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Miryeganeh M, Armitage DW. Epigenetic responses of trees to environmental stress in the context of climate change. Biol Rev Camb Philos Soc 2024. [PMID: 39192567 DOI: 10.1111/brv.13132] [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: 11/14/2023] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
In long-lived tree populations, when environmental change outpaces rates of evolutionary adaptation, plasticity in traits related to stress tolerance, dormancy, and dispersal may be vital for preventing extinction. While a population's genetic background partly determines its ability to adapt to a changing environment, so too do the many types of epigenetic modifications that occur within and among populations, which vary on timescales orders of magnitude faster than the emergence of new beneficial alleles. Consequently, phenotypic plasticity driven by epigenetic modification may be especially critical for sessile, long-lived organisms such as trees that must rely on this plasticity to keep pace with rapid anthropogenic environmental change. While studies have reported large effects of DNA methylation, histone modification, and non-coding RNAs on the expression of stress-tolerance genes and resulting phenotypic responses, little is known about the role of these effects in non-model plants and particularly in trees. Here, we review new findings in plant epigenetics with particular relevance to the ability of trees to adapt to or escape stressors associated with rapid climate change. Such findings include specific epigenetic influences over drought, heat, and salinity tolerance, as well as dormancy and dispersal traits. We also highlight promising findings concerning transgenerational inheritance of an epigenetic 'stress memory' in plants. As epigenetic information is becoming increasingly easy to obtain, we close by outlining ways in which ecologists can use epigenetic information better to inform population management and forecasting efforts. Understanding the molecular mechanisms behind phenotypic plasticity and stress memory in tree species offers a promising path towards a mechanistic understanding of trees' responses to climate change.
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Affiliation(s)
- Matin Miryeganeh
- Integrative Community Ecology Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
| | - David W Armitage
- Integrative Community Ecology Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan
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2
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de Carvalho CF, Slate J, Villoutreix R, Soria-Carrasco V, Riesch R, Feder JL, Gompert Z, Nosil P. DNA methylation differences between stick insect ecotypes. Mol Ecol 2023; 32:6809-6823. [PMID: 37864542 DOI: 10.1111/mec.17165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 10/23/2023]
Abstract
Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. Beginning to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e. ecotypes). By integrating results from sequencing of whole transcriptomes, genomes and methylomes, we investigate whether environmental, host and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in the CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, with methylation being enriched in gene bodies and impoverished in repetitive elements. Genome-wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host-plant effects. Using methylome-environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation and genetic relatedness, and with the ecologically important variable of host plant, suggests a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test whether methylation can be transmitted across generations and the extent to which it responds to experimental manipulation in field and laboratory studies.
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Affiliation(s)
| | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
| | | | | | - Rüdiger Riesch
- University of Montpellier, CEFE, CNRS, EPHE, IRD, Montpellier, France
- Department of Biological Sciences, Centre for Ecology, Evolution and Behaviour, Royal Holloway University of London, Egham, UK
| | - Jeffrey L Feder
- Department of Biology, Notre Dame University, South Bend, Indiana, USA
| | | | - Patrik Nosil
- School of Biosciences, University of Sheffield, Sheffield, UK
- University of Montpellier, CEFE, CNRS, EPHE, IRD, Montpellier, France
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3
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Prabh N, Linnenbrink M, Jovicic M, Guenther A. Fast adjustment of pace-of-life and risk-taking to changes in food quality by altered gene expression in house mice. Ecol Lett 2023; 26:99-110. [PMID: 36366786 DOI: 10.1111/ele.14137] [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: 07/04/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022]
Abstract
The pace-of-life syndrome hypothesis provides a framework for the adaptive integration of behaviour, physiology and life history between and within species. It suggests that behaviours involving a risk of death or injury should co-vary with a higher allocation to fast reproduction. Empirical support for this hypothesis is mixed, presumably because important influencing factors such as environmental variation, are usually neglected. By experimentally manipulating food quality of wild mice living under semi-natural conditions for three generations, we show that individuals adjust their life history strategies and risk-taking behaviours as well as trait covariation (Nindividuals = 1442). These phenotypic differences are correlated to differences in transcriptomic gene expression of primary metabolic processes in the liver while no changes in gene frequencies occurred. Our discussion emphasises the need to integrate the role of environmental conditions and phenotypic plasticity in shaping relationships among behaviour, physiology and life history in response to changing environmental conditions.
