Mirchandani, C. (BMEB) – Population and Evolutionary Genomics Across Ecological Scales

Sequencing technologies have transformed population and evolutionary genetics, making it possible to ask questions at scales that were intractable a decade ago. Realizing that potential depends on tailored computational approaches, and on the tools and infrastructure those approaches are built on. My dissertation works across this spectrum. Using an in vitro Drosophila cell culture system, I show that mixed Wolbachia infections resolve rapidly and deterministically, with one strain competitively excluding the other across host species and starting frequencies, offering an explanation for why mixed infections are rarely observed in nature. In a deep-sea clam and its obligate bacterial symbiont, I use two ultra-accurate sequencing methods and demographic modeling to directly estimate the effective transmission bottleneck between host generations, finding it to be roughly eight symbionts, orders of magnitude below prior cell-count estimates. I also present two tools for population genomics at scale: snpArcher, a reproducible variant calling workflow developed for the California Conservation Genomics Project and now used across hundreds of species and tens of thousands of samples; and clam, a Rust-based tool that efficiently estimates population genetic statistics by leveraging callable loci, producing results identical to existing all-sites approaches at a fraction of the computational cost. Together, these projects demonstrate how tailored computational approaches can unlock biological insight across diverse systems and scales.

Event Host: Cade Mirchandani, Ph.D. Candidate, Biomolecular Engineering & Bioinformatics

Advisors: Russ Corbett-Detig & Shelbi Russell

Zoom- https://ucsc.zoom.us/j/98034081971?pwd=L5RoKoNEFxyapNhSRoXC8os2K2YZwv.1