1
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Pollack D, Nozoe T, Kussell E. Proteolytic stability and aggregation in a key metabolic enzyme of bacteria. Proc Natl Acad Sci U S A 2024; 121:e2301458121. [PMID: 38683989 PMCID: PMC11087809 DOI: 10.1073/pnas.2301458121] [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: 01/31/2023] [Accepted: 03/07/2024] [Indexed: 05/02/2024] Open
Abstract
Proteins that are kinetically stable are thought to be less prone to both aggregation and proteolysis. We demonstrate that the classical lac system of Escherichia coli can be leveraged as a model system to study this relation. β-galactosidase (LacZ) plays a critical role in lactose metabolism and is an extremely stable protein that can persist in growing cells for multiple generations after expression has stopped. By attaching degradation tags to the LacZ protein, we find that LacZ can be transiently degraded during lac operon expression but once expression has stopped functional LacZ is protected from degradation. We reversibly destabilize its tetrameric assembly using α-complementation, and show that unassembled LacZ monomers and dimers can either be degraded or lead to formation of aggregates within cells, while the tetrameric state protects against proteolysis and aggregation. We show that the presence of aggregates is associated with cell death, and that these proteotoxic stress phenotypes can be alleviated by attaching an ssrA tag to LacZ monomers which leads to their degradation. We unify our findings using a biophysical model that enables the interplay of protein assembly, degradation, and aggregation to be studied quantitatively in vivo. This work may yield approaches to reversing and preventing protein-misfolding disease states, while elucidating the functions of proteolytic stability in constant and fluctuating environments.
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Affiliation(s)
- Dan Pollack
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
| | - Takashi Nozoe
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo153-8902, Japan
- Research Center for Complex Systems Biology, The University of Tokyo, Tokyo153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo113-0033, Japan
| | - Edo Kussell
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
- Department of Physics, New York University, New York, NY10003
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2
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Farkas BC, Baptista A, Speranza M, Wyart V, Jacquet PO. Specifying the timescale of early life unpredictability helps explain the development of internalising and externalising behaviours. Sci Rep 2024; 14:3563. [PMID: 38347055 PMCID: PMC10861493 DOI: 10.1038/s41598-024-54093-x] [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: 08/08/2023] [Accepted: 02/08/2024] [Indexed: 02/15/2024] Open
Abstract
Early life unpredictability is associated with both physical and mental health outcomes throughout the life course. Here, we classified adverse experiences based on the timescale on which they are likely to introduce variability in children's environments: variations unfolding over short time scales (e.g., hours, days, weeks) and labelled Stochasticity vs variations unfolding over longer time scales (e.g., months, years) and labelled Volatility and explored how they contribute to the development of problem behaviours. Results indicate that externalising behaviours at age 9 and 15 and internalising behaviours at age 15 were better accounted for by models that separated Stochasticity and Volatility measured at ages 3 to 5. Both externalising and internalising behaviours were specifically associated with Volatility, with larger effects for externalising behaviours. These findings are interpreted in light of evolutionary-developmental models of psychopathology and reinforcement learning models of learning under uncertainty.
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Affiliation(s)
- Bence Csaba Farkas
- Institut du Psychotraumatisme de l'Enfant et de l'Adolescent, Conseil Départemental Yvelines et Hauts-de-Seine et Centre Hospitalier des Versailles, 78000, Versailles, France.
- UVSQ, Inserm, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris-Saclay, 78000, Versailles, France.
- LNC2, Département d'études Cognitives, École Normale Supérieure, INSERM, PSL Research University, 75005, Paris, France.
| | - Axel Baptista
- UVSQ, Inserm, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris-Saclay, 78000, Versailles, France
- Centre Hospitalier de Versailles, Le Chesnay, France
| | - Mario Speranza
- Institut du Psychotraumatisme de l'Enfant et de l'Adolescent, Conseil Départemental Yvelines et Hauts-de-Seine et Centre Hospitalier des Versailles, 78000, Versailles, France
- UVSQ, Inserm, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris-Saclay, 78000, Versailles, France
- Centre Hospitalier de Versailles, Le Chesnay, France
| | - Valentin Wyart
- Institut du Psychotraumatisme de l'Enfant et de l'Adolescent, Conseil Départemental Yvelines et Hauts-de-Seine et Centre Hospitalier des Versailles, 78000, Versailles, France
- LNC2, Département d'études Cognitives, École Normale Supérieure, INSERM, PSL Research University, 75005, Paris, France
| | - Pierre Olivier Jacquet
- Institut du Psychotraumatisme de l'Enfant et de l'Adolescent, Conseil Départemental Yvelines et Hauts-de-Seine et Centre Hospitalier des Versailles, 78000, Versailles, France
- UVSQ, Inserm, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris-Saclay, 78000, Versailles, France
- LNC2, Département d'études Cognitives, École Normale Supérieure, INSERM, PSL Research University, 75005, Paris, France
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3
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Webster AK, Phillips PC. Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation. G3 (BETHESDA, MD.) 2024; 14:jkad287. [PMID: 38113034 PMCID: PMC10849368 DOI: 10.1093/g3journal/jkad287] [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: 08/03/2023] [Revised: 08/03/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Abstract
How genetic and phenotypic variation are maintained has long been one of the fundamental questions in population and quantitative genetics. A variety of factors have been implicated to explain the maintenance of genetic variation in some contexts (e.g. balancing selection), but the potential role of epigenetic regulation to influence population dynamics has been understudied. It is well recognized that epigenetic regulation, including histone methylation, small RNA expression, and DNA methylation, helps to define differences between cell types and facilitate phenotypic plasticity. In recent years, empirical studies have shown the potential for epigenetic regulation to also be heritable for at least a few generations without selection, raising the possibility that differences in epigenetic regulation can act alongside genetic variation to shape evolutionary trajectories. Heritable differences in epigenetic regulation that arise spontaneously are termed "epimutations." Epimutations differ from genetic mutations in 2 key ways-they occur at a higher rate and the loci at which they occur often revert back to their original state within a few generations. Here, we present an extension of the standard population genetic model with selection to incorporate epigenetic variation arising via epimutation. Our model assumes a diploid, sexually reproducing population with random mating. In addition to spontaneous genetic mutation, we included parameters for spontaneous epimutation and back-epimutation, allowing for 4 potential epialleles at a single locus (2 genetic alleles, each with 2 epigenetic states), each of which affect fitness. We then analyzed the conditions under which stable epialleles were maintained. Our results show that highly reversible epialleles can be maintained in long-term equilibrium under neutral conditions in a manner that depends on the epimutation and back-epimutation rates, which we term epimutation-back-epimutation equilibrium. On the other hand, epialleles that compensate for deleterious mutations cause deviations from the expectations of mutation-selection balance by a simple factor that depends on the epimutation and back-epimutation rates. We also numerically analyze several sets of fitness parameters for which large deviations from mutation-selection balance occur. Together, these results demonstrate that transient epigenetic regulation may be an important factor in the maintenance of both epigenetic and genetic variation in populations.
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Affiliation(s)
- Amy K Webster
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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4
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Fishman B, Tauber E. Epigenetics and seasonal timing in animals: a concise review. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2023:10.1007/s00359-023-01673-3. [PMID: 37695537 DOI: 10.1007/s00359-023-01673-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Seasonal adaptation in animals is a complex process that involves genetic, epigenetic, and environmental factors. The present review explores recent studies on epigenetic mechanisms implicated in seasonal adaptation in animals. The review is divided into three main sections, each focusing on a different epigenetic mechanism: DNA methylation, histone modifications, and non-coding RNA. Additionally, the review delves into the current understanding of how these epigenetic factors contribute to the regulation of circadian and seasonal cycles. Understanding these molecular mechanisms provides the first step in deciphering the complex interplay between genetics, epigenetics, and the environment in driving seasonal adaptation in animals. By exploring these mechanisms, a better understanding of how animals adapt to changing environmental conditions can be achieved.
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Affiliation(s)
- Bettina Fishman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel.
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5
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Law L, Xue B. Internal cues for optimizing reproduction in a varying environment. Proc Biol Sci 2023; 290:20230096. [PMID: 37072039 PMCID: PMC10113029 DOI: 10.1098/rspb.2023.0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 04/20/2023] Open
Abstract
In varying environments, it is beneficial for organisms to utilize available cues to infer the conditions they may encounter and express potentially favourable traits. However, external cues can be unreliable or too costly to use. We consider an alternative strategy where organisms exploit internal sources of information. Even without sensing environmental cues, their internal states may become correlated with the environment as a result of selection, which then form a memory that helps predict future conditions. To demonstrate the adaptive value of such internal cues in varying environments, we revisit the classic example of seed dormancy in annual plants. Previous studies have considered the germination fraction of seeds and its dependence on environmental cues. In contrast, we consider a model of germination fraction that depends on the seed age, which is an internal state that can serve as a memory. We show that, if the environmental variation has temporal structure, then age-dependent germination fractions will allow the population to have an increased long-term growth rate. The more the organisms can remember through their internal states, the higher the growth rate a population can potentially achieve. Our results suggest experimental ways to infer internal memory and its benefit for adaptation in varying environments.
