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Kristensen TN, Schönherz AA, Rohde PD, Sørensen JG, Loeschcke V. Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles. Sci Rep 2024; 14:17789. [PMID: 39090347 PMCID: PMC11294339 DOI: 10.1038/s41598-024-68753-5] [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: 02/29/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
There is experimental evidence that microbiomes have a strong influence on a range of host traits. Understanding the basis and importance of symbiosis between host and associated microorganisms is a rapidly developing research field, and we still lack a mechanistic understanding of ecological and genetic pressures affecting host-microbiome associations. Here Drosophila melanogaster lines from a large-scale artificial selection experiment were used to investigate whether the microbiota differ in lines selected for different stress resistance traits and longevity. Following multiple generations of artificial selection all selection regimes and corresponding controls had their microbiomes assessed. The microbiome was interrogated based on 16S rRNA sequencing. We found that the microbiome of flies from the different selection regimes differed markedly from that of the unselected control regime, and microbial diversity was consistently higher in selected relative to control regimes. Several common Drosophila bacterial species showed differentially abundance in the different selection regimes despite flies being exposed to similar environmental conditions for two generations prior to assessment. Our findings provide strong evidence for symbiosis between host and microbiomes but we cannot reveal whether the interactions are adaptive, nor whether they are caused by genetic or ecological factors.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - Anna A Schönherz
- Department of Animal and Veterinary Sciences, Aarhus University, Tjele, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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2
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McHugh KM, Burke MK. From microbes to mammals: The experimental evolution of aging and longevity across species. Evolution 2022; 76:692-707. [PMID: 35112358 DOI: 10.1111/evo.14442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/09/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023]
Abstract
Senescence, the functional deterioration of cells or organisms associated with increased age, is pervasive across the tree of life. Yet our understanding of the genetic and physiological basis underlying age-related declines in health and reproduction remains limited. Experimental evolution allows empirical examination of the question of why aging occurs; imposing selection for age-specific fitness traits shifts patterns of aging in experimental populations, enabling investigations of the variation underlying senescence and the mechanisms governing it. Whole-genome sequencing of experimentally evolved populations may reveal candidate genomic variants underlying particular aging patterns; unfortunately, most study systems suffer from limitations that weaken associations between genotypes and phenotypes. In this review, we provide a survey of experimental evolution studies that have altered population-level patterns of reproductive timing and senescence in a variety of species. We discuss the specific selection conditions that have increased longevity, the phenotypic responses and trade-offs that accompany these increases, and examine genomic data collected from these experiments. Additionally, we consider how selected field studies complement laboratory experiments on life-history evolution. Finally, we address the strengths and weaknesses of existing study systems, and evaluate which model organisms appear most promising for future genomic investigations of the evolutionary biology of aging.
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Affiliation(s)
- Kaitlin M McHugh
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
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Stazione L, Norry FM, Sambucetti P. Do Longevity and Fecundity Change by Selection on Mating Success at Elevated Temperature? Correlated Selection Responses in Drosophila buzzatii. Evol Biol 2021. [DOI: 10.1007/s11692-021-09540-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Turan ZG, Parvizi P, Dönertaş HM, Tung J, Khaitovich P, Somel M. Molecular footprint of Medawar's mutation accumulation process in mammalian aging. Aging Cell 2019; 18:e12965. [PMID: 31062469 PMCID: PMC6612638 DOI: 10.1111/acel.12965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/14/2019] [Accepted: 03/28/2019] [Indexed: 12/20/2022] Open
Abstract
Medawar's mutation accumulation hypothesis explains aging by the declining force of natural selection with age: Slightly deleterious germline mutations expressed in old age can drift to fixation and thereby lead to aging‐related phenotypes. Although widely cited, empirical evidence for this hypothesis has remained limited. Here, we test one of its predictions that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Combining 66 transcriptome datasets (including 16 tissues from five mammalian species) with sequence conservation estimates across mammals, here we report that the overall conservation level of expressed genes is lower at old age compared to young adulthood. This age‐related decrease in transcriptome conservation (ADICT) is systematically observed in diverse mammalian tissues, including the brain, liver, lung, and artery, but not in others, most notably in the muscle and heart. Where observed, ADICT is driven partly by poorly conserved genes being up‐regulated during aging. In general, the more often a gene is found up‐regulated with age among tissues and species, the lower its evolutionary conservation. Poorly conserved and up‐regulated genes have overlapping functional properties that include responses to age‐associated tissue damage, such as apoptosis and inflammation. Meanwhile, these genes do not appear to be under positive selection. Hence, genes contributing to old age phenotypes are found to harbor an excess of slightly deleterious alleles, at least in certain tissues. This supports the notion that genetic drift shapes aging in multicellular organisms, consistent with Medawar's mutation accumulation hypothesis.
