1
|
Passeri I, Vaccaro F, Mengoni A, Fagorzi C. Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges. Int J Mol Sci 2024; 25:4425. [PMID: 38674013 PMCID: PMC11050019 DOI: 10.3390/ijms25084425] [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: 02/17/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation. Here, we present an overview of the multifaceted roles of DNA methylation in prokaryotes and suggest research directions and tools which can enable us to better understand the contribution of DNA methylation to prokaryotic genome evolution and adaptation. In particular, we emphasize the need to understand the presence and role of transgenerational inheritance, as well as the impact of epigenomic signatures on adaptation and genome evolution. Research directions and the importance of novel computational tools are underlined.
Collapse
Affiliation(s)
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, 50121 Firenze, Italy; (I.P.); (F.V.); (C.F.)
| | | |
Collapse
|
2
|
Lokatis S, Jeschke JM, Bernard-Verdier M, Buchholz S, Grossart HP, Havemann F, Hölker F, Itescu Y, Kowarik I, Kramer-Schadt S, Mietchen D, Musseau CL, Planillo A, Schittko C, Straka TM, Heger T. Hypotheses in urban ecology: building a common knowledge base. Biol Rev Camb Philos Soc 2023; 98:1530-1547. [PMID: 37072921 DOI: 10.1111/brv.12964] [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: 06/21/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023]
Abstract
Urban ecology is a rapidly growing research field that has to keep pace with the pressing need to tackle the sustainability crisis. As an inherently multi-disciplinary field with close ties to practitioners and administrators, research synthesis and knowledge transfer between those different stakeholders is crucial. Knowledge maps can enhance knowledge transfer and provide orientation to researchers as well as practitioners. A promising option for developing such knowledge maps is to create hypothesis networks, which structure existing hypotheses and aggregate them according to topics and research aims. Combining expert knowledge with information from the literature, we here identify 62 research hypotheses used in urban ecology and link them in such a network. Our network clusters hypotheses into four distinct themes: (i) Urban species traits & evolution, (ii) Urban biotic communities, (iii) Urban habitats and (iv) Urban ecosystems. We discuss the potentials and limitations of this approach. All information is openly provided as part of an extendable Wikidata project, and we invite researchers, practitioners and others interested in urban ecology to contribute additional hypotheses, as well as comment and add to the existing ones. The hypothesis network and Wikidata project form a first step towards a knowledge base for urban ecology, which can be expanded and curated to benefit both practitioners and researchers.
Collapse
Affiliation(s)
- Sophie Lokatis
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, Leipzig, 04103, Germany
| | - Jonathan M Jeschke
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
| | - Maud Bernard-Verdier
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
| | - Sascha Buchholz
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, Münster, 48149, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, Potsdam, 14469, Germany
| | - Frank Havemann
- Institut für Bibliotheks- und Informationswissenschaft, Humboldt-Universität zu Berlin, Dorotheenstraße 26, Berlin, 10117, Germany
| | - Franz Hölker
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
| | - Yuval Itescu
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
| | - Ingo Kowarik
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- Institute of Ecology, Technische Universität Berlin, Rothenburgstr. 12, Berlin, 12165, Germany
| | - Stephanie Kramer-Schadt
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- Institute of Ecology, Technische Universität Berlin, Rothenburgstr. 12, Berlin, 12165, Germany
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, 10315, Germany
| | - Daniel Mietchen
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- Institute for Globally Distributed Open Research and Education (IGDORE), Gothenburg, Sweden
| | - Camille L Musseau
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
| | - Aimara Planillo
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, 10315, Germany
| | - Conrad Schittko
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- Institute of Ecology, Technische Universität Berlin, Rothenburgstr. 12, Berlin, 12165, Germany
| | - Tanja M Straka
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- Institute of Ecology, Technische Universität Berlin, Rothenburgstr. 12, Berlin, 12165, Germany
| | - Tina Heger
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 1-3, Berlin, 14195, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, Berlin, 12587, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Königin-Luise-Str. 2-4, Berlin, 14195, Germany
- Technical University of Munich, Restoration Ecology, Emil-Ramann-Str. 6, Freising, 85350, Germany
| |
Collapse
|
3
|
Li YS, Liao PC, Chang CT, Hwang SY. The Contribution of Epigenetics to Evolutionary Adaptation in Zingiber kawagoii Hayata (Zingiberaceae) Endemic to Taiwan. PLANTS (BASEL, SWITZERLAND) 2023; 12:1558. [PMID: 37050184 PMCID: PMC10096833 DOI: 10.3390/plants12071558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
We epigenotyped 211 individuals from 17 Zingiber kawagoii populations using methylation-sensitive amplification polymorphism (MSAP) and investigated the associations of methylated (mMSAP) and unmethylated (uMSAP) loci with 16 environmental variables. Data regarding genetic variation based on amplified fragment length polymorphism (AFLP) were obtained from an earlier study. We found a significant positive correlation between genetic and epigenetic variation. Significantly higher mean mMSAP and uMSAP uHE (unbiased expected heterozygosity: 0.223 and 0.131, respectively, p < 0.001) per locus than that estimated based on AFLP (uHE = 0.104) were found. Genome scans detected 10 mMSAP and 9 uMSAP FST outliers associated with various environmental variables. A significant linear fit for 11 and 12 environmental variables with outlier mMSAP and uMSAP ordination, respectively, generated using full model redundancy analysis (RDA) was found. When conditioned on geography, partial RDA revealed that five and six environmental variables, respectively, were the most important variables influencing outlier mMSAP and uMSAP variation. We found higher genetic (average FST = 0.298) than epigenetic (mMSAP and uMSAP average FST = 0.044 and 0.106, respectively) differentiation and higher genetic isolation-by-distance (IBD) than epigenetic IBD. Strong epigenetic isolation-by-environment (IBE) was found, particularly based on the outlier data, controlling either for geography (mMSAP and uMSAP βE = 0.128 and 0.132, respectively, p = 0.001) or for genetic structure (mMSAP and uMSAP βE = 0.105 and 0.136, respectively, p = 0.001). Our results suggest that epigenetic variants can be substrates for natural selection linked to environmental variables and complement genetic changes in the adaptive evolution of Z. kawagoii populations.
Collapse
Affiliation(s)
- Yi-Shao Li
- School of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei 11677, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei 11677, Taiwan
| | - Chung-Te Chang
- Department of Life Science, Tunghai University, 1727 Taiwan Boulevard, Section 4, Taichung 40704, Taiwan;
| | - Shih-Ying Hwang
- School of Life Science, National Taiwan Normal University, 88 Tingchow Road, Section 4, Taipei 11677, Taiwan
| |
Collapse
|
4
|
Tomczyk PP, Kiedrzyński M, Forma E, Zielińska KM, Kiedrzyńska E. Changes in global DNA methylation under climatic stress in two related grasses suggest a possible role of epigenetics in the ecological success of polyploids. Sci Rep 2022; 12:8322. [PMID: 35585117 PMCID: PMC9117213 DOI: 10.1038/s41598-022-12125-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022] Open
Abstract
Polyploidization drives the evolution of grasses and can result in epigenetic changes, which may have a role in the creation of new evolutionary lineages and ecological speciation. As such changes may be inherited, they can also influence adaptation to the environment. Populations from different regions and climates may also differ epigenetically; however, this phenomenon is poorly understood. The present study analyzes the effect of climatic stress on global DNA methylation based on a garden collection of two related mountain grasses (the narrow endemic diploid Festuca tatrae and the more widely distributed mixed-ploidy F. amethystina) with different geographic ranges and ecological niches. A lower level of DNA methylation was observed for F. tatrae, while a higher mean level was obtained for the diploid and tetraploid of F. amethystina; with the tetraploids having a higher level of global methylated DNA than the diploids. The weather conditions (especially insolation) measured 24 h prior to sampling appeared to have a closer relationship with global DNA methylation level than those observed seven days before sampling. Our findings suggest that the level of methylation during stress conditions (drought, high temperature and high insolation) may be significantly influenced by the ploidy level and bioclimatic provenance of specimens; however an important role may also be played by the intensity of stress conditions in a given year.
