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Santos MA, Carromeu-Santos A, Quina AS, Antunes MA, Kristensen TN, Santos M, Matos M, Fragata I, Simões P. Experimental Evolution in a Warming World: The Omics Era. Mol Biol Evol 2024; 41:msae148. [PMID: 39034684 PMCID: PMC11331425 DOI: 10.1093/molbev/msae148] [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: 11/29/2023] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
A comprehensive understanding of the genetic mechanisms that shape species responses to thermal variation is essential for more accurate predictions of the impacts of climate change on biodiversity. Experimental evolution with high-throughput resequencing approaches (evolve and resequence) is a highly effective tool that has been increasingly employed to elucidate the genetic basis of adaptation. The number of thermal evolve and resequence studies is rising, yet there is a dearth of efforts to integrate this new wealth of knowledge. Here, we review this literature showing how these studies have contributed to increase our understanding on the genetic basis of thermal adaptation. We identify two major trends: highly polygenic basis of thermal adaptation and general lack of consistency in candidate targets of selection between studies. These findings indicate that the adaptive responses to specific environments are rather independent. A review of the literature reveals several gaps in the existing research. Firstly, there is a paucity of studies done with organisms of diverse taxa. Secondly, there is a need to apply more dynamic and ecologically relevant thermal environments. Thirdly, there is a lack of studies that integrate genomic changes with changes in life history and behavioral traits. Addressing these issues would allow a more in-depth understanding of the relationship between genotype and phenotype. We highlight key methodological aspects that can address some of the limitations and omissions identified. These include the need for greater standardization of methodologies and the utilization of new technologies focusing on the integration of genomic and phenotypic variation in the context of thermal adaptation.
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Affiliation(s)
- Marta A Santos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Carromeu-Santos
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S Quina
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Almada, Portugal
| | - Marta A Antunes
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Mauro Santos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GBBE), Universitat Autonòma de Barcelona, Bellaterra, Spain
| | - Margarida Matos
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Inês Fragata
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Simões
- CE3C—Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Williams-Simon PA, Oster C, Moaton JA, Ghidey R, Ng’oma E, Middleton KM, King EG. Naturally segregating genetic variants contribute to thermal tolerance in a Drosophila melanogaster model system. Genetics 2024; 227:iyae040. [PMID: 38506092 PMCID: PMC11075556 DOI: 10.1093/genetics/iyae040] [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: 07/11/2023] [Revised: 07/11/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants within the genes that control this trait is of high importance if we want to better comprehend thermal physiology. Here, we take a multipronged approach to further dissect the genetic architecture that controls thermal tolerance in natural populations using the Drosophila Synthetic Population Resource as a model system. First, we used quantitative genetics and Quantitative Trait Loci mapping to identify major effect regions within the genome that influences thermal tolerance, then integrated RNA-sequencing to identify differences in gene expression, and lastly, we used the RNAi system to (1) alter tissue-specific gene expression and (2) functionally validate our findings. This powerful integration of approaches not only allows for the identification of the genetic basis of thermal tolerance but also the physiology of thermal tolerance in a natural population, which ultimately elucidates thermal tolerance through a fitness-associated lens.
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Affiliation(s)
- Patricka A Williams-Simon
- Department of Biology, University of Pennsylvania, 433 S University Ave., 226 Leidy Laboratories, Philadelphia, PA 19104, USA
| | - Camille Oster
- Ash Creek Forest Management, 2796 SE 73rd Ave., Hillsboro, OR 97123, USA
| | | | - Ronel Ghidey
- ECHO Data Analysis Center, Johns Hopkins Bloomberg School of Public Health, 504 Cathedral St., Baltimore, MD 2120, USA
| | - Enoch Ng’oma
- Division of Biology, University of Missouri, 226 Tucker Hall, Columbia, MO 65211, USA
| | - Kevin M Middleton
- Division of Biology, University of Missouri, 222 Tucker Hall, Columbia, MO 65211, USA
| | - Elizabeth G King
- Division of Biology, University of Missouri, 401 Tucker Hall, Columbia, MO 65211, USA
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3
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False and true positives in arthropod thermal adaptation candidate gene lists. Genetica 2021; 149:143-153. [PMID: 33963492 DOI: 10.1007/s10709-021-00122-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
Genome-wide studies are prone to false positives due to inherently low priors and statistical power. One approach to ameliorate this problem is to seek validation of reported candidate genes across independent studies: genes with repeatedly discovered effects are less likely to be false positives. Inversely, genes reported only as many times as expected by chance alone, while possibly representing novel discoveries, are also more likely to be false positives. We show that, across over 30 genome-wide studies that reported Drosophila and Daphnia genes with possible roles in thermal adaptation, the combined lists of candidate genes and orthologous groups are rapidly approaching the total number of genes and orthologous groups in the respective genomes. This is consistent with the expectation of high frequency of false positives. The majority of these spurious candidates have been identified by one or a few studies, as expected by chance alone. In contrast, a noticeable minority of genes have been identified by numerous studies with the probabilities of such discoveries occurring by chance alone being exceedingly small. For this subset of genes, different studies are in agreement with each other despite differences in the ecological settings, genomic tools and methodology, and reporting thresholds. We provide a reference set of presumed true positives among Drosophila candidate genes and orthologous groups involved in response to changes in temperature, suitable for cross-validation purposes. Despite this approach being prone to false negatives, this list of presumed true positives includes several hundred genes, consistent with the "omnigenic" concept of genetic architecture of complex traits.
