1
|
Jiang Q, Zhu L, Zeng H, Basang Z, Suolang Q, Huang J, Cai Y. Evolutionary adaptations generally reverse phenotypic plasticity to restore ancestral phenotypes during new environment adaptation in cattle. Ecol Evol 2024; 14:e11489. [PMID: 38840586 PMCID: PMC11150418 DOI: 10.1002/ece3.11489] [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] [Received: 02/07/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
Phenotype plasticity and evolution adaptations are the two main ways in which allow populations to deal with environmental changes, but the potential relationship between them remains controversial. Using a reciprocal transplant approach with cattle adapted to the Tibetan Plateau and adjacent lowlands, we aim to investigate the relative contributions of evolutionary processes and phenotypic plasticity in driving both phenotypic and transcriptomic changes under natural conditions. We observed that while numerous genetic transcriptomic changes were evident during the forward adaptation to highland environments, plastic changes predominantly facilitate the transformation of transcriptomes into a preferred state when Tibetan cattle are reintroduced to lowland habitats. Genes with ancestral plasticity are generally reversed by evolutionary adaptations and show a closer expression level to the ancestral stage in evolved Tibetan cattle. A similar trend was also observed at the phenotypes level, with a majority of biochemical and hemorheology phenotypes showing a tendency to revert to their ancestral patterns, suggesting the restoration of ancestral expression levels is a widespread evolutionary trend during adaptation. The findings of our study contribute to the debate regarding the relative contributions of plasticity and genetic changes in mammal environment adaptation. Furthermore, we highlight that the restoration of ancestral phenotypes represents a general pattern in cattle new environment adaptation.
Collapse
Affiliation(s)
- Qiang Jiang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
- Institute of Animal Science and Veterinary MedicineShandong Academy of Agricultural SciencesJinanChina
| | - Li Zhu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyYunnan Agricultural UniversityKunmingChina
| | - Hao Zeng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyYunnan Agricultural UniversityKunmingChina
| | - Zhuzha Basang
- Institute of Animal Science and Veterinary MedicineTibet Academy of Agricultural and Animal Husbandry SciencesLhasaChina
| | - Quji Suolang
- Institute of Animal Science and Veterinary MedicineTibet Academy of Agricultural and Animal Husbandry SciencesLhasaChina
| | - Jinming Huang
- Institute of Animal Science and Veterinary MedicineShandong Academy of Agricultural SciencesJinanChina
| | - Yafei Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| |
Collapse
|
2
|
Alves-Ferreira G, Fortunato DS, Katzenberger M, Fava FG, Solé M. Effects of temperature on growth, development, and survival of amphibian larvae: macroecological and evolutionary patterns. AN ACAD BRAS CIENC 2024; 96:e20230671. [PMID: 38747789 DOI: 10.1590/0001-3765202420230671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 02/23/2024] [Indexed: 05/25/2024] Open
Abstract
Temperature affects the rate of biochemical and physiological processes in amphibians, influencing metamorphic traits. Temperature patterns, as those observed in latitudinal and altitudinal clines, may impose different challenges on amphibians depending on how species are geographically distributed. Moreover, species' response to environmental temperatures may also be phylogenetically constrained. Here, we explore the effects of acclimation to higher temperatures on tadpole survival, development, and growth, using a meta-analytical approach. We also evaluate whether the latitude and climatic variables at each collection site can explain differences in species' response to increasing temperature and whether these responses are phylogenetically conserved. Our results show that species that develop at relatively higher temperatures reach metamorphosis faster. Furthermore, absolute latitude at each collection site may partially explain heterogeneity in larval growth rate. Phylogenetic signal of traits in response to temperature indicates a non-random process in which related species resemble each other less than expected under Brownian motion evolution (BM) in all traits, except survival. The integration of studies in a meta-analytic framework allowed us to explore macroecological and macroevolutionary patterns and provided a better understanding of the effects of climate change on amphibians.
Collapse
Affiliation(s)
- Gabriela Alves-Ferreira
- Universidade Estadual de Santa Cruz, Tropical Herpetology Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Departamento de Ciências Biológicas, Rodovia Jorge Amado, Km 16, Salobrinho, 45662-900 Ilhéus, BA, Brazil
| | - Danilo S Fortunato
- Universidade Federal de Goiás, DTI Program, Instituto Nacional de Ciência Tecnologia (EECBio), Instituto de Ciências Biológicas, Campus II (Samambaia), 74690-900 Goiânia, GO, Brazil
| | - Marco Katzenberger
- Universidade Federal de Pernambuco, Laboratório de Bioinformática e Biologia Evolutiva, Departamento de Genética, Av. Prof. Moraes Rego, 1235, Cidade Universitária, 50670-901 Recife, PE, Brazil
| | - Fernanda G Fava
- Universidade Estadual de Santa Cruz, Tropical Herpetology Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Departamento de Ciências Biológicas, Rodovia Jorge Amado, Km 16, Salobrinho, 45662-900 Ilhéus, BA, Brazil
| | - Mirco Solé
- Universidade Estadual de Santa Cruz, Tropical Herpetology Lab, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Departamento de Ciências Biológicas, Rodovia Jorge Amado, Km 16, Salobrinho, 45662-900 Ilhéus, BA, Brazil
- Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, North Rhine-Westphalia, Germany
| |
Collapse
|
3
|
Lai WY, Nolte V, Jakšić AM, Schlötterer C. Evolution of Phenotypic Variance Provides Insights into the Genetic Basis of Adaptation. Genome Biol Evol 2024; 16:evae077. [PMID: 38620076 PMCID: PMC11057206 DOI: 10.1093/gbe/evae077] [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: 05/11/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Most traits are polygenic, and the contributing loci can be identified by genome-wide association studies. The genetic basis of adaptation (adaptive architecture) is, however, difficult to characterize. Here, we propose to study the adaptive architecture of traits by monitoring the evolution of their phenotypic variance during adaptation to a new environment in well-defined laboratory conditions. Extensive computer simulations show that the evolution of phenotypic variance in a replicated experimental evolution setting can distinguish between oligogenic and polygenic adaptive architectures. We compared gene expression variance in male Drosophila simulans before and after 100 generations of adaptation to a novel hot environment. The variance change in gene expression was indistinguishable for genes with and without a significant change in mean expression after 100 generations of evolution. We suggest that the majority of adaptive gene expression evolution can be explained by a polygenic architecture. We propose that tracking the evolution of phenotypic variance across generations can provide an approach to characterize the adaptive architecture.
Collapse
Affiliation(s)
- Wei-Yun Lai
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
- Present address: École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
4
|
Mishra P, Rundle HD, Agrawal AF. The evolution of sexual dimorphism in gene expression in response to a manipulation of mate competition. Evolution 2024; 78:746-757. [PMID: 38270064 DOI: 10.1093/evolut/qpae004] [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: 08/16/2023] [Revised: 11/24/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
Many genes are differentially expressed between males and females and patterns of sex-biased gene expression (SBGE) vary among species. Some of this variation is thought to have evolved in response to differences in mate competition among species that cause varying patterns of sex-specific selection. We used experimental evolution to test this by quantifying SBGE and sex-specific splicing in 15 Drosophila melanogaster populations that evolved for 104 generations in mating treatments that removed mate competition via enforced monogamy, or allowed mate competition in either small, simple, or larger, structurally more complex mating environments. Consistent with sex-specific selection affecting SBGE, initially sex-biased genes diverged in expression more among treatments than unbiased genes, and there was greater expression divergence for male- than female-biased genes. It has been suggested the transcriptome should be "feminized" under monogamy because of the removal of sexual selection on males; we did not observe this, likely because selection differs in additional ways between monogamy vs. polygamy. Significant divergence in average expression dimorphism between treatments was observed and, in some treatment comparisons, the direction of the divergence differed across different sex-bias categories. There was not a generalized reduction in expression dimorphism under enforced monogamy.