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Affiliation(s)
- Leo Law
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
| | - BingKan Xue
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
- Institute for Fundamental Theory, University of Florida, Gainesville, FL 32611, USA
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6
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Sabarís G, Fitz‐James MH, Cavalli G. Epigenetic inheritance in adaptive evolution. Ann N Y Acad Sci 2023. [DOI: 10.1111/nyas.14992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Affiliation(s)
- Gonzalo Sabarís
- Institute of Human Genetics, CNRS Montpellier France
- University of Montpellier Montpellier France
| | - Maximilian H. Fitz‐James
- Institute of Human Genetics, CNRS Montpellier France
- University of Montpellier Montpellier France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS Montpellier France
- University of Montpellier Montpellier France
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7
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Edelaar P, Otsuka J, Luque VJ. A generalised approach to the study and understanding of adaptive evolution. Biol Rev Camb Philos Soc 2023; 98:352-375. [PMID: 36223883 PMCID: PMC10091731 DOI: 10.1111/brv.12910] [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: 03/30/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.
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Affiliation(s)
- Pim Edelaar
- Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Carretera Utrera km.1, 41013, Seville, Spain.,Swedish Collegium for Advanced Study, Thunbergsvägen 2, SE-75238, Uppsala, Sweden
| | - Jun Otsuka
- Department of Philosophy, Kyoto University, Yoshida-Hommachi, Sakyo, Kyoto, 606-8501, Japan.,RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Tokyo, 103-0027, Japan
| | - Victor J Luque
- Department of Philosophy, University of Valencia, Av. de Blasco Ibáñez, 30, 46010, València, Spain
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8
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Batabyal A, Lukowiak K. Tracking the path of predator recognition in a predator-naive population of the pond snail. Behav Ecol 2022. [DOI: 10.1093/beheco/arac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
Organisms evolve adaptive strategies to adjust to rapidly changing environmental stressors. Predation pressure is one of the strongest selective forces and organisms respond to predatory threats via innate and learned responses. We utilized a natural, experimental set-up, where two lakes Stoney and Margo in Canada containing natural populations of the prey Lymnaea stagnalis differed in the presence and absence of an invasive, predatory Northern crayfish, Faxonius virilis. We exploited the contrast in the predation backgrounds of the snail populations from the two lakes to test, 1) predator recognition in predator-experienced snails is innate, (2) predator-naive snails learn to detect a novel invasive predator, and 3) learning about a novel predator gets transmitted to the successive generations. We quantified predator fear memory formation using a higher-order learning paradigm called configural learning. We found that 1) predator recognition in predator-experienced snails is innate, 2) predator-naive snails learned to recognize the novel predator even after a brief exposure to predator cues highlighting the role of learning in combating invasive predators and the critical time-window during development that accounts for predator recognition, and 3) the learning and predator detection mechanism in predator-naive snails are not transmitted to successive generations. The population variation observed in the predator-detection mechanism may be due to the past and current experience of predators in one population over the other. We find an interesting study system to address how fear learning occurs and prospective future directions to understand the mechanism of innate fear recognition from a learned fear recognition.
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Affiliation(s)
- Anuradha Batabyal
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary , 3330, Hospital Drive, NW, Calgary, Alberta T2N 4N1 , Canada
- Department of Physical and Natural Sciences, FLAME University , Lavale, Off. Pune Bangalore Highway, Pune, Maharashtra 412115 , India
| | - Ken Lukowiak
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary , 3330, Hospital Drive, NW, Calgary, Alberta T2N 4N1 , Canada
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9
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Distinct Long- and Short-Term Adaptive Mechanisms in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0304322. [PMID: 36374016 PMCID: PMC9769816 DOI: 10.1128/spectrum.03043-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Heterogeneous environments such as the chronically infected cystic fibrosis lung drive the diversification of Pseudomonas aeruginosa populations into, e.g., mucoid, alginate-overproducing isolates or small-colony variants (SCVs). In this study, we performed extensive genome and transcriptome profiling on a clinical SCV isolate that exhibited high cyclic diguanylate (c-di-GMP) levels and a mucoid phenotype. We observed a delayed, stepwise decrease of the high levels of c-di-GMP as well as alginate gene expression upon passaging the SCV under noninducing, rich medium growth conditions over 7 days. Upon prolonged passaging, this lagging reduction of the high c-di-GMP levels under noninducing planktonic conditions (reminiscent of a hysteretic response) was followed by a phenotypic switch to a large-colony morphology, which could be linked to mutations in the Gac/Rsm signaling pathway. Complementation of the Gac/Rsm signaling-negative large-colony variants with a functional GacSA system restored the SCV colony morphotype but was not able to restore the high c-di-GMP levels of the SCV. Our data thus suggest that expression of the SCV colony morphotype and modulation of c-di-GMP levels are genetically separable and follow different evolutionary paths. The delayed switching of c-di-GMP levels in response to fluctuating environmental conditions might provide a unique opportunity to include a time dimension to close the gap between short-term phenotypic and long-term genetic adaptation to biofilm-associated growth conditions. IMPORTANCE Extreme environments, such as those encountered during an infection process in the human host, make effective bacterial adaptation inevitable. While bacteria adapt individually by activating stress responses, long-term adaptation of bacterial communities to challenging conditions can be achieved via genetic fixation of favorable traits. In this study, we describe a two-pronged bacterial stress resistance strategy in the opportunistic pathogen Pseudomonas aeruginosa. We show that the production of adjusted elevated c-di-GMP levels, which drive protected biofilm-associated phenotypes in vivo, resembles a stable hysteretic response which prevents unwanted frequent switching. Cellular hysteresis might provide a link between individual adaptability and evolutionary adaptation to ensure the evolutionary persistence of host-adapted stress response strategies.
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10
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Lee U, Mortola EN, Kim EJ, Long M. Evolution and maintenance of phenotypic plasticity. Biosystems 2022; 222:104791. [DOI: 10.1016/j.biosystems.2022.104791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 11/02/2022]
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11
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Vermeersch L, Cool L, Gorkovskiy A, Voordeckers K, Wenseleers T, Verstrepen KJ. Do microbes have a memory? History-dependent behavior in the adaptation to variable environments. Front Microbiol 2022; 13:1004488. [PMID: 36299722 PMCID: PMC9589428 DOI: 10.3389/fmicb.2022.1004488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
Microbes are constantly confronted with changes and challenges in their environment. A proper response to these environmental cues is needed for optimal cellular functioning and fitness. Interestingly, past exposure to environmental cues can accelerate or boost the response when this condition returns, even in daughter cells that have not directly encountered the initial cue. Moreover, this behavior is mostly epigenetic and often goes hand in hand with strong heterogeneity in the strength and speed of the response between isogenic cells of the same population, which might function as a bet-hedging strategy. In this review, we discuss examples of history-dependent behavior (HDB) or “memory,” with a specific focus on HDB in fluctuating environments. In most examples discussed, the lag time before the response to an environmental change is used as an experimentally measurable proxy for HDB. We highlight different mechanisms already implicated in HDB, and by using HDB in fluctuating carbon conditions as a case study, we showcase how the metabolic state of a cell can be a key determining factor for HDB. Finally, we consider possible evolutionary causes and consequences of such HDB.
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Affiliation(s)
- Lieselotte Vermeersch
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Lloyd Cool
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Anton Gorkovskiy
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Kevin J. Verstrepen
- VIB – KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, KU Leuven, Leuven, Belgium
- *Correspondence: Kevin J. Verstrepen,
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Hagemann J, Conejero C, Stillfried M, Mentaberre G, Castillo-Contreras R, Fickel J, López-Olvera JR. Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155126. [PMID: 35405223 DOI: 10.1016/j.scitotenv.2022.155126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/27/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.
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Affiliation(s)
- Justus Hagemann
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany; University of Potsdam, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Carles Conejero
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Milena Stillfried
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany
| | - Gregorio Mentaberre
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain; Departament de Ciència Animal, Escola Tècnica Superior d'Enginyeria Agraria (ETSEA), Universitat de Lleida (UdL), 25098 Lleida, Spain
| | - Raquel Castillo-Contreras
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Jörns Fickel
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany; University of Potsdam, Molecular Ecology and Evolution, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Jorge Ramón López-Olvera
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain.
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13
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Walzer A, Nachman G, Spangl B, Stijak M, Tscholl T. Trans- and Within-Generational Developmental Plasticity May Benefit the Prey but Not Its Predator during Heat Waves. BIOLOGY 2022; 11:biology11081123. [PMID: 36009751 PMCID: PMC9404866 DOI: 10.3390/biology11081123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary Heat waves can have fatal effects on arthropods such as insects and mites since their heat tolerance is often lower than the diurnal maximum temperatures during heat waves. Plastic modifications by the parents, however, can rapidly result in favorable adaptations in offspring traits. This question was investigated by using a prominent natural enemy/pest couple in biological control, the predatory mite Phytoseiulus persimilis and its prey, the spider mite Tetranychus urticae. We exposed both species separately to extreme or mild heat waves during their juvenile development, a vital phase of arthropod life, for two generations and assessed various fitness-relevant parameters of the offspring generation. Under extreme heat waves, adult body sizes of predator and prey males and prey females were insensitive, when they derived from parents also reared under extreme heat waves. Irrespective of their origin, offspring reached earlier adulthood under extreme heat waves. In general, prey benefitted more from parental modifications compared to the predator. However, further investigations are needed to verify whether these changes affect the interactions between the predators and their prey to an extent that it may jeopardize biological control during extreme heat waves. Abstract Theoretically, parents can adjust vital offspring traits to the irregular and rapid occurrence of heat waves via developmental plasticity. However, the direction and strength of such trait modifications are often species-specific. Here, we investigated within-generational plasticity (WGP) and trans-generational plasticity (TGP) effects induced by heat waves during the offspring development of the predator Phytoseiulus persimilis and its herbivorous prey, the spider mite Tetranychus urticae, to assess plastic developmental modifications. Single offspring individuals with different parental thermal origin (reared under mild or extreme heat waves) of both species were exposed to mild or extreme heat waves until adulthood, and food consumption, age and size at maturity were recorded. The offspring traits were influenced by within-generational plasticity (WGP), trans-generational plasticity (TGP), non-plastic trans-generational effects (TGE) and/or their interactions. When exposed to extreme heat waves, both species speeded up development (exclusively WGP), consumed more (due to the fact of WGP but also to TGP in prey females and to non-plastic TGE in predator males), and predator females got smaller (non-plastic TGE and WGP), whereas prey males and females were equally sized irrespective of their origin, because TGE, WGP and TGP acted in opposite directions. The body sizes of predator males were insensitive to parental and offspring heat wave conditions. Species comparisons indicated stronger reductions in the developmental time and reduced female predator-prey body size ratios in favor of the prey under extreme heat waves. Further investigations are needed to evaluate, whether trait modifications result in lowered suppression success of the predator on its prey under heat waves or not.