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Rolandi C, Lighton JRB, de la Vega GJ, Schilman PE, Mensch J. Genetic variation for tolerance to high temperatures in a population of Drosophila melanogaster. Ecol Evol 2018; 8:10374-10383. [PMID: 30464811 PMCID: PMC6238130 DOI: 10.1002/ece3.4409] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 07/01/2018] [Accepted: 07/02/2018] [Indexed: 12/26/2022] Open
Abstract
The range of thermal tolerance is one of the main factors influencing the geographic distribution of species. Climate change projections predict increases in average and extreme temperatures over the coming decades; hence, the ability of living beings to resist these changes will depend on physiological and adaptive responses. On an evolutionary scale, changes will occur as the result of selective pressures on individual heritable differences. In this work, we studied the genetic basis of tolerance to high temperatures in the fly Drosophila melanogaster and whether this species presents sufficient genetic variability to allow expansion of its upper thermo-tolerance limit. To do so, we used adult flies derived from a natural population belonging to the Drosophila Genetic Reference Panel, for which genomic sequencing data are available. We characterized the phenotypic variation of the upper thermal limit in 34 lines by measuring knockdown temperature (i.e., critical thermal maximum [CTmax]) by exposing flies to a ramp of increasing temperature (0.25°C/min). Fourteen percent of the variation in CTmax is explained by the genetic variation across lines, without a significant sexual dimorphism. Through a genomewide association study, 12 single nucleotide polymorphisms associated with the CTmax were identified. In most of these SNPs, the less frequent allele increased the upper thermal limit suggesting that this population harbors raw genetic variation capable of expanding its heat tolerance. This potential upper thermal tolerance increase has implications under the global warming scenario. Past climatic records show a very low incidence of days above CTmax (10 days over 25 years); however, future climate scenarios predict 243 days with extreme high temperature above CTmax from 2045 to 2070. Thus, in the context of the future climate warming, rising temperatures might drive the evolution of heat tolerance in this population by increasing the frequency of the alleles associated with higher CTmax.
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Affiliation(s)
- Carmen Rolandi
- IBBEA‐CONICET‐UBA. DBBEAFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
| | | | - Gerardo J. de la Vega
- Grupo de Ecología de Poblaciones de Insectos (GEPI)INTA EEA BarilocheBarilocheArgentina
| | - Pablo E. Schilman
- IBBEA‐CONICET‐UBA. DBBEAFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
| | - Julián Mensch
- IEGEBA‐CONICET‐UBADEGEFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina
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Kristensen TN, Ketola T, Kronholm I. Adaptation to environmental stress at different timescales. Ann N Y Acad Sci 2018; 1476:5-22. [PMID: 30259990 DOI: 10.1111/nyas.13974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 08/24/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Environments are changing rapidly, and to cope with these changes, organisms have to adapt. Adaptation can take many shapes and occur at different speeds, depending on the type of response, the trait, the population, and the environmental conditions. The biodiversity crisis that we are currently facing illustrates that numerous species and populations are not capable of adapting with sufficient speed to ongoing environmental changes. Here, we discuss current knowledge on the ability of animals and plants to adapt to environmental stress on different timescales, mainly focusing on thermal stress and ectotherms. We discuss within-generation responses that can be fast and induced within minutes or hours, evolutionary adaptations that are often slow and take several generations, and mechanisms that lay somewhere in between and that include epigenetic transgenerational effects. To understand and predict the impacts of environmental change and stress on biodiversity, we suggest that future studies should (1) have an increased focus on understanding the type and speed of responses to fast environmental changes; (2) focus on the importance of environmental fluctuations and the predictability of environmental conditions on adaptive capabilities, preferably in field studies encompassing several fitness components; and (3) look at ecosystem responses to environmental stress and their resilience when disturbed.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Bioscience, University of Aarhus, Aarhus, Denmark
| | - Tarmo Ketola
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ilkka Kronholm
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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Duan Y, Gong Z, Wu R, Miao J, Jiang Y, Li T, Wu X, Wu Y. Transcriptome analysis of molecular mechanisms responsible for light-stress response in Mythimna separata (Walker). Sci Rep 2017; 7:45188. [PMID: 28345615 PMCID: PMC5367045 DOI: 10.1038/srep45188] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 02/20/2017] [Indexed: 11/23/2022] Open
Abstract
Light is an important environmental signal for most insects. The Oriental Armyworm, Mythimna separata, is a serious pest of cereal crops worldwide, and is highly sensitive to light signals during its developmental and reproductive stages. However, molecular biological studies of its response to light stress are scarce, and related genomic information is not available. In this study, we sequenced and de novo assembled the transcriptomes of M. separata exposed to four different light conditions: dark, white light (WL), UV light (UVL) and yellow light (YL). A total of 46,327 unigenes with an average size of 571 base pairs (bp) were obtained, among which 24,344 (52.55%) matched to public databases. The numbers of genes differentially expressed between dark vs WL, dark vs UVL, dark vs YL, and UVL vs YL were 12,012, 12,950, 14,855, and 13,504, respectively. These results suggest that light exposure altered gene expression patterns in M. separata. Putative genes involved in phototransduction-fly, phototransduction, circadian rhythm-fly, olfactory transduction, and taste transduction were identified. This study thus identified a series of candidate genes and pathways potentially related to light stress in M. separata.
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Affiliation(s)
- Yun Duan
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
| | - ZhongJun Gong
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
| | - RenHai Wu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
| | - Jin Miao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
| | - YueLi Jiang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
| | - Tong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
| | - XiaoBo Wu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
| | - YuQing Wu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Crop Pest Control of Henan Province, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Zhengzhou 450002, China
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7
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Thermal fluctuations affect the transcriptome through mechanisms independent of average temperature. Sci Rep 2016; 6:30975. [PMID: 27487917 PMCID: PMC4973280 DOI: 10.1038/srep30975] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/08/2016] [Indexed: 02/05/2023] Open
Abstract
Terrestrial ectotherms are challenged by variation in both mean and variance of temperature. Phenotypic plasticity (thermal acclimation) might mitigate adverse effects, however, we lack a fundamental understanding of the molecular mechanisms of thermal acclimation and how they are affected by fluctuating temperature. Here we investigated the effect of thermal acclimation in Drosophila melanogaster on critical thermal maxima (CTmax) and associated global gene expression profiles as induced by two constant and two ecologically relevant (non-stressful) diurnally fluctuating temperature regimes. Both mean and fluctuation of temperature contributed to thermal acclimation and affected the transcriptome. The transcriptomic response to mean temperatures comprised modification of a major part of the transcriptome, while the response to fluctuations affected a much smaller set of genes, which was highly independent of both the response to a change in mean temperature and to the classic heat shock response. Although the independent transcriptional effects caused by fluctuations were relatively small, they are likely to contribute to our understanding of thermal adaptation. We provide evidence that environmental sensing, particularly phototransduction, is a central mechanism underlying the regulation of thermal acclimation to fluctuating temperatures. Thus, genes and pathways involved in phototransduction are likely of importance in fluctuating climates.
