladesh and South Asia Office, Banani, Dhaka 1213, Bangladesh; (M.A.W.); (M.N.); (M.J.R.)
| | - Md Jalilur Rahman
- WorldFish, Bangladesh and South Asia Office, Banani, Dhaka 1213, Bangladesh; (M.A.W.); (M.N.); (M.J.R.)
| | - Michael J. Phillips
- WorldFish Headquarters, Jalan Batu Maung, Batu Muang, Penang 11960, Malaysia;
| | - Songqian Huang
- Department of Aquatic Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.I.); (S.H.); (S.A.)
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; (Y.I.); (S.H.); (S.A.)
| | - Md Moshiur Rahman
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna 9208, Bangladesh;
| | - Li Lian Wong
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala-Terengganu, Terengganu 21030, Malaysia
- Correspondence: (M.A.); (L.L.W.); Tel.: +880-1717-412049 (M.A.); +609-668-3671 (L.L.W.)
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Navas Romero AL, Herrera Moratta MA, Rodríguez MR, Quiroga LB, Echegaray M, Sanabria EA. Toxicity of wine effluents and assessment of a depuration system for their control: assay with tadpoles of Rhinella arenarum (BUFONIDAE). ECOTOXICOLOGY (LONDON, ENGLAND) 2019; 28:48-61. [PMID: 30411229 DOI: 10.1007/s10646-018-1998-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
We evaluated the toxicity of the winery effluent and the efficiency of a symbiotic depuration system by means an experiment with Rhinella arenarum tadpoles. The studied effluent was taken from warehouses during the cleaning season. These effluents subsequently subjected to the purification treatment under evaluation. The effluent samples differentiated into two treatment levels: "raw" where the effluent was evaluated with field conditions and "treated" where the effluent was previously filtered with the symbiotic depuration system. The results of the bioassays compared with the physicochemical parameters determined in the effluent samples. The lethal response had a clear-cut correspondence with the effluent quality assessed utilizing physicochemical parameters. In all cases, dilution of the samples resulted in a significant reduction of their toxicity. It concluded that (a) winery effluents could be harmful to tadpoles of R. arenarum, (b) the symbiotic purification system used to treat wine effluents it would produce a significant reduction in the contaminant levels of the effluent. However, this reduction in contaminant levels does not provide sufficient safety for the release of the effluents into the environment.
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Affiliation(s)
- Ana Laura Navas Romero
- Instituto Argentino de Investigaciones en Zonas Áridas - CCT Mendoza - CONICET, Mendoza, Argentina.
| | | | | | - Lorena Beatriz Quiroga
- Instituto de Ciencias Básicas, Universidad Nacional de San Juan - CONICET, San Juan, Argentina
| | - Marcelo Echegaray
- Facultad de Ingeniería, Universidad Nacional de San Juan, San Juan, Argentina
| | - Eduardo Alfredo Sanabria
- Instituto de Ciencias Básicas, Universidad Nacional de San Juan - CONICET, San Juan, Argentina
- Facultad de Ciencias Exactas, Universidad Nacional de Cuyo, Mendoza, Argentina
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10
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Sun JT, Jin PY, Hoffmann AA, Duan XZ, Dai J, Hu G, Xue XF, Hong XY. Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates. INSECT MOLECULAR BIOLOGY 2018; 27:698-709. [PMID: 29797479 DOI: 10.1111/imb.12501] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitogenome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species that distribute across different climates. We sequenced 26 complete mitogenomes of Tetranychus truncates, which occurs in both warm and cold regions, and nine complete mitogenomes of Tetranychus pueraricola, which is restricted to warm regions. Patterns of evolution in the two species' mitogenomes were compared through a series of dN /dS methods and physicochemical profiles of amino acid replacements. We found that: (1) the mitogenomes of both species were under widespread purifying selection; (2) elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus; and (3) the strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation.
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Affiliation(s)
- J-T Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - P-Y Jin
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - A A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - X-Z Duan
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - J Dai
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - G Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-F Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-Y Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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11
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DNA barcodes of Antipode marine invertebrates in Bay of Biscay and Gulf of Lion ports suggest new biofouling challenges. Sci Rep 2018; 8:16214. [PMID: 30385812 PMCID: PMC6212436 DOI: 10.1038/s41598-018-34447-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 10/17/2018] [Indexed: 11/08/2022] Open
Abstract
Marine biological invasions threaten global biodiversity nowadays. In this article, we have studied fouling communities from 10 port areas of south Bay of Biscay (Atlantic Ocean) and Gulf of Lion (Mediterranean Sea). A total of 834 individuals were genetically barcoded and corresponded to 95 different species. A total of 76 native species 8 genera and 1 family were identified, 58 from the Bay of Biscay and 23 from the Gulf of Lion. Furthermore, 19 species were identified as non-indigenous or cryptogenic (18 from the Bay of Biscay and 4 from the Gulf of Lion). We found a high proportion of Antipode non-indigenous species (NIS) that represented the 19.3% of all sampled individuals and the 54.21% of NIS specimens of this study. A framework for inference of donor regions based on a phylogenetic screening of genetic sequences was proposed as a proof of concept and tested, as well as models for the relationship between NIS introductions, maritime imports and distance to NIS native range and inferred donor areas. Consistent generalized linear models (GLM) with positive association between NIS genetic diversity and distance, not with maritime growth weight imports, strongly suggest that distant NIS could pose higher invasion risk than closer species. Selection for wider tolerance ranges during the long travel -direct or stepwise, as well as environmental similarity between donor and receiving regions, may explain these results.