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Affiliation(s)
- Andreas Walzer
- University of Natural Resources and Life Sciences, Vienna, Department of Crop Sciences, Institute of Plant Protection, Gregor-Mendel-Straße 33, 1180 Vienna, Austria; (A.W.); (M.S.)
| | - Gösta Nachman
- Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark;
| | - Bernhard Spangl
- University of Natural Resources and Life Sciences, Vienna, Department of Landscape, Spatial and Infrastructure Sciences, Institute of Statistics, Peter-Jordan-Straße 82/I, 1190 Vienna, Austria;
| | - Miroslava Stijak
- University of Natural Resources and Life Sciences, Vienna, Department of Crop Sciences, Institute of Plant Protection, Gregor-Mendel-Straße 33, 1180 Vienna, Austria; (A.W.); (M.S.)
| | - Thomas Tscholl
- University of Natural Resources and Life Sciences, Vienna, Department of Crop Sciences, Institute of Plant Protection, Gregor-Mendel-Straße 33, 1180 Vienna, Austria; (A.W.); (M.S.)
- Correspondence: ; Tel.: +43-1-47654-95329
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14
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Spinks RK, Donelson JM, Bonzi LC, Ravasi T, Munday PL. Parents exposed to warming produce offspring lower in weight and condition. Ecol Evol 2022; 12:e9044. [PMID: 35866024 PMCID: PMC9288889 DOI: 10.1002/ece3.9044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
The parental environment can alter offspring phenotypes via the transfer of non‐genetic information. Parental effects may be viewed as an extension of (within‐generation) phenotypic plasticity. Smaller size, poorer physical condition, and skewed sex ratios are common responses of organisms to global warming, yet whether parental effects alleviate, exacerbate, or have no impact on these responses has not been widely tested. Further, the relative non‐genetic influence of mothers and fathers and ontogenetic timing of parental exposure to warming on offspring phenotypes is poorly understood. Here, we tested how maternal, paternal, and biparental exposure of a coral reef fish (Acanthochromis polyacanthus) to elevated temperature (+1.5°C) at different ontogenetic stages (development vs reproduction) influences offspring length, weight, condition, and sex. Fish were reared across two generations in present‐day and projected ocean warming in a full factorial design. As expected, offspring of parents exposed to present‐day control temperature that were reared in warmer water were shorter than their siblings reared in control temperature; however, within‐generation plasticity allowed maintenance of weight, resulting in a higher body condition. Parental exposure to warming, irrespective of ontogenetic timing and sex, resulted in decreased weight and condition in all offspring rearing temperatures. By contrast, offspring sex ratios were not strongly influenced by their rearing temperature or that of their parents. Together, our results reveal that phenotypic plasticity may help coral reef fishes maintain performance in a warm ocean within a generation, but could exacerbate the negative effects of warming between generations, regardless of when mothers and fathers are exposed to warming. Alternatively, the multigenerational impact on offspring weight and condition may be a necessary cost to adapt metabolism to increasing temperatures. This research highlights the importance of examining phenotypic plasticity within and between generations across a range of traits to accurately predict how organisms will respond to climate change.
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Affiliation(s)
- Rachel K Spinks
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia
| | - Jennifer M Donelson
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia
| | - Lucrezia C Bonzi
- Division of Biological and Environmental Sciences and Engineering, Red Sea Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Timothy Ravasi
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia.,Marine Climate Change Unit Okinawa Institute of Science and Technology Graduate University Onna Japan
| | - Philip L Munday
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia
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15
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Jablonka E. Marion Julia Lamb (29 July 1939-12 December 2021). ENVIRONMENTAL EPIGENETICS 2022; 8:dvac009. [PMID: 35496658 PMCID: PMC9049106 DOI: 10.1093/eep/dvac009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Eva Jablonka
- *Correspondence address. Cohn Institute, Tek-Aviv University, Tel Aviv 69978, Israel. Tel: +(972) 3-6409198; FAX: +(972) 3-6409463; E-mail:
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16
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Kronholm I. Evolution of anticipatory effects mediated by epigenetic changes. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac007. [PMID: 35475265 PMCID: PMC9031056 DOI: 10.1093/eep/dvac007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 05/20/2023]
Abstract
Anticipatory effects mediated by epigenetic changes occur when parents modify the phenotype of their offspring by making epigenetic changes in their gametes, guided by information from an environmental cue. To investigate when do anticipatory effects mediated by epigenetic changes evolve in a fluctuating environment, I use an individual-based simulation model with explicit genetic architecture. The model allows for the population to respond to environmental changes by evolving plasticity, bet hedging, or by tracking the environment with genetic adaptation, in addition to the evolution of anticipatory effects. The results show that anticipatory effects evolve when the environmental cue provides reliable information about the environment and the environment changes at intermediate rates, provided that fitness costs of anticipatory effects are rather low. Moreover, evolution of anticipatory effects is quite robust to different genetic architectures when reliability of the environmental cue is high. Anticipatory effects always give smaller fitness benefits than within-generation plasticity, suggesting a possible reason for generally small observed anticipatory effects in empirical studies.
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Affiliation(s)
- Ilkka Kronholm
- *Correspondence address. Department of Biological and Environmental Sciences, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland. Tel: +358 14 617 239; Fax: +358 14 617 239; E-mail:
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17
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Lemmen KD, Verhoeven KJF, Declerck SAJ. Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kimberley D. Lemmen
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Steven A. J. Declerck
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Biology Laboratory of Aquatic Ecology, Evolution and Conservation KULeuven Leuven Belgium
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18
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Patra P, Klumpp S. Role of bacterial persistence in spatial population expansion. Phys Rev E 2021; 104:034401. [PMID: 34654134 DOI: 10.1103/physreve.104.034401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/19/2021] [Indexed: 11/07/2022]
Abstract
Bacterial persistence, tolerance to antibiotics via stochastic phenotype switching, provides a survival strategy and a fitness advantage in temporally fluctuating environments. Here we study its possible benefit in spatially varying environments using a Fisher wave approach. We study the spatial expansion of a population with stochastic switching between two phenotypes in spatially homogeneous conditions and in the presence of an antibiotic barrier. Our analytical results show that the expansion speed in growth-supporting conditions depends on the fraction of persister cells at the leading edge of the population wave. The leading edge contains a small fraction of persister cells, keeping the effect on the expansion speed minimal. The fraction of persisters increases gradually in the interior of the wave. This persister pool benefits the population when it is stalled by an antibiotic environment. In that case, the presence of persister enables the population to spread deeper into the antibiotic region and to cross an antibiotic region more rapidly. Further we observe that optimal switching rates maximize the expansion speed of the population in spatially varying environments with alternating regions of growth permitting conditions and antibiotics. Overall, our results show that stochastic switching can promote population expansion in the presence of antibiotic barriers or other stressful environments.
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Affiliation(s)
- Pintu Patra
- Institute for Theoretical Physics, Heidelberg University, Heidelberg 69120, Germany
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen 37077, Germany
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19
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Calabrese F, Stryhanyuk H, Moraru C, Schlömann M, Wick LY, Richnow HH, Musat F, Musat N. Metabolic history and metabolic fitness as drivers of anabolic heterogeneity in isogenic microbial populations. Environ Microbiol 2021; 23:6764-6776. [PMID: 34472201 DOI: 10.1111/1462-2920.15756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/26/2022]
Abstract
Microbial populations often display different degrees of heterogeneity in their substrate assimilation, that is, anabolic heterogeneity. It has been shown that nutrient limitations are a relevant trigger for this behaviour. Here we explore the dynamics of anabolic heterogeneity under nutrient replete conditions. We applied time-resolved stable isotope probing and nanoscale secondary ion mass spectrometry to quantify substrate assimilation by individual cells of Pseudomonas putida, P. stutzeri and Thauera aromatica. Acetate and benzoate at different concentrations were used as substrates. Anabolic heterogeneity was quantified by the cumulative differentiation tendency index. We observed two major, opposing trends of anabolic heterogeneity over time. Most often, microbial populations started as highly heterogeneous, with heterogeneity decreasing by various degrees over time. The second, less frequently observed trend, saw microbial populations starting at low or very low heterogeneity, and remaining largely stable over time. We explain these trends as an interplay of metabolic history (e.g. former growth substrate or other nutrient limitations) and metabolic fitness (i.e. the fine-tuning of metabolic pathways to process a defined growth substrate). Our results offer a new viewpoint on the intra-population functional diversification often encountered in the environment, and suggests that some microbial populations may be intrinsically heterogeneous.
