UC Santa Cruz

Genomic conflict arises when genetic elements increase their own proliferation despite imposing costs on their hosts. This dissertation examines how these conflicts emerge, persist, and reshape genomes across evolutionary timescales through three studies integrating gamete sequencing, comparative transcriptomics, long-read isoform sequencing, and population genomics. First, I investigated pollen-acting segregation distortion in crosses within and between Arabidopsis lyrata and A. halleri populations. Distortion was absent from crosses between closely related parents but widespread and variable in more divergent crosses, including crosses within species. Repeated, opposing distortions across chromosomes and genome-wide non-independence among loci were more consistent with negative epistatic incompatibilities than with independent single-locus drivers, demonstrating that reproductive barriers can arise early during population divergence. Second, I examined transcript processing in the non-recombining UV mating-type regions of four deeply diverged Mamiellales algae. Genes in these regions exhibited consistently elevated intron retention and other forms of alternative splicing. Long-read data from Micromonas pusilla revealed abundant aberrant isoforms with shortened coding sequences and disrupted protein domains, although many genes retained at least one likely productive transcript. These findings identify reduced splicing fidelity as a persistent, transcript-level form of degeneration in chromosomes constrained to retain essential genes. Third, I characterized introner turnover across thirteen geographically diverse M. pusilla isolates. Two deeply diverged populations differed approximately fourfold in introner abundance yet showed convergent insertion patterns across genomic and functional contexts. Within the introner-rich population, allele-frequency patterns indicated ongoing gains and losses. Introner presence was associated with reduced gene expression, increased transcript isoform diversity, and greater nonsense-mediated decay, while depletion from essential genes revealed strong host filtering. Together, these results show that the evolutionary consequences of genomic conflict depend on interactions among transmission, recombination, genome architecture, molecular function, and purifying selection operating across populations, chromosomes, and molecular processes.