I-Ting Huang Thesis Defense (Colleen Cavanaugh and Christina Warinner, Co-Advisors)

Title: Microbial Evolution through the Lens of Metagenomics and Archaeogenetics

Abstract: Microbial evolution underpins processes ranging from agricultural productivity and ecosystem dynamics to pathogen emergence and human health. Host–microbial associations, in particular, are among most intimate and ancient relationships on Earth, and the coevolution of both host and symbiont is the driving force behind key biological events such as the emergence of organelles and cellular organization. Although microbial populations often display striking genetic diversity, the forces that shape this variability remain poorly understood. This gap is especially pronounced for ultra-small, largely uncultured lineages like the Candidate Phyla Radiation (CPR) – the enigmatic “microbial dark matter” thought to be symbiotic partners or parasites of other organisms - which thrive across diverse habitats spanning from hydrothermal vents to the human microbiome.

In this dissertation, I integrate comparative metagenomics, pangenomics, and archaeogenetics to track microbial populations and elucidate how genomic content mediates microbial adaptation and diversification across ecological and temporal scales.

In Chapter 1, I employ a novel inference framework that layers clonal sequencing with metagenomic sampling to track Saccharomyces cerevisiae strain dynamics across two seasons in industrial bioethanol refineries. This approach revealed contrasting population trajectories, with persistent dominance of established strains in one facility versus invasions by foreign strains at the other, highlighting the interplay of competition and community context in shaping population structure.

Chapter 2 applies a scalable pangenomics workflow alongside network analyses to over 2000 Parcubacteria genomes – revealing a minimalistic and conserved core genome dedicated to informational systems and cellular or host interaction, alongside a highly modular accessory genome rich in flexible genetic cohorts and interaction with mobile genetic elements. These findings reveal an evolutionary strategy that maintains adaptive plasticity in ultra-small genomes despite extreme size and metabolic constraints.

In Chapter 3, I leverage ancient DNA fossilized in archaeological dental calculus - from Neanderthals to modern humans spanning the past 100,000 years – together with modern oral samples from industrial andunderrepresented traditional human populations to reconstruct the evolutionary history of the CPR bacteria Saccharimonadia (TM7). I identified at least seven independent environmental-to-host transitions, and employed Bayesian tip-dated phylogenetics to calibrate the evolutionary timescales of Pleistocene-era radiations in human-associated lineages.

Together, these chapters develop new analytical workflows and illuminate the genomic strategies that underpin microbial diversity and adaptation, with broad implications for the understanding of microbialrelationships and insights into host–microbial co-evolution.

Committee: Colleen Cavanaugh (Co-Advisor), Christina Warinner (Co-Advisor), Peter Girguis, Dan Hartl, Martin Polz (U Vienna)