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12
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Díez-Del-Molino D, García-Berthou E, Araguas RM, Alcaraz C, Vidal O, Sanz N, García-Marín JL. Effects of water pollution and river fragmentation on population genetic structure of invasive mosquitofish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1372-1382. [PMID: 29801230 DOI: 10.1016/j.scitotenv.2018.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/13/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
We analyzed variation at the GPI-2 locus and eleven microsatellite loci of eastern mosquitofish Gambusia holbrooki populations introduced to the Ebro River (Spain), sampling above and below a dam (Flix Reservoir) where severe chronic pollution has been well documented. Allele frequency changes at the GPI-2 locus in the sites nearest to the polluted sediments agree with previous results from studies in mercury-exposed populations of this highly invasive fish. Genetic distinction of the mosquitofish collected close to the polluted sediments was detected at the GPI locus but also at the presumptive neutral microsatellite loci. Recent migration rates estimated from microsatellites indicated that around 30% of fish collected in a specific location were immigrants from upstream and downstream sources. Such high migration rates probably contribute to the mosquitofish's invasive success and suggest that the consequences on the mosquitofish regional genetic structured of high levels of water toxicants could be mediated by immigration from other sites, but the effect of pollutants on local diversity might be higher than observed here.
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Affiliation(s)
- David Díez-Del-Molino
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain; Dept. of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 104 05 Stockholm, Sweden.
| | | | - Rosa-Maria Araguas
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Carles Alcaraz
- IRTA Marine and Continental Waters, Carretera Poble Nou, km 5.5, 43540 Sant Carles de la Ràpita, Spain.
| | - Oriol Vidal
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Nuria Sanz
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
| | - Jose-Luis García-Marín
- Laboratori d'Ictiologia Genètica (LIG), University of Girona, Edifici AC-LEAR, Carrer M. Aurèlia Capmany, 40, 17003 Girona, Spain.
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13
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Grunst AS, Grunst ML, Thys B, Raap T, Daem N, Pinxten R, Eens M. Variation in personality traits across a metal pollution gradient in a free-living songbird. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 630:668-678. [PMID: 29494975 DOI: 10.1016/j.scitotenv.2018.02.191] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/26/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Anthropogenic contaminants could alter traits central to animal behavioral types, or personalities, including aggressiveness, boldness and activity level. Lead and other toxic metals are persistent inorganic pollutants that affect organisms worldwide. Metal exposure can alter behavior by affecting neurology, endocrinology, and health. However, the direction and magnitude of the behavioral effects of metal exposure remain equivocal. Moreover, the degree to which metal exposure simultaneously affects suites of correlated behavioral traits (behavioral syndromes) that are controlled by common mechanisms remains unclear, with most studies focusing on single behaviors. Using a model species for personality variation, the great tit (Parus major), we explored differences in multiple behavioral traits across a pollution gradient where levels of metals, especially lead and cadmium, are elevated close to a smelter. We employed the novel environment exploration test, a proxy for variation in personality type, and also measured territorial aggressiveness and nest defense behavior. At polluted sites birds of both sexes displayed slower exploration behavior, which could reflect impaired neurological or physiological function. Territorial aggression and nest defense behavior were individually consistent, but did not vary with proximity to the smelter, suggesting that metal exposure does not concurrently affect exploration and aggression. Rather, exploration behavior appears more sensitive to metal pollution. Effects of metal pollution on exploration behavior, a key animal personality trait, could have critical effects on fitness.
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Affiliation(s)
- Andrea S Grunst
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Melissa L Grunst
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Bert Thys
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Thomas Raap
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Natasha Daem
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Rianne Pinxten
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, 2610 Wilrijk, Belgium; Faculty of Social Sciences, Antwerp School of Education, University of Antwerp, 2000 Antwerp, Belgium
| | - Marcel Eens
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, 2610 Wilrijk, Belgium
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14
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Nielsen ES, Henriques R, Toonen RJ, Knapp ISS, Guo B, von der Heyden S. Complex signatures of genomic variation of two non-model marine species in a homogeneous environment. BMC Genomics 2018; 19:347. [PMID: 29743012 PMCID: PMC5944137 DOI: 10.1186/s12864-018-4721-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/23/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist. RESULTS Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region. CONCLUSIONS Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.