Collapse
Affiliation(s)
- Prashastha Mishra
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Howard D Rundle
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
5
|
She H, Hao Y, Song G, Luo X, Lei F, Zhai W, Qu Y. Gene expression plasticity followed by genetic change during colonization in a high-elevation environment. eLife 2024; 12:RP86687. [PMID: 38470231 DOI: 10.7554/elife.86687] [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] [Indexed: 03/13/2024] Open
Abstract
Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called 'plasticity first.' Herein, we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimentally implemented hypoxia acclimation (plastic stage), and colonized highland (colonized stage). Using a group of co-expressed genes from the cardiac and flight muscles, respectively, we demonstrate that gene expression plasticity to hypoxia tolerance is more often reversed than reinforced at the colonized stage. By correlating gene expression change with muscle phenotypes, we show that colonized tree sparrows reduce maladaptive plasticity that largely associated with decreased hypoxia tolerance. Conversely, adaptive plasticity that is congruent with increased hypoxia tolerance is often reinforced in the colonized tree sparrows. Genes displaying large levels of reinforcement or reversion plasticity (i.e. 200% of original level) show greater genetic divergence between ancestral and colonized populations. Overall, our work demonstrates that gene expression plasticity at the initial stage of high-elevation colonization can be reversed or reinforced through selection-driven adaptive modification.
Collapse
Affiliation(s)
- Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xu Luo
- Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
6
|
Narayan VP, Wasana N, Wilson AJ, Chenoweth SF. Misalignment of plastic and evolutionary responses of lifespan to novel carbohydrate diets. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231732. [PMID: 38234441 PMCID: PMC10791524 DOI: 10.1098/rsos.231732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Diet elicits varied effects on longevity across a wide range of animal species where dietary discordance between an organisms' evolutionary and developmental dietary history is increasingly recognized to play a critical role in shaping lifespan. However, whether such changes, predominantly assessed in a single generation, lead to evolutionary shifts in lifespan remains unclear. In this study, we used an experimental evolution approach to test whether changes in an organisms' evolutionary and developmental dietary history, specifically carbohydrate content, causes lifespan evolution in Drosophila serrata. After 30 generations, we investigated the evolutionary potential of lifespan in response to four novel diets that varied systematically in their ratio of carbohydrate-protein content. We also examined developmental plasticity effects using a set of control populations that were raised on the four novel environments allowing us to assess the extent to which plastic responses of lifespan mirrored adaptive responses observed following experimental evolution. Both high- and low-carbohydrate diets elicited plastic effects on lifespan; however, the plastic responses for lifespan to developmental diets bore little resemblance to the evolved responses on evolutionary diets. Understanding the dietary conditions regulating the match/mismatch of plastic and evolved responses will be important in determining whether a particular match/mismatch combination is adaptive for lifespan. While the differences in evolutionary diet by developmental diet interactions are only beginning to be elucidated, this study lays the foundation for future investigations of carbohydrate contributions to evolved and plastic effects on health and lifespan.
Collapse
Affiliation(s)
- Vikram P. Narayan
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia
- College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Nidarshani Wasana
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Alastair J. Wilson
- College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Stephen F. Chenoweth
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Cutter AD. Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development. Proc Biol Sci 2023; 290:20231854. [PMID: 37817601 PMCID: PMC10565415 DOI: 10.1098/rspb.2023.1854] [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: 08/16/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.
Collapse
Affiliation(s)
- Asher D. Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| |
Collapse
|
9
|
Chen P, Zhang J. Transcriptomic analysis reveals the rareness of genetic assimilation of gene expression in environmental adaptations. SCIENCE ADVANCES 2023; 9:eadi3053. [PMID: 37756399 PMCID: PMC10530075 DOI: 10.1126/sciadv.adi3053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Genetic assimilation is the evolutionary process by which an environmentally induced phenotype becomes genetically encoded and constitutive. Genetic assimilation has been proposed as a concluding step in environmental adaptation, but its prevalence has not been systematically investigated. Analyzing transcriptomic data collected upon reciprocal transplant, we address this question in the experimental evolution, domestication, or natural evolution of seven diverse species. We find that genetic assimilation of environment-induced gene expression is the exception rather than the rule and that substantially more genes retain than lose their expression plasticity upon organismal adaptations to new environments. The probability of genetic assimilation of gene expression decreases with the expression level and number of transcription factors controlling the gene, suggesting that genetic assimilation results primarily from passive losses of gene regulations that are not mutationally robust. Hence, for gene expression, our findings argue against the purported generality or importance of genetic assimilation to environmental adaptation.
Collapse
Affiliation(s)
- Piaopiao Chen
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | | |
Collapse
|
10
|
Szukala A, Bertel C, Frajman B, Schönswetter P, Paun O. Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1619-1632. [PMID: 37277969 PMCID: PMC10952512 DOI: 10.1111/tpj.16342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/07/2023]
Abstract
High levels of phenotypic plasticity are thought to be inherently costly in stable or extreme environments, but enhanced plasticity may evolve as a response to new environments and foster novel phenotypes. Heliosperma pusillum forms glabrous alpine and pubescent montane ecotypes that diverged recurrently and polytopically (parallel evolution) and can serve as evolutionary replicates. The specific alpine and montane localities are characterized by distinct temperature conditions, available moisture, and light. Noteworthy, the ecotypes show a home-site fitness advantage in reciprocal transplantations. To disentangle the relative contribution of constitutive versus plastic gene expression to altitudinal divergence, we analyze the transcriptomic profiles of two parallely evolved ecotype pairs, grown in reciprocal transplantations at native altitudinal sites. In this incipient stage of divergence, only a minor proportion of genes appear constitutively differentially expressed between the ecotypes in both pairs, regardless of the growing environment. Both derived, montane populations bear comparatively higher plasticity of gene expression than the alpine populations. Genes that change expression plastically or constitutively underlie similar ecologically relevant pathways, related to response to drought and trichome formation. Other relevant processes, such as photosynthesis, rely mainly on plastic changes. The enhanced plasticity consistently observed in the montane ecotype likely evolved as a response to the newly colonized, drier, and warmer niche. We report a striking parallelism of directional changes in gene expression plasticity. Thus, plasticity appears to be a key mechanism shaping the initial stages of phenotypic evolution, likely fostering adaptation to novel environments.
Collapse
Affiliation(s)
- Aglaia Szukala
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
- Austrian Federal Research Centre for Forests (BFW)Unit of Ecological GeneticsSeckendorff‐Gudent‐Weg 8A‐1131ViennaAustria
| | - Clara Bertel
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | - Božo Frajman
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
| | | | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| |
Collapse
|
11
|
Cavigliasso F, Savary L, Spangenberg JE, Gallart-Ayala H, Ivanisevic J, Kawecki TJ. Experimental evolution of metabolism under nutrient restriction: enhanced amino acid catabolism and a key role of branched-chain amino acids. Evol Lett 2023; 7:273-284. [PMID: 37475747 PMCID: PMC10355184 DOI: 10.1093/evlett/qrad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 07/22/2023] Open
Abstract
Periodic food shortage is a common ecological stressor for animals, likely to drive physiological and metabolic adaptations to alleviate its consequences, particularly for juveniles that have no option but to continue to grow and develop despite undernutrition. Here we study changes in metabolism associated with adaptation to nutrient shortage, evolved by replicate Drosophila melanogaster populations maintained on a nutrient-poor larval diet for over 240 generations. In a factorial metabolomics experiment we showed that both phenotypic plasticity and genetically-based adaptation to the poor diet involved wide-ranging changes in metabolite abundance; however, the plastic response did not predict the evolutionary change. Compared to nonadapted larvae exposed to the poor diet for the first time, the adapted larvae showed lower levels of multiple free amino acids in their tissues-and yet they grew faster. By quantifying accumulation of the nitrogen stable isotope 15N we show that adaptation to the poor diet led to an increased use of amino acids for energy generation. This apparent "waste" of scarce amino acids likely results from the trade-off between acquisition of dietary amino acids and carbohydrates observed in these populations. The three branched-chain amino acids (leucine, isoleucine, and valine) showed a unique pattern of depletion in adapted larvae raised on the poor diet. A diet supplementation experiment demonstrated that these amino acids are limiting for growth on the poor diet, suggesting that their low levels resulted from their expeditious use for protein synthesis. These results demonstrate that selection driven by nutrient shortage not only promotes improved acquisition of limiting nutrients, but also has wide-ranging effects on how the nutrients are used. They also show that the abundance of free amino acids in the tissues does not, in general, reflect the nutritional condition and growth potential of an animal.