Collapse
Affiliation(s)
- Przemysław P Tomczyk
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237, Lodz, Poland. .,The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland.
| | - Marcin Kiedrzyński
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237, Lodz, Poland
| | - Ewa Forma
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Katarzyna M Zielińska
- Department of Biogeography, Paleoecology and Nature Conservation, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 1/3, 90-237, Lodz, Poland
| | - Edyta Kiedrzyńska
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364, Lodz, Poland.,UNESCO Chair On Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
| |
Collapse
|
5
|
Chen Q, Zhang J, Li G. Dynamic epigenetic modifications in plant sugar signal transduction. TRENDS IN PLANT SCIENCE 2022; 27:379-390. [PMID: 34865981 DOI: 10.1016/j.tplants.2021.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 05/21/2023]
Abstract
In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research.
Collapse
Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| |
Collapse
|
6
|
Twardek WM, Ekström A, Eliason EJ, Lennox RJ, Tuononen E, Abrams AEI, Jeanson AL, Cooke SJ. Field assessments of heart rate dynamics during spawning migration of wild and hatchery-reared Chinook salmon. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200214. [PMID: 34121459 DOI: 10.1098/rstb.2020.0214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During spawning, adult Pacific salmonids (Oncorhynchus spp.) complete challenging upriver migrations during which energy and oxygen delivery must be partitioned into activities such as locomotion, maturation and spawning behaviours under the constraints of an individual's cardiac capacity. To advance our understanding of cardiac function in free-swimming fishes, we implanted migrating adult Chinook salmon (Oncorhynchus tshawytscha) collected near the mouth of the Sydenham River, Ontario, with heart rate (fH) biologgers that recorded fH every 3 min until these semelparous fish expired on spawning grounds several days later. Fundamental aspects of cardiac function were quantified, including resting, routine and maximum fH, as well as scope for fH (maximum-resting fH). Predictors of fH were explored using generalized least-squares regression, including water temperature, discharge, fish size and fish origin (wild versus hatchery). Heart rate was positively correlated with water temperature, which aligned closely with daily and seasonal shifts. Wild fish had slower resting heart rates than hatchery fish, which led to significantly higher scope for fH. Our findings suggest that wild salmon may have better cardiac capacity during migration than hatchery fish, potentially promoting migration success in wild fish. This article is part of the theme issue 'Measuring physiology in free-living animals (Part I)'.
Collapse
Affiliation(s)
- W M Twardek
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - A Ekström
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - E J Eliason
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - R J Lennox
- Norwegian Research Centre (NORCE), Laboratory for Freshwater Ecology and Inland Fisheries (LFI), Nygårdsgaten 112, 5008 Bergen, Norway
| | - E Tuononen
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - A E I Abrams
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - A L Jeanson
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - S J Cooke
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| |
Collapse
|
7
|
Hoyer-Fender S. Transgenerational effect of drug-mediated inhibition of LSD1 on eye pigment expression in Drosophila. BMC Ecol 2020; 20:62. [PMID: 33228645 PMCID: PMC7684728 DOI: 10.1186/s12898-020-00330-6] [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: 04/26/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022] Open
Abstract
Background The Drosophila melanogaster mutant white-mottled is a well-established model for position-effect variegation (PEV). Transposition of the euchromatic white gene into the vicinity of the pericentric heterochromatin caused variegated expression of white due to heterochromatin spreading. The establishment of the euchromatin-heterochromatin boundary and spreading of silencing is regulated by mutually exclusive histone modifications, i.e. the methylations of histone H3 at lysine 9 and lysine 4. Demethylation of H3K4, catalysed by lysine-specific demethylase LSD1, is required for subsequent methylation of H3K9 to establish heterochromatin. LSD1 is therefore essential for heterochromatin formation and spreading. We asked whether drug-mediated inhibition of LSD affects the expression of white and if this induced change can be transmitted to those generations that have never been exposed to the triggering signal, i.e. transgenerational epigenetic inheritance. Results We used the lysine-specific demethylase 1 (LSD1)-inhibitor Tranylcypromine to investigate its effect on eye colour expression in consecutive generations by feeding the parental and F1 generations of the Drosophila melanogaster mutant white-mottled. Quantitative Western blotting revealed that Tranylcypromine inhibits H3K4-demethylation both in vitro in S2 cells as well as in embryos when used as feeding additive. Eye colour expression in male flies was determined by optical measurement of pigment extracts and qRT-PCR of white gene expression. Flies raised in the presence of Tranylcypromine and its solvent DMSO showed increased eye pigment expression. Beyond that, eye pigment expression was also affected in consecutive generations including F3, which is the first generation without contact with the inhibitor. Conclusions Our results show that feeding of Tranylcypromine and DMSO caused desilencing of white in treated flies of generation F1. Consecutive generations, raised on standard food without further supplements, are also affected by the drug-induced alteration of histone modifications. Although eye pigment expression eventually returned to the basal state, the observed long-lasting effect points to a memory capacity of previous epigenomes. Furthermore, our results indicate that food compounds potentially affect chromatin modification and hence gene expression and that the alteration is putatively inherited not only parentally but transgenerationally.
Collapse
Affiliation(s)
- Sigrid Hoyer-Fender
- Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology-Developmental Biology, GZMB, Ernst-Caspari-Haus, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, Göttingen, Germany.
| |
Collapse
|
8
|
Wang MZ, Li HL, Li JM, Yu FH. Correlations between genetic, epigenetic and phenotypic variation of an introduced clonal herb. Heredity (Edinb) 2019; 124:146-155. [PMID: 31431739 DOI: 10.1038/s41437-019-0261-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/06/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Heritable epigenetic modifications may occur in response to environmental variation, further altering phenotypes through gene regulation, without genome sequence changes. However, epigenetic variation in wild plant populations and their correlations with genetic and phenotypic variation remain largely unknown, especially for clonal plants. We investigated genetic, epigenetic and phenotypic variation of ten populations of an introduced clonal herb Hydrocotyle vulgaris in China. Populations of H. vulgaris exhibited extremely low genetic diversity with one genotype exclusively dominant, but significantly higher epigenetic diversity. Both intra- and inter-population epigenetic variation were related to genetic variation. But there was no correlation between intra-/inter-population genetic variation and phenotypic variation. When genetic variation was controlled, intra-population epigenetic diversity was related to petiole length, specific leaf area, and leaf area variation, while inter-population epigenetic distance was correlated with leaf area differentiation. Our study provides empirical evidence that even though epigenetic variation is partly under genetic control, it could also independently play a role in shaping plant phenotypes, possibly serving as a pathway to accelerate evolution of clonal plant populations.
Collapse
Affiliation(s)
- Mo-Zhu Wang
- Institute of Wetland Ecology & Clone Ecology, Taizhou University, Taizhou, 318000, China.,Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China.,School of Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Hong-Li Li
- School of Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Jun-Min Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Fei-Hai Yu
- Institute of Wetland Ecology & Clone Ecology, Taizhou University, Taizhou, 318000, China. .,Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China.
| |
Collapse
|
9
|
Two Experiments on the Psychological and Physiological Effects of Touching-Effect of Touching on the HPA Axis-Related Parts of the Body on Both Healthy and Traumatized Experiment Participants. Behav Sci (Basel) 2018; 8:bs8100095. [PMID: 30336552 PMCID: PMC6210704 DOI: 10.3390/bs8100095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/14/2022] Open
Abstract
Two experiments were conducted to measure both the psychological and physiological effects of touching on the HPA axis related parts of the body. HPA stands for the hypothalamus, pituitary, and adrenal. One experiment was conducted with a group of healthy experiment participants, and another was with a group of traumatized participants who had Adverse Childhood Experiences (ACE). In the experiments, the back of an experiment participant was touched, where a kidney-adrenal was supposed to reside, and both the psychological and physiological effects were measured. As a result, respiratory sinus arrhythmia (RSA), an indicator of the parasympathetic nerve system function and, especially, an indicator of the social engagement system increased, by a statistically significant degree, as a consequence of HPA touching in both the healthy and the trauma group, in comparison with the control. The traumatized participants had a lower RSA, and this was increased by HPA touching, accompanied by a decrease of the heart rate. It is worth noting that the social engagement function was possibly enhanced by HPA touching, especially in the trauma group, whose members tend to have difficulty being pro-social. This touching method is very simple, so it can be administered not only by oneself, but also by psycho-therapists and body workers in order to enhance both psychological and physiological well-being.
Collapse
|
10
|
Volkova PY, Geras'kin SA. 'Omic' technologies as a helpful tool in radioecological research. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 189:156-167. [PMID: 29677564 DOI: 10.1016/j.jenvrad.2018.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.
