Epigenetics and Evolutionary Processes (2015)
(From left: Catarina Lira-Medeiros, Bob Schmitz, Josh Banta, Koen Verhoeven, Gil Smith, Liran Carmel, and Marta Robertson)
Synopsis. Scientists have abundant information on sequences for a variety of organisms, but have made little progress in understanding how the genome actually functions in creating complex traits that are adaptive in complex environments (Richards et al. 2009; Pigliucci 2010). One area that may contribute to this understanding is ecological and evolutionary epigenetics, which focuses the relationships between epigenetic variation and the axes of phenotypic variation that fuel evolutionary change. Epigenetic mechanisms can alter gene expression and organismal function without any alterations in DNA sequences (Richards 2006), leading to variation in diverse phenotypes (Cubas et al. 1999; Morgan et al. 1999; Rakyan et al. 2003; Manning et al. 2006; Kucharski et al. 2008; Cortijo et al. 2014). Furthermore, epigenetic modifications can vary among individuals and populations (Herrera and Bazaga 2010, 2011; Massicotte et al. 2011; Herrera et al. 2012; Liu et al. 2012; Massicotte and Angers 2012; Schrey et al. 2012). Epigenetic modifications can even be heritable (Jablonka and Raz 2009; Johannes et al. 2009; Verhoeven et al. 2010) and the phenotypic consequences of epigenetic changes have been observed in diverse taxa (animals: Gluckman et al. 2009; Snell-Rood et al. 2013; plants: Cubas et al. 1999; Bossdorf et al. 2010; Herrera and Bazaga 2011; Zhang et al 2013; fungi: Reyna-López et al. 1997; yeast: Herrera et al. 2012). Thus, epigenetic mechanisms are a potentially important mechanism of phenotypic change (Angers et al. 2010; Verhoeven et al. 2010; Richards et al. 2010; Cortijo et al. 2014). The study of epigenetic variation is already providing insights at both ecological and evolutionary time scales (Bossdorf et al. 2008; Richards et al. 2010; Latzel et al. 2013). Recent experimental screening for changes in methylation patterns has shown that epimutations can be induced by environmental stress, affect phenotype, and occur more rapidly than DNA sequence mutations (Johannes et al. 2009; Verhoeven et al. 2010; Cortijo et al. 2014). For this reason epigenetic effects could offer an alternative to genetic variation for rapid response to environmental challenges (Bossdorf et al. 2008), but so far few studies have begun to explore this possibility. While most of the work in ecological epigenetics to date has been done in plants, there are an increasing number of animal studies (Schrey et al 2013). This symposium highlights different approaches across systems that are making progress to understand the importance of epigenetics in evolutionary processes.
Rationale. Evolutionary biology is currently experiencing an emergence of several research areas beyond the scope of the Modern Synthesis, which merged Mendelian genetics with the study of evolution over 70 years ago (Huxley 1942). Epigenetics is one such research area of study. While epigenetics has been studied in a cellular/molecular/biomedical context for decades (Holliday 2006), it is now emerging as an active field of study in evolutionary biology, where it is being used to understand mechanisms of heritable phenotypic variation (Schrey et al. 2012). Yet because evolutionary epigenetics is still very young, it remains largely unexplored. We believe the time is ripe to start closing the gap between the number of molecular/cellular studies on epigenetics and the much smaller number of evolutionary studies on epigenetics.
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Understanding mechanisms of response to novel environments in invasive Japanese knotweed
Abstract. The expansion of invasive species provides an opportunity to investigate how organisms establish and adapt to new environments, but also challenges our understanding of the process of adaptation. Classic studies interested in adaptation have focused on DNA sequence variation, and the assumption that trait variation is based on sequence variation, but invasive species typically have low sequence based variation. There is now evidence to suggest that epigenetic effects can result in heritable, novel phenotypes even without variation in DNA sequence and could therefore provide an unappreciated source of response. We are exploring the potential role of epigenetic processes in invasive Japanese knotweed (Fallopia japonica) with a combination of classic ecological design and developing novel genomics techniques. These studies will enhance our understanding of how epigenetic variation may be shaped by environment and contribute to adaptation.
