Graduation Year

2021

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Public Health

Major Professor

Lynn B. Martin, Ph.D.

Committee Member

Thomas R. Unnasch, Ph.D.

Committee Member

Monica Uddin, Ph.D.

Committee Member

Aaron W. Schrey, Ph.D.

Committee Member

Loren Cassin Sackett, Ph.D.

Keywords

CpG sites, DNA methylation, house sparrow, invasive species, range expansion

Abstract

Epigenetic modifications play a critical role in numerous processes throughout the lifetime of an organism by influencing gene regulation. Responsive to both endogenous cues and external stimuli, epigenetic modifications are key mechanisms underlying phenotypic plasticity. Epigenetic potential, or the capacity for phenotypic plasticity mediated by epigenetic modifications, can be encoded within the genome via genetic variation underlying aspects of epigenetic modifications. For example, one type of epigenetic modification, DNA methylation, predominately occurs at CpG motifs in vertebrates. The number of CpG sites within the genome then represents the capacity for DNA methylation to occur and is one form of epigenetic potential. In certain ecological contexts, the selective value of phenotypic plasticity may be high, while canalized responses may be favored in others, leading to variation in epigenetic potential across individuals, populations, and species. For instance, phenotypic plasticity is hypothesized to be beneficial to invaders and dispersers; therefore, one might predict that epigenetic potential will be high during introductions and range expansions to impart an increased capacity for phenotypic plasticity via epigenetic modifications. This work sought to test this hypothesis and investigate other aspects of epigenetic potential in one of the most successful introduced species in the world, the house sparrow (Passer domesticus).

In the introduction, I discuss the unique natural history of house sparrows, review previous studies, and explore the characteristics which make them an exemplary system to investigate epigenetic potential. House sparrows have spread across multiple continents through natural range expansions as well as both purposeful and accidental introductions into new areas. The species has been established for over 100 years in many locations across the globe after a series of successful introduction events, yet there are still several ongoing range expansions worldwide. This allows for the comparisons of traits, such as epigenetic potential, between individuals from native, long-established, and still-invading populations. Already, substantial genetic and phenotypic differences have been identified within and between native and introduced populations, even in introduced populations with substantially lower genetic diversity than others. Further, epigenetic modifications are important in invading house sparrows, even seeming to compensate for low genetic diversity in one recent range expansion into Kenya. Overall, the house sparrow system offers exciting opportunities for studies aimed at increasing our understanding of epigenetic potential.

In Chapter One, I asked whether differences in epigenetic potential are present between native and introduced populations of house sparrows. I investigated one form of epigenetic potential, the number of CpG sites, in the putative promoter region of three different immune genes: Toll-like Receptors 1B, 2A, and 4 (TLR1B, TLR2A, and TLR4), which were chosen for their importance in house sparrow range expansions through controlling generalist microbial infections. I hypothesized that epigenetic potential would be higher in all three genes in introduced birds compared to native ones, providing more flexibility in gene regulation in the relatively novel environments they encounter. Indeed, introduced house sparrows harbor more epigenetic potential in TLR2A and TLR4 than native birds, but not in TLR1B. High epigenetic potential may provide latent phenotypic plasticity in genes that provide broad immune protection.

While I found differences in epigenetic potential across native and introduced house sparrows, the functional consequences of these differences were not known. In Chapter Two, I examined whether epigenetic potential in the promoter region of TLR4 influences gene expression. To do so, I administered a TLR4 agonist lipopolysaccharide (LPS) to wild house sparrows in order to simulate an infection and induce TLR4 expression. I predicted that when injected with LPS, individuals with higher epigenetic potential would exhibit more flexibility, or demonstrate greater inducibility and reversibility of gene expression, compared to birds with low epigenetic potential. I found that individuals with high epigenetic potential were more flexible as they showed greater induced expression overall, but only females exhibited reversibility of TLR4 expression within the experimental timeframe. Surprisingly, these results were independent of treatment with LPS. Overall, these results suggest that epigenetic potential plays a role in TLR4 gene regulation in the house sparrow.

Since epigenetic potential appears to have functional consequences in gene regulation and variation was observed across house sparrow populations, my next step was to expand this approach and investigate whether patterns of epigenetic potential could be detected on a larger scale. In Chapter Three, I used a reduced-representation, library-based sequencing approach to describe patterns of epigenetic potential and DNA methylation across a large and relatively random subset of the house sparrow genome in an on-going range expansion across Kenya. I hypothesized that epigenetic potential would be highest in birds living near the range edge due to selection for more flexibility, while those living at the site of the initial introduction would have the lowest epigenetic potential, as the core population has had the most time to adjust to local environmental conditions. Indeed, I found that house sparrows towards the range edge had the highest epigenetic potential, which seems to be driven by positive selection for CpG sites. Additionally, I found that DNA methylation was lowest but most variable towards the range edge. Together, these results suggest that epigenetic potential might allow the populations that are still invading new areas, or which have only recently established, to exhibit more phenotypic plasticity.

My dissertation work demonstrates that differences in epigenetic potential exist in both candidate genes and in a large subset of the genome between native and introduced house sparrows and even between core and edge populations that have been established for a relatively short amount of time. I found evidence of epigenetic potential influencing gene expression in one immune gene (e.g. TLR4), indicating that it contributes to flexibility in gene regulation. These results suggest that epigenetic potential is influential to house sparrow introductions and may be one mechanism underlying their invasion success. This form of epigenetic potential has the potential to be applied broadly because it can easily be measured and could lead to important insights in other ecological contexts and scenarios and across other disciplines, which I discuss in the conclusion.

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