Doctor of Philosophy (Ph.D.)
Degree Granting Department
Biology (Integrative Biology)
Lynn Martin, Ph.D.
Christina Richards, Ph.D.
Jason Rohr, Ph.D.
Toru Shimizu, Ph.D.
Aaron W. Schrey, Ph.D.
phenotypic plasticity, gene expression, introduced species, ecoimmunology
In light of human-mediated environmental change, a fundamental goal for biologists is to determine which phenotypic characteristics enable some individuals, populations or species to be more adept at coping with such change, while rendering others more vulnerable. Studying ongoing range expansions provide a unique opportunity to address this question by allowing documentation of how novel environments shape phenotypic variation on ecological timescales. At range-edges, individuals are exposed to strong selective pressures and population genetic challenges (e.g. bottlenecks and/or founder effects), which make genetic adaptation difficult. Nevertheless, certain species, such as the house sparrow (Passer domesticus), seem to thrive in their introduced ranges, despite genetic challenges, resulting in a genetic paradox. Increasing evidence suggests that rapid phenotypic differentiation at range-edges may be facilitated by phenotypic plasticity among individuals. Further, a role for epigenetic mechanisms as molecular drivers of such plasticity—particularly in genetically depauperate populations—has recently garnered empirical support across a broad range of taxa. For my dissertation, I investigated the role of epigenetic mechanisms (i.e. DNA methylation) as a potential mediator of range expansion success in vertebrates. Specifically, I proposed that success or failure at range-edges may be underlain by variation in the capacity for epigenetically-mediated plasticity (i.e. epigenetic potential) and used extant literature on an inherently plastic and highly integrated physiological system (i.e. the HPA-axis) to support this hypothesis (Chapter I). I then tested these ideas empirically by examining the relative contribution of genetic and epigenetic variation to immunological variation in Kenyan house sparrows (Chapter II) and explored whether mediators of neural plasticity (i.e. BDNF) and epigenetic potential (i.e. DNA methyltransferases; DNMTs) varied among populations of Senegalese house sparrows, including the potential for covariation among BDNF, DNMTs and corticosterone (CORT) within individuals (Chapter III).
Flexibility in the regulation of glucocorticoids (GCs) via the HPA-axis is crucial for survival at range-edges because (i) GCs act as integrators capable of coordinating diverse physiological and/or behavioral responses and (ii) the HPA-axis contains multiple regulatory checkpoints which may help to buffer organisms from maladaptive responses (via redundancy) while simultaneously allowing for the fine-tuning of phenotypic responses to future stressors contingent on current and past experiences. GC regulatory flexibility can be influenced by (and in some cases have an effect on) variation in the capacity for epigenetic mechanisms to regulate environmentally-induced phenotypic changes (i.e. epigenetic potential). DNMTs are capacitators of epigenetic change, thus provide one such example of how variation in epigenetic potential could arise via genetic (e.g. variation in coding regions of DNMT genes) and/or environmental (e.g. developmental programming of DNMT expression) factors. For my first chapter, I conducted a literature review to explore where within the HPA-axis epigenetic potential was most likely to occur and to demonstrate how such variation could promote/constrain range expansion success via its impact on GC regulatory flexibility. Results from the literature search revealed that within the HPA-axis, evidence for epigenetic regulation was highest for receptors, suggesting that variation in epigenetic potential of these targets may be most impactful for variation in GC regulatory flexibility. Using a physiological regulatory network (PRN) framework, I showed how variation in epigenetic potential can modify plasticity of PRN states by altering the regulatory relationships (e.g. connectivity) between HPA elements (e.g. GCs as central hubs) and other physiological/behavioral traits (e.g. subnetworks). As such, I portrayed how genetic forms of epigenetic potential can dictate the upper/lower limits of an individual’s homeostatic range, while environmental forms can act to further titrate GC regulatory flexibility through plasticity of PRN states or stabilization of PRN states. The concept of epigenetic potential in the HPA-axis demonstrates how plasticity at the molecular level can influence plasticity at the whole-organism level, which is likely to be important when coping with novel challenges at range-edges.