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Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland,, 7602, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland,, 7602, South Africa
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Ingrid S S Knapp
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Baocheng Guo
- The Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences, Beijing, 100101, China
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland,, 7602, South Africa.
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15
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Evolutionary Toxicology as a Tool to Assess the Ecotoxicological Risk in Freshwater Ecosystems. WATER 2018. [DOI: 10.3390/w10040490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Vittecoq M, Giraudeau M, Sepp T, Marcogliese DJ, Klaassen M, Renaud F, Ujvari B, Thomas F. Turning natural adaptations to oncogenic factors into an ally in the war against cancer. Evol Appl 2018; 11:836-844. [PMID: 29928293 PMCID: PMC5999213 DOI: 10.1111/eva.12608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/25/2018] [Indexed: 12/14/2022] Open
Abstract
Both field and experimental evolution studies have demonstrated that organisms naturally or artificially exposed to environmental oncogenic factors can, sometimes rapidly, evolve specific adaptations to cope with pollutants and their adverse effects on fitness. Although numerous pollutants are mutagenic and carcinogenic, little attention has been given to exploring the extent to which adaptations displayed by organisms living in oncogenic environments could inspire novel cancer treatments, through mimicking the processes allowing these organisms to prevent or limit malignant progression. Building on a substantial knowledge base from the literature, we here present and discuss this progressive and promising research direction, advocating closer collaboration between the fields of medicine, ecology, and evolution in the war against cancer.
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Affiliation(s)
- Marion Vittecoq
- Institut de Recherche de la Tour du Valat Arles France.,CREEC/MIVEGEC IRD CNRS University of Montpellier Montpellier France
| | - Mathieu Giraudeau
- School of Life Sciences Arizona State University Tempe AZ USA.,Centre for Ecology & Conservation College of Life and Environmental Sciences University of Exeter Penryn UK
| | - Tuul Sepp
- School of Life Sciences Arizona State University Tempe AZ USA.,Department of Zoology University of Tartu Tartu Estonia
| | - David J Marcogliese
- Aquatic Contaminants Research Division Water Science and Technology Directorate Environment and Climate Change Canada St. Lawrence Centre Montreal QC Canada.,Fisheries and Oceans Canada St. Andrews Biological Station St. Andrews NB Canada
| | - Marcel Klaassen
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Deakin Vic. Australia
| | - François Renaud
- CREEC/MIVEGEC IRD CNRS University of Montpellier Montpellier France
| | - Beata Ujvari
- School of Life and Environmental Sciences Centre for Integrative Ecology Deakin University Deakin Vic. Australia.,School of Biological Sciences University of Tasmania Hobart TAS Australia
| | - Frédéric Thomas
- CREEC/MIVEGEC IRD CNRS University of Montpellier Montpellier France
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17
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Hamilton PB, Rolshausen G, Uren Webster TM, Tyler CR. Adaptive capabilities and fitness consequences associated with pollution exposure in fish. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0042. [PMID: 27920387 PMCID: PMC5182438 DOI: 10.1098/rstb.2016.0042] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2016] [Indexed: 12/22/2022] Open
Abstract
Many fish populations are exposed to harmful levels of chemical pollution and selection pressures associated with these exposures have led to the evolution of tolerance. Our understanding of the physiological basis for these adaptations is limited, but they are likely to include processes involved with the absorption, distribution, metabolism and/or excretion of the target chemical. Other potential adaptive mechanisms include enhancements in antioxidant responses, an increased capacity for DNA and/or tissue repair and alterations to the life cycle of fish that enable earlier reproduction. Analysis of single-nucleotide polymorphism frequencies has shown that tolerance to hydrocarbon pollutants in both marine and estuarine fish species involves alteration in the expression of the xenobiotic metabolism enzyme CYP1A. In this review, we present novel data showing also that variants of the CYP1A gene have been under selection in guppies living in Trinidadian rivers heavily polluted with crude oil. Potential costs associated with these adaptations could reduce fitness in unpolluted water conditions. Integrating knowledge of local adaptation to pollution is an important future consideration in conservation practices such as for successful restocking, and improving connectivity within river systems.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Patrick B Hamilton
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Tamsyn M Uren Webster
- Department of Biosciences, Swansea University, Wallace Building, Swansea SA2 8PP, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
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18
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Brady SP, Monosson E, Matson CW, Bickham JW. Evolutionary toxicology: Toward a unified understanding of life's response to toxic chemicals. Evol Appl 2017; 10:745-751. [PMID: 29151867 PMCID: PMC5680415 DOI: 10.1111/eva.12519] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Steven P Brady
- Biology Department Southern Connecticut State University New Haven CT USA
| | - Emily Monosson
- The Ronin Institute for Independent Scholars and Department of Environmental Conservation University of Massachusetts Amherst MA USA
| | - Cole W Matson
- Department of Environmental Science and Center for Reservoir and Aquatic Systems Research (CRASR) Baylor University Waco TX USA
| | - John W Bickham
- Department of Wildlife & Fisheries Sciences Texas A&M University College Station College Station TX USA
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19
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Uren Webster TM, Williams TD, Katsiadaki I, Lange A, Lewis C, Shears JA, Tyler CR, Santos EM. Hepatic transcriptional responses to copper in the three-spined stickleback are affected by their pollution exposure history. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 184:26-36. [PMID: 28081447 DOI: 10.1016/j.aquatox.2016.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/05/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