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New levels of transcriptome complexity at upper thermal limits in wild Drosophila revealed by exon expression analysis. Genetics 2013; 195:809-30. [PMID: 24002645 DOI: 10.1534/genetics.113.156224] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
While the cellular heat-shock response has been a paradigm for studying the impact of thermal stress on RNA metabolism and gene expression, the genome-wide response to thermal stress and its connection to physiological stress resistance remain largely unexplored. Here, we address this issue using an array-based exon expression analysis to interrogate the transcriptome in recently established Drosophila melanogaster stocks during severe thermal stress and recovery. We first demonstrated the efficacy of exon-level analyses to reveal a level of thermally induced transcriptome complexity extending well beyond gene-level analyses. Next, we showed that the upper range of both the cellular and physiological thermal stress response profoundly affected message expression and processing in D. melanogaster, limiting expression to a small subset of transcripts, many that share features of known rapidly responding stress genes. As predicted from cellular heat-shock research, constitutive splicing was blocked in a set of novel genes; we did not detect changes to alternative splicing during heat stress, but rather induction of intronless isoforms of known heat-responsive genes. We observed transcriptome plasticity in the form of differential isoform expression during recovery from heat shock, mediated by multiple mechanisms including alternative transcription and alternative splicing. This affected genes involved in DNA regulation, immune response, and thermotolerance. These patterns highlight the complex nature of innate transcriptome responses under stress and potential for adaptive shifts through plasticity and evolved genetic responses at different hierarchical levels.
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Sambucetti P, Scannapieco AC, Loeschcke V, Norry FM. Heat stress survival in the pre-adult stage of the life cycle in an intercontinental set of recombinant inbred lines of Drosophila melanogaster. J Exp Biol 2013; 216:2953-9. [DOI: 10.1242/jeb.079830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Summary
In insects, pre-adult stages of the life cycle are exposed to variation in temperature that may differ from that in adults. However, the genetic basis for adaptation to environmental temperature could be similar between the pre-adult and the adult stages of the life cycle. Here, we tested quantitative trait loci (QTL) for heat-stress survival in larvae of D. melanogaster, with and without a mild-heat-stress pre-treatment. Two sets of recombinant inbred lines derived from lines artificially selected for high and low levels of knockdown resistance to high temperature in young flies were used as mapping population. There was no apparent increase in heat-shock survival between heat-pretreated and non-pretreated larvae. There was a positive correlation between the two experimental conditions of heat-shock survival (with and without a heat pre-treatment) except for males from one set of lines. Several QTL were identified involving all three major chromosomes. Many QTL for larval thermotolerance overlapped with thermotolerance-QTL identified in previous studies for adults. One new thermotolerance-QTL was found but these QTL explained only a small fraction of the phenotypic variance and were only significant in larvae that received no heat pre-treatment. Several candidate genes mapped within QTL ranges. We discuss an overall co-localization for thermotolerance-QTL between the adult fly in previous studies and the pre-adult stage of the life cycle in this study.
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Hoffmann AA, Chown SL, Clusella-Trullas S. Upper thermal limits in terrestrial ectotherms: how constrained are they? Funct Ecol 2012. [DOI: 10.1111/j.1365-2435.2012.02036.x] [Citation(s) in RCA: 447] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ary A. Hoffmann
- Departments of Zoology and Genetics; Bio21 Institute; The University of Melbourne; 30 Flemington Road; Parkville; Victoria; 3052; Australia
| | | | - Susana Clusella-Trullas
- Department of Botany and Zoology; Centre for Invasion Biology; Stellenbosch University; Private Bag X1; Matieland; 7602; South Africa
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Rand DM, Weinreich DM, Lerman D, Folk D, Gilchrist GW. Three selections are better than one: clinal variation of thermal QTL from independent selection experiments in Drosophila. Evolution 2010; 64:2921-34. [PMID: 20497214 DOI: 10.1111/j.1558-5646.2010.01039.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report the results of two independent selection experiments that have exposed distinct populations of Drosophila melanogaster to different forms of thermal selection. A recombinant population derived from Arvin California and Zimbabwe isofemale lines was exposed to laboratory natural selection at two temperatures (T(AZ): 18°C and 28°C). Microsatellite mapping identified quantitative trait loci (QTL) on the X-chromosome between the replicate "Hot" and "Cold" populations. In a separate experiment, disruptive selection was imposed on an outbred California population for the "knockdown" temperature (T(KD)) in a thermal column. Microsatellite mapping of the "High" and "Low" populations also uncovered primarily X-linked QTL. Notably, a marker in the shaggy locus at band 3A was significantly differentiated in both experiments. Finer scale mapping of the 3A region has narrowed the QTL to the shaggy gene region, which contains several candidate genes that function in circadian rhythms. The same allele that was increased in frequency in the High T(KD) populations is significantly clinal in North America and is more common at the warm end of the cline (Florida vs. Maine; however, the cline was not apparent in Australia). Together, these studies show that independent selection experiments can uncover the same target of selection and that evolution in the laboratory can recapitulate putatively adaptive clinal variation in nature.