Collapse
Affiliation(s)
- Fanny Cavigliasso
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Loriane Savary
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jorge E Spangenberg
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
12
|
Schlötterer C. How predictable is adaptation from standing genetic variation? Experimental evolution in Drosophila highlights the central role of redundancy and linkage disequilibrium. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220046. [PMID: 37004724 PMCID: PMC10067264 DOI: 10.1098/rstb.2022.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Experimental evolution is well-suited to test the predictability of evolution without the confounding effects of inaccurate forecasts about future environments. Most of the literature about parallel (and thus predictable) evolution has been carried out in asexual microorganisms, which adapt by de novo mutations. Nevertheless, parallel evolution has also been studied in sexual species at the genomic level. Here, I review the evidence for parallel evolution in Drosophila, the best-studied obligatory outcrossing model for adaptation from standing genetic variation in the laboratory. Similar to asexual microorganisms, evidence for parallel evolution varies between the focal hierarchical levels. Selected phenotypes consistently respond in a very predicable way, but the underlying allele frequency changes are much less predictable. The most important insight is that the predictability of the genomic selection response for polygenic traits depends highly on the founder population and to a much lesser extent on the selection regime. This implies that predicting adaptive genomic response is challenging and requires a good understanding of the adaptive architecture (including linkage disequilibrium) in the ancestral populations. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
Collapse
Affiliation(s)
- Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| |
Collapse
|
13
|
Kuo HC, Yao CT, Liao BY, Weng MP, Dong F, Hsu YC, Hung CM. Weak gene-gene interaction facilitates the evolution of gene expression plasticity. BMC Biol 2023; 21:57. [PMID: 36941675 PMCID: PMC10029303 DOI: 10.1186/s12915-023-01558-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation. However, we know little about what determines the evolution of phenotypic plasticity, including gene expression plasticity. Recent laboratory-based studies suggest dominance of reversing gene expression plasticity-plastic responses that move the levels of gene expression away from the new optima. Nevertheless, evidence from natural populations is still limited. RESULTS Here, we studied gene expression plasticity and its evolution in the montane and lowland populations of an elevationally widespread songbird-the Rufous-capped Babbler (Cyanoderma ruficeps)-with reciprocal transplant experiments and transcriptomic analyses; we set common gardens at altitudes close to these populations' native ranges. We confirmed the prevalence of reversing plasticity in genes associated with altitudinal adaptation. Interestingly, we found a positive relationship between magnitude and degree of evolution in gene expression plasticity, which was pertinent to not only adaptation-associated genes but also the whole transcriptomes from multiple tissues. Furthermore, we revealed that genes with weaker expressional interactions with other genes tended to exhibit stronger plasticity and higher degree of plasticity evolution, which explains the positive magnitude-evolution relationship. CONCLUSIONS Our experimental evidence demonstrates that species may initiate their adaptation to new habitats with genes exhibiting strong expression plasticity. We also highlight the role of expression interdependence among genes in regulating the magnitude and evolution of expression plasticity. This study illuminates how the evolution of phenotypic plasticity in gene expression facilitates the adaptation of species to challenging environments in nature.
Collapse
Affiliation(s)
- Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, 55244, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 97401, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
14
|
Wood DP, Holmberg JA, Osborne OG, Helmstetter AJ, Dunning LT, Ellison AR, Smith RJ, Lighten J, Papadopulos AST. Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora. Nat Ecol Evol 2023; 7:414-423. [PMID: 36702857 PMCID: PMC9998271 DOI: 10.1038/s41559-022-01975-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/12/2022] [Indexed: 01/27/2023]
Abstract
Phenotypic plasticity in ancestral populations is hypothesized to facilitate adaptation, but evidence is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel adaptive changes has not been explored. The most general finding is that ancestral responses to a new environment are reversed following adaptation (known as reversion). We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared with zinc-sensitive plants. We show that ancestral plasticity that moves expression closer to the optimum value in the new environment influences the evolution of gene expression among genes that are likely to be involved in adaptation and increases the chance that genes are recruited repeatedly during adaptation. However, despite convergence in gene expression levels between independently adapted lineages, ancestral plasticity does not influence how similar expression values of adaptive genes become. Surprisingly, we also observed that ancestral plasticity that increases fitness often becomes genetically determined and fixed, that is, genetically assimilated. These results emphasize the important role of ancestral plasticity in parallel adaptation.
Collapse
Affiliation(s)
- Daniel P Wood
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | - Jon A Holmberg
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | - Andrew J Helmstetter
- Fondation pour la Recherche sur la Biodiversité - Centre for the Synthesis and Analysis of Biodiversity, Institut Bouisson Bertrand, Montpellier, France
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, Sheffield, UK
| | - Amy R Ellison
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK
| | | | - Jackie Lighten
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor, UK.
| |
Collapse
|
15
|
Rescan M, Leurs N, Grulois D, Chevin L. Experimental evolution of environmental tolerance, acclimation, and physiological plasticity in a randomly fluctuating environment. Evol Lett 2022; 6:522-536. [PMID: 36579167 PMCID: PMC9783450 DOI: 10.1002/evl3.306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/03/2022] [Accepted: 11/07/2022] [Indexed: 12/30/2022] Open
Abstract
Environmental tolerance curves, representing absolute fitness against the environment, are an empirical assessment of the fundamental niche, and emerge from the phenotypic plasticity of underlying phenotypic traits. Dynamic plastic responses of these traits can lead to acclimation effects, whereby recent past environments impact current fitness. Theory predicts that higher levels of phenotypic plasticity should evolve in environments that fluctuate more predictably, but there have been few experimental tests of these predictions. Specifically, we still lack experimental evidence for the evolution of acclimation effects in response to environmental predictability. Here, we exposed 25 genetically diverse populations of the halotolerant microalgae Dunaliella salina to different constant salinities, or to randomly fluctuating salinities, for over 200 generations. The fluctuating treatments differed in their autocorrelation, which determines the similarity of subsequent values, and thus environmental predictability. We then measured acclimated tolerance surfaces, mapping population growth rate against past (acclimation) and current (assay) environments. We found that experimental mean and variance in salinity caused the evolution of niche position (optimal salinity) and breadth, with respect to not only current but also past (acclimation) salinity. We also detected weak but significant evidence for evolutionary changes in response to environmental predictability, with higher predictability leading notably to lower optimal salinities and stronger acclimation effect of past environment on current fitness. We further showed that these responses are related to the evolution of plasticity for intracellular glycerol, the major osmoregulatory mechanism in this species. However, the direction of plasticity evolution did not match simple theoretical predictions. Our results underline the need for a more explicit consideration of the dynamics of environmental tolerance and its underlying plastic traits to reach a better understanding of ecology and evolution in fluctuating environments.
Collapse
Affiliation(s)
- Marie Rescan
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRDMontpellier34090France,Université Perpignan Via Domitia, Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110Perpignan66860France,CNRS, Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110Perpignan66860France,Catalan Institute for Water Research (ICRA)Scientific and Technologic Park of the University of GironaEmili Grahit 101GironaGirona17003Spain
| | - Nicolas Leurs
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRDMontpellier34090France,ISEM, CNRS, IRD, EPHE, Univ. MontpellierMontpellier34095France
| | - Daphné Grulois
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRDMontpellier34090France
| | - Luis‐Miguel Chevin
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier 3, EPHE, IRDMontpellier34090France
| |
Collapse
|
16
|
Yu Y, Bergland AO. Distinct signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster. Evolution 2022; 76:2758-2768. [PMID: 36097359 PMCID: PMC9710195 DOI: 10.1111/evo.14617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/31/2022] [Accepted: 08/17/2022] [Indexed: 01/22/2023]
Abstract
Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. Local adaptation can be reflected on both phenotypic and genetic levels, and it has been documented in many organisms. Although complex fitness-related phenotypes have been shown to vary across latitudinal clines and seasons in similar ways in Drosophila melanogaster populations, the comparative signals of local adaptation across space and time remain poorly understood. Here, we examined patterns of allele frequency change across a latitudinal cline and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by using differential expression profiles of fly populations collected across latitudinal clines or exposed to different environmental conditions. In general, we find that eQTLs are enriched for clinally varying polymorphisms, and that these eQTLs change in frequency in concordant ways across the cline and in response to starvation and chill-coma. The enrichment of eQTLs among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTLs appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is at least partially distinct from seasonal adaptation.