Some fish populations inhabiting contaminated environments show evidence of increased chemical tolerance, however the mechanisms contributing to this tolerance, and whether this is heritable, are poorly understood. We investigated the responses of two populations of wild three-spined stickleback (Gasterosteus aculeatus) with different histories of contaminant exposure to an oestrogen and copper, two widespread aquatic pollutants. Male stickleback originating from two sites, the River Aire, with a history of complex pollution discharges, and Siblyback Lake, with a history of metal contamination, were depurated and then exposed to copper (46μg/L) and the synthetic oestrogen ethinyloestradiol (22ng/L). The hepatic transcriptomic response was compared between the two populations and to a reference population with no known history of exposure (Houghton Springs, Dorset). Gene responses included those typical for both copper and oestrogen, with no discernable difference in response to oestrogen between populations. There was, however, some difference in the magnitude of response to copper between populations. Siblyback fish showed an elevated baseline transcription of genes encoding metallothioneins and a lower level of metallothionein induction following copper exposure, compared to those from the River Aire. Similarly, a further experiment with an F1 generation of Siblyback fish bred in the laboratory found evidence for elevated transcription of genes encoding metallothioneins in unexposed fish, together with an altered transcriptional response to 125μg/L copper, compared with F1 fish originating from the clean reference population exposed to the same copper concentration. These data suggest that the stickleback from Siblyback Lake have a differential response to copper, which is inherited by the F1 generation in laboratory conditions, and for which the underlying mechanism may include an elevation of baseline transcription of genes encoding metallothioneins. The genetic and/or epigenetic mechanisms contributing to this inherited alteration of metallothionein transcription have yet to be established.
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Affiliation(s)
- Tamsyn M Uren Webster
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Tim D Williams
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Ioanna Katsiadaki
- Centre for Environment, Fisheries and Aquaculture Science, Cefas Weymouth Laboratory, Weymouth DT4 8UB, UK
| | - Anke Lange
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Ceri Lewis
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Janice A Shears
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Eduarda M Santos
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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20
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Bernatchez L. On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes. JOURNAL OF FISH BIOLOGY 2016; 89:2519-2556. [PMID: 27687146 DOI: 10.1111/jfb.13145] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/23/2016] [Indexed: 05/18/2023]
Abstract
The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.
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Affiliation(s)
- L Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1Y 2T8, Canada
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21
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Byers KJRP, Xu S, Schlüter PM. Molecular mechanisms of adaptation and speciation: why do we need an integrative approach? Mol Ecol 2016; 26:277-290. [DOI: 10.1111/mec.13678] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Kelsey J. R. P. Byers
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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22
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Milan M, Matozzo V, Pauletto M, Di Camillo B, Giacomazzo M, Boffo L, Binato G, Marin MG, Patarnello T, Bargelloni L. Can ecological history influence response to pollutants? Transcriptomic analysis of Manila clam collected in different Venice lagoon areas and exposed to heavy metal. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 174:123-133. [PMID: 26945539 DOI: 10.1016/j.aquatox.2016.02.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/26/2016] [Accepted: 02/27/2016] [Indexed: 06/05/2023]
Abstract
Chronic exposure to environmental pollutants can exert strong selective pressures on natural populations, favoring the transmission over generations of traits that enable individuals to survive and thrive in highly impacted environments. The lagoon of Venice is an ecosystem subject to heavy anthropogenic impact, mainly due to the industrial activities of Porto Marghera (PM), which led to a severe chemical contamination of soil, groundwater, and sediments. Gene expression analysis on wild Manila clams collected in different Venice lagoon areas enabled to identify differences in gene expression profiles between clams collected in PM and those sampled in clean areas, and the definition of molecular signatures of chemical stress. However, it remains largely unexplored to which extent modifications of gene expression patterns persists after removing the source of contamination. It is also relatively unknown whether chronic exposure to xenobiotics affects the response to other chemical pollutants. To start exploring such issues, in the present study a common-garden experiment was coupled with transcriptomic analysis, to compare gene expression profiles of PM clams with those of clams collected in the less impacted area of Chioggia (CH) during a period under the same control conditions. Part of the two experimental groups were also exposed to copper for seven days to assess whether different "ecological history" does influence response to such pollutant. The results obtained suggest that the chronic exposure to chemical pollution generated a response at the transcriptional level that persists after removal for the contaminated site. These transcriptional changes are centered on key biological processes, such as defense against either oxidative stress or tissue/protein damage, and detoxification, suggesting an adaptive strategy for surviving in the deeply impacted environment of Porto Marghera. On the other hand, CH clams appeared to respond more effectively to copper exposure than PM animals, proposing that chronic exposure to chemical toxicants either lowers the sensitivity to additional toxicants or blunts the capacity to respond to novel chemical challenges in PM clams.