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Affiliation(s)
- Neel Prabh
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Milan Jovicic
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Anja Guenther
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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4
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Vigneaud J, Maury S. [Developmental plasticity in plants: an interaction between hormones and epigenetics at the meristem level]. Biol Aujourdhui 2020; 214:125-135. [PMID: 33357371 DOI: 10.1051/jbio/2020011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 12/25/2022]
Abstract
Plants are fixed organisms with continuous development throughout their life and great sensitivity to environmental variations. They react in this way by exhibiting large developmental phenotypic plasticity. This plasticity is partly controlled by (phyto)hormones, but recent studies also suggest the involvement of epigenetic mechanisms. It seems that these two factors may interact in a complex way and especially in the stem cells grouped together in meristems. The objective of this review is to present the current arguments about this interaction which would promote developmental plasticity. Three major points are thus addressed to justify this interaction between hormonal control and epigenetics (control at the chromatin level) for the developmental plasticity of plants: the arguments in favor of an effect of hormones on chromatin and vice versa, the arguments in favor of their roles on developmental plasticity and finally the arguments in favor of the central place of these interactions, the meristems. Various perspectives and applications are discussed.
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Affiliation(s)
- Julien Vigneaud
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAe, Université d'Orléans, EA1207 USC1328, 45067 Orléans, France
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAe, Université d'Orléans, EA1207 USC1328, 45067 Orléans, France
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5
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Abstract
The importance of tree genetic variability in the ability of forests to respond and adapt to environmental changes is crucial in forest management and conservation. Along with genetics, recent advances have highlighted “epigenetics” as an emerging and promising field of research for the understanding of tree phenotypic plasticity and adaptive responses. In this paper, we review recent advances in this emerging field and their potential applications for tree researchers and breeders, as well as for forest managers. First, we present the basics of epigenetics in plants before discussing its potential for trees. We then propose a bibliometric and overview of the literature on epigenetics in trees, including recent advances on tree priming. Lastly, we outline the promises of epigenetics for forest research and management, along with current gaps and future challenges. Research in epigenetics could use highly diverse paths to help forests adapt to global change by eliciting different innovative silvicultural approaches for natural- and artificial-based forest management.
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6
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Vasil’ev AG. Evolutionary Ecology in the 21st Century: New Concepts and Development Prospects. RUSS J ECOL+ 2019. [DOI: 10.1134/s1067413619020103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Macagno ALM, Zattara EE, Ezeakudo O, Moczek AP, Ledón-Rettig CC. Adaptive maternal behavioral plasticity and developmental programming mitigate the transgenerational effects of temperature in dung beetles. OIKOS 2018. [DOI: 10.1111/oik.05215] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Anna L. M. Macagno
- Dept of Biology; Indiana Univ.; 915 E. Third Street Myers Hall 150 Bloomington IN 47405-7107 USA
| | - Eduardo E. Zattara
- Dept of Biology; Indiana Univ.; 915 E. Third Street Myers Hall 150 Bloomington IN 47405-7107 USA
- INIBIOMA, Univ. Nacional del Comahue - CONICET; Bariloche Argentina
| | | | - Armin P. Moczek
- Dept of Biology; Indiana Univ.; 915 E. Third Street Myers Hall 150 Bloomington IN 47405-7107 USA
| | - Cristina C. Ledón-Rettig
- Dept of Biology; Indiana Univ.; 915 E. Third Street Myers Hall 150 Bloomington IN 47405-7107 USA
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8
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Baranov VY, Vasil’ev AG. Morphological Diversity and Variability of Sympatric Populations of Crucian and Prussian Carps in Radionuclide Contaminated Lakes in the Southern Urals. RUSS J ECOL+ 2018. [DOI: 10.1134/s1067413618010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Hu J, Barrett RDH. Epigenetics in natural animal populations. J Evol Biol 2017; 30:1612-1632. [PMID: 28597938 DOI: 10.1111/jeb.13130] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 12/22/2022]
Abstract
Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally-mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.
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Affiliation(s)
- J Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
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10
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Vasil’ev AG, Bol’shakov VN, Vasil’eva IA, Evdokimov NG, Sineva NV. Assessment of nonselective elimination effects in rodent communities by methods of geometric morphometrics. RUSS J ECOL+ 2016. [DOI: 10.1134/s1067413616040159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Metzger DCH, Schulte PM. Epigenomics in marine fishes. Mar Genomics 2016; 30:43-54. [PMID: 26833273 DOI: 10.1016/j.margen.2016.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
Epigenetic mechanisms are an underappreciated and often ignored component of an organism's response to environmental change and may underlie many types of phenotypic plasticity. Recent technological advances in methods for detecting epigenetic marks at a whole-genome scale have launched new opportunities for studying epigenomics in ecologically relevant non-model systems. The study of ecological epigenomics holds great promise to better understand the linkages between genotype, phenotype, and the environment and to explore mechanisms of phenotypic plasticity. The many attributes of marine fish species, including their high diversity, variable life histories, high fecundity, impressive plasticity, and economic value provide unique opportunities for studying epigenetic mechanisms in an environmental context. To provide a primer on epigenomic research for fish biologists, we start by describing fundamental aspects of epigenetics, focusing on the most widely studied and most well understood of the epigenetic marks: DNA methylation. We then describe the techniques that have been used to investigate DNA methylation in marine fishes to date and highlight some new techniques that hold great promise for future studies. Epigenomic research in marine fishes is in its early stages, so we first briefly discuss what has been learned about the establishment, maintenance, and function of DNA methylation in fishes from studies in zebrafish and then summarize the studies demonstrating the pervasive effects of the environment on the epigenomes of marine fishes. We conclude by highlighting the potential for ongoing research on the epigenomics of marine fishes to reveal critical aspects of the interaction between organisms and their environments.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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12
