1
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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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Linder RA, Zabanavar B, Majumder A, Hoang HCS, Delgado VG, Tran R, La VT, Leemans SW, Long AD. Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes. Mol Biol Evol 2022; 39:msac248. [PMID: 36366952 PMCID: PMC9728589 DOI: 10.1093/molbev/msac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We carried out a 200 generation Evolve and Resequence (E&R) experiment initiated from an outbred diploid recombined 18-way synthetic base population. Replicate populations were evolved at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing resulted in an average between adjacent-gene per cell division recombination rate of ∼0.0008. Despite attempts to force weekly sex, roughly half of our populations evolved cheaters and appear to be evolving asexually. Focusing on seven chemical stressors and 55 total evolved populations that remained sexual we observed large fitness gains and highly repeatable patterns of genome-wide haplotype change within chemical challenges, with limited levels of repeatability across chemical treatments. Adaptation appears highly polygenic with almost the entire genome showing significant and consistent patterns of haplotype change with little evidence for long-range linkage disequilibrium in a subset of populations for which we sequenced haploid clones. That is, almost the entire genome is under selection or drafting with selected sites. At any given locus adaptation was almost always dominated by one of the 18 founder's alleles, with that allele varying spatially and between treatments, suggesting that selection acts primarily on rare variants private to a founder or haplotype blocks harboring multiple mutations.
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Affiliation(s)
- Robert A Linder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Behzad Zabanavar
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Arundhati Majumder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Hannah Chiao-Shyan Hoang
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vanessa Genesaret Delgado
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Ryan Tran
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vy Thoai La
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Simon William Leemans
- Department of Biomedical Engineering, School of Engineering, University of California, Irvine
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
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3
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Henry LP, Ayroles JF. Meta-analysis suggests the microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster. BMC Microbiol 2021; 21:108. [PMID: 33836662 PMCID: PMC8034159 DOI: 10.1186/s12866-021-02168-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/31/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Experimental evolution has a long history of uncovering fundamental insights into evolutionary processes, but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also respond to selection. However, the microbial contribution to host evolution remains poorly understood. Here, we re-analyzed genomic data to characterize the metagenomes from ten Evolve and Resequence (E&R) experiments in Drosophila melanogaster to determine how the microbiome changed in response to host selection. RESULTS Bacterial diversity was significantly different in 5/10 studies, primarily in traits associated with metabolism or immunity. Duration of selection did not significantly influence bacterial diversity, highlighting the importance of associations with specific host traits. CONCLUSIONS Our genomic re-analysis suggests the microbiome often responds to host selection; thus, the microbiome may contribute to the response of Drosophila in E&R experiments. We outline important considerations for incorporating the microbiome into E&R experiments. The E&R approach may provide critical insights into host-microbiome interactions and fundamental insight into the genomic basis of adaptation.
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Affiliation(s)
- Lucas P Henry
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
| | - Julien F Ayroles
- Department of Ecology & Evolutionary Biology, 150 Carl Icahn Laboratory, Princeton University, Princeton, NJ, 08544, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
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4
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Kawecki TJ, Erkosar B, Dupuis C, Hollis B, Stillwell RC, Kapun M. The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila. Mol Biol Evol 2021; 38:2732-2749. [PMID: 33677563 PMCID: PMC8233504 DOI: 10.1093/molbev/msab061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Periods of nutrient shortage impose strong selection on animal populations. Experimental studies of genetic adaptation to nutrient shortage largely focus on resistance to acute starvation at adult stage; it is not clear how conclusions drawn from these studies extrapolate to other forms of nutritional stress. We studied the genomic signature of adaptation to chronic juvenile malnutrition in six populations of Drosophila melanogaster evolved for 150 generations on an extremely nutrient-poor larval diet. Comparison with control populations evolved on standard food revealed repeatable genomic differentiation between the two set of population, involving >3,000 candidate SNPs forming >100 independently evolving clusters. The candidate genomic regions were enriched in genes implicated in hormone, carbohydrate, and lipid metabolism, including some with known effects on fitness-related life-history traits. Rather than being close to fixation, a substantial fraction of candidate SNPs segregated at intermediate allele frequencies in all malnutrition-adapted populations. This, together with patterns of among-population variation in allele frequencies and estimates of Tajima’s D, suggests that the poor diet results in balancing selection on some genomic regions. Our candidate genes for tolerance to larval malnutrition showed a high overlap with genes previously implicated in acute starvation resistance. However, adaptation to larval malnutrition in our study was associated with reduced tolerance to acute adult starvation. Thus, rather than reflecting synergy, the shared genomic architecture appears to mediate an evolutionary trade-off between tolerances to these two forms of nutritional stress.