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Affiliation(s)
- Zeliha Gözde Turan
- Department of Biological Sciences Middle East Technical University Ankara Turkey
| | - Poorya Parvizi
- Department of Biological Sciences Middle East Technical University Ankara Turkey
- Usher Institute of Population Health Sciences and Informatics University of Edinburgh Edinburgh UK
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL‐EBI Wellcome Trust Genome Campus Cambridge UK
| | - Jenny Tung
- Department of Evolutionary Anthropology Duke University Durham North Carolina
- Department of Biology Duke University Durham North Carolina
- Duke Population Research Institute Duke University Durham North Carolina
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration Skolkovo Institute of Science and Technology Moscow Russia
- CAS Key Laboratory of Computational Biology, CAS‐MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
| | - Mehmet Somel
- Department of Biological Sciences Middle East Technical University Ankara Turkey
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Golubev A, Panchenko A, Anisimov V. Applying parametric models to survival data: tradeoffs between statistical significance, biological plausibility, and common sense. Biogerontology 2018; 19:341-365. [PMID: 29869230 DOI: 10.1007/s10522-018-9759-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022]
Abstract
Parametric models for survival data help to differentiate aging from other lifespan determinants. However, such inferences suffer from small sizes of experimental animal samples and variable animals handling by different labs. We analyzed control data from a single laboratory where interventions in murine lifespan were studied over decades. The minimal Gompertz model (GM) was found to perform best with most murine strains. However, when several control datasets related to a particular strain are fitted to GM, strikingly rigid interdependencies between GM parameters emerge, consistent with the Strehler-Mildvan correlation (SMC). SMC emerges even when survival patterns do not conform to GM, as with cancer-prone HER2/neu mice, which die at a log-normally distributed age. Numerical experiments show that SMC includes an artifact whose magnitude depends on dataset deviation from conformance to GM irrespectively of the noisiness of small datasets, another contributor to SMC. Still another contributor to SMC is the compensation effect of mortality (CEM): a real tradeoff between the physiological factors responsible for initial vitality and the rate of its decline. To avoid misinterpretations, we advise checking experimental results against a SMC based on historical controls or on subgroups obtained by randomization of control animals. An apparent acceleration of aging associated with a decrease in the initial mortality is invalid if it is not greater than SMC suggests. This approach applied to published data suggests that the effects of calorie restriction and of drugs believed to mimic it are different. SMC and CEM relevance to human survival patterns is discussed.
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Affiliation(s)
- Alexey Golubev
- N.N. Petrov Research Institute of Oncology, Pesochny-2, Saint-Petersburg, 197758, Russia.
| | - Andrei Panchenko
- N.N. Petrov Research Institute of Oncology, Pesochny-2, Saint-Petersburg, 197758, Russia
| | - Vladimir Anisimov
- N.N. Petrov Research Institute of Oncology, Pesochny-2, Saint-Petersburg, 197758, Russia
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Michalak P, Kang L, Sarup PM, Schou MF, Loeschcke V. Nucleotide diversity inflation as a genome-wide response to experimental lifespan extension in Drosophila melanogaster. BMC Genomics 2017; 18:84. [PMID: 28088192 PMCID: PMC5237518 DOI: 10.1186/s12864-017-3485-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/10/2017] [Indexed: 11/20/2022] Open
Abstract
Background Evolutionary theory predicts that antagonistically selected alleles, such as those with divergent pleiotropic effects in early and late life, may often reach intermediate population frequencies due to balancing selection, an elusive process when sought out empirically. Alternatively, genetic diversity may increase as a result of positive frequency-dependent selection and genetic purging in bottlenecked populations. Results While experimental evolution systems with directional phenotypic selection typically result in at least local heterozygosity loss, we report that selection for increased lifespan in Drosophila melanogaster leads to an extensive genome-wide increase of nucleotide diversity in the selected lines compared to replicate control lines, pronounced in regions with no or low recombination, such as chromosome 4 and centromere neighborhoods. These changes, particularly in coding sequences, are most consistent with the operation of balancing selection and the antagonistic pleiotropy theory of aging and life history traits that tend to be intercorrelated. Genes involved in antioxidant defenses, along with multiple lncRNAs, were among those most affected by balancing selection. Despite the overwhelming genetic diversification and the paucity of selective sweep regions, two genes with functions important for central nervous system and memory, Ptp10D and Ank2, evolved under positive selection in the longevity lines. Conclusions Overall, the ‘evolve-and-resequence’ experimental approach proves successful in providing unique insights into the complex evolutionary dynamics of genomic regions responsible for longevity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3485-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pawel Michalak
- Biocomplexity Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA.
| | - Lin Kang
- Biocomplexity Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA
| | - Pernille M Sarup
- Department of Bioscience, Aarhus University, Ny Munkegade 114-116, Aarhus, DK-8000, Denmark
| | - Mads F Schou
- Department of Bioscience, Aarhus University, Ny Munkegade 114-116, Aarhus, DK-8000, Denmark
| | - Volker Loeschcke
- Department of Bioscience, Aarhus University, Ny Munkegade 114-116, Aarhus, DK-8000, Denmark.
