Genetic Novelty and Short-Term Evolutionary Dynamics in Drosophila yakuba mayottensis

1Understanding how genetic novelty arises and contributes to population divergence is central to evolutionary biology. On short evolutionary timescales, the relative roles of new mutations and standing variation remain underexplored among structural variation. Here, we compare the contributions of chromosomal rearrangements, tandem duplications, and single-nucleotide polymorphisms (SNPs) to early genomic differentiation in a recently colonized island population, Drosophila yakuba mayottensis, from the island of Mayotte. By comparing the relative impacts of these mutation classes, along with the involvement of transposable elements (TEs), we assess whether certain mutations are more likely to contribute to rapid divergence. We show that TEs are disproportionately involved in the formation of novel structural variants shortly after colonization, particularly through direct insertions. Our results suggest that TE-associated rearrangements may bypass the clocklike pace of SNP accumulation and divergence, where the contributions of coding SNPs, tandem duplications, and TE-facilitated ectopic recombination are constrained to standing variation on short timescales. Although TEs can drive the rapid emergence of novel variants, their full contribution to adaptation likely depends on evolutionary context and time since colonization. Together, our findings reveal time-dependent mutational dynamics and highlight the importance of structural variation, particularly TE-associated rearrangements, in shaping early genomic divergence following habitat shifts.