Collapse
Affiliation(s)
- Polina Yu Volkova
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia.
| | - Stanislav A Geras'kin
- Institute of Radiology and Agroecology, 249032, Kievskoe shosse, 109 km, Obninsk, Russia
| |
Collapse
|
11
|
Li YS, Chang CT, Wang CN, Thomas P, Chung JD, Hwang SY. The Contribution of Neutral and Environmentally Dependent Processes in Driving Population and Lineage Divergence in Taiwania ( Taiwania cryptomerioides). FRONTIERS IN PLANT SCIENCE 2018; 9:1148. [PMID: 30135693 PMCID: PMC6092574 DOI: 10.3389/fpls.2018.01148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The question of what determines divergence both between and within species has been the central topic in evolutionary biology. Neutral drift and environmentally dependent divergence are predicted to play roles in driving population and lineage divergence. However, neutral drift may preclude adaptation if the rate of gene flow between populations is high. Here, we sampled populations of three Taiwania (Taiwania cryptomerioides) lineages occurring in Taiwan, the mainland of China (Yunnan-Myanmar border), and northern Vietnam, and tested the relative strength of neutral drift and divergent selection in shaping divergence of those populations and lineages. We quantified genetic and epigenetic variation, respectively, using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP). Analysis of 1413 AFLP and 462 MSAP loci using frequency-based genome scan methods and generalized linear models (GLMs) found no potential selective outliers when only Taiwanese populations were examined, suggesting that neutral drift was the predominant evolutionary process driving differentiation between those populations. However, environmentally associated divergence was found when lineages were compared. Thirty-two potential selective outliers were identified based on genome scans and their associations with environmental variables were tested with GLMs, generalized linear mixed effect models (GLMMs), and model selection with a model averaging approach. Ten loci (six AFLP and four MSAP) were found to be strongly associated with environmental variables, particularly monthly temperature variation and normalized difference vegetation index (NDVI) using model selection and a model averaging approach. Because only a small portion of genetic and epigenetic loci were found to be potential selective outliers, neutral evolutionary process might also have played crucial roles in driving lineage divergence, particularly between geographically and genetically isolated island and mainland Asia lineages. Nevertheless, the vast amount of neutral drift causing genetic and epigenetic variations might have the potential for adaptation to future climate changes. These could be important for the survival of Taiwania in different geographic areas.
Collapse
Affiliation(s)
- Yi-Shao Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, Taipei, Taiwan
| | - Chun-Neng Wang
- Institute of Ecology and Evolution, National Taiwan University, Taipei, Taiwan
| | - Philip Thomas
- International Conifer Conservation Programme of the Royal Botanic Garden, Edinburgh, United Kingdom
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| |
Collapse
|
12
|
Yang SX, Guo C, Zhao XT, Sun JT, Hong XY. Divergent methylation pattern in adult stage between two forms of Tetranychus urticae (Acari: Tetranychidae). INSECT SCIENCE 2018; 25:667-678. [PMID: 28217963 DOI: 10.1111/1744-7917.12444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
The two-spotted spider mite, Tetranychus urticae Koch has two forms: green form and red form. Understanding the molecular basis of how these two forms established without divergent genetic background is an intriguing area. As a well-known epigenetic process, DNA methylation has particularly important roles in gene regulation and developmental variation across diverse organisms that do not alter genetic background. Here, to investigate whether DNA methylation could be associated with different phenotypic consequences in the two forms of T. urticae, we surveyed the genome-wide cytosine methylation status and expression level of DNA methyltransferase 3 (Tudnmt3) throughout their entire life cycle. Methylation-sensitive amplification polymorphism (MSAP) analyses of 585 loci revealed variable methylation patterns in the different developmental stages. In particular, principal coordinates analysis (PCoA) indicates a significant epigenetic differentiation between female adults of the two forms. The gene expression of Tudnmt3 was detected in all examined developmental stages, which was significantly different in the adult stage of the two forms. Together, our results reveal the epigenetic distance between the two forms of T. urticae, suggesting that DNA methylation might be implicated in different developmental demands, and contribute to different phenotypes in the adult stage of these two forms.
Collapse
Affiliation(s)
- Si-Xia Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Chao Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiu-Ting Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| |
Collapse
|
13
|
Lee K, Seo PJ. Dynamic Epigenetic Changes during Plant Regeneration. TRENDS IN PLANT SCIENCE 2018; 23:235-247. [PMID: 29338924 DOI: 10.1016/j.tplants.2017.11.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 05/18/2023]
Abstract
Plants have the remarkable ability to drive cellular dedifferentiation and regeneration. Changes in epigenetic landscapes accompany the cell fate transition. Notably, modifications of chromatin structure occur primarily during callus formation via an in vitro tissue culture process and, thus, pluripotent callus cells have unique epigenetic signatures. Here, we highlight the latest progress in epigenetic regulation of callus formation in plants, which addresses fundamental questions related to cell fate changes and pluripotency establishment. Global and local modifications of chromatin structure underlie callus formation, and the combination and sequence of epigenetic modifications further shape intricate cell fate changes. This review illustrates how a series of chromatin marks change dynamically during callus formation and their biological relevance in plant regeneration.
Collapse
Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| |
Collapse
|
14
|
Vršanský P, OruŘinský R, Aristov D, Wei DD, Vidlička Ľ, Ren D. Temporary deleterious mass mutations relate to originations of cockroach families. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0096] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
15
|
Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon. Proc Natl Acad Sci U S A 2017; 114:12964-12969. [PMID: 29162695 DOI: 10.1073/pnas.1711229114] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon (Oncorhynchus kisutch) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatchery-born smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon.
Collapse
|
16
|
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: 84] [Impact Index Per Article: 12.0] [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.
Collapse
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
| |
Collapse
|
17
|
Cortez MJV, Rabajante JF, Tubay JM, Babierra AL. From epigenetic landscape to phenotypic fitness landscape: Evolutionary effect of pathogens on host traits. INFECTION GENETICS AND EVOLUTION 2017; 51:245-254. [PMID: 28408285 DOI: 10.1016/j.meegid.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
The epigenetic landscape illustrates how cells differentiate through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here, we formulate a multistable decision-switch model involving several phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior through negative frequency-dependent selection. Furthermore, novel predictions of our model show that parasitism can steer the dynamics of phenotype specification from multistable equilibrium convergence to oscillations. This oscillatory behavior could explain pathogen-mediated epimutations and excessive phenotypic plasticity. The Red Queen dynamics also occur in certain parameter space of the model, which demonstrates winnerless cyclic phenotype-switching in hosts and in pathogens. The results of our simulations elucidate the association between the epigenetic and phenotypic fitness landscapes and how parasitism facilitates non-genetic phenotypic diversity.
Collapse
Affiliation(s)
- Mark Jayson V Cortez
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Jomar F Rabajante
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines.
| | - Jerrold M Tubay
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Ariel L Babierra
- Institute of Mathematical Sciences and Physics, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| |
Collapse
|
18
|
Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives. BIOLOGY 2016; 5:biology5020024. [PMID: 27231949 PMCID: PMC4929538 DOI: 10.3390/biology5020024] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/26/2016] [Accepted: 05/11/2016] [Indexed: 01/08/2023]
Abstract
Epigenetics increasingly occupies a pivotal position in our understanding of inheritance, natural selection and, perhaps, even evolution. A survey of the PubMed database, however, reveals that the great majority (>93%) of epigenetic papers have an intra-, rather than an inter-generational focus, primarily on mechanisms and disease. Approximately ~1% of epigenetic papers even mention the nexus of epigenetics, natural selection and evolution. Yet, when environments are dynamic (e.g., climate change effects), there may be an “epigenetic advantage” to phenotypic switching by epigenetic inheritance, rather than by gene mutation. An epigenetically-inherited trait can arise simultaneously in many individuals, as opposed to a single individual with a gene mutation. Moreover, a transient epigenetically-modified phenotype can be quickly “sunsetted”, with individuals reverting to the original phenotype. Thus, epigenetic phenotype switching is dynamic and temporary and can help bridge periods of environmental stress. Epigenetic inheritance likely contributes to evolution both directly and indirectly. While there is as yet incomplete evidence of direct permanent incorporation of a complex epigenetic phenotype into the genome, doubtlessly, the presence of epigenetic markers and the phenotypes they create (which may sort quite separately from the genotype within a population) will influence natural selection and, so, drive the collective genotype of a population.
