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Sadler DE, Watts PC, Uusi-Heikkilä S. Directional selection, not the direction of selection, affects telomere length and copy number at ribosomal RNA loci. Sci Rep 2024; 14:12162. [PMID: 38802448 PMCID: PMC11130246 DOI: 10.1038/s41598-024-63030-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024] Open
Abstract
Many fisheries exert directional selection on traits such as body size and growth rate. Whether directional selection impacts regions of the genome associated with traits related to growth is unknown. To address this issue, we characterised copy number variation in three regions of the genome associated with cell division, (1) telomeric DNA, (2) loci transcribed as ribosomal RNA (rDNA), and (3) mitochondrial DNA (mtDNA), in three selection lines of zebrafish reared at three temperatures (22 °C, 28 °C, and 34 °C). Selection lines differed in (1) the direction of selection (two lines experienced directional selection for large or small body size) and (2) whether they experienced any directional selection itself. Lines that had experienced directional selection were smaller, had lower growth rate, shorter telomeres, and lower rDNA copy number than the line that experiencing no directional selection. Neither telomere length nor rDNA copy number were affected by temperature. In contrast, mtDNA content increased at elevated temperature but did not differ among selection lines. Though directional selection impacts rDNA and telomere length, direction of such selection did not matter, whereas mtDNA acts as a stress marker for temperature. Future work should examine the consequences of these genomic changes in natural fish stocks.
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Affiliation(s)
- Daniel E Sadler
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Silva Uusi-Heikkilä
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
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Car C, Quevarec L, Gilles A, Réale D, Bonzom JM. Evolutionary approach for pollution study: The case of ionizing radiation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123692. [PMID: 38462194 DOI: 10.1016/j.envpol.2024.123692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/12/2024]
Abstract
Estimating the consequences of environmental changes, specifically in a global change context, is essential for conservation issues. In the case of pollutants, the interest in using an evolutionary approach to investigate their consequences has been emphasized since the 2000s, but these studies remain rare compared to the characterization of direct effects on individual features. We focused on the study case of anthropogenic ionizing radiation because, despite its potential strong impact on evolution, the scarcity of evolutionary approaches to study the biological consequences of this stressor is particularly true. In this study, by investigating some particular features of the biological effects of this stressor, and by reviewing existing studies on evolution under ionizing radiation, we suggest that evolutionary approach may help provide an integrative view on the biological consequences of ionizing radiation. We focused on three topics: (i) the mutagenic properties of ionizing radiation and its disruption of evolutionary processes, (ii) exposures at different time scales, leading to an interaction between past and contemporary evolution, and (iii) the special features of contaminated areas called exclusion zones and how evolution could match field and laboratory observed effects. This approach can contribute to answering several key issues in radioecology: to explain species differences in the sensitivity to ionizing radiation, to improve our estimation of the impacts of ionizing radiation on populations, and to help identify the environmental features impacting organisms (e.g., interaction with other pollution, migration of populations, anthropogenic environmental changes). Evolutionary approach would benefit from being integrated to the ecological risk assessment process.
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Affiliation(s)
- Clément Car
- Laboratoire de Recherche sur Les Effets des Radionucléides sur L'écosystème (LECO), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Saint-Paul Lèz Durance, France
| | - Loïc Quevarec
- Laboratoire de Recherche sur Les Effets des Radionucléides sur L'écosystème (LECO), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Saint-Paul Lèz Durance, France.
| | - André Gilles
- UMR Risques, ECOsystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix-Marseille Université (AMU), Marseille, France
| | - Denis Réale
- Département des Sciences Biologiques, Université Du Québec à Montréal, (UQAM), Montréal, Canada
| | - Jean-Marc Bonzom
- Laboratoire de Recherche sur Les Effets des Radionucléides sur L'écosystème (LECO), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Saint-Paul Lèz Durance, France
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Jernfors T, Lavrinienko A, Vareniuk I, Landberg R, Fristedt R, Tkachenko O, Taskinen S, Tukalenko E, Mappes T, Watts PC. Association between gut health and gut microbiota in a polluted environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169804. [PMID: 38184263 DOI: 10.1016/j.scitotenv.2023.169804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/28/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, digestion of otherwise undigestible foodstuffs, and impacts on host behaviour. Exposure to stressors, such as environmental pollution, parasites, and/or predators, can alter the composition of the gut microbiome, potentially affecting host-microbiome interactions that can be manifest in the host as, for example, metabolic dysfunction or inflammation. However, whether a change in gut microbiota in wild animals associates with a change in host condition is seldom examined. Thus, we quantified whether wild bank voles inhabiting a polluted environment, areas where there are environmental radionuclides, exhibited a change in gut microbiota (using 16S amplicon sequencing) and concomitant change in host health using a combined approach of transcriptomics, histological staining analyses of colon tissue, and quantification of short-chain fatty acids in faeces and blood. Concomitant with a change in gut microbiota in animals inhabiting contaminated areas, we found evidence of poor gut health in the host, such as hypotrophy of goblet cells and likely weakened mucus layer and related changes in Clca1 and Agr2 gene expression, but no visible inflammation in colon tissue. Through this case study we show that inhabiting a polluted environment can have wide reaching effects on the gut health of affected animals, and that gut health and other host health parameters should be examined together with gut microbiota in ecotoxicological studies.
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Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland.
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Igor Vareniuk
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Rikard Fristedt
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Olena Tkachenko
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Sara Taskinen
- Department of Mathematics and Statistics, University of Jyväskylä, FI-40014, Finland
| | - Eugene Tukalenko
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, 020000, Ukraine
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
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Sadler DE, van Dijk S, Karjalainen J, Watts PC, Uusi‐Heikkilä S. Does size-selective harvesting erode adaptive potential to thermal stress? Ecol Evol 2024; 14:e11007. [PMID: 38333098 PMCID: PMC10850808 DOI: 10.1002/ece3.11007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Overharvesting is a serious threat to many fish populations. High mortality and directional selection on body size can cause evolutionary change in exploited populations via selection for a specific phenotype and a potential reduction in phenotypic diversity. Whether the loss of phenotypic diversity that accompanies directional selection impairs response to environmental stress is not known. To address this question, we exposed three zebrafish selection lines to thermal stress. Two lines had experienced directional selection for (1) large and (2) small body size, and one was (3) subject to random removal of individuals with respect to body size (i.e. line with no directional selection). Selection lines were exposed to three temperatures (elevated, 34°C; ambient, 28°C; low, 22°C) to determine the response to an environmental stressor (thermal stress). We assessed differences among selection lines in their life history (growth and reproduction), physiological traits (metabolic rate and critical thermal max) and behaviour (activity and feeding behaviour) when reared at different temperatures. Lines experiencing directional selection (i.e. size selected) showed reduced growth rate and a shift in average phenotype in response to lower or elevated thermal stress compared with fish from the random-selected line. Our data indicate that populations exposed to directional selection can have a more limited capacity to respond to thermal stress compared with fish that experience a comparable reduction in population size (but without directional selection). Future studies should aim to understand the impacts of environmental stressors on natural fish stocks.
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Affiliation(s)
- Daniel E. Sadler
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Stephan van Dijk
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Juha Karjalainen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Phillip C. Watts
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Silva Uusi‐Heikkilä
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Impact of anthropogenic contamination on glacier surface biota. Curr Opin Biotechnol 2023; 80:102900. [PMID: 36764028 DOI: 10.1016/j.copbio.2023.102900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 02/11/2023]
Abstract
Glaciers are ecosystems and they host active biological communities. Despite their remoteness, glaciers act as cold condensers where high precipitation rates and cold temperatures favor the deposition of pollutants. These contaminants include a broad range of substances, including legacy pollutants, but also compounds still largely used. Some of these compounds are monitored in the environment and their effects on the ecosystems are known, in contrast others can be defined as emerging pollutants since their presence and their impact on the environment are still poorly understood (e.g. microplastics, radionuclides). This review aim to provide an overview of the studies that have investigated the effects of pollutants on the supraglacial ecosystem so far. Despite the distribution of the pollutants in glacier environments has been discussed in several studies, no review paper has summarized the current knowledge on the effects of these substances on the ecological communities living in glacier ecosystems.
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de Moraes RLR, Sassi FDMC, Marinho MMF, Ráb P, Porto JIR, Feldberg E, Cioffi MDB. Small Body, Large Chromosomes: Centric Fusions Shaped the Karyotype of the Amazonian Miniature Fish Nannostomus anduzei (Characiformes, Lebiasinidae). Genes (Basel) 2023; 14:192. [PMID: 36672933 PMCID: PMC9858914 DOI: 10.3390/genes14010192] [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: 11/11/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Miniature refers to species with extraordinarily small adult body size when adult and can be found within all major metazoan groups. It is considered that miniature species have experienced severe alteration of numerous morphological traits during evolution. For a variety of reasons, including severe labor concerns during collecting, chromosomal acquisition, and taxonomic issues, miniature fishes are neglected and understudied. Since some available studies indicate possible relationship between diploid chromosome number (2n) and body size in fishes, we aimed to study one of the smallest Neotropical fish Nannostomus anduzei (Teleostei, Characiformes, Lebiasinidae), using both conventional (Giemsa staining, C-banding) and molecular cytogenetic methods (FISH mapping of rDNAs, microsatellites, and telomeric sequences). Our research revealed that N. anduzei possesses one of the lowest diploid chromosome numbers (2n = 22) among teleost fishes, and its karyotype is entirely composed of large metacentric chromosomes. All chromosomes, except for pair number 11, showed an 18S rDNA signal in the pericentromeric region. 5S rDNA signals were detected in the pericentromeric regions of chromosome pair number 1 and 6, displaying synteny to 18S rDNA signals. Interstitial telomeric sites (ITS) were identified in the centromeric region of pairs 6 and 8, indicating that centric fusions played a significant role in karyotype evolution of studied species. Our study provides further evidence supporting the trend of diploid chromosome number reduction along with miniaturization of adult body size in fishes.