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Epigenome of tomato (Solanum lycopersicum) and its implications on the domestication process of this species
Abstract. Changes in DNA methylation of cytosines can be used as markers of biodiversity in wild species. The cytosine DNA methylation is an epigenetic phenomenon related to different processes such as genome stability and regulation of gene expression. Through the next-generation sequencing techniques, large scale epigenome studies have been carried out with model and wild plant species. Tomato is a species of great interest for agriculture and can be used in functional studies because of its wide range of genomic tools available. Moreover, little is known about the epigenetic process during its domestication. In order to elucidate about the epigenetic alterations resulted from the tomato domestication, we sequenced in Illumina bisulfite-treated libraries of two accessions of Solanum lycopersicum (domesticated tomato) and three accessions of S. pimpinellifolium (wild relative of tomato). All epigenomes were aligned with the reference genome of S. lycopersicum 2.50 from Solgenomics database using Bismark. Mapping efficiency was high for all libraries. Percentages of methylation in CpG, CHG and CHH context were similar to all libraries sequenced, 11%, 42%, 47%, respectivelly, showing proportionally less methylation in CpG regions. Also CpG methylation was not correlated to repeated regions nor centromeric regions. Preliminary comparative results show several genes with CpG regions differentially methylated between domesticated and wild tomato species (S. lycopersicum vs. S. pimpinellifolium). Further analysis are needed to comprehend the relation of differentially metylated CpG regions inside genes and promoters with differentially expressed genes within and between these two species of tomato and its accessions.
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Epigenetic inheritance in asexual plants: causes and consequences of heritable DNA methylation variation within apomictic dandelion lineages
Abstract. Heritable epigenetic modulation of gene expression is a candidate mechanism to explain parental environmental effects on offspring phenotypes, but current evidence for environment-induced epigenetic changes that persist in offspring generations is scarce. In apomictic dandelions, exposure to various stresses was previously shown to heritably alter DNA methylation patterns. In this study we explore whether these induced changes are accompanied by heritable effects on offspring phenotypes. We observed effects of parental jasmonic acid treatment on offspring specific leaf area and on offspring interaction with a generalist herbivore; and of parental nutrient stress on offspring root-shoot biomass ratio, tissue P-content and leaf morphology. Some of the effects appeared to enhance offspring ability to cope with the same stresses that their parents experienced. Effects differed between apomictic genotypes and were not always consistently observed between different experiments, especially in the case of parental nutrient stress. While this context-dependency of the effects remains to be further clarified, the total set of results provides evidence for the existence of transgenerational effects in apomictic dandelions. Zebularine treatment affected the within-generation response to nutrient stress, pointing at a role of DNA methylation in phenotypic plasticity to nutrient environments. This study shows that stress exposure in apomictic dandelions can cause transgenerational phenotypic effects, in addition to previously demonstrated transgenerational DNA methylation effects.
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Comparative epigenomics of DNA methylation within flowering plants
Abstract. Methylation of cytosines in plants is a prominent epigenomic feature and is involved in critical functions such as transposon silencing and regulating gene expression. We have compared the methylomes of >35 different plant species from across the angiosperms using whole genome bisulfite sequencing data. These results indicate widespread variance in the amount of CG, CHG, and CHH methylation across species which is indicative of the diversity of silencing pathways being used by plant genomes. Genes with CG gene-body methylation, associated stable gene expression and non-CG methylation, associated with silencing, were classified for each species. Molecular evolutionary analysis of CG gene-body genes shows that these genes are generally conserved in multiple features. Differences in the use of CHG and CHH methylation suggests that different methylation pathways may predominate in different species.
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Genome‐wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus)
Abstract. Epigenetic marks such as DNA methylation play important biological roles in gene expression regulation and cellular differentiation during development. The role of epigenetic variation in evolution has been highly contested, yet information on naturally occurring epigenetic variation across species is lacking. To examine whether DNA methylation patterns are potentially associated with naturally occurring phenotypic differences, we examined genome-wide DNA methylation within G. aculeatus, using reduced representation bisulfite sequencing (RRBS). We sequenced the genomes of two stickleback phenotypes: complete lateral plate morphs (associated with marine populations) and low plate morphs (associated with freshwater populations). First, we identified highly methylated regions of the stickleback genome, determining the genomic locations of methylated regions and the genes associated with them. Next, we identified differentially methylated regions (DMRs) of the genome between complete and low lateral plate morphs, their genomic locations and associated genes.
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Paleo‐epigenetics: the DNA methylation maps of archaic humans
Abstract. A widely accepted evolutionary notion is that many phenotypic differences between closely related species may be attributed to changes in regulatory programs rather than to changes in protein sequence. Recent advances in ancient DNA sequencing yielded archaic human genomes at a quality that rivals that of present-day humans. This opens up an unprecedented opportunity to use genomic information in studying the recent evolution of gene regulation in humans. Here I present a novel method to reconstruct the complete DNA methylation map along ancient genomes, based on asymmetry between the deamination of methylated and unmethylated cytosines. I revealed ~2000 differentially methylated regions (DMRs) between archaic and present-day humans, and compiled a list of genes whose activity level had recently changed along our lineage. Examples include the HOXD9 and HOXD10 genes that may underlie the unique morphology of present-day humans. In general, these genes have high tendency to be associated with human diseases. This work comprises the first epigenetic map of an ancient genome, and provides the first insight to gene activity in archaic humans. Our method can be implicated on any future high-coverage ancient genome, and thus opens a window to a new field – paleo-epigenetics.
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