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Alton LA, Kutz T, Bywater CL, Lombardi E, Cockerell FE, Layh S, Winwood-Smith H, Arnold PA, Beaman JE, Walter GM, Monro K, Mirth CK, Sgrò CM, White CR. Temperature and nutrition do not interact to shape the evolution of metabolic rate. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220484. [PMID: 38186272 PMCID: PMC10772606 DOI: 10.1098/rstb.2022.0484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/22/2023] [Indexed: 01/09/2024] Open
Abstract
Metabolic cold adaptation, or Krogh's rule, is the controversial hypothesis that predicts a monotonically negative relationship between metabolic rate and environmental temperature for ectotherms living along thermal clines measured at a common temperature. Macrophysiological patterns consistent with Krogh's rule are not always evident in nature, and experimentally evolved responses to temperature have failed to replicate such patterns. Hence, temperature may not be the sole driver of observed variation in metabolic rate. We tested the hypothesis that temperature, as a driver of energy demand, interacts with nutrition, a driver of energy supply, to shape the evolution of metabolic rate to produce a pattern resembling Krogh's rule. To do this, we evolved replicate lines of Drosophila melanogaster at 18, 25 or 28°C on control, low-calorie or low-protein diets. Contrary to our prediction, we observed no effect of nutrition, alone or interacting with temperature, on adult female and male metabolic rates. Moreover, support for Krogh's rule was only in females at lower temperatures. We, therefore, hypothesize that observed variation in metabolic rate along environmental clines arises from the metabolic consequences of environment-specific life-history optimization, rather than because of the direct effect of temperature on metabolic rate. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.
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Affiliation(s)
- Lesley A. Alton
- Centre for Geometric Biology, Monash University, Melbourne, Victoria 3800, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Teresa Kutz
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Candice L. Bywater
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Emily Lombardi
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Fiona E. Cockerell
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Sean Layh
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Hugh Winwood-Smith
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Pieter A. Arnold
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Julian E. Beaman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Greg M. Walter
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Keyne Monro
- Centre for Geometric Biology, Monash University, Melbourne, Victoria 3800, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Christen K. Mirth
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Carla M. Sgrò
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Craig R. White
- Centre for Geometric Biology, Monash University, Melbourne, Victoria 3800, Australia
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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2
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Erkosar B, Dupuis C, Cavigliasso F, Savary L, Kremmer L, Gallart-Ayala H, Ivanisevic J, Kawecki TJ. Evolutionary adaptation to juvenile malnutrition impacts adult metabolism and impairs adult fitness in Drosophila. eLife 2023; 12:e92465. [PMID: 37847744 PMCID: PMC10637773 DOI: 10.7554/elife.92465] [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: 09/03/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Juvenile undernutrition has lasting effects on adult metabolism of the affected individuals, but it is unclear how adult physiology is shaped over evolutionary time by natural selection driven by juvenile undernutrition. We combined RNAseq, targeted metabolomics, and genomics to study the consequences of evolution under juvenile undernutrition for metabolism of reproductively active adult females of Drosophila melanogaster. Compared to Control populations maintained on standard diet, Selected populations maintained for over 230 generations on a nutrient-poor larval diet evolved major changes in adult gene expression and metabolite abundance, in particular affecting amino acid and purine metabolism. The evolved differences in adult gene expression and metabolite abundance between Selected and Control populations were positively correlated with the corresponding differences previously reported for Selected versus Control larvae. This implies that genetic variants affect both stages similarly. Even when well fed, the metabolic profile of Selected flies resembled that of flies subject to starvation. Finally, Selected flies had lower reproductive output than Controls even when both were raised under the conditions under which the Selected populations evolved. These results imply that evolutionary adaptation to juvenile undernutrition has large pleiotropic consequences for adult metabolism, and that they are costly rather than adaptive for adult fitness. Thus, juvenile and adult metabolism do not appear to evolve independently from each other even in a holometabolous species where the two life stages are separated by a complete metamorphosis.