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Affiliation(s)
- David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA.
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Mahapatra CT, Bond J, Rand DM, Rand MD. Identification of methylmercury tolerance gene candidates in Drosophila. Toxicol Sci 2010; 116:225-38. [PMID: 20375079 DOI: 10.1093/toxsci/kfq097] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Methylmercury (MeHg) is a ubiquitous environmental contaminant that preferentially targets the developing nervous system. Variable outcomes of prenatal MeHg exposure within a population point to a genetic component that regulates MeHg toxicity. We therefore sought to identify fundamental MeHg tolerance genes using the Drosophila model for genetic and molecular dissection of a MeHg tolerance trait. We observe autosomal dominance in a MeHg tolerance trait (development on MeHg food) in both wild-derived and laboratory-selected MeHg-tolerant strains of flies. We performed whole-genome transcript profiling of larval brains of tolerant (laboratory selected) and nontolerant (control) strains in the presence and absence of MeHg stress. Pairwise transcriptome comparisons of four conditions (+/-selection and +/-MeHg) identified a "down-down-up" expression signature, whereby MeHg alone and selection alone resulted in a greater number of downregulated transcripts, and the combination of selection + MeHg resulted in a greater number of upregulated transcripts. Functional annotation cluster analyses showed enrichment for monooxygenases/oxidoreductases, which include cytochrome P450 (CYP) family members. Among the 10 CYPs upregulated with selection + MeHg in tolerant strains, CYP6g1, previously identified as the dichlorodiphenyl trichloroethane resistance allele in flies, was the most highly expressed and responsive to MeHg. Among all the genes, Turandot A (TotA), an immune pathway-regulated humoral response gene, showed the greatest upregulation with selection + MeHg. Neural-specific transgenic overexpression of TotA enhanced MeHg tolerance during pupal development. Identification of TotA and CYP genes as MeHg tolerance genes is an inroad to investigating the conserved function of immune signaling and phase I metabolism pathways in MeHg toxicity and tolerance in higher organisms.
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Affiliation(s)
- Cecon T Mahapatra
- Department of Anatomy and Neurobiology, College of Medicine, University of Vermont, Burlington, Vermont 05405, USA
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Jensen LT, Cockerell FE, Kristensen TN, Rako L, Loeschcke V, McKechnie SW, Hoffmann AA. Adult heat tolerance variation in Drosophila melanogaster is not related to Hsp70 expression. ACTA ACUST UNITED AC 2010; 313:35-44. [PMID: 19739085 DOI: 10.1002/jez.573] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Expression of heat-inducible Hsp70 is considered closely linked to thermotolerance in Drosophila melanogaster and other ectotherms. However, intra-specific variation of Hsp70 expression levels and its relationship to heat resistance has only been investigated in a few studies. Although in Drosophila larvae Hsp70 expression may be a key determinant of heat tolerance, the evidence for this in adults is equivocal. We therefore examined heat-induced Hsp70 expression and several measurements of adult heat tolerance in three independent collections of D. melanogaster, measured in three laboratories and using slightly different protocols. Expression levels of Hsp70 were quantified using ELISA or Western blots on extracts from adult females. Both Hsp70 and heat tolerance exhibited substantial within-population variation as previously reported. However, in all experiments there were no significant correlation between Hsp70 expression and laboratory assays of adult heat tolerance commonly used in Drosophila. When combining data across three studies we had high power to detect associations but the results showed that variation in Hsp70 expression is only likely to explain a small proportion of variation in adult heat tolerance. Therefore, although Hsp70 expression is a major component of the cellular heat stress response, its influence on intra-specific heat tolerance variation may be life-stage specific.