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Affiliation(s)
- Federica Calabrese
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Michael Schlömann
- Department of Environmental Microbiology, Institute of Biosciences, TU-Bergakademie Freiberg, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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20
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Phenotypic plasticity in plant defense across life stages: Inducibility, transgenerational induction, and transgenerational priming in wild radish. Proc Natl Acad Sci U S A 2021; 118:2005865118. [PMID: 34389664 PMCID: PMC8379918 DOI: 10.1073/pnas.2005865118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As they develop, many plants deploy shifts in antiherbivore defense allocation due to changing costs and benefits of their defensive traits. Plant defenses are known to be primed or directly induced by herbivore damage within generations and across generations by long-lasting epigenetic mechanisms. However, little is known about the differences between life stages of epigenetically inducible defensive traits across generations. To help fill this knowledge gap, we conducted a multigenerational experiment to determine whether defense induction in wild radish plants was reflected in chromatin modifications (DNA methylation); we then examined differences between seedlings and reproductive plants in current and transgenerational plasticity in chemical (glucosinolates) and physical (trichomes) defenses in this species. Herbivory triggered genome methylation both in targeted plants and their offspring. Within one generation, both defenses were highly inducible at the seedling stage, but only chemical defenses were inducible in reproductive plants. Across generations, herbivory experienced by mother plants caused strong direct induction of physical defenses in their progeny, with effects lasting from seedling to reproductive stages. For chemical defenses, however, this transgenerational induction was evident only in adults. Transgenerational priming was observed in physical and chemical defenses, particularly in adult plants. Our results show that transgenerational plasticity in plant defenses in response to herbivore offense differs for physical and chemical defense and changes across plant life stages.
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21
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McLeod DV, Wild G, Úbeda F. Epigenetic memories and the evolution of infectious diseases. Nat Commun 2021; 12:4273. [PMID: 34257309 PMCID: PMC8277771 DOI: 10.1038/s41467-021-24580-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Genes with identical DNA sequence may show differential expression because of epigenetic marks. Where epigenetic marks respond to past conditions, they represent a form of "memory". Despite their medical relevance, the impact of memories on the evolution of infectious diseases has rarely been considered. Here we explore the evolution of virulence in pathogens that carry memories of the sex of their previous host. We show that this form of memory provides information about the sex of present and future hosts when the sexes differ in their pathogen's transmission pattern. Memories of past hosts enable the evolution of greater virulence in infections originating from one sex and infections transmitted across sexes. Thus, our results account for patterns of virulence that have, to date, defied medical explanation. In particular, it has been observed that girls infected by boys (or boys infected by girls) are more likely to die from measles, chickenpox and polio than girls infected by girls (or boys infected by boys). We also evaluate epigenetic therapies that tamper with the memories of infecting pathogens. More broadly, our findings imply that pathogens can be selected to carry memories of past environments other than sex. This identifies new directions in personalised medicine.
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Affiliation(s)
- David V McLeod
- Centre D'Ecologie Fonctionnelle & Evolutive, CNRS, Montpellier, France
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Geoff Wild
- Department of Applied Mathematics, The University of Western Ontario, London, ON, Canada
| | - Francisco Úbeda
- Department of Biology, Royal Holloway University of London, Egham, Surrey, UK.
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22
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Eckmann JP, Tlusty T. Dimensional reduction in complex living systems: Where, why, and how. Bioessays 2021; 43:e2100062. [PMID: 34245050 DOI: 10.1002/bies.202100062] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/20/2022]
Abstract
The unprecedented prowess of measurement techniques provides a detailed, multi-scale look into the depths of living systems. Understanding these avalanches of high-dimensional data-by distilling underlying principles and mechanisms-necessitates dimensional reduction. We propose that living systems achieve exquisite dimensional reduction, originating from their capacity to learn, through evolution and phenotypic plasticity, the relevant aspects of a non-random, smooth physical reality. We explain how geometric insights by mathematicians allow one to identify these genuine hallmarks of life and distinguish them from universal properties of generic data sets. We illustrate these principles in a concrete example of protein evolution, suggesting a simple general recipe that can be applied to understand other biological systems.
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Affiliation(s)
- Jean-Pierre Eckmann
- Département de Physique Théorique and Section de Mathématiques, Université de Genève, Geneva 4, Switzerland
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.,Departments of Physics and Chemistry, UNIST, Ulsan, Republic of Korea
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23
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Sobral M. All Traits Are Functional: An Evolutionary Viewpoint. TRENDS IN PLANT SCIENCE 2021; 26:674-676. [PMID: 33994092 DOI: 10.1016/j.tplants.2021.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
There is increasing confusion regarding the term 'functional trait' and its links with ecosystem functioning. Functional traits are defined as traits that affect individual fitness. I use an evolutionary rationale that considers the integration of the phenotype, the environmental variation, and the relationship between both, to propose that all traits are functional.
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Affiliation(s)
- Mar Sobral
- Departamento de Bioloxía Funcional, Area de Ecoloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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24
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McGuigan K, Hoffmann AA, Sgrò CM. How is epigenetics predicted to contribute to climate change adaptation? What evidence do we need? Philos Trans R Soc Lond B Biol Sci 2021; 376:20200119. [PMID: 33866811 PMCID: PMC8059617 DOI: 10.1098/rstb.2020.0119] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
Transgenerational effects that are interpreted in terms of epigenetics have become an important research focus at a time when rapid environmental changes are occurring. These effects are usually interpreted as enhancing fitness extremely rapidly, without depending on the slower process of natural selection changing DNA-encoded (fixed) genetic variants in populations. Supporting evidence comes from a variety of sources, including environmental associations with epialleles, cross-generation responses of clonal material exposed to different environmental conditions, and altered patterns of methylation or frequency changes in epialleles across time. Transgenerational environmental effects have been postulated to be larger than those associated with DNA-encoded genetic changes, based on (for instance) stronger associations between epialleles and environmental conditions. Yet environmental associations for fixed genetic differences may always be weak under polygenic models where multiple combinations of alleles can lead to the same evolutionary outcome. The ultimate currency of adaptation is fitness, and few transgenerational studies have robustly determined fitness effects, particularly when compared to fixed genetic variants. Not all transgenerational modifications triggered by climate change will increase fitness: stressful conditions often trigger negative fitness effects across generations that can eliminate benefits. Epigenetic responses and other transgenerational effects will undoubtedly play a role in climate change adaptation, but further, well-designed, studies are required to test their importance relative to DNA-encoded changes. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Katrina McGuigan
- School of Biological Science, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Ary A. Hoffmann
- School of Biosciences and Bio21 Institute, The University of Melbourne, Melbourne 3010, Australia
| | - Carla M. Sgrò
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
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25
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Kuijper B, Johnstone RA. Evolution of epigenetic transmission when selection acts on fecundity versus viability. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200128. [PMID: 33866808 DOI: 10.1098/rstb.2020.0128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Existing theory on the evolution of parental effects and the inheritance of non-genetic factors has mostly focused on the role of environmental change. By contrast, how differences in population demography and life history affect parental effects is poorly understood. To fill this gap, we develop an analytical model to explore how parental effects evolve when selection acts on fecundity versus viability in spatio-temporally fluctuating environments. We find that regimes of viability selection, but not fecundity selection, are most likely to favour parental effects. In the case of viability selection, locally adapted phenotypes have a higher survival than maladapted phenotypes and hence become enriched in the local environment. Hence, simply by being alive, a parental phenotype becomes correlated to its environment (and hence informative to offspring) during its lifetime, favouring the evolution of parental effects. By contrast, in regimes of fecundity selection, correlations between phenotype and environment develop more slowly: this is because locally adapted and maladapted parents survive at equal rates (no survival selection), so that parental phenotypes, by themselves, are uninformative about the local environment. However, because locally adapted parents are more fecund, they contribute more offspring to the local patch than maladapted parents. In case these offspring are also likely to inherit the adapted parents' phenotypes (requiring pre-existing inheritance), locally adapted offspring become enriched in the local environment, resulting in a correlation between phenotype and environment, but only in the offspring's generation. Because of this slower build-up of a correlation between phenotype and environment essential to parental effects, fecundity selection is more sensitive to any distortions owing to environmental change than viability selection. Hence, we conclude that viability selection is most conducive to the evolution of parental effects. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Bram Kuijper
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, UK
| | - Rufus A Johnstone
- Behaviour and Evolution Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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26
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27
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Browning AP, Sharp JA, Mapder T, Baker CM, Burrage K, Simpson MJ. Persistence as an Optimal Hedging Strategy. Biophys J 2020; 120:133-142. [PMID: 33253635 DOI: 10.1016/j.bpj.2020.11.2260] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/07/2020] [Accepted: 11/05/2020] [Indexed: 02/02/2023] Open
Abstract
Bacteria invest in a slow-growing subpopulation, called persisters, to ensure survival in the face of uncertainty. This hedging strategy is remarkably similar to financial hedging, where diversifying an investment portfolio protects against economic uncertainty. We provide a new, to our knowledge, theoretical foundation for understanding cellular hedging by unifying the study of biological population dynamics and the mathematics of financial risk management through optimal control theory. Motivated by the widely accepted role of volatility in the emergence of persistence, we consider several models of environmental volatility described by continuous-time stochastic processes. This allows us to study an emergent cellular hedging strategy that maximizes the expected per capita growth rate of the population. Analytical and simulation results probe the optimal persister strategy, revealing results that are consistent with experimental observations and suggest new opportunities for experimental investigation and design. Overall, we provide a new, to our knowledge, way of conceptualizing and modeling cellular decision making in volatile environments by explicitly unifying theory from mathematical biology and finance.