Collapse
Affiliation(s)
- Yang Yu
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
| | - Alan O. Bergland
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
| |
Collapse
|
17
|
Tadmor E, Juravel K, Morin S, Santos-Garcia D. Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host. Genome Biol Evol 2022; 14:6649882. [PMID: 35880721 PMCID: PMC9372648 DOI: 10.1093/gbe/evac118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 11/14/2022] Open
Abstract
Although generalist insect herbivores can migrate and rapidly adapt to a broad range of host plants, they can face significant difficulties when accidentally migrating to novel and marginally-suitable hosts. What happens, both in performance and gene expression regulation, if these marginally-suitable hosts must be used for multiple generations before migration to a suitable host can take place, largely remains unknown. In this study, we established multigenerational colonies of the whitefly Bemisia tabaci, a generalist phloem-feeding species, adapted to a marginally-suitable host (habanero pepper) or an optimal host (cotton). We used reciprocal host tests to estimate the differences in performance of the populations on both hosts under optimal (30 oC) and mild-stressful (24 oC) temperature conditions, and documented the associated transcriptomic changes. The habanero pepper-adapted population greatly improved its performance on habanero pepper but did not reach its performance level on cotton, the original host. It also showed reduced performance on cotton, relative to the non-adapted population, and an antagonistic effect of the lower-temperature stressor. The transcriptomic data revealed that most of the expression changes, associated with long-term adaptation to habanero pepper, can be categorized as "evolved" with no initial plastic response. Three molecular functions dominated: enhanced formation of cuticle structural constituents, enhanced activity of oxidation-reduction processes involved in neutralization of phytotoxins and reduced production of proteins from the cathepsin B family. Taken together, these findings indicate that generalist insects can adapt to novel host plants by modifying the expression of a relatively small set of specific molecular functions.
Collapse
Affiliation(s)
- Ella Tadmor
- Department of Entomology, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Ksenia Juravel
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agricultural, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Morin
- Department of Entomology, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Diego Santos-Garcia
- Laboratory of Biometry and Evolutionary Biology University Lyon 1 - UMR CNRS 5558, Villeurbanne, France
| |
Collapse
|
18
|
Oliver A, Cavalheri HB, Lima TG, Jones NT, Podell S, Zarate D, Allen E, Burton RS, Shurin JB. Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation. PLoS One 2022; 17:e0265103. [PMID: 35834446 PMCID: PMC9282536 DOI: 10.1371/journal.pone.0265103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.
Collapse
Affiliation(s)
- Aaron Oliver
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Hamanda B. Cavalheri
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Thiago G. Lima
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Natalie T. Jones
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Daniela Zarate
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
| | - Eric Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Ronald S. Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan B. Shurin
- Department of Biological Sciences, Ecology Behavior and Evolution Section, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
19
|
Swaegers J, Koch EL. Gene expression studies of plastic and evolutionary responses to global warming. CURRENT OPINION IN INSECT SCIENCE 2022; 51:100918. [PMID: 35390507 DOI: 10.1016/j.cois.2022.100918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Phenotypic plasticity can be a rapid response for coping with global warming, yet may be insufficient to protect species from extinction. Evolutionary adaptation may reinforce adaptive or oppose maladaptive plastic responses. With advances in technology whole transcriptomes can provide us with an unprecedented overview of genes and functional processes underlying the interplay between plasticity and evolution. We advocate that insects provide ideal opportunities to study plasticity in non-adapted and thermally adapted populations to infer reaction norms across the whole transcriptome ('reactionomes'). This can advance our understanding of how the interplay between plasticity and evolution shapes responses to warming. So far, a limited number of studies suggest predominantly maladaptive plastic responses to novel environments that are reduced with time, but much more research is needed to infer general patterns.
Collapse
Affiliation(s)
- Janne Swaegers
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Charles Deberiotstraat 32, Leuven B-3000, Belgium.
| | - Eva L Koch
- School of Biociences, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
20
|
Govaert L, Pantel JH, De Meester L. Quantifying eco‐evolutionary contributions to trait divergence in spatially structured systems. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lynn Govaert
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, B‐3000 Leuven Belgium
- Department of Evolutionary Biology and Environmental Studies University of Zurich, Winterthurerstrasse 190 Zürich Switzerland
- Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133 Dübendorf Switzerland
| | - Jelena H. Pantel
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, B‐3000 Leuven Belgium
- Department of Computer Science, Mathematics, and Environmental Science The American University of Paris, 6 rue du Colonel Combes Paris France
- Ecological Modelling, Faculty of Biology University of Duisburg‐Essen, Universitätsstraße 5 Essen Germany
| | - Luc De Meester
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, B‐3000 Leuven Belgium
- Institute of Biology, Freie Universität Berlin Berlin Germany
| |
Collapse
|
21
|
Huang Y, Lack JB, Hoppel GT, Pool JE. Gene Regulatory Evolution in Cold-Adapted Fly Populations Neutralizes Plasticity and May Undermine Genetic Canalization. Genome Biol Evol 2022; 14:evac050. [PMID: 35380655 PMCID: PMC9017818 DOI: 10.1093/gbe/evac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 11/12/2022] Open
Abstract
The relationships between adaptive evolution, phenotypic plasticity, and canalization remain incompletely understood. Theoretical and empirical studies have made conflicting arguments on whether adaptive evolution may enhance or oppose the plastic response. Gene regulatory traits offer excellent potential to study the relationship between plasticity and adaptation, and they can now be studied at the transcriptomic level. Here, we take advantage of three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. We measure the transcriptome-wide plasticity in gene expression levels and alternative splicing (intron usage) between warm and cold laboratory environments. We find that suspected adaptive changes in both gene expression and alternative splicing tend to neutralize the ancestral plastic response. Further, we investigate the hypothesis that adaptive evolution can lead to decanalization of selected gene regulatory traits. We find strong evidence that suspected adaptive gene expression (but not splicing) changes in cold-adapted populations are more vulnerable to the genetic perturbation of inbreeding than putatively neutral changes. We find some evidence that these patterns may reflect a loss of genetic canalization accompanying adaptation, although other processes including hitchhiking recessive deleterious variants may contribute as well. Our findings augment our understanding of genetic and environmental effects on gene regulation in the context of adaptive evolution.
Collapse
Affiliation(s)
- Yuheng Huang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Grant T Hoppel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| |
Collapse
|
22
|
Brennan RS, deMayo JA, Dam HG, Finiguerra MB, Baumann H, Pespeni MH. Loss of transcriptional plasticity but sustained adaptive capacity after adaptation to global change conditions in a marine copepod. Nat Commun 2022; 13:1147. [PMID: 35241657 PMCID: PMC8894427 DOI: 10.1038/s41467-022-28742-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/04/2022] [Indexed: 12/04/2022] Open
Abstract
Adaptive evolution and phenotypic plasticity will fuel resilience in the geologically unprecedented warming and acidification of the earth’s oceans, however, we have much to learn about the interactions and costs of these mechanisms of resilience. Here, using 20 generations of experimental evolution followed by three generations of reciprocal transplants, we investigated the relationship between adaptation and plasticity in the marine copepod, Acartia tonsa, in future global change conditions (high temperature and high CO2). We found parallel adaptation to global change conditions in genes related to stress response, gene expression regulation, actin regulation, developmental processes, and energy production. However, reciprocal transplantation showed that adaptation resulted in a loss of transcriptional plasticity, reduced fecundity, and reduced population growth when global change-adapted animals were returned to ambient conditions or reared in low food conditions. However, after three successive transplant generations, global change-adapted animals were able to match the ambient-adaptive transcriptional profile. Concurrent changes in allele frequencies and erosion of nucleotide diversity suggest that this recovery occurred via adaptation back to ancestral conditions. These results demonstrate that while plasticity facilitated initial survival in global change conditions, it eroded after 20 generations as populations adapted, limiting resilience to new stressors and previously benign environments. Rapid adaptation will facilitate species resilience under global climate change, but its effects on plasticity are less commonly investigated. This study shows that 20 generations of experimental adaptation in a marine copepod drives a rapid loss of plasticity that carries costs and might have impacts on future resilience to environmental change.