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Liu S, Sun K, Jiang T, Feng J. Natural epigenetic variation in bats and its role in evolution. ACTA ACUST UNITED AC 2015; 218:100-6. [PMID: 25568456 DOI: 10.1242/jeb.107243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When facing the challenges of environmental change, such as habitat fragmentation, organisms have to adjust their phenotype to adapt to various environmental stresses. Recent studies show that epigenetic modifications could mediate environmentally induced phenotypic variation, and this epigenetic variance could be inherited by future generations, indicating that epigenetic processes have potential evolutionary effects. Bats living in diverse environments show geographic variations in phenotype, and the females usually have natal philopatry, presenting an opportunity to explore how environments shape epigenetic marks on the genome and the evolutionary potential of epigenetic variance in bat populations for adaptation. We have explored the natural epigenetic diversity and structure of female populations of the great roundleaf bat (Hipposideros armiger), the least horseshoe bat (Rhinolophus pusillus) and the eastern bent-winged bat (Miniopterus fuliginosus) using a methylation-sensitive amplified polymorphism technique. We have also estimated the effects of genetic variance and ecological variables on epigenetic diversification. All three bat species have a low level of genomic DNA methylation and extensive epigenetic diversity that exceeds the corresponding genetic variance. DNA sequence divergence, epigenetic drift and environmental variables contribute to the epigenetic diversities of each species. Environment-induced epigenetic variation may be inherited as a result of both mitosis and meiosis, and their potential roles in evolution for bat populations are also discussed in this review.
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Affiliation(s)
- Sen Liu
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo 454000, Henan, China
| | - Keping Sun
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China
| | - Tinglei Jiang
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China
| | - Jiang Feng
- Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, Jilin, China
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13
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Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P. Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl 2014; 7:1008-25. [PMID: 25553064 PMCID: PMC4231592 DOI: 10.1111/eva.12149] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
| | | | - Paul Sunnucks
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
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14
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Warner DA. Fitness Consequences of Maternal and Embryonic Responses to Environmental Variation: Using Reptiles as Models for Studies of Developmental Plasticity. Integr Comp Biol 2014; 54:757-73. [DOI: 10.1093/icb/icu099] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Schulz B, Eckstein RL, Durka W. Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb. Mol Ecol 2014; 23:3523-37. [DOI: 10.1111/mec.12835] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Benjamin Schulz
- Institute of Landscape Ecology and Resource Management; Interdisciplinary Research Centre (IFZ); Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 D-35393 Giessen Germany
| | - Rolf Lutz Eckstein
- Institute of Landscape Ecology and Resource Management; Interdisciplinary Research Centre (IFZ); Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 D-35393 Giessen Germany
| | - Walter Durka
- Department of Community Ecology (BZF); Helmholtz Centre for Environmental Research-UFZ; Theodor-Lieser-Straße 4 D-06120 Halle (Saale) Germany
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16
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Crespi EJ, Unkefer MK. Development of food intake controls: neuroendocrine and environmental regulation of food intake during early life. Horm Behav 2014; 66:74-85. [PMID: 24727079 DOI: 10.1016/j.yhbeh.2014.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/01/2014] [Accepted: 04/05/2014] [Indexed: 01/18/2023]
Abstract
This article is part of a Special Issue "Energy Balance". The development of neuroendocrine regulation of food intake during early life has been shaped by natural selection to allow for optimal growth and development rates needed for survival. In vertebrates, neonates or early larval forms typically exhibit "feeding drive," characterized by a developmental delay in 1) responsiveness of the hypothalamus to satiety signals (e.g., leptin, melanocortins) and 2) sensitivity to environmental cues that suppress food intake. Homeostatic regulation of food intake develops once offspring transition to later life history stages when growth is slower, neuroendocrine systems are more mature, and appetite becomes more sensitive to environmental or social cues. Across vertebrate groups, there is a tremendous amount of developmental plasticity in both food intake regulation and stress responsiveness depending on the environmental conditions experienced during early life history stages or by pregnant/brooding mothers. This plasticity is mediated through the organizing effects of hormones acting on the food intake centers of the hypothalamus during development, which alter epigenetic expression of genes associated with ingestive behaviors. Research is still needed to reveal the mechanisms through which environmental conditions during development generate and maintain these epigenetic modifications within the lifespan or across generations. Furthermore, more research is needed to determine whether observed patterns of plasticity are adaptive or pathological. It is clear, however, that developmental programming of food intake has important effects on fitness, and therefore, has ecological and evolutionary implications.
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Affiliation(s)
- Erica J Crespi
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.
| | - Margaret K Unkefer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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