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Affiliation(s)
- Alexander P Browning
- School of Mathematical Sciences, Queensland University of Technology, Queensland, Australia; ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Queensland, Australia.
| | - Jesse A Sharp
- School of Mathematical Sciences, Queensland University of Technology, Queensland, Australia; ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Queensland, Australia
| | - Tarunendu Mapder
- School of Mathematical Sciences, Queensland University of Technology, Queensland, Australia; ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Queensland, Australia; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Christopher M Baker
- School of Mathematical Sciences, Queensland University of Technology, Queensland, Australia; ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Queensland, Australia; School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Kevin Burrage
- School of Mathematical Sciences, Queensland University of Technology, Queensland, Australia; ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Queensland, Australia; Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Matthew J Simpson
- School of Mathematical Sciences, Queensland University of Technology, Queensland, Australia
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28
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Zhang J, Luo S, Gu Z, Deng Y, Jiao Y. Genome-wide DNA Methylation Analysis of Mantle Edge and Mantle Central from Pearl Oyster Pinctada fucata martensii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:380-390. [PMID: 32140888 DOI: 10.1007/s10126-020-09957-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
DNA methylation is a type of epigenetic modification that alters gene expression without changing the DNA sequence and mediates some cases of phenotypic plasticity. In this study, we identified six DNA methyltransferase (DNMT) genes and two methyl-CpG binding domain protein2 (MBD2) gene from Pinctada fucata martensii. We also analyzed the genome-wide DNA methylation levels of mantle edge (ME) and mantle central (MC) from P. f. martensii via methylated immunoprecipitation sequencing (MeDIP-Seq). Results revealed that both ME and MC had 122 million reads, and had 58,702 and 55,721 peaks, respectively. The obtained methylation patterns of gene elements and repeats showed that the methylation of the protein-coding genes, particularly intron and coding exons (CDSs), was more frequent than that of other genomic elements in the pearl oyster genome. We combined the methylation data with the RNA-seq data of the ME and MC of P. f. martensii and found that promoter, CDS, and intron methylation levels were positively correlated with gene expression levels except the highest gene expression level. We also identified 313 differential methylation genes (DMGs) and annotated 212 of them. These DMGs were significantly enriched in 30 pathways, such as amino acid and protein metabolism, energy metabolism, terpenoid synthesis, and immune-related pathways. This study comprehensively analyzed the methylomes of biomineralization-related tissues and helped enhance our understanding of the regulatory mechanism underlying shell formation.
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Affiliation(s)
- Jiabin Zhang
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Shaojie Luo
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zefeng Gu
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yuewen Deng
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China
- Pearl Breeding and Processing Engineering Technology Research Center of Guangdong Province, Zhanjiang, 524088, China
| | - Yu Jiao
- Fisheries College of Guangdong Ocean University, Zhanjiang, 524088, China.
- Pearl Breeding and Processing Engineering Technology Research Center of Guangdong Province, Zhanjiang, 524088, China.
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29
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Suriyampola PS, Lopez M, Ellsworth BE, Martins EP. Reversibility of Multimodal Shift: Zebrafish Shift to Olfactory Cues When the Visual Environment Changes. Integr Comp Biol 2020; 60:33-42. [DOI: 10.1093/icb/icaa036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Synopsis
Animals can shift their reliance on different sensory modalities in response to environmental conditions, and knowing the degree to which traits are reversible may help us to predict their chances of survival in a changing environment. Here, using adult zebrafish (Danio rerio), we found that 6 weeks in different light environments alone were sufficient to shift whether fish approached visual or chemical cues first, and that a subsequent reversal of lighting conditions also reversed their sensory preferences. In addition, we measured simple behavioral responses to sensory stimuli presented alone, and found that zebrafish housed in dim light for 6 weeks responded weakly to an optomotor assay, but strongly to an olfactory cue, whereas fish experiencing bright light for 6 weeks responded strongly to the visual optomotor stimulus and weakly in an olfactory assay. Visual and olfactory responses were equally reversible, and shifted to the opposite pattern when we reversed lighting conditions for 6 weeks. In contrast, we did not find a change in activity level, suggesting that changes in multiple sensory modalities can buffer animals from changes in more complex forms of behavior. This reversal of sensory response provides insight into how animals may use sensory shifts to keep up with environmental change.
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Affiliation(s)
| | - Melissa Lopez
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | | | - Emília P Martins
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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30
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Paul SC, Putra R, Müller C. Early life starvation has stronger intra-generational than transgenerational effects on key life-history traits and consumption measures in a sawfly. PLoS One 2019; 14:e0226519. [PMID: 31856200 PMCID: PMC6922382 DOI: 10.1371/journal.pone.0226519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/26/2019] [Indexed: 11/19/2022] Open
Abstract
Resource availability during development shapes not only adult phenotype but also the phenotype of subsequent offspring. When resources are absent and periods of starvation occur in early life, such developmental stress often influences key life-history traits in a way that benefits individuals and their offspring when facing further bouts of starvation. Here we investigated the impacts of different starvation regimes during larval development on life-history traits and measures of consumption in the turnip sawfly, Athalia rosae (Hymenoptera: Tenthredinidae). We then assessed whether offspring of starved and non-starved parents differed in their own life-history if reared in conditions that either matched that of their parents or were a mismatch. Early life starvation effects were more pronounced within than across generations in A. rosae, with negative impacts on adult body mass and increases in developmental time, but no effects on adult longevity in either generation. We found some evidence of higher growth rates in larvae having experienced starvation, although this did not ameliorate the overall negative effect of larval starvation on adult size. However, further work is necessary to disentangle the effects of larval size and instar from those of starvation treatment. Finally, we found weak evidence for transgenerational effects on larval growth, with intra-generational larval starvation experience being more decisive for life-history traits. Our study demonstrates that intra-generational effects of starvation are stronger than transgenerational effects on life-history traits and consumption measures in A. rosae.
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Affiliation(s)
| | - Rocky Putra
- Chemical Ecology, Bielefeld University, Bielefeld, Germany
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Caroline Müller
- Chemical Ecology, Bielefeld University, Bielefeld, Germany
- * E-mail:
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31
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Nichol D, Robertson-Tessi M, Anderson ARA, Jeavons P. Model genotype-phenotype mappings and the algorithmic structure of evolution. J R Soc Interface 2019; 16:20190332. [PMID: 31690233 PMCID: PMC6893500 DOI: 10.1098/rsif.2019.0332] [Citation(s) in RCA: 20] [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] [Received: 05/13/2019] [Accepted: 10/04/2019] [Indexed: 12/13/2022] Open
Abstract
Cancers are complex dynamic systems that undergo evolution and selection. Personalized medicine approaches in the clinic increasingly rely on predictions of tumour response to one or more therapies; these predictions are complicated by the inevitable evolution of the tumour. Despite enormous amounts of data on the mutational status of cancers and numerous therapies developed in recent decades to target these mutations, many of these treatments fail after a time due to the development of resistance in the tumour. The emergence of these resistant phenotypes is not easily predicted from genomic data, since the relationship between genotypes and phenotypes, termed the genotype-phenotype (GP) mapping, is neither injective nor functional. We present a review of models of this mapping within a generalized evolutionary framework that takes into account the relation between genotype, phenotype, environment and fitness. Different modelling approaches are described and compared, and many evolutionary results are shown to be conserved across studies despite using different underlying model systems. In addition, several areas for future work that remain understudied are identified, including plasticity and bet-hedging. The GP-mapping provides a pathway for understanding the potential routes of evolution taken by cancers, which will be necessary knowledge for improving personalized therapies.
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Affiliation(s)
- Daniel Nichol
- Department of Computer Science, University of Oxford, Oxford, UK
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alexander R. A. Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Peter Jeavons
- Department of Computer Science, University of Oxford, Oxford, UK
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32
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Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. Mol Cell 2019; 77:266-278.e6. [PMID: 31757756 DOI: 10.1016/j.molcel.2019.10.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/29/2019] [Accepted: 10/17/2019] [Indexed: 02/08/2023]
Abstract
Theory and experiments suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors, but the mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.
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Donelan SC, Hellmann JK, Bell AM, Luttbeg B, Orrock JL, Sheriff MJ, Sih A. Transgenerational Plasticity in Human-Altered Environments. Trends Ecol Evol 2019; 35:115-124. [PMID: 31706627 DOI: 10.1016/j.tree.2019.09.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/06/2019] [Accepted: 09/11/2019] [Indexed: 01/04/2023]
Abstract
Our ability to predict how species will respond to human-induced rapid environmental change (HIREC) may depend upon our understanding of transgenerational plasticity (TGP), which occurs when environments experienced by previous generations influence phenotypes of subsequent generations. TGP evolved to help organisms cope with environmental stressors when parental environments are highly predictive of offspring environments. HIREC can alter conditions that favored TGP in historical environments by reducing parents' ability to detect environmental conditions, disrupting previous correlations between parental and offspring environments, and interfering with the transmission of parental cues to offspring. Because of the propensity to produce errors in these processes, TGP will likely generate negative fitness outcomes in response to HIREC, though beneficial fitness outcomes may occur in some cases.