Collapse
Affiliation(s)
- Reid S Brennan
- Department of Biology, University of Vermont, Burlington, VT, USA. .,Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
| | - James A deMayo
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Hans G Dam
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Michael B Finiguerra
- Department of Ecology and Evolutionary Biology, University of Connecticut, Groton, CT, USA
| | - Hannes Baumann
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | | |
Collapse
|
23
|
Valenza‐Troubat N, Davy M, Storey R, Wylie MJ, Hilario E, Ritchie P, Wellenreuther M. Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally ( Pseudocaranx georgianus). Evol Appl 2022; 15:237-248. [PMID: 35233245 PMCID: PMC8867707 DOI: 10.1111/eva.13332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/01/2022] Open
Abstract
Ectotherm species, such as marine fishes, depend on environmental temperature to regulate their vital functions. In finfish aquaculture production, being able to predict physiological responses in growth and other economic traits to temperature is crucial to address challenges inherent in the selection of grow-out locations. This will become an even more significant issue under the various predicted future climate change scenarios. In this study, we used the marine teleost silver trevally (Pseudocaranx georgianus), a species currently being explored as a candidate for aquaculture in New Zealand, as a model to study plasticity in gene expression patterns and growth in response to different temperatures. Using a captive study population, temperature conditions were experimentally manipulated for 1 month to mimic seasonal extremes. Phenotypic differences in growth were measured in 400 individuals, and gene expression patterns of pituitary gland and liver were determined in a subset of 100 individuals. Results showed that growth increased 50% in the warmer compared with the colder condition, suggesting that temperature has a large impact on metabolic activities associated with growth. A total of 265,116,678 single-end RNA sequence reads were aligned to the trevally genome, and 28,416 transcript models were developed (27,887 of these had GenBank accessions, and 17,980 unique gene symbols). Further filtering reduced this set to 8597 gene models. 39 and 238 differentially expressed genes (DEGs) were found in the pituitary gland and the liver, respectively (|log2FC| > 0.26, p-value < 0.05). Of these, 6 DEGs showed a common expression pattern between both tissues, all involved in housekeeping functions. Temperature-modulated growth responses were linked to major pathways affecting metabolism, cell regulation and signalling, previously shown to be important for temperature tolerance in other fish species. An interesting finding of this study was that genes linked to the reproductive system were up-regulated in both tissues in the high treatment, indicating the onset of sexual maturation. Few studies have investigated the thermal plasticity of the gene expression in the main organs of the somatotropic axis simultaneously. Our findings indicate that trevally exhibit substantial growth differences and predictable plastic regulatory responses to different temperature conditions. We identified a set of genes that provide a list of candidates for further investigations for selective breeding objectives and how populations may adapt to increasing temperatures.
Collapse
Affiliation(s)
| | - Marcus Davy
- The New Zealand Institute for Plant and Food Research LimitedTe PukeNew Zealand
| | - Roy Storey
- The New Zealand Institute for Plant and Food Research LimitedTe PukeNew Zealand
| | - Matthew J. Wylie
- The New Zealand Institute for Plant and Food Research LimitedNelsonNew Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research LimitedTe PukeNew Zealand
| | - Peter Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research LimitedNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| |
Collapse
|
24
|
Campbell-Staton SC, Velotta JP, Winchell KM. Selection on adaptive and maladaptive gene expression plasticity during thermal adaptation to urban heat islands. Nat Commun 2021; 12:6195. [PMID: 34702827 PMCID: PMC8548502 DOI: 10.1038/s41467-021-26334-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
Phenotypic plasticity enables a single genotype to produce multiple phenotypes in response to environmental variation. Plasticity may play a critical role in the colonization of novel environments, but its role in adaptive evolution is controversial. Here we suggest that rapid parallel regulatory adaptation of Anolis lizards to urban heat islands is due primarily to selection for reduced and/or reversed heat-induced plasticity that is maladaptive in urban thermal conditions. We identify evidence for polygenic selection across genes of the skeletal muscle transcriptome associated with heat tolerance. Forest lizards raised in common garden conditions exhibit heat-induced changes in expression of these genes that largely correlate with decreased heat tolerance, consistent with maladaptive regulatory response to high-temperature environments. In contrast, urban lizards display reduced gene expression plasticity after heat challenge in common garden and a significant increase in gene expression change that is congruent with greater heat tolerance, a putatively adaptive state in warmer urban environments. Genes displaying maladaptive heat-induced plasticity repeatedly show greater genetic divergence between urban and forest habitats than those displaying adaptive plasticity. These results highlight the role of selection against maladaptive regulatory plasticity during rapid adaptive modification of complex systems in the wild.
Collapse
Affiliation(s)
- Shane C Campbell-Staton
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08540, USA.
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
- Institute for Society and Genetics, University of California, Los Angeles, CA, 90095, USA.
| | - Jonathan P Velotta
- Department of Biological Sciences, University of Denver, Denver, CO, 80208, USA
| | | |
Collapse
|
25
|
Chevin LM, Leung C, Le Rouzic A, Uller T. Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map. Genetica 2021; 150:209-221. [PMID: 34617196 DOI: 10.1007/s10709-021-00135-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Deciphering the genotype-phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype-phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype-environment-phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.
Collapse
Affiliation(s)
- Luis-Miguel Chevin
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Christelle Leung
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Arnaud Le Rouzic
- Laboratoire Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
26
|
Voigt S, Kost L. Differences in temperature-sensitive expression of PcG-regulated genes among natural populations of Drosophila melanogaster. G3 (BETHESDA, MD.) 2021; 11:jkab237. [PMID: 34544136 PMCID: PMC8496320 DOI: 10.1093/g3journal/jkab237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
Environmental temperature can affect chromatin-based gene regulation, in particular in ectotherms such as insects. Genes regulated by the Polycomb group (PcG) vary in their transcriptional output in response to changes in temperature. Expression of PcG-regulated genes typically increases with decreasing temperatures. Here, we examined variations in temperature-sensitive expression of PcG target genes in natural populations from different climates of Drosophila melanogaster, and differences thereof across different fly stages and tissues. Temperature-induced expression plasticity was found to be stage- and sex-specific with differences in the specificity between the examined PcG target genes. Some tissues and stages, however, showed a higher number of PcG target genes with temperature-sensitive expression than others. Overall, we found higher levels of temperature-induced expression plasticity in African tropical flies from the ancestral species range than in flies from temperate Europe. We also observed differences between temperate flies, however, with more reduction of expression plasticity in warm-temperate than in cold-temperate populations. Although in general, temperature-sensitive expression appeared to be detrimental in temperate climates, there were also cases in which plasticity was increased in temperate flies, as well as no changes in expression plasticity between flies from different climates.
Collapse
Affiliation(s)
- Susanne Voigt
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden 01217, Germany
| | - Luise Kost
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden 01217, Germany
| |
Collapse
|
27
|
Josephs EB, Van Etten ML, Harkess A, Platts A, Baucom RS. Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed. Evol Lett 2021; 5:432-440. [PMID: 34367667 PMCID: PMC8327940 DOI: 10.1002/evl3.241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/29/2021] [Accepted: 05/20/2021] [Indexed: 11/09/2022] Open
Abstract
Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive. Predicting whether and how organisms will adapt to environmental change is a crucial goal. However, this goal can be complicated because environmental change can alter traits, in a process called plasticity. The extent and fitness consequences of plasticity will have important effects on the adaptive process. In this study, we use adaptation to herbicide in the agricultural weed, the common morning glory, as a model for understanding the extent and fitness consequences of plasticity in gene expression. We find evidence that gene expression plasticity is adaptive in the presence of herbicide, suggesting that understanding plasticity is crucial for understanding how organisms adapt to new environments.
Collapse
Affiliation(s)
- Emily B Josephs
- Department of Plant Biology Michigan State University East Lansing Michigan 48824.,Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan 48824
| | - Megan L Van Etten
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109.,Biology Department Pennsylvania State University Dunmore Pennsylvania 18512
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences Auburn University Auburn Alabama 36849.,HudsonAlpha Institute for Biotechnology Huntsville Alabama 35806
| | - Adrian Platts
- Department of Plant Biology Michigan State University East Lansing Michigan 48824
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109
| |
Collapse
|
28
|
He F, Steige KA, Kovacova V, Göbel U, Bouzid M, Keightley PD, Beyer A, de Meaux J. Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity. Nat Commun 2021; 12:3376. [PMID: 34099660 PMCID: PMC8184852 DOI: 10.1038/s41467-021-23558-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
Phenotypic plasticity is the variation in phenotype that a single genotype can produce in different environments and, as such, is an important component of individual fitness. However, whether the effect of new mutations, and hence evolution, depends on the direction of plasticity remains controversial. Here, we identify the cis-acting modifications that have reshaped gene expression in response to dehydration stress in three Arabidopsis species. Our study shows that the direction of effects of most cis-regulatory variants differentiating the response between A. thaliana and the sister species A. lyrata and A. halleri depends on the direction of pre-existing plasticity in gene expression. A comparison of the rate of cis-acting variant accumulation in each lineage indicates that the selective forces driving adaptive evolution in gene expression favors regulatory changes that magnify the stress response in A. lyrata. The evolutionary constraints measured on the amino-acid sequence of these genes support this interpretation. In contrast, regulatory changes that mitigate the plastic response to stress evolved more frequently in A. halleri. Our results demonstrate that pre-existing plasticity may be a stepping stone for adaptation, but its selective remodeling differs between lineages.
