Differential equations in life science and environmental engineering

Plant breeding; quantitative genetics; plant genomics

Epidemiology; foodborne pathogens; infectious diseases; swine

Program: Ph.D.

Advisor: Dr. Sarah Adamowicz

Research:

Biodiversity is important for ecosystem function. Building large and comprehensive phylogenetic trees, i.e., reconstructing the evolutionary relatedness among species, is valuable for diverse studies, including biomonitoring, evolutionary biology, and conservation biology. With phylogenetic trees, we can ask: how much unique evolutionary history is represented at a given site? High-throughput sequencing technologies are providing a great opportunity to build larger trees than ever before, but there is a gap in the literature regarding the performance of existing bioinformatics tools. Therefore, the objective of this study is to test and develop new approaches for quantifying evolutionary history and identifying biodiversity using molecular data. My approach is to combine the best of two methods: DNA barcoding projects sequence many species for few genes, while phylogenomics projects study few species for many genes. I am benchmarking existing methods for phylogenetic placement, including distance-based and likelihood-based methods, considering the taxonomic coverage of backbone phylogenies, phylogenetic patterns in missing data, and generality of the findings across animal taxa. In combining these techniques, this project will open new avenues for biodiversity, evolutionary, and conservation research in species-rich groups of life and under-studied environments.