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Affiliation(s)
- Sarah C Donelan
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD 21037, USA
| | - Jennifer K Hellmann
- Department of Evolution, Ecology and Behavior, Carl R. Woese Institute for Genomic Biology, Program in Neuroscience, Program in Ecology, Evolution and Conservation, University of Illinois, Urbana Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, USA.
| | - Alison M Bell
- Department of Evolution, Ecology and Behavior, Carl R. Woese Institute for Genomic Biology, Program in Neuroscience, Program in Ecology, Evolution and Conservation, University of Illinois, Urbana Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Barney Luttbeg
- Department of Integrative Biology, 501 Life Sciences West, Oklahoma State University, Stillwater, OK 74078, USA
| | - John L Orrock
- Department of Integrative Biology, 145 Noland Hall, 250 North Mills Street, University of Wisconsin, Madison, WI 53706, USA
| | - Michael J Sheriff
- Biology Department, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Andrew Sih
- Department of Environmental Science and Policy, University of California, One Shields Avenue, Davis, CA 95616, USA
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34
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Gómez-Schiavon M, Buchler NE. Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise. PLoS Comput Biol 2019; 15:e1007364. [PMID: 31658246 PMCID: PMC6837633 DOI: 10.1371/journal.pcbi.1007364] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 11/07/2019] [Accepted: 08/30/2019] [Indexed: 11/30/2022] Open
Abstract
Epigenetic switches are bistable, molecular systems built from self-reinforcing feedback loops that can spontaneously switch between heritable phenotypes in the absence of DNA mutation. It has been hypothesized that epigenetic switches first evolved as a mechanism of bet-hedging and adaptation, but the evolutionary trajectories and conditions by which an epigenetic switch can outcompete adaptation through genetic mutation remain unknown. Here, we used computer simulations to evolve a mechanistic, biophysical model of a self-activating genetic circuit, which can both adapt genetically through mutation and exhibit epigenetic switching. We evolved these genetic circuits under a fluctuating environment that alternatively selected for low and high protein expression levels. In all tested conditions, the population first evolved by genetic mutation towards a region of genotypes where genetic adaptation can occur faster after each environmental transition. Once in this region, the self-activating genetic circuit can exhibit epigenetic switching, which starts competing with genetic adaptation. We show a trade-off between either minimizing the adaptation time or increasing the robustness of the phenotype to biochemical noise. Epigenetic switching was superior in a fast fluctuating environment because it adapted faster than genetic mutation after an environmental transition, while still attenuating the effect of biochemical noise on the phenotype. Conversely, genetic adaptation was favored in a slowly fluctuating environment because it maximized the phenotypic robustness to biochemical noise during the constant environment between transitions, even if this resulted in slower adaptation. This simple trade-off predicts the conditions and trajectories under which an epigenetic switch evolved to outcompete genetic adaptation, shedding light on possible mechanisms by which bet-hedging strategies might emerge and persist in natural populations. Epigenetic switches regulate cell fate decisions during development in multicellular organisms, but their origin predates multicellularity because they are found in viruses, bacteria, and unicellular eukaryotes. It has been suggested that epigenetic switches first evolved as a mechanism of bet-hedging and adaptation to fluctuating environments. To discern the evolutionary pressures that select for epigenetic switches, we used computer simulations to evolve a mechanistic, biophysical model of a self-activating genetic circuit, which can both adapt genetically and exhibit epigenetic switching. Unlike laboratory evolution experiments, this in silico experiment was run many times over a range of evolutionary parameters (population size, selection pressure, mutation step-size, fluctuation frequency) and different model assumptions to uncover statistical regularities in the evolutionary trajectories. Using this computational approach, we could elucidate simple principles that predict the conditions that favor adaptation by epigenetic switching over genetic mutation in a fluctuating environment.
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Affiliation(s)
- Mariana Gómez-Schiavon
- Program in Computational Biology & Bioinformatics, Duke University, Durham, North Carolina, United States of America
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Nicolas E. Buchler
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Department of Physics, Duke University, Durham, North Carolina, United States of America
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35
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Epigenetic patterns associated with an ascidian invasion: a comparison of closely related clades in their native and introduced ranges. Sci Rep 2019; 9:14275. [PMID: 31582771 PMCID: PMC6776620 DOI: 10.1038/s41598-019-49813-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 08/29/2019] [Indexed: 12/12/2022] Open
Abstract
Environmentally induced epigenetic modifications have been proposed as one mechanism underlying rapid adaptive evolution of invasive species. Didemnum vexillum is an invasive colonial ascidian that has established in many coastal waters worldwide. Phylogenetic analyses have revealed that D. vexillum populations consist of two distinct clades; clade B appears to be restricted to the native range (Japan), whereas clade A is found in many regions throughout the world, including New Zealand. The spread of D. vexillum clade A suggests that it might be intrinsically more invasive than clade B, despite low levels of genetic diversity compared to populations from the native region. This study investigated whether D. vexillum clade A exhibits epigenetic signatures (specifically differences in DNA methylation) associated with invasiveness. Global DNA methylation patterns were significantly different between introduced clade A colonies, and both clades A and B in the native range. Introduced colonies also showed a significant reduction in DNA methylation levels, which could be a mechanism for increasing phenotypic plasticity. High levels of DNA methylation diversity were maintained in the introduced population, despite reduced levels of genetic diversity, which may allow invasive populations to respond quickly to changes in new environments. Epigenetic changes induced during the invasion process could provide a means for rapid adaptation despite low levels of genetic variation in introduced populations.
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36
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Simpson KJ, Olofsson JK, Ripley BS, Osborne CP. Frequent fires prime plant developmental responses to burning. Proc Biol Sci 2019; 286:20191315. [PMID: 31431130 DOI: 10.1098/rspb.2019.1315] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Coping with temporal variation in fire requires plants to have plasticity in traits that promote persistence, but how plastic responses to current conditions are affected by past fire exposure remains unknown. We investigate phenotypic divergence between populations of four resprouting grasses exposed to differing experimental fire regimes (annually burnt or unburnt for greater than 35 years) and test whether divergence persists after plants are grown in a common environment for 1 year. Traits relating to flowering and biomass allocation were measured before plants were experimentally burnt, and their regrowth was tracked. Genetic differentiation between populations was investigated for a subset of individuals. Historic fire frequency influenced traits relating to flowering and below-ground investment. Previously burnt plants produced more inflorescences and invested proportionally more biomass below ground, suggesting a greater capacity for recruitment and resprouting than unburnt individuals. Tiller-scale regrowth rate did not differ between treatments, but prior fire exposure enhanced total regrown biomass in two species. We found no consistent genetic differences between populations suggesting trait differences arose from developmental plasticity. Grass development is influenced by prior fire exposure, independent of current environmental conditions. This priming response to fire, resulting in adaptive trait changes, may produce communities more resistant to future fire regime changes.
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Affiliation(s)
- Kimberley J Simpson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Brad S Ripley
- Department of Botany, Rhodes University, PO Box 94, Grahamstown 6140, South Africa
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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37
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Yin J, Zhou M, Lin Z, Li QQ, Zhang YY. Transgenerational effects benefit offspring across diverse environments: a meta-analysis in plants and animals. Ecol Lett 2019; 22:1976-1986. [PMID: 31436014 DOI: 10.1111/ele.13373] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/10/2019] [Accepted: 07/25/2019] [Indexed: 12/15/2022]
Abstract
The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical evidence remains equivocal. Here, we conducted a meta-analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life-history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer-lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life-history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta-analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.
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Affiliation(s)
- Junjie Yin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Ming Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zeru Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
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38
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Kordes A, Grahl N, Koska M, Preusse M, Arce-Rodriguez A, Abraham WR, Kaever V, Häussler S. Establishment of an induced memory response in Pseudomonas aeruginosa during infection of a eukaryotic host. THE ISME JOURNAL 2019; 13:2018-2030. [PMID: 30952997 PMCID: PMC6775985 DOI: 10.1038/s41396-019-0412-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 12/28/2022]
Abstract
In a given habitat, bacterial cells often experience recurrent exposures to the same environmental stimulus. The ability to memorize the past event and to adjust current behaviors can lead to efficient adaptation to the recurring stimulus. Here we demonstrate that the versatile bacterium Pseudomonas aeruginosa adopts a virulence phenotype after serial passage in the invertebrate model host Galleria mellonella. The virulence phenotype was not linked to the acquisition of genetic variations and was sustained for several generations, despite cultivation of the ex vivo virulence-adapted P. aeruginosa cells under rich medium conditions in vitro. Transcriptional reprogramming seemed to be induced by a host-specific food source, as reprogramming was also observed upon cultivation of P. aeruginosa in rich medium supplemented with polyunsaturated long-chain fatty acids. The establishment of induced memory responses adds a time dimension and seems to fill the gap between long-term evolutionary genotypic adaptation and short-term induced individual responses. Efforts to unravel the fundamental mechanisms that underlie the carry-over effect to induce such memory responses will continue to be of importance as hysteretic behavior can serve survival of bacterial populations in changing and challenging habitats.