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Affiliation(s)
- Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Berra Erkosar
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Brian Hollis
- EPFL, Department of Systems Biology, Lausanne, Switzerland.,Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - R Craig Stillwell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
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5
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Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Transposable Element Landscape in Drosophila Populations Selected for Longevity. Genome Biol Evol 2021; 13:6141024. [PMID: 33595657 PMCID: PMC8355499 DOI: 10.1093/gbe/evab031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) inflict numerous negative effects on health and fitness as they replicate by integrating into new regions of the host genome. Even though organisms employ powerful mechanisms to demobilize TEs, transposons gradually lose repression during aging. The rising TE activity causes genomic instability and was implicated in age-dependent neurodegenerative diseases, inflammation, and the determination of lifespan. It is therefore conceivable that long-lived individuals have improved TE silencing mechanisms resulting in reduced TE expression relative to their shorter-lived counterparts and fewer genomic insertions. Here, we test this hypothesis by performing the first genome-wide analysis of TE insertions and expression in populations of Drosophila melanogaster selected for longevity through late-life reproduction for 50–170 generations from four independent studies. Contrary to our expectation, TE families were generally more abundant in long-lived populations compared with nonselected controls. Although simulations showed that this was not expected under neutrality, we found little evidence for selection driving TE abundance differences. Additional RNA-seq analysis revealed a tendency for reducing TE expression in selected populations, which might be more important for lifespan than regulating genomic insertions. We further find limited evidence of parallel selection on genes related to TE regulation and transposition. However, telomeric TEs were genomically and transcriptionally more abundant in long-lived flies, suggesting improved telomere maintenance as a promising TE-mediated mechanism for prolonging lifespan. Our results provide a novel viewpoint indicating that reproduction at old age increases the opportunity of TEs to be passed on to the next generation with little impact on longevity.
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Affiliation(s)
- Daniel K Fabian
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
- Corresponding author: E-mail:
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Matías Fuentealba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Linda Partridge
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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6
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Zeng L, Jiang HL, Ashraf GM, Li ZR, Liu R. MicroRNA and mRNA profiling of cerebral cortex in a transgenic mouse model of Alzheimer's disease by RNA sequencing. Neural Regen Res 2021; 16:2099-2108. [PMID: 33642400 PMCID: PMC8343333 DOI: 10.4103/1673-5374.308104] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In a previous study, we found that long non-coding genes in Alzheimer’s disease (AD) are a result of endogenous gene disorders caused by the recruitment of microRNA (miRNA) and mRNA, and that miR-200a-3p and other representative miRNAs can mediate cognitive impairment and thus serve as new biomarkers for AD. In this study, we investigated the abnormal expression of miRNA and mRNA and the pathogenesis of AD at the epigenetic level. To this aim, we performed RNA sequencing and an integrative analysis of the cerebral cortex of the widely used amyloid precursor protein and presenilin-1 double transgenic mouse model of AD. Overall, 129 mRNAs and 68 miRNAs were aberrantly expressed. Among these, eight down-regulated miRNAs and seven up-regulated miRNAs appeared as promising noninvasive biomarkers and therapeutic targets. The main enriched signaling pathways involved mitogen-activated kinase protein, phosphatidylinositol 3-kinase-protein kinase B, mechanistic target of rapamycin kinase, forkhead box O, and autophagy. An miRNA-mRNA network between dysregulated miRNAs and corresponding target genes connected with AD progression was also constructed. These miRNAs and mRNAs are potential biomarkers and therapeutic targets for new treatment strategies, early diagnosis, and prevention of AD. The present results provide a novel perspective on the role of miRNAs and mRNAs in AD. This study was approved by the Experimental Animal Care and Use Committee of Institute of Medicinal Biotechnology of Beijing, China (approval No. IMB-201909-D6) on September 6, 2019.
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Affiliation(s)
- Li Zeng
- Organic Chemistry and Function Laboratory, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Lun Jiang
- Organic Chemistry and Function Laboratory, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zhuo-Rong Li
- Organic Chemistry and Function Laboratory, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Liu
- Organic Chemistry and Function Laboratory, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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7
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Phillips MA, Kutch IC, Long AD, Burke MK. Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change. Mol Ecol 2020; 29:4898-4912. [PMID: 33135198 DOI: 10.1111/mec.15687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/28/2022]
Abstract
"Evolve and resequence" (E&R) studies combine experimental evolution and whole-genome sequencing to interrogate the genetics underlying adaptation. Due to ease of handling, E&R work with asexual organisms such as bacteria can employ optimized experimental design, with large experiments and many generations of selection. By contrast, E&R experiments with sexually reproducing organisms are more difficult to implement, and design parameters vary dramatically among studies. Thus, efforts have been made to assess how these differences, such as number of independent replicates, or size of experimental populations, impact inference. We add to this work by investigating the role of time sampling-the number of discrete time points sequence data are collected from evolving populations. Using data from an E&R experiment with outcrossing Saccharomyces cerevisiae in which populations were sequenced 17 times over ~540 generations, we address the following questions: (a) Do more time points improve the ability to identify candidate regions underlying selection? And (b) does high-resolution sampling provide unique insight into evolutionary processes driving adaptation? We find that while time sampling does not improve the ability to identify candidate regions, high-resolution sampling does provide valuable opportunities to characterize evolutionary dynamics. Increased time sampling reveals three distinct trajectories for adaptive alleles: one consistent with classic population genetic theory (i.e., models assuming constant selection coefficients), and two where trajectories suggest more context-dependent responses (i.e., models involving dynamic selection coefficients). We conclude that while time sampling has limited impact on candidate region identification, sampling eight or more time points has clear benefits for studying complex evolutionary dynamics.