Collapse
Affiliation(s)
- F He
- CEPLAS, University of Cologne, Cologne, Germany
| | - K A Steige
- CEPLAS, University of Cologne, Cologne, Germany
| | - V Kovacova
- CECAD, University of Cologne, Cologne, Germany
| | - U Göbel
- CEPLAS, University of Cologne, Cologne, Germany
| | - M Bouzid
- CEPLAS, University of Cologne, Cologne, Germany
| | - P D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - A Beyer
- CEPLAS, University of Cologne, Cologne, Germany
| | - J de Meaux
- CEPLAS, University of Cologne, Cologne, Germany.
| |
Collapse
|
29
|
Bittner NKJ, Mack KL, Nachman MW. Gene expression plasticity and desert adaptation in house mice. Evolution 2021; 75:1477-1491. [PMID: 33458812 PMCID: PMC8218737 DOI: 10.1111/evo.14172] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 12/10/2020] [Accepted: 12/27/2020] [Indexed: 12/26/2022]
Abstract
Understanding how organisms adapt to new environments is a key problem in evolution, yet it remains unclear whether phenotypic plasticity generally facilitates or hinders this process. Here we studied evolved and plastic responses to water-stress in lab-born descendants of wild house mice (Mus musculus domesticus) collected from desert and non-desert environments and measured gene expression and organismal phenotypes under control and water-stressed conditions. After many generations in the lab, desert mice consumed significantly less water than mice from other localities, indicating that this difference has a genetic basis. Under water-stress, desert mice maintained more weight than non-desert mice, and exhibited differences in blood chemistry related to osmoregulatory function. Gene expression in the kidney revealed evolved differences between mice from different environments as well as plastic responses between hydrated and dehydrated mice. Desert mice showed reduced expression plasticity under water-stress compared to non-desert mice. Importantly, non-desert mice under water-stress generally showed shifts toward desert-like expression, consistent with adaptive plasticity. Finally, we identify several co-expression modules linked to phenotypes of interest. These findings provide evidence for local adaptation after a recent invasion and suggest that adaptive plasticity may have facilitated colonization of the desert environment.
Collapse
Affiliation(s)
- Noëlle K J Bittner
- Deparment of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, 94720
| | - Katya L Mack
- Deparment of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, 94720
- Department of Biology, Stanford University, Stanford, California, 94305
| | - Michael W Nachman
- Deparment of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, 94720
| |
Collapse
|
30
|
Rahi ML, Mather PB, Hurwood DA. Do plasticity in gene expression and physiological responses in Palaemonid prawns facilitate adaptive response to different osmotic challenges? Comp Biochem Physiol A Mol Integr Physiol 2021; 251:110810. [DOI: 10.1016/j.cbpa.2020.110810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/20/2022]
|
31
|
Mallard F, Nolte V, Schlötterer C. The Evolution of Phenotypic Plasticity in Response to Temperature Stress. Genome Biol Evol 2020; 12:2429-2440. [PMID: 33022043 PMCID: PMC7846148 DOI: 10.1093/gbe/evaa206] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 12/23/2022] Open
Abstract
Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to environmental variation. The importance of phenotypic plasticity in natural populations and its contribution to phenotypic evolution during rapid environmental change is widely debated. Here, we show that thermal plasticity of gene expression in natural populations is a key component of its adaptation: evolution to novel thermal environments increases ancestral plasticity rather than mean genetic expression. We determined the evolution of plasticity in gene expression by conducting laboratory natural selection on a Drosophila simulans population in hot and cold environments. After more than 60 generations in the hot environment, 325 genes evolved a change in plasticity relative to the natural ancestral population. Plasticity increased in 75% of these genes, which were strongly enriched for several well-defined functional categories (e.g., chitin metabolism, glycolysis, and oxidative phosphorylation). Furthermore, we show that plasticity in gene expression of populations exposed to different temperatures is rather similar across species. We conclude that most of the ancestral plasticity can evolve further in more extreme environments.
Collapse
Affiliation(s)
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Austria
| | | |
Collapse
|
32
|
Němcová L, Marková S, Kotlík P. Gene Expression Variation of Candidate Endogenous Control Genes Across Latitudinal Populations of the Bank Vole (Clethrionomys glareolus). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.562065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
33
|
Signor SA. Evolution of Plasticity in Response to Ethanol between Sister Species with Different Ecological Histories ( Drosophila melanogaster and D. simulans). Am Nat 2020; 196:620-633. [PMID: 33064591 DOI: 10.1086/710763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractWhen populations evolve adaptive reaction norms in response to novel environments, it can occur through a process termed genetic accommodation. Under this model, the initial response to the environment is widely variable between genotypes as a result of cryptic genetic variation, which is then refined by selection to a single adaptive response. Here, I empirically test these predictions from genetic accommodation by measuring reaction norms in individual genotypes and across several time points. I compare two species of Drosophila that differ in their adaptation to ethanol (D. melanogaster and D. simulans). Both species are human commensals with a recent cosmopolitan expansion, but only D. melanogaster is adapted to ethanol exposure. Using gene expression as a phenotype and an approach that combines information about expression and alternative splicing, I find that D. simulans exhibits cryptic genetic variation in the response to ethanol, while D. melanogaster has almost no genotype-specific variation in reaction norm. This is evidence for adaptation to ethanol through genetic accommodation, suggesting that the evolution of phenotypic plasticity could be an important contributor to the ability to exploit novel resources.
Collapse
|
34
|
Jallet AJ, Le Rouzic A, Genissel A. Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici. Front Microbiol 2020; 11:573829. [PMID: 33042084 PMCID: PMC7517895 DOI: 10.3389/fmicb.2020.573829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/17/2020] [Indexed: 11/28/2022] Open
Abstract
Most species live in a variable environment in nature. Yet understanding the evolutionary processes underlying molecular adaptation to fluctuations remains a challenge. In this study we investigate the transcriptome of the fungal wheat pathogen Zymoseptoria tritici after experimental evolution under stable or fluctuating temperature, by comparing ancestral and evolved populations simultaneously. We found that temperature regimes could have a large and pervasive effect on the transcriptome evolution, with as much as 38% of the genes being differentially expressed between selection regimes. Although evolved lineages showed different changes of gene expression based on ancestral genotypes, we identified a set of genes responding specifically to fluctuation. We found that transcriptome evolution in fluctuating conditions was repeatable between parallel lineages initiated from the same genotype for about 60% of the differentially expressed genes. Further, we detected several hotspots of significantly differentially expressed genes in the genome, in regions known to be enriched in repetitive elements, including accessory chromosomes. Our findings also evidenced gene expression evolution toward a gain of robustness (loss of phenotypic plasticity) associated with the fluctuating regime, suggesting robustness is adaptive in changing environment. This work provides valuable insight into the role of transcriptional rewiring for rapid adaptation to abiotic changes in filamentous plant pathogens.
Collapse
Affiliation(s)
- Arthur J. Jallet
- UMR BIOGER, Université Paris Saclay – INRAE – AgroParisTech, Thiverval-Grignon, France
| | - Arnaud Le Rouzic
- UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay – CNRS – IRD, Gif-sur-Yvette, France
| | - Anne Genissel
- UMR BIOGER, Université Paris Saclay – INRAE – AgroParisTech, Thiverval-Grignon, France
| |
Collapse
|
35
|
Koch EL, Guillaume F. Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum. Mol Ecol 2020; 29:3938-3953. [PMID: 32844494 DOI: 10.1111/mec.15607] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 06/19/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
Plasticity and evolution are two processes allowing populations to respond to environmental changes, but how both are related and impact each other remains controversial. We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after exposure of the beetles to new environments that differed from ancestral conditions in temperature, humidity or both. Using experimental evolution with 10 replicated lines per condition, we were able to demonstrate adaptation after 20 generations. We measured whole-transcriptome gene expression with RNA-sequencing to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between the proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line.