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Affiliation(s)
- Adrian Kordes
- Department of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
| | - Nora Grahl
- Department of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
| | - Michal Koska
- Department of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Alejandro Arce-Rodriguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Wolf-Rainer Abraham
- Department of Chemical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, 30625, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, 30625, Germany.
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany.
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Bell AM, Hellmann JK. An Integrative Framework for Understanding the Mechanisms and Multigenerational Consequences of Transgenerational Plasticity. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2019; 50:97-118. [PMID: 36046014 PMCID: PMC9427003 DOI: 10.1146/annurev-ecolsys-110218-024613] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Transgenerational plasticity (TGP) occurs when the environment experienced by a parent influences the development of their offspring. In this article, we develop a framework for understanding the mechanisms and multi-generational consequences of TGP. First, we conceptualize the mechanisms of TGP in the context of communication between parents (senders) and offspring (receivers) by dissecting the steps between an environmental cue received by a parent and its resulting effects on the phenotype of one or more future generations. Breaking down the problem in this way highlights the diversity of mechanisms likely to be involved in the process. Second, we review the literature on multigenerational effects and find that the documented patterns across generations are diverse. We categorize different multigenerational patterns and explore the proximate and ultimate mechanisms that can generate them. Throughout, we highlight opportunities for future work in this dynamic and integrative area of study.
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Affiliation(s)
- Alison M Bell
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Program in Neuroscience and Program in Ecology, Evolution and Conservation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jennifer K Hellmann
- Department of Evolution, Ecology and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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40
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Oborny B. The plant body as a network of semi-autonomous agents: a review. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180371. [PMID: 31006361 PMCID: PMC6553591 DOI: 10.1098/rstb.2018.0371] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2018] [Indexed: 01/31/2023] Open
Abstract
Plants can solve amazingly difficult tasks while adjusting their growth and development to the environment. They can explore and exploit several resources simultaneously, even when the distributions of these vary in space and time. The systematic study of plant behaviour goes back to Darwin's book The power of movement in plants. Current research has highlighted that modularity is a key to understanding plant behaviour, as the production, functional specialization and death of modules enable the plant to adjust its movement to the environment. The adjustment is assisted by a flow of information and resources among the modules. Experiments have yielded many results about these processes in various plant species. Theoretical research, however, has lagged behind the empirical studies, possibly owing to the lack of a proper modelling framework that could encompass the high number of components and interactions. In this paper, I propose such a framework on the basis of network theory, viewing the plant as a group of connected, semi-autonomous agents. I review some characteristic plant responses to the environment through changing the states of agents and/or links. I also point out some unexplored areas, in which a dialogue between plant science and network theory could be mutually inspiring. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.
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Affiliation(s)
- Beata Oborny
- Institute of Biology, Loránd Eötvös University, Budapest, Hungary
- GINOP Sustainable Ecosystems Group, Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary
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41
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Gluckman PD, Hanson MA, Low FM. Evolutionary and developmental mismatches are consequences of adaptive developmental plasticity in humans and have implications for later disease risk. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180109. [PMID: 30966891 PMCID: PMC6460082 DOI: 10.1098/rstb.2018.0109] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2018] [Indexed: 01/29/2023] Open
Abstract
A discrepancy between the phenotype of an individual and that which would confer optimal responses in terms of fitness in an environment is termed 'mismatch'. Phenotype results from developmental plasticity, conditioned partly by evolutionary history of the species and partly by aspects of the developmental environment. We discuss two categories of such mismatch with reference primarily to nutrition and in the context of evolutionary medicine. The categories operate over very different timescales. A developmental mismatch occurs when the phenotype induced during development encounters a different environment post-development. This may be the result of wider environmental changes, such as nutritional transition between generations, or because maternal malnutrition or placental dysfunction give inaccurate information about the organism's likely future environment. An evolutionary mismatch occurs when there is an evolutionarily novel environment. Developmental plasticity may involve immediate adaptive responses (IARs) to preserve survival if an environmental challenge is severe, and/or predictive adaptive responses (PARs) if the challenge does not threaten survival, but there is a fitness advantage in developing a phenotype that will be better adapted later. PARs can have long-term adverse health consequences if there is a developmental mismatch. For contemporary humans, maternal constraint of fetal growth makes PARs likely even if there is no obvious IAR, and this, coupled with the pervasive nutritionally dense modern environment, can explain the widespread observations of developmental mismatch, particularly in populations undergoing nutritional transition. Both developmental and evolutionary mismatch have important public health consequences and implications for where policy interventions may be most effective. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
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Affiliation(s)
- Peter D. Gluckman
- Liggins Institute, University of Auckland, New Zealand
- Singapore Institute for Clinical Sciences, Singapore
| | - Mark A. Hanson
- Institute of Developmental Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Danchin É, Pocheville A, Huneman P. Early in life effects and heredity: reconciling neo-Darwinism with neo-Lamarckism under the banner of the inclusive evolutionary synthesis. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180113. [PMID: 30966884 PMCID: PMC6460090 DOI: 10.1098/rstb.2018.0113] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2018] [Indexed: 12/22/2022] Open
Abstract
Recent discoveries show that early in life effects often have long-lasting influences, sometimes even spanning several generations. Such intergenerational effects of early life events appear not easily reconcilable with strict genetic inheritance. However, an integrative evolutionary medicine of early life effects needs a sound view of inheritance in development and evolution. Here, we show how to articulate the gene-centred and non-gene-centred visions of inheritance. We first recall the coexistence of two gene concepts in scientific discussions, a statistical one (focused on patterns of parent-offspring resemblance, and implicitly including non-DNA-sequence-based resemblance), and a molecular one (based on the DNA sequence). We then show how all the different mechanisms of inheritance recently discovered can be integrated into an inclusive theory of evolution where different mechanisms would enable adaptation to changing environments at different timescales. One surprising consequence of this integrative vision of inheritance is that early in life effects start much earlier than fertilization. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
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Affiliation(s)
- Étienne Danchin
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Arnaud Pocheville
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
- Department of Philosophy and Charles Perkins Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Philippe Huneman
- Institut d'Histoire et de Philosophie des Sciences et des Techniques, CNRS/Université Paris I Panthéon-Sorbonne, Paris, France
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Crocker KC, Hunter MD. Social density, but not sex ratio, drives ecdysteroid hormone provisioning to eggs by female house crickets ( Acheta domesticus). Ecol Evol 2018; 8:10257-10265. [PMID: 30397463 PMCID: PMC6206184 DOI: 10.1002/ece3.4502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 11/08/2022] Open
Abstract
Social environment profoundly influences the fitness of animals, affecting their probability of survival to adulthood, longevity, and reproductive output. The social conditions experienced by parents at the time of reproduction can predict the social environments that offspring will face. Despite clear challenges in predicting future environmental conditions, adaptive maternal effects provide a mechanism of passing environmental information from parent to offspring and are now considered pervasive in natural systems. Maternal effects have been widely studied in vertebrates, especially in the context of social environment, and are often mediated by steroid hormone (SH) deposition to eggs. In insects, although many species dramatically alter phenotype and life-history traits in response to social density, the mechanisms of these alterations, and the role of hormone deposition by insect mothers into their eggs, remains unknown. In the experiments described here, we assess the effects of social environment on maternal hormone deposition to eggs in house crickets (Acheta domesticus). Specifically, we tested the hypotheses that variable deposition of ecdysteroid hormones (ESH) to eggs is affected by both maternal (a) social density and (b) social composition. We found that while maternal hormone deposition to eggs does not respond to social composition (sex ratio), it does reflect social density; females provision their eggs with higher ESH doses under low-density conditions. This finding is consistent with the interpretation that variable ESH provisioning is an adaptive maternal response to social environment and congruent with similar patterns of variable maternal provisioning across the tree of life. Moreover, our results confirm that maternal hormone provisioning may mediate delayed density dependence by introducing a time lag in the response of offspring phenotype to population size.