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Affiliation(s)
- Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Francisco de Menezes Cavalcante Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Manoela Maria Ferreira Marinho
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Cidade Universitária, Castelo Branco, João Pessoa 58051-900, PB, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Jorge Ivan Rebelo Porto
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus 69067-375, AM, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
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Watts PC, Mappes T, Tukalenko E, Mousseau TA, Boratyński Z, Møller AP, Lavrinienko A. Interpretation of gut microbiota data in the 'eye of the beholder': A commentary and re-evaluation of data from 'Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone'. J Anim Ecol 2022; 91:1535-1545. [PMID: 35694772 PMCID: PMC9541917 DOI: 10.1111/1365-2656.13667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Evidence that exposure to environmental pollutants can alter the gut microbiota composition of wildlife includes studies of rodents exposed to radionuclides. Antwis et al. (2021) used amplicon sequencing to characterise the gut microbiota of four species of rodent (Myodes glareolus, Apodemus agrarius, A. flavicollis and A. sylvaticus) inhabiting the Chernobyl Exclusion Zone (CEZ) to examine possible changes in gut bacteria (microbiota) and gut fungi (mycobiota) associated with exposure to radionuclides and whether the sample type (from caecum or faeces) affected the analysis. The conclusions derived from the analyses of gut mycobiota are based on data that represent a mixture of ingested fungi (e.g. edible macrofungi, polypores, lichens and ectomycorrhizae) and gut mycobiota (e.g. microfungi and yeasts), which mask the patterns of inter‐ and intraspecific variation in the authentic gut mycobiota. Implying that ‘faecal samples are not an accurate indicator of gut composition’ creates an unnecessary controversy about faecal sampling because the comparison of samples from the caecum and faeces confounds many other possible drivers (including different animals from different locations, sampled in different years) of variation in gut microbiota. It is relevant also that Antwis et al.'s (2021) data lack statistical power to detect an effect of exposure to radionuclides on the gut microbiota because (1) all of their samples of Apodemus mice had experienced a medium or high total absorbed dose rate and (2) they did not collect samples of bank voles (M. glareolus) from replicate contaminated and uncontaminated locations. Discussion of Antwis et al.'s (2021) analysis, especially the claims presented in the Abstract, is important to prevent controversy about the outcome of research on the biological impacts of wildlife inhabiting the CEZ.
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Affiliation(s)
- Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Eugene Tukalenko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,National Research Center for Radiation Medicine of the National Academy of Medical Science, Kyiv, Ukraine
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Zbyszek Boratyński
- CIBIO/InBio, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Anders P Møller
- Laboratoire d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud 11, Orsay Cedex, France
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model. Genes (Basel) 2021; 12:genes12101524. [PMID: 34680920 PMCID: PMC8535310 DOI: 10.3390/genes12101524] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 12/18/2022] Open
Abstract
The pericentric satellite III (SatIII or Sat3) and II tandem repeats recently appeared to be transcribed under stress conditions, and the transcripts were shown to play an essential role in the universal stress response. In this paper, we review the role of human-specific SatIII copy number variation (CNV) in normal stress response, aging and pathology, with a focus on 1q12 loci. We postulate a close link between transcription of SatII/III repeats and their CNV. The accrued body of data suggests a hypothetical universal mechanism, which provides for SatIII copy gain during the stress response, alongside with another, more hypothetical reverse mechanism that might reduce the mean SatIII copy number, likely via the selection of cells with excessively large 1q12 loci. Both mechanisms, working alternatively like swings of the pendulum, may ensure the balance of SatIII copy numbers and optimum stress resistance. This model is verified on the most recent data on SatIII CNV in pathology and therapy, aging, senescence and response to genotoxic stress in vitro.
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