Detecting Evolutionary Outliers in The Tree of Life

Abstract

This thesis investigates genome scrambling, the progressive disruption of gene order over evolutionary time, across diverse lineages. Using whole-genome alignments, I compared pairwise nucleotide divergence and structural rearrangement, and examined how these relationships vary among clades. I also assessed how alignment settings, missing data, and distance definitions influence downstream clustering and interpretation. Benchmarking showed that simple alignment-based distance measures can become unreliable at deeper divergences, whereas coverage-aware corrections improve their use as evolutionary proxies. Across the analysed groups, the results suggest that structural genome evolution is not always tightly coupled to sequence divergence and may proceed at different rates in different clades. Together, these results support the use of genome scrambling as a measurable comparative trait and lay the groundwork for broader, phylogeny-wide studies of chromosome-scale structural evolution across the Tree of Life.