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Overgaard J, Sørensen JG, Jensen LT, Loeschcke V, Kristensen TN. Field tests reveal genetic variation for performance at low temperatures inDrosophila melanogaster. Funct Ecol 2010. [DOI: 10.1111/j.1365-2435.2009.01615.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Transcriptional regulation of metabolism associated with the increased desiccation resistance of the cactophilic Drosophila mojavensis. Genetics 2009; 182:1279-88. [PMID: 19487561 DOI: 10.1534/genetics.109.104927] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Drosophila, adaptation to xeric environments presents many challenges, greatest among them the maintenance of water balance. Drosophila mojavensis, a cactophilic species from the deserts of North America, is one of the most desiccation resistant in the genus, surviving low humidity primarily by reducing its metabolic rate. Genetic control of reduced metabolic rate, however, has yet to be elucidated. We utilized the recently sequenced genome of D. mojavensis to create an oligonucleotide microarray to pursue the identities of the genes involved in metabolic regulation during desiccation. We observed large differences in gene expression between male and female D. mojavensis as well as both quantitative and qualitative sex differences in their ability to survive xeric conditions. As expected, genes associated with metabolic regulation and carbohydrate metabolism were differentially regulated between stress treatments. Most importantly, we identified four points in central metabolism (Glyceraldehyde 3-phosphate dehydrogenase, transaldolase, alcohol dehydrogenase, and phosphoenolpyruvate carboxykinase) that indicate the potential mechanisms controlling metabolic rate reduction associated with desiccation resistance. Furthermore, a large number of genes associated with vision pathways also were differentially expressed between stress treatments, especially in females, that may underlie the initial detection of stressful environments and trigger subsequent metabolic changes.
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Norry FM, Scannapieco AC, Sambucetti P, Bertoli CI, Loeschcke V. QTL for the thermotolerance effect of heat hardening, knockdown resistance to heat and chill-coma recovery in an intercontinental set of recombinant inbred lines of Drosophila melanogaster. Mol Ecol 2008; 17:4570-81. [PMID: 18986501 DOI: 10.1111/j.1365-294x.2008.03945.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The thermotolerance effect of heat hardening (also called short-term acclimation), knockdown resistance to high temperature (KRHT) with and without heat hardening and chill-coma recovery (CCR) are important phenotypes of thermal adaptation in insects and other organisms. Drosophila melanogaster from Denmark and Australia were previously selected for low and high KRHT, respectively. These flies were crossed to construct recombinant inbred lines (RIL). KRHT was higher in heat-hardened than in nonhardened RIL. We quantify the heat-hardening effect (HHE) as the ratio in KRHT between heat-hardened and nonhardened RIL. Composite interval mapping revealed a more complex genetic architecture for KRHT without heat-hardening than for KRHT in heat-hardened insects. Five quantitative trait loci (QTL) were found for KRHT, but only two of them were significant after heat hardening. KRHT and CCR showed trade-off associations for QTL both in the middle of chromosome 2 and the right arm of chromosome 3, which should be the result of either pleiotropy or linkage. The major QTL on chromosome 2 explained 18% and 27-33% of the phenotypic variance in CCR and KRHT in nonhardened flies, respectively, but its KRHT effects decreased by heat hardening. We discuss candidate loci for each QTL. One HHE-QTL was found in the region of small heat-shock protein genes. However, HHE-QTL explained only a small fraction of the phenotypic variance. Most heat-resistance QTL did not colocalize with CCR-QTL. Large-effect QTL for CCR and KRHT without hardening (basal thermotolerance) were consistent across continents, with apparent transgressive segregation for CCR. HHE (inducible thermotolerance) was not regulated by large-effect QTL.
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Affiliation(s)
- Fabian M Norry
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. (C-1428-EHA) Buenos Aires, Argentina.
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D'Ávila MF, Garcia RN, Loreto ELS, Valente VLDS. Analysis of phenotypes altered by temperature stress and hipermutability in Drosophila willistoni. IHERINGIA. SERIE ZOOLOGIA 2008. [DOI: 10.1590/s0073-47212008000300009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Drosophila willistoni (Sturtevant, 1916) is a species of the willistoni group of Drosophila having wide distribution from the South of USA (Florida) and Mexico to the North of Argentina. It has been subject of many evolutionary studies within the group, due to its considerable ability to successfully occupy a wide range of environments and also because of its great genetic variability expressed by different markers. The D. willistoni 17A2 strain was collected in 1991 in the state of Rio Grande do Sul, Brazil (30°05'S, 51°39'W), and has been maintained since then at the Drosophila laboratory of UFRGS. Different to the other D. willistoni strains maintained in the laboratory, the 17A2 strain spontaneously produced mutant males white-like (white eyes) and sepia-like (brown eyes) in stocks held at 17°C. In order to discover if this strain is potentially hypermutable, we submitted it to temperature stress tests. Eighteen isofemale strains were used in our tests and, after the first generation, all the individuals produced in each strain were maintained at 29°C. Different phenotype alterations were observed in subsequent generations, similar to mutations already well characterized in D. melanogaster (white, sepia, blistered and curly). In addition, an uncommon phenotype alteration with an apparent fusion of the antennae was observed, but only in the isofemale line nº 31. This last alteration has not been previously described as a mutation in the D. melanogaster species. Our results indicate that the D. willistoni 17A2 strain is a candidate for hypermutability, which presents considerable cryptic genetic variability. Different factors may be operating for the formation of this effect, such as the mobilization of transposable elements, effect of inbreeding and alteration of the heat-shock proteins functions.
