Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological ...experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non‐model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non‐model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.
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Epigenetics for ecologists Bossdorf, Oliver; Richards, Christina L; Pigliucci, Massimo
Ecology letters,
February 2008, Volume:
11, Issue:
2
Journal Article
Peer reviewed
There is now mounting evidence that heritable variation in ecologically relevant traits can be generated through a suite of epigenetic mechanisms, even in the absence of genetic variation. Moreover, ...recent studies indicate that epigenetic variation in natural populations can be independent from genetic variation, and that in some cases environmentally induced epigenetic changes may be inherited by future generations. These novel findings are potentially highly relevant to ecologists because they could significantly improve our understanding of the mechanisms underlying natural phenotypic variation and the responses of organisms to environmental change. To understand the full significance of epigenetic processes, however, it is imperative to study them in an ecological context. Ecologists should therefore start using a combination of experimental approaches borrowed from ecological genetics, novel techniques to analyse and manipulate epigenetic variation, and genomic tools, to investigate the extent and structure of epigenetic variation within and among natural populations, as well as the interrelations between epigenetic variation, phenotypic variation and ecological interactions.
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Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole‐genome measures of gene expression with microarrays and RNAseq ...(i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.
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The expansion of invasive species challenges our understanding of the process of adaptation. Given that the invasion process often entails population bottlenecks, it is surprising that many invasives ...appear to thrive even with low levels of sequence‐based genetic variation. Using Amplified Fragment Length Polymorphism (AFLP) and methylation sensitive‐AFLP (MS‐AFLP) markers, we tested the hypothesis that differentiation of invasive Japanese knotweed in response to new habitats is more correlated with epigenetic variation than DNA sequence variation. We found that the relatively little genetic variation present was differentiated among species, with less differentiation among sites within species. In contrast, we found a great deal of epigenetic differentiation among sites within each species and evidence that some epigenetic loci may respond to local microhabitat conditions. Our findings indicate that epigenetic effects could contribute to phenotypic variation in genetically depauperate invasive populations. Deciphering whether differences in methylation patterns are the cause or effect of habitat differentiation will require manipulative studies.
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Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed ...genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ∼110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PC(veg)) correlate to temperature and precipitation occurrence in the field. The largest PC(veg) axes included thermoregulatory genes while the second major PC(veg) was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract Understanding the mechanisms that underlie plant invasions is critical for management and conservation of biodiversity. At the same time, invasive species also provide a unique opportunity ...to study rapid adaptation to complex environmental conditions. Using four replicate reciprocal transplant experiments across three habitats, we described patterns of phenotypic response and assessed the degree of local adaptation in knotweed populations. We found plants from beach habitats were generally smaller than plants from marsh and roadside habitats when grown in their home habitat. In the marsh habitat, marsh plants were generally larger than beach plants, but not different from roadside plants. There were no differences among plants grown in the roadside habitat. We found mixed evidence for local adaptation: plants from the marsh habitat had greater biomass in their “home” sites, while plants from beaches and roadsides had greater survival in their “home” sites compared to other plants. In sum, we found phenotypic differentiation and some support for the hypothesis of rapid local adaptation of plants from beach, marsh and roadside habitats. Identifying whether these patterns of differentiation result from genetic or heritable non-genetic mechanisms will require further work.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
To explore the potential evolutionary relevance of heritable epigenetic variation, the National Evolutionary Synthesis Center recently hosted a catalysis meeting that brought together molecular ...epigeneticists, experimental evolutionary ecologists, and theoretical population and quantitative geneticists working across a wide variety of systems. The group discussed the methods available to investigate epigenetic variation and epigenetic inheritance, and how to evaluate their importance for phenotypic evolution. We found that understanding the relevance of epigenetic effects in phenotypic evolution will require clearly delineating epigenetics within existing terminology and expanding research efforts into ecologically relevant circumstances across model and nonmodel organisms. In addition, a critical component of understanding epigenetics will be the development of new and current statistical approaches and expansion of quantitative and population genetic theory. Although the importance of heritable epigenetic effects on evolution is still under discussion, investigating them in the context of a multidisciplinary approach could transform the field.
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Epigenetics refers to chemical modifications of chromatin or transcribed DNA that can influence gene activity and expression without changes in DNA sequence. The last 20 years have yielded ...breakthroughs in our understanding of epigenetic processes that impact many fields of biology. In this review, we discuss how epigenetics relates to quantitative genetics and evolution. We argue that epigenetics is important for quantitative genetics because: (1) quantitative genetics is increasingly being combined with genomics, and therefore we should expand our thinking to include cellular-level mechanisms that can account for phenotypic variance and heritability besides just those that are hard-coded in the DNA sequence; and (2) epigenetic mechanisms change how phenotypic variance is partitioned, and can thereby change the heritability of traits and how those traits are inherited. To explicate these points, we show that epigenetics can influence all aspects of the phenotypic variance formula: V
(total phenotypic variance) = V
(genetic variance) + V
(environmental variance) + V
(genotype-by-environment interaction) + 2COV
(the genotype-environment covariance) + V
(residual variance), requiring new strategies to account for different potential sources of epigenetic effects on phenotypic variance. We also demonstrate how each of the components of phenotypic variance not only can be influenced by epigenetics, but can also have evolutionary consequences. We argue that no sources of epigenetic effects on phenotypic variance can be easily cast aside in a quantitative genetic research program that seeks to understand evolutionary processes.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Investigating the features and implications of epigenetic mechanisms across the breadth of organisms and ecosystems is important for understanding the ecological relevance of epigenetics. Several ...cost-effective reduced representation bisulfite sequencing approaches (RRBS) have been recently developed and applied to different organisms that lack a well annotated reference genome. These new approaches improve the assessment of epigenetic diversity in ecological settings and may provide functional insights. We assess here the opportunities and limitations of RRBS in nonmodel plant species. Well thought out experimental designs that include complementary gene expression studies, and the improvement of genomics resources for the target group, promise to maximize the effect of future RRBS studies.
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Epigenetics and the success of invasive plants Mounger, Jeannie; Ainouche, Malika L; Bossdorf, Oliver ...
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
06/2021, Volume:
376, Issue:
1826
Journal Article
Peer reviewed
Open access
Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the ...evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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