Collapse
|
19
|
Mainigi MA, Sapienza C, Butts S, Coutifaris C. A Molecular Perspective on Procedures and Outcomes with Assisted Reproductive Technologies. Cold Spring Harb Perspect Med 2016; 6:a023416. [PMID: 26747835 DOI: 10.1101/cshperspect.a023416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emerging association of assisted reproductive technologies with adverse perinatal outcomes has prompted the in-depth examination of clinical and laboratory protocols and procedures and their possible effects on epigenetic regulatory mechanism(s). The application of various approaches to study epigenetic regulation to problems in reproductive medicine has the potential to identify relative risk indicators for particular conditions, diagnostic biomarkers of disease state, and prognostic indicators of outcome. Moreover, when applied genome-wide, these techniques are likely to find novel pathways of disease pathogenesis and identify new targets for intervention. The analysis of DNA methylation, histone modifications, transcription factors, enhancer binding and other chromatin proteins, DNase-hypersensitivity and, micro- and other noncoding RNAs all provide overlapping and often complementary snapshots of chromatin structure and resultant "gene activity." In terms of clinical application, the predictive power and utility of epigenetic information will depend on the power of individual techniques to discriminate normal levels of interindividual variation from variation linked to a disease state. At present, quantitative analysis of DNA methylation at multiple loci seems likely to hold the greatest promise for achieving the level of precision, reproducibility, and throughput demanded in a clinical setting.
Collapse
Affiliation(s)
- Monica A Mainigi
- Department of Obstetrics and Gynecology and the Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Carmen Sapienza
- Fels Institute for Cancer Research and Molecular Biology and Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania 19140
| | - Samantha Butts
- Department of Obstetrics and Gynecology and the Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology and the Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
20
|
Kesäniemi JE, Heikkinen L, Knott KE. DNA Methylation and Potential for Epigenetic Regulation in Pygospio elegans. PLoS One 2016; 11:e0151863. [PMID: 27008314 PMCID: PMC4805255 DOI: 10.1371/journal.pone.0151863] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/04/2016] [Indexed: 01/24/2023] Open
Abstract
Transitions in developmental mode are common evolutionarily, but how and why they occur is not understood. Developmental mode describes larval phenotypes, including morphology, ecology and behavior of larvae, which typically are generalized across different species. The polychaete worm Pygospio elegans is one of few species polymorphic in developmental mode, with multiple larval phenotypes, providing a possibility to examine the potential mechanisms allowing transitions in developmental mode. We investigated the presence of DNA methylation in P. elegans, and, since maternal provisioning is a key factor determining eventual larval phenotype, we compared patterns of DNA methylation in females during oogenesis in this species. We demonstrate that intragenic CpG site DNA methylation and many relevant genes necessary for DNA methylation occur in P. elegans. Methylation-sensitive AFLP analysis showed that gravid females with offspring differing in larval developmental mode have significantly different methylation profiles and that the females with benthic larvae and non-reproductive females from the same location also differ in their epigenetic profiles. Analysis of CpG sites in transcriptome data supported our findings of DNA methylation in this species and showed that CpG observed/expected ratios differ among females gravid with embryos destined to different developmental modes. The differences in CpG site DNA methylation patterns seen among the samples suggest a potential for epigenetic regulation of gene expression (through DNA methylation) in this species.
Collapse
Affiliation(s)
- Jenni E. Kesäniemi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- * E-mail:
| | - Liisa Heikkinen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - K. Emily Knott
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| |
Collapse
|
21
|
Ward TD, Algera DA, Gallagher AJ, Hawkins E, Horodysky A, Jørgensen C, Killen SS, McKenzie DJ, Metcalfe JD, Peck MA, Vu M, Cooke SJ. Understanding the individual to implement the ecosystem approach to fisheries management. CONSERVATION PHYSIOLOGY 2016; 4:cow005. [PMID: 27293757 PMCID: PMC4825417 DOI: 10.1093/conphys/cow005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/25/2016] [Accepted: 02/08/2016] [Indexed: 05/20/2023]
Abstract
Ecosystem-based approaches to fisheries management (EAFMs) have emerged as requisite for sustainable use of fisheries resources. At the same time, however, there is a growing recognition of the degree of variation among individuals within a population, as well as the ecological consequences of this variation. Managing resources at an ecosystem level calls on practitioners to consider evolutionary processes, and ample evidence from the realm of fisheries science indicates that anthropogenic disturbance can drive changes in predominant character traits (e.g. size at maturity). Eco-evolutionary theory suggests that human-induced trait change and the modification of selective regimens might contribute to ecosystem dynamics at a similar magnitude to species extirpation, extinction and ecological dysfunction. Given the dynamic interaction between fisheries and target species via harvest and subsequent ecosystem consequences, we argue that individual diversity in genetic, physiological and behavioural traits are important considerations under EAFMs. Here, we examine the role of individual variation in a number of contexts relevant to fisheries management, including the potential ecological effects of rapid trait change. Using select examples, we highlight the extent of phenotypic diversity of individuals, as well as the ecological constraints on such diversity. We conclude that individual phenotypic diversity is a complex phenomenon that needs to be considered in EAFMs, with the ultimate realization that maintaining or increasing individual trait diversity may afford not only species, but also entire ecosystems, with enhanced resilience to environmental perturbations. Put simply, individuals are the foundation from which population- and ecosystem-level traits emerge and are therefore of central importance for the ecosystem-based approaches to fisheries management.
Collapse
Affiliation(s)
- Taylor D. Ward
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, CanadaK1S 5B6
- Corresponding author: Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6.
| | - Dirk A. Algera
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, CanadaK1S 5B6
| | - Austin J. Gallagher
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, CanadaK1S 5B6
| | - Emily Hawkins
- Department of Biology, University of Ottawa, 30 Marie-Curie Private, Ottawa, ON, CanadaK1N 9B4
| | - Andrij Horodysky
- Department of Marine and Environmental Science, Hampton University, Hampton, VA 23668, USA
| | - Christian Jørgensen
- Department of Biology and Hjort Centre for Marine Ecosystem Dynamics, University of Bergen, PO Box 7803, Bergen 5020, Norway
| | - Shaun S. Killen
- Institute of Biodiversity, Animal Health, and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - David J. McKenzie
- Equipe Diversité et Ecologie des Poissons, UMR5119 Ecologie des Systèmes Marins Côtiers, Université Montpellier, Place Eugène Bataillon, Montpellier cedex 5 34095, France
| | - Julian D. Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft Laboratory, Suffolk NR33 0HT, UK
| | - Myron A. Peck
- Institute of Hydrobiology and Fisheries Science, Center for Earth System Research and Sustainability, Olbersweg 24, Hamburg 22767, Germany
| | - Maria Vu
- Department of Biology, University of Ottawa, 30 Marie-Curie Private, Ottawa, ON, CanadaK1N 9B4
| | - Steven J. Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, CanadaK1S 5B6
| |
Collapse
|
22
|
Yagi K, Pawełkowicz M, Osipowski P, Siedlecka E, Przybecki Z, Tagashira N, Hoshi Y, Malepszy S, Pląder W. Molecular Cytogenetic Analysis of Cucumis Wild Species Distributed in Southern Africa: Physical Mapping of 5S and 45S rDNA with DAPI. Cytogenet Genome Res 2015; 146:80-7. [PMID: 26112877 DOI: 10.1159/000433572] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/19/2022] Open
Abstract
Wild Cucumis species have been divided into Australian/Asian and African groups using morphological and phylogenetic characteristics, and new species have been described recently. No molecular cytogenetic information is available for most of these species. The crossability between 5 southern African Cucumis species (C. africanus, C. anguria, C. myriocarpus, C. zeyheri, and C. heptadactylus) has been reported; however, the evolutionary relationship among them is still unclear. Here, a molecular cytogenetic analysis using FISH with 5S and 45 S ribosomal DNA (rDNA) was used to investigate these Cucumis species based on sets of rDNA-bearing chromosomes (rch) types I, II and III. The molecular cytogenetic and phylogenetic results suggested that at least 2 steps of chromosomal rearrangements may have occurred during the evolution of tetraploid C. heptadactylus. In step 1, an additional 45 S rDNA site was observed in the chromosome (type III). In particular, C. myriocarpus had a variety of rch sets. Our results suggest that chromosomal rearrangements may have occurred in the 45 S rDNA sites. We propose that polyploid evolution occurred in step 2. This study provides insights into the chromosomal characteristics of African Cucumis species and contributes to the understanding of chromosomal evolution in this genus.