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Bettencourt BR, Hogan CC, Nimali M, Drohan BW. Inducible and constitutive heat shock gene expression responds to modification of Hsp70 copy number in Drosophila melanogaster but does not compensate for loss of thermotolerance in Hsp70 null flies. BMC Biol 2008; 6:5. [PMID: 18211703 PMCID: PMC2257928 DOI: 10.1186/1741-7007-6-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 01/22/2008] [Indexed: 06/12/2024] Open
Abstract
Background The heat shock protein Hsp70 promotes inducible thermotolerance in nearly every organism examined to date. Hsp70 interacts with a network of other stress-response proteins, and dissecting the relative roles of these interactions in causing thermotolerance remains difficult. Here we examine the effect of Hsp70 gene copy number modification on thermotolerance and the expression of multiple stress-response genes in Drosophila melanogaster, to determine which genes may represent mechanisms of stress tolerance independent of Hsp70. Results Hsp70 copy number in four strains is positively associated with Hsp70 expression and inducible thermotolerance of severe heat shock. When assayed at carefully chosen temperatures, Hsp70 null flies are almost entirely deficient in thermotolerance. In contrast to expectations, increasing Hsp70 expression levels induced by thermal pretreatment are associated with increasing levels of seven other inducible Hsps across strains. In addition, complete Hsp70 loss causes upregulation of the inducible Hsps and six constitutive stress-response genes following severe heat shocks. Conclusion Modification of Hsp70 copy number quantitatively and qualitatively affects the expression of multiple other stress-response genes. A positive association between absolute expression levels of Hsp70 and other Hsps after thermal pretreatment suggests novel regulatory mechanisms. Severe heat shocks induce both novel gene expression patterns and almost total mortality in the Hsp70 null strain: alteration of gene expression in this strain does not compensate for Hsp70 loss but suggests candidates for overexpression studies.
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Affiliation(s)
- Brian R Bettencourt
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA.
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Abstract
Global environmental change is altering the selection regime for all biota. The key selective factors are altered mean, variance and seasonality of climatic variables and increase in CO(2) concentration itself. We review recent studies that document rapid evolution to global climate change at the phenotypic and genetic level, as a response to shifts in these factors. Among the traits that have changed are photoperiod responses, stress tolerance and traits associated with enhanced dispersal. The genetic basis of two traits with a critical role under climate change, stress tolerance and photoperiod behaviour, is beginning to be understood for model organisms, providing a starting point for candidate gene approaches in targeted nonmodel species. Most studies that have documented evolutionary change are correlative, while selection experiments that manipulate relevant variables are rare. The latter are particularly valuable for prediction because they provide insight into heritable change to simulated future conditions. An important gap is that experimental selection regimes have mostly been testing one variable at a time, while synergistic interactions are likely under global change. The expanding toolbox available to molecular ecologists holds great promise for identifying the genetic basis of many more traits relevant to fitness under global change. Such knowledge, in turn, will significantly advance predictions on global change effects because presence and polymorphism of critical genes can be directly assessed. Moreover, knowledge of the genetic architecture of trait correlations will provide the necessary framework for understanding limits to phenotypic evolution; in particular as lack of critical gene polymorphism or entire pathways, metabolic costs of tolerance and linkage or pleiotropy causing negative trait correlations. Synergism among stressor impacts on organismal function may be causally related to conflict among transcriptomic syndromes specific to stressor types. Because adaptation to changing environment is always contingent upon the spatial distribution of genetic variation, high-resolution estimates of gene flow and hybridization should be used to inform predictions of evolutionary rates.
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Affiliation(s)
- Thorsten B H Reusch
- Plant Evolutionary Ecology, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr.1, 48149 Münster, Germany.