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Shenoi VN, Banerjee SM, Guruswamy B, Sen S, Ali SZ, Prasad NG. Drosophila melanogaster males evolve increased courtship as a correlated response to larval crowding. Anim Behav 2016. [DOI: 10.1016/j.anbehav.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sepil I, Carazo P, Perry JC, Wigby S. Insulin signalling mediates the response to male-induced harm in female Drosophila melanogaster. Sci Rep 2016; 6:30205. [PMID: 27457757 PMCID: PMC4960482 DOI: 10.1038/srep30205] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/29/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic manipulations in nutrient-sensing pathways are known to both extend lifespan and modify responses to environmental stressors (e.g., starvation, oxidative and thermal stresses), suggesting that similar mechanisms regulate lifespan and stress resistance. However, despite being a key factor reducing female lifespan and affecting female fitness, male-induced harm has rarely been considered as a stressor mediated by nutrient sensing pathways. We explored whether a lifespan-extending manipulation also modifies female resistance to male-induced harm. To do so, we used long-lived female Drosophila melanogaster that had their insulin signalling pathway downregulated by genetically ablating the median neurosecretory cells (mNSC). We varied the level of exposure to males for control and ablated females and tested for interacting effects on female lifespan and fitness. As expected, we found that lifespan significantly declined with exposure to males. However, mNSC-ablated females maintained significantly increased lifespan across all male exposure treatments. Furthermore, lifespan extension and relative fitness of mNSC-ablated females were maximized under intermediate exposure to males, and minimized under low and high exposure to males. Overall, our results suggest that wild-type levels of insulin signalling reduce female susceptibility to male-induced harm under intense sexual conflict, and may also protect females when mating opportunities are sub-optimally low.
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Affiliation(s)
- Irem Sepil
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Pau Carazo
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
- Instituto Cavanilles of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Jennifer C. Perry
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
- Jesus College, University of Oxford, Turl Street, Oxford OX1 3DW, UK
| | - Stuart Wigby
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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Bosa CF, Cruz-López L, Zepeda-Cisneros CS, Valle-Mora J, Guillén-Navarro K, Liedo P. Sexual behavior and male volatile compounds in wild and mass-reared strains of the Mexican fruit fly Anastrepha ludens (Diptera: Tephritidae) held under different colony management regimes. INSECT SCIENCE 2016; 23:105-116. [PMID: 25339372 DOI: 10.1111/1744-7917.12180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/02/2014] [Indexed: 06/04/2023]
Abstract
We compared the calling and mating behavior and volatile release of wild males Anastrepha ludens (Loew) with males from 4 mass-reared strains: (i) a standard mass-reared colony (control), (ii) a genetic sexing strain (Tap-7), (iii) a colony started from males selected on their survival and mating competitiveness abilities (selected), and (iv) a hybrid colony started by crossing wild males with control females. Selected and wild males were more competitive, achieving more matings under field cage conditions. Mass-reared strains showed higher percentages of pheromone calling males under field conditions except for Tap-7 males, which showed the highest percentages of pheromone calling males under laboratory cage conditions. For mature males of all strains, field-cage calling behavior increased during the last hour before sunset, with almost a 2 fold increase exhibited by wild males during the last half hour. The highest peak mating activity of the 4 mass-reared strains occurred 30 min earlier than for wild males. By means of solid phase microextraction (SPME) plus gas chromatography-mass spectrometry (GC-MS), the composition of volatiles released by males was analyzed and quantified. Wild males emitted significantly less amounts of (E,E)-α-farnesene but emitted significantly more amounts of (E,E)-suspensolide as they aged than mass-reared males. Within the 4 mass-reared strains, Tap-7 released significantly more amounts of (E,E)-α-farnesene and hybrid more of (E,E)-suspensolide. Differences in chemical composition could be explained by the intrinsic characteristics of the strains and the colony management regimes. Characterization of calling behavior and age changes of volatile composition between wild and mass-reared strains could explain the differences in mating competitiveness and may be useful for optimizing the sterile insect technique in A. ludens.
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Affiliation(s)
- Carlos Felipe Bosa
- El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto km 2.5, Chiapas, 30700, Mexico
| | - Leopoldo Cruz-López
- El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto km 2.5, Chiapas, 30700, Mexico
| | | | - Javier Valle-Mora
- El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto km 2.5, Chiapas, 30700, Mexico
| | - Karina Guillén-Navarro
- El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto km 2.5, Chiapas, 30700, Mexico
| | - Pablo Liedo
- El Colegio de la Frontera Sur, Carretera Antiguo Aeropuerto km 2.5, Chiapas, 30700, Mexico
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Briga M, Verhulst S. What can long-lived mutants tell us about mechanisms causing aging and lifespan variation in natural environments? Exp Gerontol 2015; 71:21-6. [DOI: 10.1016/j.exger.2015.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/01/2015] [Accepted: 09/03/2015] [Indexed: 12/14/2022]
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