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Affiliation(s)
- Katherine C Crocker
- Department of Environmental Health Sciences Mailman School of Public Health at Columbia University New York New York
| | - Mark D Hunter
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan
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Kristensen TN, Ketola T, Kronholm I. Adaptation to environmental stress at different timescales. Ann N Y Acad Sci 2018; 1476:5-22. [PMID: 30259990 DOI: 10.1111/nyas.13974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 08/24/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Environments are changing rapidly, and to cope with these changes, organisms have to adapt. Adaptation can take many shapes and occur at different speeds, depending on the type of response, the trait, the population, and the environmental conditions. The biodiversity crisis that we are currently facing illustrates that numerous species and populations are not capable of adapting with sufficient speed to ongoing environmental changes. Here, we discuss current knowledge on the ability of animals and plants to adapt to environmental stress on different timescales, mainly focusing on thermal stress and ectotherms. We discuss within-generation responses that can be fast and induced within minutes or hours, evolutionary adaptations that are often slow and take several generations, and mechanisms that lay somewhere in between and that include epigenetic transgenerational effects. To understand and predict the impacts of environmental change and stress on biodiversity, we suggest that future studies should (1) have an increased focus on understanding the type and speed of responses to fast environmental changes; (2) focus on the importance of environmental fluctuations and the predictability of environmental conditions on adaptive capabilities, preferably in field studies encompassing several fitness components; and (3) look at ecosystem responses to environmental stress and their resilience when disturbed.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Bioscience, University of Aarhus, Aarhus, Denmark
| | - Tarmo Ketola
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ilkka Kronholm
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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Danchin E, Pocheville A, Rey O, Pujol B, Blanchet S. Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis. Biol Rev Camb Philos Soc 2018. [PMCID: PMC6378602 DOI: 10.1111/brv.12453] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
After decades of debate about the existence of non‐genetic inheritance, the focus is now slowly shifting towards dissecting its underlying mechanisms. Here, we propose a new mechanism that, by integrating non‐genetic and genetic inheritance, may help build the long‐sought inclusive vision of evolution. After briefly reviewing the wealth of evidence documenting the existence and ubiquity of non‐genetic inheritance in a table, we review the categories of mechanisms of parent–offspring resemblance that underlie inheritance. We then review several lines of argument for the existence of interactions between non‐genetic and genetic components of inheritance, leading to a discussion of the contrasting timescales of action of non‐genetic and genetic inheritance. This raises the question of how the fidelity of the inheritance system can match the rate of environmental variation. This question is central to understanding the role of different inheritance systems in evolution. We then review and interpret evidence indicating the existence of shifts from inheritance systems with low to higher transmission fidelity. Based on results from different research fields we propose a conceptual hypothesis linking genetic and non‐genetic inheritance systems. According to this hypothesis, over the course of generations, shifts among information systems allow gradual matching between the rate of environmental change and the inheritance fidelity of the corresponding response. A striking conclusion from our review is that documented shifts between types of inherited non‐genetic information converge towards epigenetics (i.e. inclusively heritable molecular variation in gene expression without change in DNA sequence). We then interpret the well‐documented mutagenicity of epigenetic marks as potentially generating a final shift from epigenetic to genetic encoding. This sequence of shifts suggests the existence of a relay in inheritance systems from relatively labile ones to gradually more persistent modes of inheritance, a relay that could constitute a new mechanistic basis for the long‐proposed, but still poorly documented, hypothesis of genetic assimilation. A profound difference between the genocentric and the inclusive vision of heredity revealed by the genetic assimilation relay proposed here lies in the fact that a given form of inheritance can affect the rate of change of other inheritance systems. To explore the consequences of such inter‐connection among inheritance systems, we briefly review published theoretical models to build a model of genetic assimilation focusing on the shift in the engraving of environmentally induced phenotypic variation into the DNA sequence. According to this hypothesis, when environmental change remains stable over a sufficient number of generations, the relay among inheritance systems has the potential to generate a form of genetic assimilation. In this hypothesis, epigenetics appears as a hub by which non‐genetically inherited environmentally induced variation in traits can become genetically encoded over generations, in a form of epigenetically facilitated mutational assimilation. Finally, we illustrate some of the major implications of our hypothetical framework, concerning mutation randomness, the central dogma of molecular biology, concepts of inheritance and the curing of inherited disorders, as well as for the emergence of the inclusive evolutionary synthesis.
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Affiliation(s)
- Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
| | - Arnaud Pocheville
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
- Department of Philosophy and Charles Perkins Centre; University of Sydney; Sydney NSW 2006 Australia
| | - Olivier Rey
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321; 09200 Moulis France
- Université de Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Université de Montpellier; F-66860 Perpignan France
| | - Benoit Pujol
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
| | - Simon Blanchet
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174); Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1; 31062 Toulouse Cedex 9 France
- CNRS, Station d'Ecologie Théorique et Expérimentale (SETE), UMR5321; 09200 Moulis France
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Le Gac AL, Lafon-Placette C, Chauveau D, Segura V, Delaunay A, Fichot R, Marron N, Le Jan I, Berthelot A, Bodineau G, Bastien JC, Brignolas F, Maury S. Winter-dormant shoot apical meristem in poplar trees shows environmental epigenetic memory. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4821-4837. [PMID: 30107545 PMCID: PMC6137975 DOI: 10.1093/jxb/ery271] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/02/2018] [Indexed: 05/04/2023]
Abstract
Trees have a long lifespan and must continually adapt to environmental pressures, notably in the context of climate change. Epigenetic mechanisms are doubtless involved in phenotypic plasticity and in stress memory; however, little evidence of the role of epigenetic processes is available for trees growing in fields. Here, we analyzed the possible involvement of epigenetic mechanisms in the winter-dormant shoot apical meristem of Populus × euramericana clones in memory of the growing conditions faced during the vegetative period. We aimed to estimate the range of genetic and environmentally induced variations in global DNA methylation and to evaluate their correlation with changes in biomass production, identify differentially methylated regions (DMRs), and characterize common DMRs between experiments. We showed that the variations in global DNA methylation between conditions were genotype dependent and correlated with biomass production capacity. Microarray chip analysis allowed detection of DMRs 6 months after the stressful summer period. The 161 DMRs identified as common to three independent experiments most notably targeted abiotic stress and developmental response genes. Results are consistent with a winter-dormant shoot apical meristem epigenetic memory of stressful environmental conditions that occurred during the preceding summer period. This memory may facilitate tree acclimation.
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Affiliation(s)
| | | | | | | | | | - Régis Fichot
- LBLGC, INRA, Université d’Orléans, Orléans, France
| | - Nicolas Marron
- Silva, INRA Grand Est, Nancy, AgroParisTech, Université de Lorraine, UMR, Nancy, France
| | | | - Alain Berthelot
- FCBA Délégation Territoriale Nord-Est, Charrey-Sur-Saône, France
| | | | | | | | - Stéphane Maury
- LBLGC, INRA, Université d’Orléans, Orléans, France
- Correspondence:
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Crocker KC, Hunter MD. Environmental causes and transgenerational consequences of ecdysteroid hormone provisioning in Acheta domesticus. JOURNAL OF INSECT PHYSIOLOGY 2018; 109:69-78. [PMID: 29890170 DOI: 10.1016/j.jinsphys.2018.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
An animal's phenotype may be shaped by its genes, but also reflects its own environment and often that of its parents. Nongenetic parental effects are often mediated by steroid hormones, and operate between parents and offspring through mechanisms that are well described in vertebrate and model systems. However, less is understood about the strength and frequency of hormone mediated nongenetic parental effects across more than one generation of descendants, and in nonmodel systems. Here we show that the concentration of active ecdysteroid hormones provided by a female house cricket (Acheta domesticus) affects the growth rate of her offspring. We also reveal that variation in the active ecdysteroid hormones provided by a female house cricket to her eggs derives primarily from the quality of nutrition available to her maternal grandmother, regardless of genetic background. This finding is in stark contrast to most previous work that documents a decline in the strength of environmentally based parental effects with each passing generation. Strong grandparental effects may be adaptive under predictable, cyclical changes in the environment. Our results also suggest that hormone-mediated grand-maternal effects represent an important potential mechanism by which organisms can respond to environmental variability, and that further study of hormone-mediated carryover effects in this context could be profitable.
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Affiliation(s)
- Katherine C Crocker
- 1105 North University Ave, Kraus Natural Sciences Building, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1085, USA.
| | - Mark D Hunter
- 1105 North University Ave, Kraus Natural Sciences Building, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1085, USA
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48
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Marzen SE, Crutchfield JP. Optimized bacteria are environmental prediction engines. Phys Rev E 2018; 98:012408. [PMID: 30110764 DOI: 10.1103/physreve.98.012408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Indexed: 06/08/2023]
Abstract
Experimentalists observe phenotypic variability even in isogenic bacteria populations. We explore the hypothesis that in fluctuating environments this variability is tuned to maximize a bacterium's expected log-growth rate, potentially aided by epigenetic (all inheritable nongenetic) markers that store information about past environments. Crucially, we assume a time delay between sensing and action, so that a past epigenetic marker is used to generate the present phenotypic variability. We show that, in a complex, memoryful environment, the maximal expected log-growth rate is linear in the instantaneous predictive information-the mutual information between a bacterium's epigenetic markers and future environmental states. Hence, under resource constraints, optimal epigenetic markers are causal states-the minimal sufficient statistics for prediction-or lossy approximations thereof. We propose new theoretical investigations into and new experiments on bacteria phenotypic bet-hedging in fluctuating complex environments.
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Affiliation(s)
- Sarah E Marzen
- Department of Physics, Physics of Living Systems Group, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - James P Crutchfield
- Complexity Sciences Center and Department of Physics, University of California at Davis, Davis, California 95616, USA
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Frankenhuis WE, Nettle D, McNamara JM. Echoes of Early Life: Recent Insights From Mathematical Modeling. Child Dev 2018; 89:1504-1518. [PMID: 29947096 PMCID: PMC6175464 DOI: 10.1111/cdev.13108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the last decades, developmental origins of health and disease (DOHaD) has emerged as a central framework for studying early‐life effects, that is, the impact of fetal and early postnatal experience on adult functioning. Apace with empirical progress, theoreticians have built mathematical models that provide novel insights for DOHaD. This article focuses on three of these insights, which show the power of environmental noise (i.e., imperfect indicators of current and future conditions) in shaping development. Such noise can produce: (a) detrimental outcomes even in ontogenetically stable environments, (b) individual differences in sensitive periods, and (c) early‐life effects tailored to predicted future somatic states. We argue that these insights extend DOHaD and offer new research directions.
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50
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Hawes NA, Fidler AE, Tremblay LA, Pochon X, Dunphy BJ, Smith KF. Understanding the role of DNA methylation in successful biological invasions: a review. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1703-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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