Collapse
Affiliation(s)
- Eva L Koch
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| |
Collapse
|
36
|
Stamp MA, Hadfield JD. The relative importance of plasticity versus genetic differentiation in explaining between population differences; a meta‐analysis. Ecol Lett 2020; 23:1432-1441. [DOI: 10.1111/ele.13565] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/25/2019] [Accepted: 05/14/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Megan A. Stamp
- Institute of Evolutionary Biology University of Edinburgh Edinburgh UK
| | | |
Collapse
|
37
|
Koch EL, Guillaume F. Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum. PLoS Genet 2020; 16:e1008768. [PMID: 32379753 PMCID: PMC7238888 DOI: 10.1371/journal.pgen.1008768] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 05/19/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Gene expression is known to be highly responsive to the environment and important for adjustment of metabolism but there is also growing evidence that differences in gene regulation contribute to species divergence and differences among locally adapted populations. However, most studies so far investigated populations when divergence had already occurred. Selection acting on expression levels at the onset of adaptation to an environmental change has not been characterized. Understanding the mechanisms is further complicated by the fact that environmental change is often multivariate, meaning that organisms are exposed to multiple stressors simultaneously with potentially interactive effects. Here we use a novel approach by combining fitness and whole-transcriptome data in a large-scale experiment to investigate responses to drought, heat and their combination in Tribolium castaneum. We found that fitness was reduced by both stressors and their combined effect was almost additive. Expression data showed that stressor responses were acting independently and did not interfere physiologically. Since we measured expression and fitness within the same individuals, we were able to estimate selection on gene expression levels. We found that variation in fitness can be attributed to gene expression variation and that selection pressures were environment dependent and opposite between control and stress conditions. We could further show that plastic responses of expression were largely adaptive, i.e. in the direction that should increase fitness.
Collapse
Affiliation(s)
- Eva L. Koch
- Department of Evolutionary Biology and Environmental Studies, University
of Zürich, Zürich, Switzerland
- Department of Animal and Plant Science, University of Sheffield, Western
Bank, Sheffield, United Kingdom
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University
of Zürich, Zürich, Switzerland
| |
Collapse
|
38
|
Gene Expression and Diet Breadth in Plant-Feeding Insects: Summarizing Trends. Trends Ecol Evol 2019; 35:259-277. [PMID: 31791830 DOI: 10.1016/j.tree.2019.10.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/18/2019] [Accepted: 10/29/2019] [Indexed: 11/20/2022]
Abstract
Transcriptomic studies lend insights into the role of transcriptional plasticity in adaptation and specialization. Recently, there has been growing interest in understanding the relationship between variation in herbivorous insect gene expression and the evolution of diet breadth. We review the studies that have emerged on insect gene expression and host plant use, and outline the questions and approaches in the field. Many candidate genes underlying herbivory and specialization have been identified, and a few key studies demonstrate increased transcriptional plasticity associated with generalist compared with specialist species. Addressing the roles that transcriptional variation plays in insect diet breadth will have important implications for our understanding of the evolution of specialization and the genetic and environmental factors that govern insect-plant interactions.
Collapse
|
39
|
Velotta JP, Cheviron ZA. Remodeling Ancestral Phenotypic Plasticity in Local Adaptation: A New Framework to Explore the Role of Genetic Compensation in the Evolution of Homeostasis. Integr Comp Biol 2019; 58:1098-1110. [PMID: 30272147 DOI: 10.1093/icb/icy117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Phenotypic plasticity is not universally adaptive. In certain cases, plasticity can result in phenotypic shifts that reduce fitness relative to the un-induced state. A common cause of such maladaptive plasticity is the co-option of ancestral developmental and physiological response systems to meet novel challenges. Because these systems evolved to meet specific challenges in an ancestral environment (e.g., localized and transient hypoxia), their co-option to meet a similar, but novel, stressor (e.g., reductions in ambient pO2 at high elevation) can lead to misdirected responses that reduce fitness. In such cases, natural selection should act to remodel phenotypic plasticity to suppress the expression of these maladaptive responses. Because these maladaptive responses reduce the fitness of colonizers in new environments, this remodeling of ancestral plasticity may be among the earliest steps in adaptive walks toward new local optima. Genetic compensation has been proposed as a general form of adaptive evolution that leads to the suppression of maladaptive plasticity to restore the ancestral trait value in the face of novel stimuli. Given their central role in the regulation of basic physiological functions, we argue that genetic compensation may often be achieved by modifications of homeostatic regulatory systems. We further suggest that genetic compensation to modify homeostatic systems can be achieved by two alternative strategies that differ in their mechanistic underpinnings; to our knowledge, these strategies have not been formally recognized by previous workers. We then consider how the mechanistic details of these alternative strategies may constrain their evolution. These considerations lead us to argue that genetic compensation is most likely to evolve by compensatory physiological changes that safeguard internal homeostatic conditions to prevent the expression of maladaptive portions of conserved reaction norms, rather than direct evolution of plasticity itself. Finally, we outline a simple experimental framework to test this hypothesis. Our goal is to stimulate research aimed at providing a deeper mechanistic understanding of whether and how phenotypic plasticity can be remodeled following environmental shifts that render ancestral responses maladaptive, an issue with increasing importance in our current era of rapid environmental change.
Collapse
Affiliation(s)
- Jonathan P Velotta
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| |
Collapse
|
40
|
Wang A, Singh A, Huang Y, Agrawal AF. Ecological specialization in populations adapted to constant versus heterogeneous environments. Evolution 2019; 73:1309-1317. [PMID: 30912125 DOI: 10.1111/evo.13725] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/26/2019] [Indexed: 11/27/2022]
Abstract
Populations vary in their degree of ecological specialization. An intuitive, but often untested, hypothesis is that populations evolving under greater environmental heterogeneity will evolve to be less specialized. How important is environmental heterogeneity in explaining among-population variation in specialization? We assessed juvenile viability of 20 Drosophila melanogaster populations evolving under one of four regimes: (1) a salt-enriched environment, (2) a cadmium-enriched environment, (3) a temporally varying environment, and (4) a spatially varying environment. Juvenile viability was tested in both the original selective environments and a set of novel environments. In both the original and novel environments, populations from the constant cadmium regime had the lowest average viability and the highest variance in viability across environments but populations from the other three regimes were similar. Our results suggest that variation in specialization among these populations is most simply explained as a pleiotropic by-product of adaptation to specific environments rather than resulting from a history of exposure to environmental heterogeneity.
Collapse
Affiliation(s)
- Ao Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Amardeep Singh
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Yuheng Huang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Aneil F Agrawal
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
41
|
Sikkink KL, Reynolds RM, Ituarte CM, Cresko WA, Phillips PC. Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei. G3 (BETHESDA, MD.) 2019; 9:969-982. [PMID: 30679247 PMCID: PMC6404610 DOI: 10.1534/g3.118.200017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/23/2019] [Indexed: 11/18/2022]
Abstract
Organisms can cope with stressful environments via a combination of phenotypic plasticity at the individual level and adaptation at the population level. Changes in gene expression can play an important role in both. Significant advances in our understanding of gene regulatory plasticity and evolution have come from comparative studies in the field and laboratory. Experimental evolution provides another powerful path by which to learn about how differential regulation of genes and pathways contributes to both acclimation and adaptation. Here we present results from one such study using the nematode Caenorhabditis remanei We selected one set of lines to withstand heat stress and another oxidative stress. We then compared transcriptional responses to acute heat stress of both and an unselected control to the ancestral population using a weighted gene coexpression network analysis, finding that the transcriptional response is primarily dominated by a plastic response that is shared in the ancestor and all evolved populations. In addition, we identified several modules that respond to artificial selection by (1) changing the baseline level of expression, (2) altering the magnitude of the plastic response, or (3) a combination of the two. Our findings therefore reveal that while patterns of transcriptional response can be perturbed with short bouts of intense selection, the overall ancestral structure of transcriptional plasticity is largely maintained over time.