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Sørensen JG, Nielsen MM, Loeschcke V. Gene expression profile analysis of Drosophila melanogaster selected for resistance to environmental stressors. J Evol Biol 2007; 20:1624-36. [PMID: 17584255 DOI: 10.1111/j.1420-9101.2007.01326.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we report a detailed analysis of changes in gene expression in Drosophila melanogaster selected for ecologically relevant environmental stress resistance traits. We analysed females from seven replicated selection regimes and one control regime using whole genome gene expression arrays. When compared with gene expression profiles of control lines, we were able to detect consistent selection responses at the transcript level in each specific selection regime and also found a group of differentially expressed genes that were changed among all selected lines. Replicated selection lines showed similar changes in gene expression (compared with controls) and thus showed that 10 generations of artificial selection give a clear signal with respect to the resulting gene expression profile. The changes in gene expression in lines selected for increased longevity, desiccation and starvation resistance, respectively, showed high similarities. Cold resistance-selected lines showed little differentiation from controls. Different methods of heat selection (heat survival, heat knock down and constant 30 degrees C) showed little similarity verifying that different mechanisms are involved in high temperature adaptation. For most individual selection regimes, and in the comparison of all selected lines and controls, the gene expression changes were exclusively in one direction, although the different selection regimes varied in the direction of response. The responses to selection restricted to individual selection regimes can be interpreted as stress specific, whereas the response shared among all selected lines can be considered as a general stress response. Here, we identified genes belonging to both types of responses to selection for stress resistance.
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Affiliation(s)
- J G Sørensen
- Department of Ecology and Genetics, University of Aarhus, Aarhus C, Denmark.
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Sørensen JG, Loeschcke V. Studying stress responses in the post-genomic era: its ecological and evolutionary role. J Biosci 2007; 32:447-56. [PMID: 17536164 DOI: 10.1007/s12038-007-0044-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most investigations on the effects of and responses to stress exposures have been performed on a limited number of model organisms in the laboratory. Here much progress has been made in terms of identifying and describing beneficial and detrimental effects of stress, responses to stress and the mechanisms behind stress tolerance. However, to gain further understanding of which genes are involved in stress resistance and how the responses are regulated from an ecological and evolutionary perspective there is a need to combine studies on multiple levels of biological organization from DNA to phenotypes. Furthermore,we emphasize the importance of studying ecologically relevant traits and natural or semi-natural conditions to verify whether the results obtained are representative of the ecological and evolutionary processes in the field. Here,we will review what we currently know about thermal adaptation and the role of different stress responses to thermal challenges in insects, particularly Drosophila.Furthermore,we address some key questions that require future attention.
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Affiliation(s)
- Jesper G Sørensen
- Aarhus Centre for Environmental Stress Research (ACES), Department of Genetics and Ecology, Institute of Biological Sciences, University of Aarhus, Aarhus, Denmark.
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Kristensen TN, Loeschcke V, Hoffmann AA. Can artificially selected phenotypes influence a component of field fitness? Thermal selection and fly performance under thermal extremes. Proc Biol Sci 2007; 274:771-8. [PMID: 17251092 PMCID: PMC2093976 DOI: 10.1098/rspb.2006.0247] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Artificially selected lines are widely used to investigate the genetic basis of quantitative traits and make inferences about evolutionary trajectories. Yet, the relevance of selected traits to field fitness is rarely tested. Here, we assess the relevance of thermal stress resistance artificially selected in the laboratory to one component of field fitness by investigating the likelihood of adult Drosophila melanogaster reaching food bait under different temperatures. Lines resistant to heat reached the bait more often than controls under hot and cold conditions, but less often at intermediate temperatures, suggesting a fitness cost of increased heat resistance but not at temperature extremes. Cold-resistant lines were more common at baits than controls under cold as well as hot field conditions, and there was no cost at intermediate temperatures. One of the replicate heat-resistant lines was caught less often than the others under hot conditions. Direct and correlated patterns of responses in laboratory tests did not fully predict the low performance of the heat selected lines at intermediate temperatures, nor the high performance of the cold selected lines under hot conditions. Therefore, lines selected artificially not only behaved partly as expected based on laboratory assays but also evolved patterns only evident in the field releases.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Center for Environmental Stress and Adaptation Research, Department of Genetics, The University of Melbourne, Victoria, Australia.
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