Collapse
Affiliation(s)
- Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Isaksson C. Urbanization, oxidative stress and inflammation: a question of evolving, acclimatizing or coping with urban environmental stress. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12477] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
24
|
Zhang W, Cao Y, Wang M, Ji L, Chen L, Deater-Deckard K. The Dopamine D2 Receptor Polymorphism (DRD2 TaqIA) Interacts with Maternal Parenting in Predicting Early Adolescent Depressive Symptoms: Evidence of Differential Susceptibility and Age Differences. J Youth Adolesc 2015; 44:1428-40. [PMID: 25941120 DOI: 10.1007/s10964-015-0297-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/27/2015] [Indexed: 01/16/2023]
Abstract
Most gene-environment interaction research on depression has largely focused on negative environment and to a lesser extent on positive environment. Moreover, to date few studies have directly examined G × E at different periods in development, particularly during early adolescence. The present study addressed these issues by examining the concurrent and prospective longitudinal effects of maternal parenting, DRD2 TaqIA polymorphism, and their interaction on adolescent depressive symptoms in a sample of 1026 Chinese adolescents (Mage = 11.33 ± 0.47 years at T1, 50.3% girls) in a three-wave longitudinal study from age 11 to 13. Results indicated that maternal positive and negative parenting significantly concurrently predicted adolescent depressive symptoms at all three waves, whereas TaqIA polymorphism had no main effect on depressive symptoms. TaqIA polymorphism interacted with negative parenting in predicting concurrent depressive symptoms at age 11 and 12. A1 carriers were more susceptible to negative parenting compared to A2A2 homozygotes, such that adolescents carrying A1 alleles experiencing high negative parenting reported more depressive symptoms but fared better when experiencing low negative parenting. However, the interaction became nonsignificant at age 13, indicating the interaction of TaqIA polymorphism and maternal parenting may vary with development. Also, there was no G × E effect on longitudinal change in depression. The findings provided evidence in support of the differential susceptibility hypothesis and shed light on the potential for dynamic change in gene-environment interactions over development.
Collapse
Affiliation(s)
- Wenxin Zhang
- Department of Psychology, Shandong Normal University, No. 88 East Wenhua Road, Jinan, 250014, Shandong Province, China,
| | | | | | | | | | | |
Collapse
|
25
|
Bateson P, Gluckman P, Hanson M. The biology of developmental plasticity and the Predictive Adaptive Response hypothesis. J Physiol 2015; 592:2357-68. [PMID: 24882817 DOI: 10.1113/jphysiol.2014.271460] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Many forms of developmental plasticity have been observed and these are usually beneficial to the organism. The Predictive Adaptive Response (PAR) hypothesis refers to a form of developmental plasticity in which cues received in early life influence the development of a phenotype that is normally adapted to the environmental conditions of later life. When the predicted and actual environments differ, the mismatch between the individual's phenotype and the conditions in which it finds itself can have adverse consequences for Darwinian fitness and, later, for health. Numerous examples exist of the long-term effects of cues indicating a threatening environment affecting the subsequent phenotype of the individual organism. Other examples consist of the long-term effects of variations in environment within a normal range, particularly in the individual's nutritional environment. In mammals the cues to developing offspring are often provided by the mother's plane of nutrition, her body composition or stress levels. This hypothetical effect in humans is thought to be important by some scientists and controversial by others. In resolving the conflict, distinctions should be drawn between PARs induced by normative variations in the developmental environment and the ill effects on development of extremes in environment such as a very poor or very rich nutritional environment. Tests to distinguish between different developmental processes impacting on adult characteristics are proposed. Many of the mechanisms underlying developmental plasticity involve molecular epigenetic processes, and their elucidation in the context of PARs and more widely has implications for the revision of classical evolutionary theory.
Collapse
Affiliation(s)
- Patrick Bateson
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Peter Gluckman
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Mark Hanson
- Institute of Developmental Sciences, Faculty of Medicine, University of Southampton and NIHR Nutrition Biomedical Research Centre, Universazity Hospital Southampton, Southampton, UK
| |
Collapse
|
26
|
Tricker PJ. Transgenerational inheritance or resetting of stress-induced epigenetic modifications: two sides of the same coin. FRONTIERS IN PLANT SCIENCE 2015; 6:699. [PMID: 26442015 PMCID: PMC4561384 DOI: 10.3389/fpls.2015.00699] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/21/2015] [Indexed: 05/06/2023]
Abstract
The transgenerational inheritance of stress-induced epigenetic modifications is still controversial. Despite several examples of defense "priming" and induced genetic rearrangements, the involvement and persistence of transgenerational epigenetic modifications is not known to be general. Here I argue that non-transmission of epigenetic marks through meiosis may be regarded as an epigenetic modification in itself, and that we should understand the implications for plant evolution in the context of both selection for and selection against transgenerational epigenetic memory. Recent data suggest that both epigenetic inheritance and resetting are mechanistically directed and targeted. Stress-induced epigenetic modifications may buffer against DNA sequence-based evolution to maintain plasticity, or may form part of plasticity's adaptive potential. To date we have tended to concentrate on the question of whether and for how long epigenetic memory persists. I argue that we should now re-direct our question to investigate the differences between where it persists and where it does not, to understand the higher order evolutionary methods in play and their contribution.
Collapse
Affiliation(s)
- Penny J. Tricker
- *Correspondence: Penny J. Tricker, Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Hartley Grove, Urrbrae, SA 5064, Australia,
| |
Collapse
|
27
|
Smith G, Smith C, Kenny JG, Chaudhuri RR, Ritchie MG. Genome-wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus). Mol Biol Evol 2014; 32:888-95. [PMID: 25534027 DOI: 10.1093/molbev/msu344] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Epigenetic marks such as DNA methylation play important biological roles in gene expression regulation and cellular differentiation during development. To examine whether DNA methylation patterns are potentially associated with naturally occurring phenotypic differences, we examined genome-wide DNA methylation within Gasterosteus aculeatus, using reduced representation bisulfite sequencing. First, we identified highly methylated regions of the stickleback genome, finding such regions to be located predominantly within genes, and associated with genes functioning in metabolism and biosynthetic processes, cell adhesion, signaling pathways, and blood vessel development. Next, we identified putative differentially methylated regions (DMRs) of the genome between complete and low lateral plate morphs of G. aculeatus. We detected 77 DMRs that were mainly located in intergenic regions. Annotations of genes associated with these DMRs revealed potential functions in a number of known divergent adaptive phenotypes between G. aculeatus ecotypes, including cardiovascular development, growth, and neuromuscular development.
Collapse
Affiliation(s)
- Gilbert Smith
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - Carl Smith
- School of Biology, University of St Andrews, St. Andrews, Fife, United Kingdom
| | - John G Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Roy R Chaudhuri
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Michael G Ritchie
- School of Biology, University of St Andrews, St. Andrews, Fife, United Kingdom
| |
Collapse
|
28
|
Kishida O, Tezuka A, Ikeda A, Takatsu K, Michimae H. Adaptive acceleration in growth and development of salamander hatchlings in cannibalistic situations. Funct Ecol 2014. [DOI: 10.1111/1365-2435.12361] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Osamu Kishida
- Teshio Experimental Forest, Field Science Center for Northern Biosphere Hokkaido University Toikanbetsu 131 Horonobe, Hokkaido 098‐2943 Japan
| | - Ayumi Tezuka
- Teshio Experimental Forest, Field Science Center for Northern Biosphere Hokkaido University Toikanbetsu 131 Horonobe, Hokkaido 098‐2943 Japan
- Department of Bioscience and Bioinformatics Kyushu Institute of Technology Kawazu 680‐4 Iizuka Fukuoka 820‐8502 Japan
| | - Akiko Ikeda
- Graduate School of Environmental Science Hokkaido University Toikanbetsu 131 Horonobe Hokkaido 098‐2943 Japan
| | - Kunio Takatsu
- Graduate School of Environmental Science Hokkaido University Toikanbetsu 131 Horonobe Hokkaido 098‐2943 Japan
| | - Hirofumi Michimae
- Division of Biostatistics School of Pharmaceutical Sciences Kitasato University Shirokane 5‐9‐1Minato‐ku Tokyo 108‐8641 Japan
| |
Collapse
|
29
|
Why are individuals so different from each other? Heredity (Edinb) 2014; 115:285-92. [PMID: 25407080 DOI: 10.1038/hdy.2014.103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/10/2014] [Accepted: 07/24/2014] [Indexed: 02/07/2023] Open
Abstract
An important contributor to the differences between individuals derives from their plasticity. Such plasticity is widespread in organisms from the simple to the most complex. Adaptability plasticity enables the organism to cope with a novel challenge not previously encountered by its ancestors. Conditional plasticity appears to have evolved from repeated challenges from the environment so that the organism responds in a particular manner to the environment in which it finds itself. The resulting phenotypic variation can be triggered during development in a variety of ways, some mediated through the parent's phenotype. Sometimes the organism copes in suboptimal conditions trading off reproductive success against survival. Whatever the adaptedness of the phenotype, each of the many types of plasticity demonstrates how a given genotype will express itself differently in different environmental conditions-a field of biology referred to as the study of epigenetics. The ways in which epigenetic mechanisms may have evolved are discussed, as are the potential impacts on the evolution of their descendants.