Collapse
Affiliation(s)
- Kristin L Sikkink
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Rose M Reynolds
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Department of Biology, William Jewell College, Liberty, Missouri 64068
| | - Catherine M Ituarte
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
King JG, Hadfield JD. The evolution of phenotypic plasticity when environments fluctuate in time and space. Evol Lett 2019; 3:15-27. [PMID: 30788139 PMCID: PMC6369965 DOI: 10.1002/evl3.100] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/04/2018] [Indexed: 12/17/2022] Open
Abstract
Most theoretical studies have explored the evolution of plasticity when the environment, and therefore the optimal trait value, varies in time or space. When the environment varies in time and space, we show that genetic adaptation to Markovian temporal fluctuations depends on the between-generation autocorrelation in the environment in exactly the same way that genetic adaptation to spatial fluctuations depends on the probability of philopatry. This is because both measure the correlation in parent-offspring environments and therefore the effectiveness of a genetic response to selection. If the capacity to genetically respond to selection is stronger in one dimension (e.g., space), then plasticity mainly evolves in response to fluctuations in the other dimension (e.g., time). If the relationships between the environments of development and selection are the same in time and space, the evolved plastic response to temporal fluctuations is useful in a spatial context and genetic differentiation in space is reduced. However, if the relationships between the environments of development and selection are different, the optimal level of plasticity is different in the two dimensions. In this case, the plastic response that evolves to cope with temporal fluctuations may actually be maladaptive in space, resulting in the evolution of hyperplasticity or negative plasticity. These effects can be mitigated by spatial genetic differentiation that acts in opposition to plasticity resulting in counter-gradient variation. These results highlight the difficulty of making space-for-time substitutions in empirical work but identify the key parameters that need to be measured in order to test whether space-for-time substitutions are likely to be valid.
Collapse
Affiliation(s)
- Jessica G King
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3JT United Kingdom
| |
Collapse
|
44
|
Hsu SK, Jakšić AM, Nolte V, Barghi N, Mallard F, Otte KA, Schlötterer C. A 24 h Age Difference Causes Twice as Much Gene Expression Divergence as 100 Generations of Adaptation to a Novel Environment. Genes (Basel) 2019; 10:E89. [PMID: 30696109 PMCID: PMC6410183 DOI: 10.3390/genes10020089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 01/19/2019] [Accepted: 01/23/2019] [Indexed: 02/08/2023] Open
Abstract
Gene expression profiling is one of the most reliable high-throughput phenotyping methods, allowing researchers to quantify the transcript abundance of expressed genes. Because many biotic and abiotic factors influence gene expression, it is recommended to control them as tightly as possible. Here, we show that a 24 h age difference of Drosophilasimulans females that were subjected to RNA sequencing (RNA-Seq) five and six days after eclosure resulted in more than 2000 differentially expressed genes. This is twice the number of genes that changed expression during 100 generations of evolution in a novel hot laboratory environment. Importantly, most of the genes differing in expression due to age introduce false positives or negatives if an adaptive gene expression analysis is not controlled for age. Our results indicate that tightly controlled experimental conditions, including precise developmental staging, are needed for reliable gene expression analyses, in particular in an evolutionary framework.
Collapse
Affiliation(s)
- Sheng-Kai Hsu
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Neda Barghi
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - François Mallard
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | - Kathrin A Otte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria.
| | | |
Collapse
|
45
|
Morphological novelty emerges from pre-existing phenotypic plasticity. Nat Ecol Evol 2018; 2:1289-1297. [PMID: 29988161 DOI: 10.1038/s41559-018-0601-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/08/2018] [Indexed: 02/01/2023]
Abstract
Plasticity-first evolution (PFE) posits that novel features arise when selection refines pre-existing phenotypic plasticity into an adaptive phenotype. However, PFE is controversial because few tests have been conducted in natural populations. Here we present evidence that PFE fostered the origin of an evolutionary novelty that allowed certain amphibians to invade a new niche-a distinctive carnivore morph. We compared morphology, gene expression and growth of three species of spadefoot toad tadpoles when reared on alternative diets: Scaphiopus holbrookii, which (like most frogs) never produce carnivores; Spea multiplicata, which sometimes produce carnivores, but only through diet-induced plasticity; and Spea bombifrons, which often produce carnivores regardless of diet. Consistent with PFE, we found diet-induced plasticity-in morphology and gene expression-in Sc. holbrookii, adaptive refinement of this plasticity in Sp. multiplicata, and further refinement of the carnivore phenotype in Sp. bombifrons. Generally, phenotypic plasticity might play a significant, if underappreciated, role in evolutionary innovation.
Collapse
|
46
|
Wagner MR, Mitchell-Olds T. Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta. Evolution 2018. [PMID: 29522254 DOI: 10.1111/evo.13469] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection ("adaptive" plasticity) or disfavored ("nonadaptive" plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, United States. Glucosinolate profiles-including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds-were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats.
Collapse
Affiliation(s)
- Maggie R Wagner
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708.,Current Address: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695
| | - Thomas Mitchell-Olds
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708
| |
Collapse
|
47
|
Rittschof CC, Hughes KA. Advancing behavioural genomics by considering timescale. Nat Commun 2018; 9:489. [PMID: 29434301 PMCID: PMC5809431 DOI: 10.1038/s41467-018-02971-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022] Open
Abstract
Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity.
Collapse
Affiliation(s)
- Clare C Rittschof
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA.
| | - Kimberly A Hughes
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 32306, USA
| |
Collapse
|
48
|
Lea AJ, Tung J, Archie EA, Alberts SC. Developmental plasticity: Bridging research in evolution and human health. Evol Med Public Health 2018; 2017:162-175. [PMID: 29424834 PMCID: PMC5798083 DOI: 10.1093/emph/eox019] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/19/2017] [Indexed: 02/06/2023] Open
Abstract
Early life experiences can have profound and persistent effects on traits expressed throughout the life course, with consequences for later life behavior, disease risk, and mortality rates. The shaping of later life traits by early life environments, known as 'developmental plasticity', has been well-documented in humans and non-human animals, and has consequently captured the attention of both evolutionary biologists and researchers studying human health. Importantly, the parallel significance of developmental plasticity across multiple fields presents a timely opportunity to build a comprehensive understanding of this phenomenon. We aim to facilitate this goal by highlighting key outstanding questions shared by both evolutionary and health researchers, and by identifying theory and empirical work from both research traditions that is designed to address these questions. Specifically, we focus on: (i) evolutionary explanations for developmental plasticity, (ii) the genetics of developmental plasticity and (iii) the molecular mechanisms that mediate developmental plasticity. In each section, we emphasize the conceptual gains in human health and evolutionary biology that would follow from filling current knowledge gaps using interdisciplinary approaches. We encourage researchers interested in developmental plasticity to evaluate their own work in light of research from diverse fields, with the ultimate goal of establishing a cross-disciplinary understanding of developmental plasticity.
Collapse
Affiliation(s)
- Amanda J Lea
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, Karen, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| |
Collapse
|
49
|
|
50
|
de Francisco P, Martín-González A, Turkewitz AP, Gutiérrez JC. Extreme metal adapted, knockout and knockdown strains reveal a coordinated gene expression among different Tetrahymena thermophila metallothionein isoforms. PLoS One 2017; 12:e0189076. [PMID: 29206858 PMCID: PMC5716537 DOI: 10.1371/journal.pone.0189076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/17/2017] [Indexed: 01/01/2023] Open
Abstract
Metallothioneins (MT) constitute a superfamily of small cytosolic proteins that are able to bind metal cations through numerous cysteine (Cys) residues. Like other organisms the ciliate Tetrahymena thermophila presents several MT isoforms, which have been classified into two subfamilies (Cd- and Cu-metallothioneins). The main aim of this study was to examine the specific functions and transcriptional regulation of the five MT isoforms present in T. thermophila, by using several strains of this ciliate. After a laboratory evolution experiment over more than two years, three different T. thermophila strains adapted to extreme metal stress (Cd2+, Cu2+ or Pb2+) were obtained. In addition, three knockout and/or knockdown strains for different metallothionein (MT) genes were generated. These strains were then analyzed for expression of the individual MT isoforms. Our results provide a strong basis for assigning differential roles to the set of MT isoforms. MTT1 appears to have a key role in adaptation to Cd. In contrast, MTT2/4 are crucial for Cu-adaptation and MTT5 appears to be important for Pb-adaptation and might be considered as an “alarm” MT gene for responding to metal stress. Moreover, results indicate that likely a coordinated transcriptional regulation exists between the MT genes, particularly among MTT1, MTT5 and MTT2/4. MTT5 appears to be an essential gene, a first such report in any organism of an essential MT gene.
Collapse
Affiliation(s)
- Patricia de Francisco
- Departamento de Microbiología-III, Facultad de Biología, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Ana Martín-González
- Departamento de Microbiología-III, Facultad de Biología, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Aaron P. Turkewitz
- Department of Molecular Genetics and Cell Biology, Cummings Life Sciences Center, University of Chicago, Chicago, Illinois, United States of America
| | - Juan Carlos Gutiérrez
- Departamento de Microbiología-III, Facultad de Biología, Universidad Complutense de Madrid (UCM), Madrid, Spain
- * E-mail:
| |
Collapse
|