Research

Research Focus

In my research, I am primarily interested in the evolutionary mechanisms and genomic forces shaping the genetic landscape of chromosomes in natural populations. I am fascinated with how the simple four nucleotide base structure of DNA can change and be altered over time leading to complex species. My work tries to explain interesting phenomena observed in nature at the sequence level. With the recent explosion of high-throughput sequencing technologies, unprecedented opportunities await to understand how genes and genomes change over time and construct the astounding complexity of life. With these great opportunities, however, come computational and statistical challenges, so I am also interested in employing and developing new techniques to assemble genomes and analyze sequences.

Current Work

My current research is conducted in the lab of Dr. Steve Schaeffer at Penn State. Chromosomal inversions are genetic rearrangements in which the sequence is reversed end to end and are prevalent throughout nature. Many human diseases and abnormalities are caused by inversions and heterozygotes often have reduced fitness because of unbalanced gametes produced during meiosis. However, in many populations chromosomal inversions can exist at high frequencies and actually may be adaptive. The fruit fly, Drosophila pseudoobscura, is an excellent model system to study the evolution of chromosomal rearrangements and the evolutionary mechanisms responsible for their spread and maintenance because the species is polymorphic for over 30 well-characterized widespread inversions on the third chromosome. In fact, the frequencies of particular inversions form a cline across the Southwestern United States and major frequency shifts occur along climatic zones. My work analyzes the full chromosome sequences produced from next-generation technology to test hypotheses about how inversions spread in populations. In addition, the environment of reduced recombination produced by the inversions allow interesting studies into the effect of decreased genetic exchange on codon usage bias, genetic variation and haplotype structure. Our lab is also using transcriptome data to profile the gene expression pattern of different chromosome arrangements to further understand the molecular genetic basis underlying inversion evolution. Because the reference genome of D. pseudoobscura is of one arrangement type, I am also working to assemble each chromosome inversion de novo with potential applications to other large-scale population resequencing projects including humans.

Previous Work

I completed a rotation in the lab Dr. Webb Miller when I was first at Penn State in the department of bioinformatics. In a collaboration with Dr. Christina Grozinger, I was involved in a project examining the full genomic sequences of different populations of Kenyan honeybees, Apis mellifera. Bee populations in Kenya are currently suffering from the well-publicized colony collapse disorder, and our goal was to utilize genomics to help both understand the cause of this phenomenon as well as gain information that can be used to inform local apiaries of strategies to prevent further population declines. I analyzed polymorphism data to detect genes potentially under selection and examined the population structure and phylogeny of the different populations used in the study. As a student in the lab, I also helped to design tools written in Python to detect so called “signatures of selection” that are publicly available on the web-based genomics platform www.galaxy.org.

Undergraduate Work

I received a B.S. in Biology from Creighton University in 2012. While an undergraduate, I worked in the lab of Dr. Soochin Cho on two major projects, the first of which was involved with sex-chromosome evolution. The South American genus of field mouse Akodon has a peculiar and widespread sex-reversal trait where some XY individuals are actually phenotypically female, even though they are a genetic male. Here, my work amplified, cloned and sequenced several candidate genes possibly involved in this strange sex-reversal trait. Through phylogenetic and molecular evolutionary approaches, I analyzed the sequences of these genes to determine if any were linked to the XY sex-reversal phenotype. A second project in Dr. Cho’s lab examined the evolutionary history of large gene families, specifically ribonucleases in the Giant Panda, Ailuropoda melanoleuca.The goal of this project was to functionally characterize different ribonucleases and understand the multiple gene duplications within this gene family specific to the Giant Panda.