Collapse
|
30
|
Hanson MA, Gluckman PD. Early developmental conditioning of later health and disease: physiology or pathophysiology? Physiol Rev 2014; 94:1027-76. [PMID: 25287859 PMCID: PMC4187033 DOI: 10.1152/physrev.00029.2013] [Citation(s) in RCA: 698] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Extensive experimental animal studies and epidemiological observations have shown that environmental influences during early development affect the risk of later pathophysiological processes associated with chronic, especially noncommunicable, disease (NCD). This field is recognized as the developmental origins of health and disease (DOHaD). We discuss the extent to which DOHaD represents the result of the physiological processes of developmental plasticity, which may have potential adverse consequences in terms of NCD risk later, or whether it is the manifestation of pathophysiological processes acting in early life but only becoming apparent as disease later. We argue that the evidence suggests the former, through the operation of conditioning processes induced across the normal range of developmental environments, and we summarize current knowledge of the physiological processes involved. The adaptive pathway to later risk accords with current concepts in evolutionary developmental biology, especially those concerning parental effects. Outside the normal range, effects on development can result in nonadaptive processes, and we review their underlying mechanisms and consequences. New concepts concerning the underlying epigenetic and other mechanisms involved in both disruptive and nondisruptive pathways to disease are reviewed, including the evidence for transgenerational passage of risk from both maternal and paternal lines. These concepts have wider implications for understanding the causes and possible prevention of NCDs such as type 2 diabetes and cardiovascular disease, for broader social policy and for the increasing attention paid in public health to the lifecourse approach to NCD prevention.
Collapse
Affiliation(s)
- M A Hanson
- Academic Unit of Human Development and Health, University of Southampton, and NIHR Nutrition Biomedical Research Centre, University Hospital, Southampton, United Kingdom; and Liggins Institute and Gravida (National Centre for Growth and Development), University of Auckland, Auckland, New Zealand
| | - P D Gluckman
- Academic Unit of Human Development and Health, University of Southampton, and NIHR Nutrition Biomedical Research Centre, University Hospital, Southampton, United Kingdom; and Liggins Institute and Gravida (National Centre for Growth and Development), University of Auckland, Auckland, New Zealand
| |
Collapse
|
31
|
Duncan EJ, Gluckman PD, Dearden PK. Epigenetics, plasticity, and evolution: How do we link epigenetic change to phenotype? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:208-20. [PMID: 24719220 DOI: 10.1002/jez.b.22571] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/13/2014] [Accepted: 03/15/2014] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms are proposed as an important way in which the genome responds to the environment. Epigenetic marks, including DNA methylation and Histone modifications, can be triggered by environmental effects, and lead to permanent changes in gene expression, affecting the phenotype of an organism. Epigenetic mechanisms have been proposed as key in plasticity, allowing environmental exposure to shape future gene expression. While we are beginning to understand how these mechanisms have roles in human biology and disease, we have little understanding of their roles and impacts on ecology and evolution. In this review, we discuss different types of epigenetic marks, their roles in gene expression and plasticity, methods for assaying epigenetic changes, and point out the future advances we require to understand fully the impact of this field.
Collapse
Affiliation(s)
- Elizabeth J Duncan
- Genetics Otago and Gravida, The National Centre for Growth and Development, Biochemistry Department, University of Otago, Dunedin, New Zealand
| | | | | |
Collapse
|
32
|
Schlichting CD, Wund MA. Phenotypic plasticity and epigenetic marking: an assessment of evidence for genetic accommodation. Evolution 2014; 68:656-72. [PMID: 24410266 DOI: 10.1111/evo.12348] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/22/2013] [Indexed: 12/16/2022]
Abstract
The relationship between genotype (which is inherited) and phenotype (the target of selection) is mediated by environmental inputs on gene expression, trait development, and phenotypic integration. Phenotypic plasticity or epigenetic modification might influence evolution in two general ways: (1) by stimulating evolutionary responses to environmental change via population persistence or by revealing cryptic genetic variation to selection, and (2) through the process of genetic accommodation, whereby natural selection acts to improve the form, regulation, and phenotypic integration of novel phenotypic variants. We provide an overview of models and mechanisms for how such evolutionary influences may be manifested both for plasticity and epigenetic marking. We point to promising avenues of research, identifying systems that can best be used to address the role of plasticity in evolution, as well as the need to apply our expanding knowledge of genetic and epigenetic mechanisms to our understanding of how genetic accommodation occurs in nature. Our review of a wide variety of studies finds widespread evidence for evolution by genetic accommodation.
Collapse
Affiliation(s)
- Carl D Schlichting
- Department of Ecology & Evolutionary Biology, U-3043, University of Connecticut, Storrs, Connecticut 06269.
| | | |
Collapse
|
33
|
|
34
|
Adaptation or malignant transformation: the two faces of epigenetically mediated response to stress. BIOMED RESEARCH INTERNATIONAL 2013; 2013:954060. [PMID: 24187667 PMCID: PMC3803131 DOI: 10.1155/2013/954060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 01/22/2023]
Abstract
Adaptive response to stress is a fundamental property of living systems. At the cellular level, many different types of stress elicit an essentially limited repertoire of adaptive responses. Epigenetic changes are the main mechanism for medium- to long-term adaptation to accumulated (intense, long-term, or repeated) stress. We propose the adaptive deregulation of the epigenome in response to stress (ADERS) hypothesis which assumes that the unspecific adaptive stress response grows stronger with the increasing stress level, epigenetically activating response gene clusters while progressively deregulating other cellular processes. The balance between the unspecific adaptive response and the general epigenetic deregulation is critical because a strong response can lead to pathology, particularly to malignant transformation. The main idea of our hypothesis is the continuum traversed by a cell subjected to accumulated stress, which lies between an unspecific adaptive response and pathological deregulation--the two extremes sharing the same underlying cause, which is a manifestation of a unified epigenetically mediated adaptive response to stress. The evolutionary potential of epigenetic regulation in multigenerational adaptation is speculatively discussed in the light of neo-Lamarckism. Finally, an approach to testing the proposed hypothesis is presented, relying on either the publicly available datasets or on conducting new experiments.
Collapse
|
35
|
Tricker PJ, Rodríguez López CM, Hadley P, Wagstaff C, Wilkinson MJ. Pre-conditioning the epigenetic response to high vapor pressure deficit increases the drought tolerance of Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2013; 8:25974. [PMID: 24270688 PMCID: PMC4091208 DOI: 10.4161/psb.25974] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/30/2013] [Accepted: 07/31/2013] [Indexed: 05/22/2023]
Abstract
Epigenetic modification of the genome via cytosine methylation is a dynamic process that responds to changes in the growing environment. This modification can also be heritable. The combination of both properties means that there is the potential for the life experiences of the parental generation to modify the methylation profiles of their offspring and so potentially to “pre-condition” them to better accommodate abiotic conditions encountered by their parents. We recently identified high vapor pressure deficit (vpd)-induced DNA methylation at 2 gene loci in the stomatal development pathway and an associated reduction in leaf stomatal frequency.1 Here, we test whether this epigenetic modification pre-conditioned parents and their offspring to the more severe water stress of periodic drought. We found that 3 generations of high vpd-grown plants were better able to withstand periodic drought stress over 2 generations. This resistance was not directly associated with de novo methylation of the target stomata genes, but was associated with the cmt3 mutant’s inability to maintain asymmetric sequence context methylation. If our finding applies widely, it could have significant implications for evolutionary biology and breeding for stressful environments.
