In recent years, a surge in genetic evidence has illuminated the phenomenon of fluctuating selection in Drosophila and other species. This has been identified by observing temporal oscillations in thousands of alleles. However, we currently lack an understanding of the effect of fluctuating selection on population genetic statistics and its influence on genome-wide genetic diversity. The ages of these fluctuating alleles also remain ambiguous, as their oscillations are observed over merely short time scales.
In this study, we use forward simulations to produce seasonally fluctuating selection. We then characterize the resulting genomic patterns across various time scales, employing a wide range of population genetic summary statistics. These patterns were compared against those arising from classical forms of positive and balancing selection. Further, we evaluated the capability of different summary statistics in pinpointing loci influenced by fluctuating selection.
Our findings reveal that while long-term fluctuating selection is distinct from positive selection, it exhibits considerable parallels with genomic patterns characteristic of balancing selection. Diversity and site frequency spectrum based statistics face challenges in pinpointing fluctuating selection, but haplotype-based approaches present promising avenues. In conclusion, fluctuating selection can substantially influence genome-wide genetic diversity, suggesting a pivotal role in determining genetic diversity in many species.