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Affiliation(s)
- Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy.
| | - Valerio Matozzo
- Department of Biology, University of Padova, via G. Colombo 3, 35131 Padova, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | | | - Matteo Giacomazzo
- Department of Biology, University of Padova, via G. Colombo 3, 35131 Padova, Italy; Department of Environmental Sciences University of Quèbec at Trois-Rivières, Canada
| | | | - Giovanni Binato
- Laboratory of Chemistry, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
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Pottinger TG, Matthiessen P. Disruption of the stress response in wastewater treatment works effluent-exposed three-spined sticklebacks persists after translocation to an unpolluted environment. ECOTOXICOLOGY (LONDON, ENGLAND) 2016; 25:538-547. [PMID: 26821232 DOI: 10.1007/s10646-016-1612-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/18/2016] [Indexed: 06/05/2023]
Abstract
The hypothalamic-pituitary-adrenal/interrenal (HPA/I) axis plays a key role in responding to biotic and abiotic challenges in all vertebrates. Recent studies have shown that the apical response of the HPI axis to stressors in three-spined sticklebacks varies in proportion to the concentration of wastewater treatment works (WWTW) effluent to which the fish are exposed. This study was conducted to determine whether between-site variation in stress responsiveness among WWTW effluent-exposed sticklebacks is persistent or reversible. Sticklebacks from eight sites in north-west England affected by WWTW effluent and exhibiting between-population variation in HPI axis reactivity, were moved to a clean-water aquarium environment. After five months in the contaminant-free environment the responsiveness of these fish to a standardised stressor was determined, by measuring the rate of stress-induced cortisol release across the gills, and compared with the responses of fish newly sampled from the eight original capture sites. Inter-site differences in the reactivity of the HPI axis, proportional to the effluent concentration at each site, persisted among the translocated female sticklebacks for at least 5 months. In male fish however, the direct relationship between stress responsiveness and site-specific effluent was not evident 5 months post-translocation. These results support previous observations that the HPA/I axis, a non-reproductive endocrine system, is vulnerable to modulation by anthropogenic factors in fish and show for the first time that, in female fish at least, this modulation is not transient. The mechanisms underlying these observations, and the implications for the fitness and resilience of affected populations, requires investigation.
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Affiliation(s)
- Tom G Pottinger
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK.
| | - Peter Matthiessen
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
- Dolfan Barn, Beulah, Llanwrtyd Wells, Powys, LD5 4UE, UK
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Bougas B, Normandeau E, Grasset J, Defo MA, Campbell PGC, Couture P, Bernatchez L. Transcriptional response of yellow perch to changes in ambient metal concentrations-A reciprocal field transplantation experiment. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 173:132-142. [PMID: 26867186 DOI: 10.1016/j.aquatox.2015.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/18/2015] [Accepted: 12/20/2015] [Indexed: 06/05/2023]
Abstract
Recent local adaptation to pollution has been evidenced in several organisms inhabiting environments heavily contaminated by metals. Nevertheless, the molecular mechanisms underlying adaptation to high metal concentrations are poorly understood, especially in fishes. Yellow perch (Perca flavescens) populations from lakes in the mining area of Rouyn-Noranda (QC, Canada) have been faced with metal contamination for about 90 years. Here, we examine gene transcription patterns of fish reciprocally transplanted between a reference and a metal-contaminated lake and also fish caged in their native lake. After four weeks, 111 genes were differentially transcribed in metal-naïve fish transferred to the metal-contaminated lake, revealing a plastic response to metal exposure. Genes involved in the citric cycle and beta-oxidation pathways were under-transcribed, suggesting a potential strategy to mitigate the effects of metal stress by reducing energy turnover. However, metal-contaminated fish transplanted to the reference lake did not show any transcriptomic response, indicating a reduced plastic response capability to sudden reduction in metal concentrations. Moreover, the transcription of other genes, especially ones involved in energy metabolism, was affected by caging. Overall, our results highlight environmental stress response mechanisms in yellow perch at the transcriptomic level and support a rapid adaptive response to metal exposure through genetic assimilation.
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Affiliation(s)
- Bérénice Bougas
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec) G1V 0A6, Canada.