Collapse
Affiliation(s)
- Penny J Tricker
- School of Biological Sciences; University of Reading; Whiteknights; Reading, UK
| | - Carlos M Rodríguez López
- Institute of Biological; Environmental and Rural Sciences; Edward Llywd Building; University of Aberystwyth; Aberystwyth, Ceredigion, UK
| | - P Hadley
- School of Biological Sciences; University of Reading; Whiteknights; Reading, UK
| | - C Wagstaff
- Department of Food and Nutritional Sciences; University of Reading; Whiteknights; Reading, UK
| | - Mike J Wilkinson
- Institute of Biological; Environmental and Rural Sciences; Edward Llywd Building; University of Aberystwyth; Aberystwyth, Ceredigion, UK
- Correspondence to: Mike J Wilkinson,
| |
Collapse
|
36
|
Pathways by which the interplay of organismic and environmental factors lead to phenotypic variation within and across generations. ADVANCES IN CHILD DEVELOPMENT AND BEHAVIOR 2013; 44:325-54. [PMID: 23834011 DOI: 10.1016/b978-0-12-397947-6.00012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The range of responses made to environmental exigencies by animals, including humans, may be impacted by the experiences of their progenitors. In mammals, pathways have been documented ranging from transactions between a mother and her developing fetus in the womb through continuity of parenting practices and cultural inheritance. In addition, phenotypic plasticity may be constrained by factors transmitted by the gametes that are involved in the regulation of gene expression rather than modifications to the genome itself. Possible mediators for this kind of inheritance are examined, and the conditions that might have led to the evolution of such transmission are considered. Anticipatory adjustments to possible environmental exigencies are likely to occur when such conditions recur regularly, but intermittently across generations and endure for substantial periods of time, and when adjusting to them after the fact is likely to be biologically costly, even life-threatening. It appears that physical growth and responses to nutrient availability are domains in which anticipatory, epigenetically inherited adjustments occur. In addition, given the fact that humans have oppressed one another repeatedly and for relatively long periods of time, such behavioral tendencies as boldness or innovativeness may be behavioral traits subject to such effects. The implications of these factors for research and policy are discussed.
Collapse
|
37
|
Ashman TL, Kwok A, Husband BC. Revisiting the dioecy-polyploidy association: alternate pathways and research opportunities. Cytogenet Genome Res 2013; 140:241-55. [PMID: 23838528 DOI: 10.1159/000353306] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The evolutionary transition from hermaphroditism (combined sexes) to dioecy (separate sexes) is associated with whole genome duplication (polyploidy) in several flowering plant genera. Moreover, there is evidence for transitions in the opposite direction, i.e. a loss of dioecy with an increase in ploidy. Here, we review evidence for these associations, synthesize previous ideas on the mechanism underlying the patterns and explore alternative pathways. Specifically, we examine potential ecological and genetic mechanisms, differentiated by whether ploidy or gender (functional sex expression of the plant) changes are the primary cause and whether the effect is direct or indirect. An analysis of 22 genera variable for both ploidy and gender indicates that gender monomorphism (hermaphroditism, monoecy) is more common among diploid than polyploid species, whereas gender dimorphism (dioecy, gynodioecy, subdioecy) is more frequent among polyploid species. The transition from diploid hermaphroditic to polyploid gender-dimorphic taxa may arise directly through changes in gender as a result of genome duplication through genomic rearrangements or homeologous recombination, or changes in gender may result in increased unreduced gamete production leading to polyploid formation. Alternatively, the transition may occur through the indirect effects of genome duplication on mating system and inbreeding depression, which favor selection for unisexuality, or habitat shifts associated with unisexuality may simultaneously cause increased unreduced gamete production. Novel mechanisms for transitions in the opposite direction (from dioecy to hermaphroditism with increase in ploidy) include disruption of genetic sex determination and the benefits of reproductive assurance. We highlight key questions requiring further attention and promising approaches for answering them and better clarifying the genesis of sexual system polyploidy associations. See also the sister article focusing on animals by Wertheim et al. in this themed issue.
Collapse
Affiliation(s)
- T-L Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260-3929, USA. tia1 @ pitt.edu
| | | | | |
Collapse
|
38
|
Sharif J, Shinkai Y, Koseki H. Is there a role for endogenous retroviruses to mediate long-term adaptive phenotypic response upon environmental inputs? Philos Trans R Soc Lond B Biol Sci 2013; 368:20110340. [PMID: 23166400 DOI: 10.1098/rstb.2011.0340] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Endogenous retroviruses (ERVs) are long terminal repeat-containing virus-like elements that have colonized approximately 10 per cent of the present day mammalian genomes. The intracisternal A particles (IAPs) are a class of ERVs that is currently highly active in the rodents. IAP elements can influence the transcription profile of nearby genes by providing functional promoter elements and modulating local epigenetic landscape through changes in DNA methylation and histone (H3K9) modifications. Despite the potential role for IAPs in gene regulation, the precise genomic locations where these elements are integrated are not well understood. To address this issue, we have identified more than 400 novel IAP insertion sites within/near annotated genes by searching the murine genome, which suggests that the impact of IAP elements on local and/or global gene regulation could be more profound than was previously expected. On the basis of our independent analyses and already published reports, here we argue that IAPs and ERV elements in general could have an evolutionary role for modulating phenotypic plasticity upon environmental inputs, and that this could be mediated through specific stages of embryonic development such as placentation during which the epigenetic constraints on IAP elements are partially relaxed.
Collapse
Affiliation(s)
- Jafar Sharif
- Developmental Genetics Group, RIKEN Research Center for Allergy & Immunology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Kanagawa, Japan.
| | | | | |
Collapse
|
39
|
Carja O, Liberman U, Feldman MW. Evolution with stochastic fitnesses: a role for recombination. Theor Popul Biol 2013; 86:29-42. [PMID: 23517905 DOI: 10.1016/j.tpb.2013.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 12/16/2022]
Abstract
Phenotypic adaptation to fluctuating environments has been an important focus in the population genetic literature. Previous studies have shown that evolution under temporal variation is determined not only by expected fitness in a given generation, but also by the degree of variation in fitness over generations; in an uncertain environment, alleles that increase the geometric mean fitness can invade a randomly mating population at equilibrium. This geometric mean principle governs the evolutionary interplay of genes controlling mean phenotype and genes controlling phenotypic variation, such as genetic regulators of the epigenetic machinery. Thus, it establishes an important role for stochastic epigenetic variation in adaptation to fluctuating environments: by modifying the geometric mean fitness, variance-modifying genes can change the course of evolution and determine the long-term trajectory of the evolving system. The role of phenotypic variance has previously been studied in systems in which the only driving force is natural selection, and there is no recombination between mean- and variance-modifying genes. Here, we develop a population genetic model to investigate the effect of recombination between mean- and variance-modifiers of phenotype on the geometric mean principle under different environmental regimes and fitness landscapes. We show that interactions of recombination with stochastic epigenetic variation and environmental fluctuations can give rise to complex evolutionary dynamics that differ from those in systems with no recombination.
Collapse
Affiliation(s)
- Oana Carja
- Department of Biology, Stanford University, Stanford, CA, 94305, United States.
| | | | | |
Collapse
|
40
|
Snell-Rood EC, Troth A, Moczek AP. DNA methylation as a mechanism of nutritional plasticity: limited support from horned beetles. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:22-34. [PMID: 22951993 PMCID: PMC3708545 DOI: 10.1002/jez.b.22479] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 06/01/2012] [Accepted: 07/23/2012] [Indexed: 01/30/2023]
Abstract
Epigenetic changes to DNA, potentially heritable alterations above the sequence level, such as DNA methylation, are thought to underlie many instances of adaptive phenotypic plasticity. Our understanding of the links between epigenetic variation and adaptive phenotypic plasticity in natural populations is limited. If DNA methylation underlies adaptive responses to different nutritional environments, methylation patterns should be correlated with differences in performance across nutritional environments, and respond to changes in the environment. Additionally, genotypes that can cope with a broader range of nutritional environments are expected to have greater flexibility in methylation patterns. We tested these predictions using horned beetles (genus Onthophagus), which can cope with a wide range of variation in larval nutrition. We surveyed levels of methylation across several methylated loci in lab-reared beetles originating from natural populations using a methylation-specific amplified fragment length polymorphism (AFLP) analysis. For less than half the of the loci investigated, methylation level was correlated with performance, measured as adult body size attained on a given diet, in different nutritional environments, with an overall greater effect in males (the more nutritionally plastic sex) than females. Methylation levels at most sites were influenced more by genotype (iso-female line) than by environment (dung type). Only 1 site (of 12) showed a significant genotype-by-environment interaction. Taken together, our results provide modest support for the hypothesis that DNA methylation underlies nutritional plasticity, as only 8-16% of methylated sites conformed to all of our predictions.
