Research
Current Research
My current work as a data scientist in Jeremy Day's lab at UAB focuses on analyzing gene expression data to answer questions about changes in the brain with substance abuse, using the rat as a model. Projects include bulk RNA-seq, as well as single-cell RNA-seq and ATAC-seq datasets.
Research Background
My research background in biology is in phylogeography and ecology of amphibians in the US Gulf Coastal Plain, including studies of biogeography, population genetics, systematics, seasonality, and conservation to better understand the patterns and processes of the evolution of biodiversity in the southeastern US.
Phylogeography of Plethodontid Salamanders
My dissertation research used the southern red-back salamander Plethodon serratus as a model for investigating the processes driving "multi-disjunct" amphibian species ranges in the Southeast. This region is home to at least 30 vertebrate species with geographic ranges consisting of >3 isolated regions, including 18 amphibians. I used genetic data and natural history collection and environmental data (through ecological niche modeling and palaeodistribution modeling) to describe patterns of genetic variation within P. serratus and test hypotheses about biogeographic history.
Salamander genomes can be up to 40 times the size of the human genome! Large genomes pose unique challenges for methods of generating large genetic data sets with next-generation sequencing (NGS). I tested the effectiveness of standard NGS protocols for generating a large multilocus phylogenetic data set for P. serratus to further clarify the population relationships within this species.
Evolution of Genome Size
The family Plethodontidae is one of the most diverse in genome size, with genomes ranging from about 18-70 Gb. There are 55 species of Plethodon, but genome size has been measured for only 25% of those species. The genome size of my own study species, P. serratus, was not known, so I collaborated with Ryan Gregory at the University of Guelph to collect this data and used ancestral character state reconstruction to study how genome size has expanded and contracted in the diversification of Plethodontidae.
Leopard Frogs
I was one of two lead researchers on a collaboration among several institutions investigating multiple leopard frog populations of interest in the northeastern U.S. Several populations had mating calls that sounded different from both of the known leopard frog species in the area. Our genetic analyses showed that the region is host to a previously undescribed cryptic species, which we named Rana kauffeldi, the Atlantic Coast leopard frog.