Investigating the role of structural variant interaction in accelerating adaptation : a test in field crickets

Understanding how genomic architecture shapes rapid adaptive evolution is a central challenge in modern evolutionary biology. This thesis integrates comparative and population-genomic approaches in crickets (Orthoptera: Gryllidae) to address this question across both macro- and micro-evolutionary scales. First, I generated high-quality de novo genome assemblies for several cricket species—including Teleogryllus oceanicus, T. commodus, Gryllodes sigillatus, and Lebinthus luae—thereby greatly expanding genomic resources for singing insects. Comparative analyses using these and other Orthopteran genomes reveal striking dynamism in genome size and structural evolution. Transposable-element activity and extensive chromosomal rearrangements emerge as major drivers of genome diversification, producing highly dynamic autosomes, whereas the X chromosome is remarkably conserved. These findings provide new insights into the mechanisms underlying insect genome evolution and position crickets as an emerging model for functional and evolutionary genomics. Second, this thesis investigates the rapid spread of the adaptive “flatwing” phenotype in the Hawaiian species T. oceanicus, which recently evolved under strong selection from a lethal parasitoid fly. Integrating a pangenome framework with population-scale whole-genome resequencing, I uncover a multi-layered genomic architecture underlying flatwing evolution. Convergent adaptation is driven in part by small structural variants—primarily non-coding insertions and deletions—affecting key regulatory genes such as doublesex, highlighting the importance of regulatory evolution. In addition, a large polymorphic X-linked inversion, although not directly causal, plays a crucial indirect role. This ancient inversion provides a genomic background that facilitates the spread and persistence of adaptive haploblocks through partial linkage and acts as a regulatory scaffold that reshapes gene expression networks, particularly sex-biased genes, via both cis- and trans-effects. Together, these findings show how direct regulatory mutations, indirect linkage effects, and broader genomic architecture interact to drive rapid phenotypic innovation under natural selection.