Collapse
|
41
|
Schnurr ME, Yin Y, Scott GR. Temperature during embryonic development has persistent effects on metabolic enzymes in the muscle of zebrafish. J Exp Biol 2013; 217:1370-80. [DOI: 10.1242/jeb.094037] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Summary
Global warming is intensifying interest in the physiological consequences of temperature change in ectotherms, but we still have a relatively poor understanding of the effects of temperature on early life stages. This study determined how embryonic temperature (TE) affects development and the activity of metabolic enzymes in the swimming muscle of zebrafish. Embryos developed successfully to hatching (survival ≥ 88%) from 22°C to 32°C, but suffered sharp increases in mortality outside of this range. Embryos that were incubated until hatching at a control TE (27°C) or near the extremes for successful development (22°C or 32°C) were next raised to adulthood under control conditions at 27°C. Growth trajectories after hatching were altered in the 22°C and 32°C TE groups compared to 27°C TE controls, but growth slowed after 3 months of age in all groups. Maximal enzyme activities of cytochrome c oxidase (COX), citrate synthase (CS), hydroxyacyl-coA dehydrogenase (HOAD), pyruvate kinase (PK), and lactate dehydrogenase (LDH) were measured across a range of assay temperatures (22°C, 27°C, 32°C, 36°C) in adults from each TE group that were acclimated to 27°C or 32°C. Substrate affinities (Km) were also determined for COX and LDH. In adult fish acclimated to 27°C, COX and PK activities were higher in 22°C and 32°C TE groups than in 27°C TE controls, and the temperature optimum for COX activity was higher in the 32°C TE group than in the 22°C TE group. Warm acclimation reduced COX, CS, and/or PK activities in the 22°C and 32°C TE groups, possibly to compensate for thermal effects on molecular activity. This response did not occur in the 27°C TE controls, which instead increased LDH and HOAD activities. Warm acclimation also increased thermal sensitivity (Q10) of HOAD to cool temperatures across all TE groups. We conclude that the temperature experienced during early development can have a persistent impact on energy metabolism pathways and acclimation capacity in later life.
Collapse
Affiliation(s)
| | - Yi Yin
- McMaster University, Canada
| | | |
Collapse
|
42
|
Bell CG, Wilson GA, Butcher LM, Roos C, Walter L, Beck S. Human-specific CpG "beacons" identify loci associated with human-specific traits and disease. Epigenetics 2012; 7:1188-99. [PMID: 22968434 PMCID: PMC3469460 DOI: 10.4161/epi.22127] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. Here we provide evidence that CpG dinucleotides play a special role in this process. CpGs enable epigenome variability via DNA methylation, and this epigenetic mark functions as a regulatory mechanism. Therefore, species-specific CpGs may influence species-specific regulation. We report non-polymorphic species-specific CpG dinucleotides (termed “CpG beacons”) as a distinct genomic feature associated with CpG island (CGI) evolution, human traits and disease. Using an inter-primate comparison, we identified 21 extreme CpG beacon clusters (≥ 20/kb peaks, empirical p < 1.0 × 10−3) in humans, which include associations with four monogenic developmental and neurological disease related genes (Benjamini-Hochberg corrected p = 6.03 × 10−3). We also demonstrate that beacon-mediated CpG density gain in CGIs correlates with reduced methylation in these species in orthologous CGIs over time, via human, chimpanzee and macaque MeDIP-seq. Therefore mapping into both the genomic and epigenomic space the identified CpG beacon clusters define points of intersection where a substantial two-way interaction between genetic sequence and epigenetic state has occurred. Taken together, our data support a model for CpG beacons to contribute to CGI evolution from genesis to tissue-specific to constitutively active CGIs.
Collapse
Affiliation(s)
- Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK.
| | | | | | | | | | | |
Collapse
|
43
|
Tattersall GJ, Sinclair BJ, Withers PC, Fields PA, Seebacher F, Cooper CE, Maloney SK. Coping with Thermal Challenges: Physiological Adaptations to Environmental Temperatures. Compr Physiol 2012; 2:2151-202. [DOI: 10.1002/cphy.c110055] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
44
|
Carja O, Feldman MW. An equilibrium for phenotypic variance in fluctuating environments owing to epigenetics. J R Soc Interface 2012; 9:613-23. [PMID: 21849387 PMCID: PMC3284130 DOI: 10.1098/rsif.2011.0390] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 07/26/2011] [Indexed: 01/13/2023] Open
Abstract
The connection between random environments and genetic and phenotypic variability has been a major focus in the population genetic literature. By providing differential access to the underlying genetic information, epigenetic variation could play an important role in the interaction between environmental and phenotypic variation. Using simulation, we model epigenetic plasticity during development by investigating the dynamics of genetic regulators of the epigenetic machinery that change the variance of the phenotype, while having no effect on the phenotype's mean. Previous studies have found that increased phenotypic variance is selected for if the environment is fluctuating. Here, we find that when a variance-increasing allele achieves a sufficiently high frequency, it can be out-competed by a variance-reducing allele, with the consequence that the population evolves to an equilibrium phenotypic variability. This equilibrium is shown to be robust to different initial conditions, but to depend heavily on parameters of the model, such as the mutation rate, the fitness landscape and the nature of the environmental fluctuation. Indeed, if there is no mutation at the genes controlling the variance of the phenotype, reduction of this variance is favoured.
Collapse
Affiliation(s)
- Oana Carja
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | | |
Collapse
|
45
|
Valena S, Moczek AP. Epigenetic mechanisms underlying developmental plasticity in horned beetles. GENETICS RESEARCH INTERNATIONAL 2012; 2012:576303. [PMID: 22567393 PMCID: PMC3335661 DOI: 10.1155/2012/576303] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/05/2011] [Indexed: 11/18/2022]
Abstract
All developmental plasticity arises through epigenetic mechanisms. In this paper we focus on the nature, origins, and consequences of these mechanisms with a focus on horned beetles, an emerging model system in evolutionary developmental genetics. Specifically, we introduce the biological significance of developmental plasticity and summarize the most important facets of horned beetle biology. We then compare and contrast the epigenetic regulation of plasticity in horned beetles to that of other organisms and discuss how epigenetic mechanisms have facilitated innovation and diversification within and among taxa. We close by highlighting opportunities for future studies on the epigenetic regulation of plastic development in these and other organisms.
Collapse
Affiliation(s)
- Sophie Valena
- Department of Biology, Indiana University, 915 E Third Street, Myers Hall 150, Bloomington, IN 47405-7107, USA
| | - Armin P. Moczek
- Department of Biology, Indiana University, 915 E Third Street, Myers Hall 150, Bloomington, IN 47405-7107, USA
| |
Collapse
|
46
|
|
47
|
Wolf C, Linden DEJ. Biological pathways to adaptability - interactions between genome, epigenome, nervous system and environment for adaptive behavior. GENES BRAIN AND BEHAVIOR 2011; 11:3-28. [DOI: 10.1111/j.1601-183x.2011.00752.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
48
|
The impact of the organism on its descendants. GENETICS RESEARCH INTERNATIONAL 2011; 2012:640612. [PMID: 22567396 PMCID: PMC3335618 DOI: 10.1155/2012/640612] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/30/2011] [Accepted: 10/24/2011] [Indexed: 11/18/2022]
Abstract
Historically, evolutionary biologists have taken the view that an understanding of development is irrelevant to theories of evolution. However, the integration of several disciplines in recent years suggests that this position is wrong. The capacity of the organism to adapt to challenges from the environment can set up conditions that affect the subsequent evolution of its descendants. Moreover, molecular events arising from epigenetic processes can be transmitted from one generation to the next and influence genetic mutation. This in turn can facilitate evolution in the conditions in which epigenetic change was first initiated.
Collapse
|
49
|
Cocozza S, Akhtar MM, Miele G, Monticelli A. CpG islands undermethylation in human genomic regions under selective pressure. PLoS One 2011; 6:e23156. [PMID: 21829712 PMCID: PMC3149076 DOI: 10.1371/journal.pone.0023156] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 07/07/2011] [Indexed: 11/18/2022] Open
Abstract
DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE) Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more "protected" from methylation when compared with other regions of the genome.
Collapse
Affiliation(s)
- Sergio Cocozza
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli Federico II - Università di Salerno, Naples, Italy.
| | | | | | | |
Collapse
|
50
|
A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics 2011; 186:1085-93. [PMID: 21156958 DOI: 10.1534/genetics.110.124180] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as "transposable elements" in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work.
Collapse
|