Study System: Threespine Stickleback
Because of stickleback’s abundance and variation, there is a rich history of stickleback research leading to their emergence as a model organism for behavior, ecology, immunology, and evolution. Marine stickleback repeatedly colonized freshwater lakes following deglaciation ~12,000 years ago, essentially creating thousands of natural replicates of an evolution experiment. As a result, researchers have catalogued a vast array of ecological and genetic information on stickleback populations around that world that can be leveraged to ask novel and exciting questions. Perhaps most recently, stickleback are emerging as a model for studying immune system evolution. This is an exciting new turn because historically, most biomedical research has been conducted on inbred genetic lines reared in controlled laboratory settings. Using the genetic and environmentally variable stickleback, we can assess health outcomes to immune challenges in a way that more closely reflects the variation found in humans.
Mechanisms of plasticity: DNA methylation
Phenotypic plasticity is the ability of an individual with a single genotype to produce alternative phenotypes. Arguably, all plasticity requires a change in gene expression, which ultimately leads to alternative trait expression. Epigenetics is an umbrella term for chemical modifications to DNA and proteins that influence which genes are activated, with DNA methylation (DNAm) being among the most well studied epigenetic modifications. DNA methylation is required for healthy development and cell function, but dysregulated DNAm has also been implicated in a variety of ailments, including cancers and autoimmune disorders. Where DNAm is found in the genome is both heritable and environmentally sensitive (plastic), leading to heated debate regarding the role DNAm may play in evolution. While DNAm is just one epigenetic marker, and epigenetics is just one of countless mechanism of mediating plastic responses, it integrates many historically disparate fields (molecular biology, physiology, development, ecology, evolution) and is at the center of contemporary controversy in evolution. It is for these reasons that much of my PhD research centers on understanding how DNAm varies in natural populations, how selection acts on methylation, and how methylation can influence the phenotype.
How do sequencing and bioinformatic methods influence our ability to capture DNA methylation variation?
DNA methylation (DNAm) is the most commonly studied epigenetic marker in ecological epigenetics, yet the performance of the most popular sequencing and bioinformatic tools have seldom been assessed in natural populations. Therefore, I used reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (WGBS) to sequence five ecologically-divergent populations of threespine stickleback with unknown polymorphisms. I also compared how the most commonly used read mapper and methylation caller performs next to two alternative tools. The major findings of this experiment were:
The most commonly used tool for read mapping may result in a significant loss of data.
Relatively few CpG sites were sequenced between individuals using the same method, or within technical replicates using different sequencing methods (RRBS vs WGBS).
RRBS fails to recover many CpG sites that are not stably (un)methylated between cells.
I presented this work at Evolution in 2024, and am preparing to submit the manuscript for publication.
How does selection influence hybridization in a killifish hybrid zone?
Fundulus heteroclitus is a killifish that inhabits coastal habitats along most of the east coast of the United States, while F. grandis inhabits the coastlines of the Gulf of Mexico. The ranges of these two fish species overlap in a ~45km region in central Florida, where they sometimes interbreed to form hybrid offspring. As an undergraduate at the University of North Florida, I completed a capstone project in Dr. Matthew Gilg’s lab to assess the frequency of hybridization and selection against hybrids. We found that while advanced hybridization is common, F1 hybrids were rare. Additionally, frequency of hybridization within the hybrid zone followed a mosaic pattern and hybrids were selected against, but only in some years. The inconsistent selection pattern and mosaic structure of hybridization indicated that selection may have been environmentally-induced. Therefore, we also assessed the microgeographic structure of hybridization within the region and potential associations with environmental parameters, finding that multiple environmental factors and propensity to hybridize were likely driving the hybridization structure.
Associated publications:
