This document discusses the role of epigenetics in ecology and evolution. It addresses how epigenetic marks are inherited, reset, and influence phenotypic plasticity and responses to stress. Several model organisms are studied including plants, insects, fish and algae. Research presented includes studies on DNA methylation patterns in fish in response to heat shock, and variable phenotypes in dandelions and nectar yeast in response to stress. The role of transposons in establishing epigenetic patterns is discussed. Epigenetic marks can increase phenotypic variation in fluctuating environments and may allow faster adaptive changes by decoupling genotype from phenotype. Understanding both genetics and ecology is important for studying the role of epigenetics.
2. Questions Addressed The role of epigenetics in evolution: How much is inherited How is it inherited What and how much is reset Chromatin modification Theory The role of epigenetics in ecology Natural variation Phenotypic plasticity Response to stress What ecologically relevant organisms can we/should we study
4. Tools Bisulfite sequencing ChIP/MeDIP-seq& ChIP/MeDIP-chip RNA-seq MSAP – CE, GeneMapper SureSelect Target Enrichment System (Agilent) Software: ChIPDiff, SICER
5. Study Systems Arabidopsis, Drosophila..yawn ;) Nectar yeasts Dandilions Mimulus Insects: wasps, locusts Algae Fish
6. Fish European Sea Bass (F. Piferrer) EPIGEN-AQUA heat shock of embryo suppresses aromatase what is mechanism? Bisulfite sequenced promoter found differential methylation in promoter of males and females relationship between expression and methylation is weak Darters (T. Smith) AFLP and MSAP in populations from the same river Guppies (A. Lopez-Sepulchre) Cool system, ‘ecotypes’ in high predation and low predation environments – interested in epigenetics http://www.cnas.ucr.edu/guppy/
7. Theory Carja et al 2011 – Equilibrium for phenotypic variance in fluctuating environments Jason Wolf – epistatic selection can favor imprinting when interacting loci share imprinting status Sinead Collins- ephemeral mutations (e.g. DNA methylation) can speed up fitness increases Decouples timing of adaptive changes in phenotype from genotype, “hand over hand”
8. What ‘writes’ DNA methylation How do marks know where to go? Arabidopsis (numerous) role of transposons was greatly discussed transposons are silenced by DNA methylation lots of experimental examples shown (e.g. epiRILs, DDM mutants) C.elegans (B. Kelly) transcription itself can write epigenetics Cancer Cells (A. Bar) ‘microevolution’ – 350 generations local v. regional (signaling from ind.CpG or lifiting of repressive chromatin state)
9. DNA Methylation and Stress Mostly shown in plants different stresses: salinity, heat Different levels of ‘inheritance’ e.g. extreme heat stress ‘primed’ plants only when exposed for 2 generations phenotype & epigenetic mark still being understood Most ecologically relevant model: nectar yeast (Carlos Herrera)
10. Examples of Increased Variation Dandilions(K. Verhoeven) stress = increased variability in phenotype zebularine treatment – results variable in phenotype (‘no robust response’) Nectar Yeast (C. Herrera) add 5-aza = no effect in optimized environments, big effect in non-optimized (but phenotypes variable between these)
12. Best Things Incorporated genetics – must be considered together (e.g. epigenetic status effects recombination, transposons effect epigenetic status) Ecology – need to study relevant stressors, understand natural populations Major challenges – each stress has a different response, may need to look at bigger picture (fitness as variation, instead of specific response?) Kava, swimming, x2 desserts/day