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec) G1V 0A6, Canada
| | - Julie Grasset
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Michel A Defo
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Peter G C Campbell
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Patrice Couture
- Institut National de la Recherche Scientifique, Centre Eau Terre Environnement 490, rue de la Couronne, Québec (Québec) G1K 9A9, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec (Québec) G1V 0A6, Canada
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25
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Vera M, Díez-del-Molino D, García-Marín JL. Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki). Mol Ecol 2016; 25:1089-105. [PMID: 26825431 DOI: 10.1111/mec.13545] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/10/2015] [Accepted: 01/15/2016] [Indexed: 01/26/2023]
Abstract
Biological invasions rank among the main global threats for biodiversity. The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100 world worst invasive species due to its high adaptation capability to new environments. Using the restriction-site-associated DNA tags (RADtags), introduced European locations were compared against native US mosquitofish populations to analyse genomic changes that occurred during invasive process of European locations. After filtering, 7724 RADtags containing only one SNP were retained for population studies. Comparative genomics indicated that 186 of these RADtags matched sequences in the transcriptome of Xyphophorus maculatus, the most closely related genome available. Genomic analyses showed that invasive populations show high reductions in diversity. Further, analyses of population structuring based on these data are concordant with previous analyses based on microsatellites. It is concluded that during the invasion process genetic drift was the main evolutionary force affecting patterns of diversity and population structure. While recognizing that positive selection could be masked by the strong drift during founder events, adaptive processes were evidenced in a reduced number of RADtags (<2%), with only one of these in a putative coding region. Surprisingly, balancing selection was detected in several coding RADtags, suggesting that the preservation of polymorphism in specific genes could be more important than the average population diversity for the population maintenance at any location, particularly for the survival of introduced populations.
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Affiliation(s)
- Manuel Vera
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - David Díez-del-Molino
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - José-Luis García-Marín
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
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26
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Laporte M, Pavey SA, Rougeux C, Pierron F, Lauzent M, Budzinski H, Labadie P, Geneste E, Couture P, Baudrimont M, Bernatchez L. RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels. Mol Ecol 2015; 25:219-37. [DOI: 10.1111/mec.13466] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/06/2015] [Accepted: 11/06/2015] [Indexed: 12/14/2022]
Affiliation(s)
- M. Laporte
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
| | - S. A. Pavey
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- Institut National de la Recherche Scientifique (INRS); Centre Eau Terre et Environnement; 490, rue de la Couronne Québec QC G1K 9A9 Canada
- Department of Biology; University of New Brunswick; PO Box 5050 Saint-John NB E2L 4L5 Canada
| | - C. Rougeux
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
| | - F. Pierron
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - M. Lauzent
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - H. Budzinski
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - P. Labadie
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - E. Geneste
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - P. Couture
- Institut National de la Recherche Scientifique (INRS); Centre Eau Terre et Environnement; 490, rue de la Couronne Québec QC G1K 9A9 Canada
| | - M. Baudrimont
- UMR EPOC CNRS 5805; Université de Bordeaux; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
- CNRS, EPOC; UMR 5805; allée Geoffroy Saint-Hilaire, CS 50023 33615 Pessac France
| | - L. Bernatchez
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand Québec QC G1V 0A6 Canada
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27
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Jacobsen MW, da Fonseca RR, Bernatchez L, Hansen MM. Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.). Mol Phylogenet Evol 2015; 95:161-70. [PMID: 26654959 DOI: 10.1016/j.ympev.2015.11.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 11/29/2022]
Abstract
Several studies have recently reported evidence for positive selection acting on the mitochondrial genome (mitogenome), emphasizing its potential role in adaptive divergence and speciation. In this study we searched 107 full mitogenomes of recently diverged species and lineages of whitefish (Coregonus ssp.) for signals of positive selection. These salmonids show several distinct morphological and ecological differences that may be associated with energetics and therefore potentially positive selection at the mitogenome level. We found that purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, the NADH dehydrogenase 2 gene (ND2) showed a highly elevated dN/dS ratio compared to the other mitochondrial genes, which was significantly higher in whitefish compared to other salmonids. We therefore further examined nonsynonymous evolution in ND2 by (i) mapping amino acid changes to a protein model structure which showed that they were located away from key functional residues of the protein, (ii) locating them in the sequences of other species of fish (Salmonidae, Anguillidae, Scombridae and Percidae) only to find pronounced overlap of nonsynonymous regions. We thus conclude that relaxed purifying selection is driving the evolution of ND2 by affecting mostly regions that have lower functional relevance.