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Affiliation(s)
- Mark A Phillips
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Ian C Kutch
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
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8
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Roberts KE, Meaden S, Sharpe S, Kay S, Doyle T, Wilson D, Bartlett LJ, Paterson S, Boots M. Resource quality determines the evolution of resistance and its genetic basis. Mol Ecol 2020; 29:4128-4142. [PMID: 32860314 DOI: 10.1111/mec.15621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 10/23/2022]
Abstract
Parasites impose strong selection on their hosts, but the level of any evolved resistance may be constrained by the availability of resources. However, studies identifying the genomic basis of such resource-mediated selection are rare, particularly in nonmodel organisms. Here, we investigated the role of nutrition in the evolution of resistance to a DNA virus (PiGV), and any associated trade-offs in a lepidopteran pest species (Plodia interpunctella). Through selection experiments and whole-genome resequencing, we identify genetic markers of resistance that vary between the nutritional environments during selection. We do not find consistent evolution of resistance in the presence of virus but rather see substantial variation among replicate populations. Resistance in a low-nutrition environment is negatively correlated with growth rate, consistent with an established trade-off between immunity and development, but this relationship is highly context dependent. Whole-genome resequencing of the host shows that resistance mechanisms are likely to be highly polygenic and although the underlying genetic architecture may differ between high and low-nutrition environments, similar mechanisms are commonly used. As a whole, our results emphasize the importance of the resource environment on influencing the evolution of resistance.
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Affiliation(s)
- Katherine E Roberts
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Sean Meaden
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Stephen Sharpe
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Suzanne Kay
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Toby Doyle
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Drew Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | | | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mike Boots
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK.,Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
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9
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Hoedjes KM, van den Heuvel J, Kapun M, Keller L, Flatt T, Zwaan BJ. Distinct genomic signals of lifespan and life history evolution in response to postponed reproduction and larval diet in Drosophila. Evol Lett 2019; 3:598-609. [PMID: 31867121 PMCID: PMC6906992 DOI: 10.1002/evl3.143] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/08/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Reproduction and diet are two major factors controlling the physiology of aging and life history, but how they interact to affect the evolution of longevity is unknown. Moreover, although studies of large-effect mutants suggest an important role of nutrient sensing pathways in regulating aging, the genetic basis of evolutionary changes in lifespan remains poorly understood. To address these questions, we analyzed the genomes of experimentally evolved Drosophila melanogaster populations subjected to a factorial combination of two selection regimes: reproductive age (early versus postponed), and diet during the larval stage ("low," "control," "high"), resulting in six treatment combinations with four replicate populations each. Selection on reproductive age consistently affected lifespan, with flies from the postponed reproduction regime having evolved a longer lifespan. In contrast, larval diet affected lifespan only in early-reproducing populations: flies adapted to the "low" diet lived longer than those adapted to control diet. Here, we find genomic evidence for strong independent evolutionary responses to either selection regime, as well as loci that diverged in response to both regimes, thus representing genomic interactions between the two. Overall, we find that the genomic basis of longevity is largely independent of dietary adaptation. Differentiated loci were not enriched for "canonical" longevity genes, suggesting that naturally occurring genic targets of selection for longevity differ qualitatively from variants found in mutant screens. Comparing our candidate loci to those from other "evolve and resequence" studies of longevity demonstrated significant overlap among independent experiments. This suggests that the evolution of longevity, despite its presumed complex and polygenic nature, might be to some extent convergent and predictable.