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Affiliation(s)
- Berra Erkosar
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Fanny Cavigliasso
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Loriane Savary
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Laurent Kremmer
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Hector Gallart-Ayala
- Metabolomics Unit, Faculty of Biology and Medicine, University of LausanneLausanneSwitzerland
| | - Julijana Ivanisevic
- Metabolomics Unit, Faculty of Biology and Medicine, University of LausanneLausanneSwitzerland
| | - Tadeusz J Kawecki
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
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3
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Zakharenko LP, Petrovskii DV, Bobrovskikh MA, Gruntenko NE, Yakovleva EY, Markov AV, Putilov AA. Motus Vita Est: Fruit Flies Need to Be More Active and Sleep Less to Adapt to Either a Longer or Harder Life. Clocks Sleep 2023; 5:98-115. [PMID: 36975551 PMCID: PMC10047790 DOI: 10.3390/clockssleep5010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Background: Activity plays a very important role in keeping bodies strong and healthy, slowing senescence, and decreasing morbidity and mortality. Drosophila models of evolution under various selective pressures can be used to examine whether increased activity and decreased sleep duration are associated with the adaptation of this nonhuman species to longer or harder lives. Methods: For several years, descendants of wild flies were reared in a laboratory without and with selection pressure. To maintain the “salt” and “starch” strains, flies from the wild population (called “control”) were reared on two adverse food substrates. The “long-lived” strain was maintained through artificial selection for late reproduction. The 24 h patterns of locomotor activity and sleep in flies from the selected and unselected strains (902 flies in total) were studied in constant darkness for at least, 5 days. Results: Compared to the control flies, flies from the selected strains demonstrated enhanced locomotor activity and reduced sleep duration. The most profound increase in locomotor activity was observed in flies from the starch (short-lived) strain. Additionally, the selection changed the 24 h patterns of locomotor activity and sleep. For instance, the morning and evening peaks of locomotor activity were advanced and delayed, respectively, in flies from the long-lived strain. Conclusion: Flies become more active and sleep less in response to various selection pressures. These beneficial changes in trait values might be relevant to trade-offs among fitness-related traits, such as body weight, fecundity, and longevity.
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Affiliation(s)
- Lyudmila P. Zakharenko
- Department of Insect Genetics, Institute of Cytology and Genetics of the Siberian Branch, The Russian Academy of Sciences, Novosibirsk 630000, Russia
| | - Dmitrii V. Petrovskii
- Department of Insect Genetics, Institute of Cytology and Genetics of the Siberian Branch, The Russian Academy of Sciences, Novosibirsk 630000, Russia
| | - Margarita A. Bobrovskikh
- Department of Insect Genetics, Institute of Cytology and Genetics of the Siberian Branch, The Russian Academy of Sciences, Novosibirsk 630000, Russia
| | - Nataly E. Gruntenko
- Department of Insect Genetics, Institute of Cytology and Genetics of the Siberian Branch, The Russian Academy of Sciences, Novosibirsk 630000, Russia
| | | | - Alexander V. Markov
- Department of Biological Evolution, The Moscow State University, Moscow 101000, Russia
- Borisyak Paleontological Institute of the Russian Academy of Sciences, Moscow 101000, Russia
| | - Arcady A. Putilov
- Research Group for Math-Modeling of Biomedical Systems, Research Institute for Molecular Biology and Biophysics of the Federal Research Centre for Fundamental and Translational Medicine, Novosibirsk 630000, Russia
- Laboratory of Sleep/Wake Neurobiology, Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, Moscow 101000, Russia
- Correspondence: ; Tel.: +49-30-53674643 or +49-30-61290031
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4
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Hoedjes KM, Kostic H, Flatt T, Keller L. A Single Nucleotide Variant in the PPARγ-homolog Eip75B Affects Fecundity in Drosophila. Mol Biol Evol 2023; 40:7005670. [PMID: 36703226 PMCID: PMC9922802 DOI: 10.1093/molbev/msad018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/04/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Single nucleotide polymorphisms are the most common type of genetic variation, but how these variants contribute to the adaptation of complex phenotypes is largely unknown. Experimental evolution and genome-wide association studies have demonstrated that variation in the PPARγ-homolog Eip75B has associated with longevity and life-history differences in the fruit fly Drosophila melanogaster. Using RNAi knockdown, we first demonstrate that reduced expression of Eip75B in adult flies affects lifespan, egg-laying rate, and egg volume. We then tested the effects of a naturally occurring SNP within a cis-regulatory domain of Eip75B by applying two complementary approaches: a Mendelian randomization approach using lines of the Drosophila Genetic Reference Panel, and allelic replacement using precise CRISPR/Cas9-induced genome editing. Our experiments reveal that this natural polymorphism has a significant pleiotropic effect on fecundity and egg-to-adult viability, but not on longevity or other life-history traits. Our results provide a rare functional validation at the nucleotide level and identify a natural allelic variant affecting fitness and life-history adaptation.