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Affiliation(s)
- Magnus W Jacobsen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
| | - Rute R da Fonseca
- Department of Bioinformatics and RNA Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 København N, Denmark
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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28
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Defo MA, Bernatchez L, Campbell PGC, Couture P. Transcriptional and biochemical markers in transplanted Perca flavescens to characterize cadmium- and copper-induced oxidative stress in the field. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 162:39-53. [PMID: 25770975 DOI: 10.1016/j.aquatox.2015.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 06/04/2023]
Abstract
Despite recent progress achieved in elucidating the mechanisms underlying local adaptation to pollution, little is known about the evolutionary change that may be occurring at the molecular level. The goal of this study was to examine patterns of gene transcription and biochemical responses induced by metal accumulation in clean yellow perch (Perca flavescens) and metal depuration in contaminated fish in a mining and smelting region of Canada. Fish were collected from a reference lake (lake Opasatica) and a Cd, Cu and Zn contaminated lake (lake Dufault) located in the Rouyn-Noranda region (Qc, Canada) and caged for one or four weeks in their own lake or transplanted in the other lake. Free-ranging fish from the same lakes were also collected. Kidney Cd and Cu concentrations in clean fish caged in the contaminated lake increased with the time of exposure, but metal depuration did not occur in contaminated fish caged in the clean lake. After 4 weeks, the major retinoid metabolites analysed, the percentage of free dehydroretinol (dROH) and the retinol dehydrogenase-2 (rdh-2) transcription level in liver decreased in clean fish transplanted into the metal-contaminated lake, suggesting that metal exposure negatively impacted retinoid metabolism. However, we observed an increase in almost all of the retinoid parameters analysed in fish from the metal-impacted lake caged in the same lake, which we interpret as an adaptation response to higher ambient metal concentration. In support of this hypothesis, liver transcription levels of microsomal glutathione-S-transferase-3 (mgst-3) and glucose-6-phosphate dehydrogenase (g6pdh) were enhanced in clean fish transplanted into the metal-contaminated lake and this up-regulation was accompanied by an increase in the activities of corresponding enzymes, involved in antioxidant response. However, although in the same fish the transcription level of Cu/Zn superoxide dismutase (Cu/Zn sod) was also increased, this did not lead to a change in the activity of the SOD enzyme, suggesting that this upregulation was aimed at maintaining SOD-related antioxidant capacities. In contrast, the transcription level of the cat gene, which did not change in contaminated fish, did not compensate for the decrease of CAT activity. After 4 weeks of exposure, some plastic responses of the clean fish were observed when they were transplanted in the metal-contaminated lake. However, probably as a consequence of the prior 80 years of exposure to metals, the contaminated population showed a limited plastic response in the expression of the majority of the candidate genes tested, when they were transplanted in the reference lake. The overall findings of this field investigation highlight how yellow perch molecularly and biochemically responded to a sudden or relatively long-term exposure (4 weeks) to a cocktail of metals.
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Affiliation(s)
- Michel A Defo
- Institut National De La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 De La Couronne, Québec, QC G1K 9A9, Canada
| | - Louis Bernatchez
- Institut De Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
| | - Peter G C Campbell
- Institut National De La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 De La Couronne, Québec, QC G1K 9A9, Canada
| | - Patrice Couture
- Institut National De La Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 De La Couronne, Québec, QC G1K 9A9, Canada
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29
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Vega-Retter C, Vila I, Véliz D. Signatures of Directional and Balancing Selection in the Silverside Basilichthys microlepidotus (Teleostei: Atherinopsidae) Inhabiting a Polluted River. Evol Biol 2015. [DOI: 10.1007/s11692-015-9307-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Bouétard A, Côte J, Besnard AL, Collinet M, Coutellec MA. Environmental versus anthropogenic effects on population adaptive divergence in the freshwater snail Lymnaea stagnalis. PLoS One 2014; 9:e106670. [PMID: 25207985 PMCID: PMC4160221 DOI: 10.1371/journal.pone.0106670] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/07/2014] [Indexed: 12/11/2022] Open
Abstract
Repeated pesticide contaminations of lentic freshwater systems located within agricultural landscapes may affect population evolution in non-target organisms, especially in species with a fully aquatic life cycle and low dispersal ability. The issue of evolutionary impact of pollutants is therefore conceptually important for ecotoxicologists. The impact of historical exposure to pesticides on genetic divergence was investigated in the freshwater gastropod Lymnaea stagnalis, using a set of 14 populations from contrasted environments in terms of pesticide and other anthropogenic pressures. The hypothesis of population adaptive divergence was tested on 11 life-history traits, using Q(ST)-F(ST) comparisons. Despite strong neutral differentiation (mean F(ST) = 0.291), five adult traits or parameters were found to be under divergent selection. Conversely, two early expressed traits showed a pattern consistent with uniform selection or trait canalization, and four adult traits appeared to evolve neutrally. Divergent selection patterns were mostly consistent with a habitat effect, opposing pond to ditch and channel populations. Comparatively, pesticide and other human pressures had little correspondence with evolutionary patterns, despite hatching rate impairment associated with global anthropogenic pressure. Globally, analyses revealed high genetic variation both at neutral markers and fitness-related traits in a species used as model in ecotoxicology, providing empirical support for the need to account for genetic and evolutionary components of population response in ecological risk assessment.