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Affiliation(s)
- Katja M. Hoedjes
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Joost van den Heuvel
- Laboratory of Genetics, Plant Sciences GroupWageningen UniversityWageningenThe Netherlands
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle Upon TyneUnited Kingdom
| | - Martin Kapun
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Current Address: Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Laurent Keller
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Thomas Flatt
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Bas J. Zwaan
- Laboratory of Genetics, Plant Sciences GroupWageningen UniversityWageningenThe Netherlands
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10
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Sex and age specific reduction in stress resistance and mitochondrial DNA copy number in Drosophila melanogaster. Sci Rep 2019; 9:12305. [PMID: 31444377 PMCID: PMC6707197 DOI: 10.1038/s41598-019-48752-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023] Open
Abstract
Environmental stresses such as extreme temperatures, dehydration and food deprivation may have distinct consequences for different age-classes and for males and females across species. Here we investigate a natural population of the model organism Drosophila melanogaster. Males and females at ages 3, 19 and 35 days were tested for stress resistance; i.e. the ability of flies to cope with starvation and both cold and hot temperatures. Further, we tested a measure of metabolic efficiency, namely mitochondrial DNA copy number (mtDNA CN) in both sexes at all three age-classes. We hypothesize that stress resistance is reduced at old age and more so in males, and that mtDNA CN is a biomarker for sex- and age-dependent reductions in the ability to cope with harsh environments. We show that: (1) males exhibit reduced starvation tolerance at old age, whereas older females are better in coping with periods without food compared to younger females, (2) heat tolerance decreases with increasing age in males but not in females, (3) cold tolerance is reduced at old age in both sexes, and (4) old males have reduced mtDNA CN whereas mtDNA CN slightly increases with age in females. In conclusion, our data provide strong evidence for trait and sex specific consequences of aging with females generally being better at coping with environmental stress at old age. The reduced mtDNA CN in old males suggests reduced metabolic efficiency and this may partly explain why males are less stress tolerant at old age than females. We suggest that mtDNA CN might be a suitable biomarker for physiological robustness. Our findings likely extend to other taxa than Drosophila and therefore we discuss the observations in relation to aging and sex specific lifespan across species.
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11
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Kelly JK, Hughes KA. Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans. Genetics 2019; 211:943-961. [PMID: 30593495 PMCID: PMC6404262 DOI: 10.1534/genetics.118.301824] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/15/2018] [Indexed: 11/18/2022] Open
Abstract
We develop analytical and simulation tools for evolve-and-resequencing experiments and apply them to a new study of rapid evolution in Drosophila simulans Likelihood test statistics applied to pooled population sequencing data suggest parallel evolution of 138 SNPs across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from Drosophila genetic data sets indicate that major features of the genome-wide response could be explained by as few as 30 loci under strong directional selection with a corresponding hitchhiking effect. Smaller effect loci are likely also responding, but are below the detection limit of the experiment. Finally, SNPs showing strong parallel evolution in the experiment are intermediate in frequency in the natural population (usually 30-70%) indicative of balancing selection in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans, suggesting environmental heterogeneity as a potential balancing mechanism.
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Affiliation(s)
- John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - Kimberly A Hughes
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
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12
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Michalak P, Kang L, Schou MF, Garner HR, Loeschcke V. Genomic signatures of experimental adaptive radiation in Drosophila. Mol Ecol 2018; 28:600-614. [PMID: 30375065 DOI: 10.1111/mec.14917] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/03/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022]
Abstract
Abiotic environmental factors play a fundamental role in determining the distribution, abundance and adaptive diversification of species. Empowered by new technologies enabling rapid and increasingly accurate examination of genomic variation in populations, researchers may gain new insights into the genomic background of adaptive radiation and stress resistance. We investigated genomic variation across generations of large-scale experimental selection regimes originating from a single founder population of Drosophila melanogaster, diverging in response to ecologically relevant environmental stressors: heat shock, heat knock down, cold shock, desiccation and starvation. When compared to the founder population, and to parallel unselected controls, there were more than 100,000 single nucleotide polymorphisms (SNPs) displaying consistent allelic changes in response to selective pressures across generations. These SNPs were found in both coding and noncoding sequences, with the highest density in promoter regions, and involved a broad range of functionalities, including molecular chaperoning by heat-shock proteins. The SNP patterns were highly stressor-specific despite considerable variation among line replicates within each selection regime, as reflected by a principal component analysis, and co-occurred with selective sweep regions. Only ~15% of SNPs with putatively adaptive changes were shared by at least two selective regimes, while less than 1% of SNPs diverged in opposite directions. Divergent stressors driving evolution in the experimental system of adaptive radiation left distinct genomic signatures, most pronounced in starvation and heat-shock selection regimes.
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Affiliation(s)
- Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia.,One Health Research Center, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia.,Institute of Evolution, University of Haifa, Haifa, Israel
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia
| | - Mads F Schou
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Harold R Garner
- Edward Via College of Osteopathic Medicine, Blacksburg, Virginia.,The Gibbs Cancer Center and Research Institute, Spartanburg, SC, USA
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13
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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