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Affiliation(s)
| | - Hristina Kostic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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5
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Hoedjes KM, Kostic H, Keller L, Flatt T. Natural alleles at the Doa locus underpin evolutionary changes in Drosophila lifespan and fecundity. Proc Biol Sci 2022; 289:20221989. [PMID: 36350205 PMCID: PMC9653240 DOI: 10.1098/rspb.2022.1989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
'Evolve and resequence' (E&R) studies in Drosophila melanogaster have identified many candidate loci underlying the evolution of ageing and life history, but experiments that validate the effects of such candidates remain rare. In a recent E&R study we have identified several alleles of the LAMMER kinase Darkener of apricot (Doa) as candidates for evolutionary changes in lifespan and fecundity. Here, we use two complementary approaches to confirm a functional role of Doa in life-history evolution. First, we used transgenic RNAi to study the effects of Doa at the whole-gene level. Ubiquitous silencing of expression in adult flies reduced both lifespan and fecundity, indicating pleiotropic effects. Second, to characterize segregating variation at Doa, we examined four candidate single nucleotide polymorphisms (SNPs; Doa-1, -2, -3, -4) using a genetic association approach. Three candidate SNPs had effects that were qualitatively consistent with expectations based on our E&R study: Doa-2 pleiotropically affected both lifespan and late-life fecundity; Doa-1 affected lifespan (but not fecundity); and Doa-4 affected late-life fecundity (but not lifespan). Finally, the last candidate allele (Doa-3) also affected lifespan, but in the opposite direction from predicted.
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Affiliation(s)
- Katja M. Hoedjes
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Hristina Kostic
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland,Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
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6
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Malod K, Roets PD, Bosua H, Archer CR, Weldon CW. Selecting on age of female reproduction affects lifespan in both sexes and age-dependent reproductive effort in female (but not male) Ceratitis cosyra. Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-03063-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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7
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Ferguson KB, Visser S, Dalíková M, Provazníková I, Urbaneja A, Pérez‐Hedo M, Marec F, Werren JH, Zwaan BJ, Pannebakker BA, Verhulst EC. Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest. INSECT MOLECULAR BIOLOGY 2021; 30:188-209. [PMID: 33305885 PMCID: PMC8048687 DOI: 10.1111/imb.12688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/25/2020] [Accepted: 12/07/2020] [Indexed: 05/14/2023]
Abstract
Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.
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Affiliation(s)
- K. B. Ferguson
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - S. Visser
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - M. Dalíková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - I. Provazníková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- European Molecular Biology LaboratoryHeidelbergGermany
| | - A. Urbaneja
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - M. Pérez‐Hedo
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - F. Marec
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
| | - J. H. Werren
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - B. J. Zwaan
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - B. A. Pannebakker
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - E. C. Verhulst
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
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8
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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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9
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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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10
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Ng'oma E, Williams-Simon PA, Rahman A, King EG. Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population. BMC Genomics 2020; 21:84. [PMID: 31992183 PMCID: PMC6988245 DOI: 10.1186/s12864-020-6467-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/08/2020] [Indexed: 12/19/2022] Open
Abstract
Background Environmental variation in the amount of resources available to populations challenge individuals to optimize the allocation of those resources to key fitness functions. This coordination of resource allocation relative to resource availability is commonly attributed to key nutrient sensing gene pathways in laboratory model organisms, chiefly the insulin/TOR signaling pathway. However, the genetic basis of diet-induced variation in gene expression is less clear. Results To describe the natural genetic variation underlying nutrient-dependent differences, we used an outbred panel derived from a multiparental population, the Drosophila Synthetic Population Resource. We analyzed RNA sequence data from multiple female tissue samples dissected from flies reared in three nutritional conditions: high sugar (HS), dietary restriction (DR), and control (C) diets. A large proportion of genes in the experiment (19.6% or 2471 genes) were significantly differentially expressed for the effect of diet, and 7.8% (978 genes) for the effect of the interaction between diet and tissue type (LRT, Padj. < 0.05). Interestingly, we observed similar patterns of gene expression relative to the C diet, in the DR and HS treated flies, a response likely reflecting diet component ratios. Hierarchical clustering identified 21 robust gene modules showing intra-modularly similar patterns of expression across diets, all of which were highly significant for diet or diet-tissue interaction effects (FDR Padj. < 0.05). Gene set enrichment analysis for different diet-tissue combinations revealed a diverse set of pathways and gene ontology (GO) terms (two-sample t-test, FDR < 0.05). GO analysis on individual co-expressed modules likewise showed a large number of terms encompassing many cellular and nuclear processes (Fisher exact test, Padj. < 0.01). Although a handful of genes in the IIS/TOR pathway including Ilp5, Rheb, and Sirt2 showed significant elevation in expression, many key genes such as InR, chico, most insulin peptide genes, and the nutrient-sensing pathways were not observed. Conclusions Our results suggest that a more diverse network of pathways and gene networks mediate the diet response in our population. These results have important implications for future studies focusing on diet responses in natural populations.