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Affiliation(s)
- Anthony Bouétard
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Jessica Côte
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Anne-Laure Besnard
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Marc Collinet
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Marie-Agnès Coutellec
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
- * E-mail:
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31
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Defo MA, Bernatchez L, Campbell PGC, Couture P. Waterborne cadmium and nickel impact oxidative stress responses and retinoid metabolism in yellow perch. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 154:207-220. [PMID: 24915613 DOI: 10.1016/j.aquatox.2014.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/18/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
In this experiment, we studied the transcriptional and functional (enzymatic) responses of yellow perch (Perca flavescens) to metal stress, with a focus on oxidative stress and vitamin A metabolism. Juvenile yellow perch were exposed to two environmentally relevant concentrations of waterborne cadmium (Cd) and nickel (Ni) for a period of 6 weeks. Kidney Cd and Ni bioaccumulation significantly increased with increasing metal exposure. The major retinoid metabolites analyzed in liver and muscle decreased with metal exposure except at high Cd exposure where no variation was reported in liver. A decrease in free plasma dehydroretinol was also observed with metal exposure. In the liver of Cd-exposed fish, both epidermal retinol dehydrogenase 2 transcription level and corresponding enzyme activities retinyl ester hydrolase and lecithin dehydroretinyl acyl transferase increased. In contrast, muscle epidermal retinol dehydrogenase 2 transcription level decreased with Cd exposure. Among antioxidant defences, liver transcription levels of catalase, microsomal glutathione-S-transferase-3 and glucose-6-phosphate dehydrogenase were generally enhanced in Cd-exposed fish and this up-regulation was accompanied by an increase in the activities of corresponding enzymes, except for microsomal glutathione-S-transferase. No consistent pattern in antioxidant defence responses was observed between molecular and biochemical response when fish were exposed to Ni, suggesting a non-synchronous response of antioxidant defence in fish exposed to waterborne Ni. There was a general lack of consistency between muscle transcription level and enzyme activities analyzed. The overall findings from this investigation highlight the usefulness of transcriptional and biochemical endpoints in the identification of oxidative stress and vitamin A metabolism impairment biomarkers and the potential use of multi-level biological approaches when assessing environmental risk in fish.
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Affiliation(s)
- Michel A Defo
- Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, 490 de la Couronne, Québec, Québec G1K 9A9, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec G1V 0A6, Canada
| | - Peter G C Campbell
- Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, 490 de la Couronne, Québec, Québec G1K 9A9, Canada
| | - Patrice Couture
- Institut national de la recherche scientifique (INRS), Centre Eau Terre Environnement, 490 de la Couronne, Québec, Québec G1K 9A9, Canada.
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32
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Bougas B, Normandeau E, Pierron F, Campbell PGC, Bernatchez L, Couture P. How does exposure to nickel and cadmium affect the transcriptome of yellow perch (Perca flavescens)--results from a 1000 candidate-gene microarray. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 142-143:355-64. [PMID: 24084258 DOI: 10.1016/j.aquatox.2013.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 05/25/2023]
Abstract
The molecular mechanisms underlying nickel (Ni) and cadmium (Cd) toxicity and their specific effects on fish are poorly understood. Documenting gene transcription profiles offers a powerful approach toward identifying the molecular mechanisms affected by these metals and to discover biomarkers of their toxicity. However, confounding environmental factors can complicate the interpretation of the results and the detection of biomarkers for fish captured in their natural environment. In the present study, a 1000 candidate-gene microarray, developed from a previous RNA-seq study on a subset of individual fish from contrasting level of metal contamination, was used to investigate the transcriptional response to metal (Ni and Cd) and non metal (temperature, oxygen, and diet) stressors in yellow perch (Perca flavescens). Specifically, we aimed at (1) identifying transcriptional signatures specific to Ni and Cd exposure, (2) investigating the mechanisms of their toxicity, and (3) developing a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments. A total of 475 genes displayed significantly different transcription levels when temperature varied while 287 and 176 genes were differentially transcribed at different concentrations of Ni and Cd, respectively. These metals were found to mainly affect the transcription level of genes involved in iron metabolism, transcriptional and translational processes, vitamin metabolism, blood coagulation, and calcium transport. In addition, a linear discriminant analysis (LDA) made using gene transcription levels yielded 94% correctly reassigned samples regarding their level of metal contamination, which indicates the potential of the microarray to detect perch response to Cd or Ni effects.
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Affiliation(s)
- Bérénice Bougas
- Institut National de la Recherche Scientifique, Centre INRS Eau Terre et Environnement, 490, rue de la Couronne, Québec, Québec G1K 9A9, Canada; Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec G1V 0A6, Canada.
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