Among the strongest of selective pressures faced by range-edge populations is exposure to parasites, particularly those with which individuals have little to no evolutionary history. Previous work from our lab on house sparrows in Kenya—site of an ongoing range expansion—revealed that range-edge birds had higher expression of Toll-like receptor 4 (TLR4—a microbial surveillance gene) than birds from the range-core. Moreover, extensive inter-individual variation in genome-wide DNA methylation was found among Kenyan house sparrows, including an inverse relationship between epigenetic diversity and genetic diversity across populations. For my second chapter, I investigated whether these two observations were related, asking whether and how DNA methylation and/or genetic variation within the putative promoter of the TLR4 gene contributed to variation in TLR4 expression. I found that DNA methylation status at CpG1, which varied from only ~73-100%, was a strong predictor of TLR4 expression within individuals. Interestingly, other studies have shown that similar magnitudes of variation in DNA methylation of TLR4 can result in differences in the susceptibility/resistance to bacterial pathogens, thus, it’s plausible that the variation we observed could have functional implications for host defense. I also discovered four genetically linked polymorphisms within the TLR4 promoter that grouped into two general genotypes. We revealed a trend that suggests that genotype differences may influence TLR4 expression, confirmation of which may be possible with increased representation from individuals with the rare genotype. Given that DNA methylation did not vary systematically among populations and evidence for extensive genetic admixture at the Kenyan range-edge, it seems likely that individual-level factors (e.g. genotype, early-life experience, infection history, etc.) may be more predictive of variation in DNA methylation of TLR4 than population-level processes.
Coping with novel challenges often requires coordinated adjustments to environmentally-sensitive (i.e. plastic) traits. Findings from my first dissertation chapter, as well as previous research from the Martin lab, revealed that CORT regulation, exploratory behavior and epigenetic mechanisms likely contribute to range expansion success in house sparrows. Within the hippocampus, mediators of neural plasticity such as brain-derived neurotrophic factor (BDNF), play a unique role in the bidirectional regulation of CORT and exploratory behavior, with important implications for hippocampal-dependent learning and memory. Moreover, evidence suggests that the regulatory capacity of CORT and BDNF to influence learning and memory relies heavily on the catalytic capacity of epigenetic modification enzymes—including DNA methyltransferases (DNMTs). For my third chapter, I explored whether previous CORT/behavioral/epigenetic patterns contributed to population-level differences in hippocampal BDNF expression and/or hippocampal expression of DNMTs (mediators of epigenetic potential), including potential covariation among CORT, BDNF and DNMTs within individuals. I collected house sparrows from three populations in Senegal—site of an ongoing range expansion—and measured stressor-induced CORT, hippocampal BDNF, DNMT1 and DNMT3a expression. Given the potential importance of neural plasticity and epigenetic potential for coping with novel challenges, I hypothesized that BDNF and DNMT expression would be highest at the range-edge, while positive covariation would occur between CORT, BDNF and/or DNMT expression within individuals. I found that intermediate levels of CORT resulted in the highest BDNF expression within individuals, suggesting that interactions between CORT and BDNF are likely important for balancing homeostatic and progressive (e.g. cognitive) changes within the hippocampus in response to environmental challenges. I also found that CORT positively covaried with DNMT1 expression in one, but not both, range-edge populations, while the reverse was true at the range-core. These findings suggest that in newly established population, CORT may promote epigenetic potential, allowing for rapid and fine-tuned organism-wide responses to novel stressors, while at the range-core, where stressors are presumably less novel, CORT may inhibit epigenetic potential as a means of diverting resources away from cognitive processes and towards maintaining homeostasis.
Altogether, my dissertation has demonstrated how inherently plastic sub-organismal level traits (i.e. molecular, physiological, and neurological) may interact and contribute to range expansion success in an introduced bird. Specifically, my research has not only shown that epigenetic variation can influence an ecologically-relevant trait, but also that variation in the regulatory potential of epigenetic mechanisms can be mediated by intrinsic and extrinsic factors. These studies have expanded our understanding about how epigenetic mechanisms act as regulatory mediators of plasticity at the molecular level and can influence (and be influenced by) variation at multiple phenotypic levels, with implications for whole-organism performance in natural populations. I hope that my work contributes to the field of ecological epigenetics by providing the framework for epigenetic potential as an additional tool for assessing how epigenetic processes contribute to phenotypic outcomes in the face of rapid environmental change.
Scholar Commons Citation
Kilvitis, Holly J., "Ecological Epigenetics of Avian Range Expansions" (2017). Graduate Theses and Dissertations.