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Affiliation(s)
- E Ng'oma
- University of Missouri, 401 Tucker Hall, Columbia, MO, 65211, USA.
| | | | - A Rahman
- University of Missouri, 401 Tucker Hall, Columbia, MO, 65211, USA
| | - E G King
- University of Missouri, 401 Tucker Hall, Columbia, MO, 65211, USA
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11
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Flatt T. Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster. Genetics 2020; 214:3-48. [PMID: 31907300 PMCID: PMC6944413 DOI: 10.1534/genetics.119.300160] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Life-history traits or "fitness components"-such as age and size at maturity, fecundity and fertility, age-specific rates of survival, and life span-are the major phenotypic determinants of Darwinian fitness. Analyzing the evolution and genetics of these phenotypic targets of selection is central to our understanding of adaptation. Due to its simple and rapid life cycle, cosmopolitan distribution, ease of maintenance in the laboratory, well-understood evolutionary genetics, and its versatile genetic toolbox, the "vinegar fly" Drosophila melanogaster is one of the most powerful, experimentally tractable model systems for studying "life-history evolution." Here, I review what has been learned about the evolution and genetics of life-history variation in D. melanogaster by drawing on numerous sources spanning population and quantitative genetics, genomics, experimental evolution, evolutionary ecology, and physiology. This body of work has contributed greatly to our knowledge of several fundamental problems in evolutionary biology, including the amount and maintenance of genetic variation, the evolution of body size, clines and climate adaptation, the evolution of senescence, phenotypic plasticity, the nature of life-history trade-offs, and so forth. While major progress has been made, important facets of these and other questions remain open, and the D. melanogaster system will undoubtedly continue to deliver key insights into central issues of life-history evolution and the genetics of adaptation.
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Affiliation(s)
- Thomas Flatt
- Department of Biology, University of Fribourg, CH-1700, Switzerland
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12
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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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May CM, van den Heuvel J, Doroszuk A, Hoedjes KM, Flatt T, Zwaan BJ. Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly. J Evol Biol 2019; 32:425-437. [PMID: 30735275 PMCID: PMC6850652 DOI: 10.1111/jeb.13425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 02/04/2019] [Indexed: 11/30/2022]
Abstract
Experimental evolution (EE) is a powerful tool for addressing how environmental factors influence life-history evolution. While in nature different selection pressures experienced across the lifespan shape life histories, EE studies typically apply selection pressures one at a time. Here, we assess the consequences of adaptation to three different developmental diets in combination with classical selection for early or late reproduction in the fruit fly Drosophila melanogaster. We find that the response to each selection pressure is similar to that observed when they are applied independently, but the overall magnitude of the response depends on the selection regime experienced in the other life stage. For example, adaptation to increased age at reproduction increased lifespan across all diets; however, the extent of the increase was dependent on the dietary selection regime. Similarly, adaptation to a lower calorie developmental diet led to faster development and decreased adult weight, but the magnitude of the response was dependent on the age-at-reproduction selection regime. Given that multiple selection pressures are prevalent in nature, our findings suggest that trade-offs should be considered not only among traits within an organism, but also among adaptive responses to different-sometimes conflicting-selection pressures, including across life stages.
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Affiliation(s)
- Christina M May
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands
| | - Joost van den Heuvel
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Agnieszka Doroszuk
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands.,Rijk Zwaan, Hague, the Netherlands
| | - Katja M Hoedjes
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands
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