Graduation Year

2015

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Biology (Integrative Biology)

Major Professor

V. Jody Harwood, Ph.D.

Co-Major Professor

Christina L. Richards, Ph.D.

Committee Member

Gordon Fox, Ph.D.

Committee Member

Marc Lajeunesse, Ph.D.

Committee Member

Aaron W. Schrey, Ph.D.

Keywords

epigenetics, DNA methylation, Spartina alterniflora, Borrichia frutescens

Abstract

Phenotypic plasticity is the ability of a given genotype to exhibit different phenotypes in response to environmental variables, which can impact population level processes. Plasticity of ecologically-relevant traits is important to an organism’s environmental response; however, the underlying mechanisms of plasticity are largely unknown. Ecological epigenetics may offer mechanisms (e.g. DNA methylation) underlying phenotypic plasticity. Epigenetics can be defined as the underlying molecular mechanisms that allow one genotype to exhibit different phenotypes. Differential DNA methylation is one epigenetic mechanism that has been correlated with a number of ecologically-relevant traits; including, differential herbivory in Viola cazorlensis, spinescence in Ilex aquifolium, flower morphology in Linaria vulgaris, and fitness in Arabidopsis thaliana. The epigenetic correlations with traits found in these studies are interesting, but they are also partially confounded by a potential correlation between genetic and epigenetic variation.

Teasing apart the correlation between genetic and epigenetic variation is one of the challenges within ecological epigenetics. This correlation has resulted in epigenetic variation being partitioned into three types by researchers: obligate, facilitated, and pure. Changes in obligate epigenetic variation are directly correlated with genetic variation. Changes in pure epigenetic variation are completely independent from genetic variation. Changes in facilitated epigenetic variation are partially dependent on genetic variation, but the outcome of the phenotype is context-dependent based on environmental conditions. Since our predictions about the outcome of phenotypic variation are driven largely by population genetics theories, which make no room for variation that operates in non-Mendelian ways, epigenetics research needs to utilize unique ways to tease apart the interaction between genetic and epigenetic variation where facilitated or pure epigenetic variation exists outside of the realm of population genetics theory.

To address these issues, I performed a literature review and two research-based studies. In Chapter 1 I performed a literature review on the topic of population epigenetics addressing the correlation with genetic variation and recommending an extension to the Modern Synthesis to accommodate the non-Mendelian nature of DNA methylation. While population genetics has approximately 85-years of data to support it, epigenetics is beginning to show some of the limitations associated with predictions made using populations genetics models. One of these limitations is that population genetics as defined by the Modern Synthesis does not allow for violations of Mendelian genetics (i.e. random assortment and segregation of alleles). This limitation does not allow for phenotypic variation that is directly due to environmental conditions; however, recent ecological epigenetics data shows that this can, indeed, occur. Within this review I propose epigenetic questions that we should focus on at the population level, and I make recommendations for how to approach these questions in future studies.

In the second and third research-based chapters, I investigated whether an independent component of epigenetic variation was correlated with habitat, while controlling for a correlation with genetic variation, for Spartina alterniflora and Borrichia frutescens, respectively. Previous work has shown that there is no consistent genetic response to environment in these species. I, therefore, hypothesized that there would be a significant epigenetic correlation with habitat instead. To test this hypothesis, I collected leaf samples from five different sites for each species on Sapelo Island, GA. Within each site I established three 10m transects (n=20 for each microhabitat) in low, middle, and high marsh microhabitats, respectively. Plants of both species exhibit different phenotypes for height (tall, intermediate, short, respectively) based on their location within the marsh. I screened AFLP and methylation-sensitive AFLP (MS-AFLP) markers for genetic and epigenetic variation, respectively. I used a variety of statistical tests to attempt to tease apart a potential correlation between genetic and epigenetic variation and found that when genetic population structure is controlled for, significant epigenetic population structure persists across all populations for S. alterniflora and within 3 of 5 populations for B. frutescens. These results suggest that regulation of certain genomic elements via DNA methylation may play an important role in dealing with environmental variables. To fully determine the significance of these findings, future studies should examine the interaction between environmentally-mediated epigenetic variation and gene expression to determine its importance to phenotypic plasticity and habitat differentiation.

The body of work I produced supports that epigenetics may play a role in environmental response in populations within relatively small spatial scales. I used a combination of statistical tests to control for potential correlations with genetic variation which allowed me to see patterns that may normally be hidden. These findings expand upon traditional views of evolution by suggesting that environment can play a role in phenotypic variation, and other research supports that the variation due to epigenetic mechanisms can be inherited in future generations. Much of the current epigenetic research is based upon studies involving model species in highly controlled studies. While this research is been incredibly informative about some of the mechanisms underlying epigenetics, to fully understand the role of epigenetics to environmental response and evolution we must pair these data with field studies of non-model organisms. Only then will we begin to see the full role of epigenetics in organisms.

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