Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking

Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown. We generated high-frequency, genome-wide allele frequency data from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December, a period of ~12 generations. Adaptation throughout the fundamental ecological phases of population expansion, peak density, and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of allele frequency change to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveal fitness-r..., , , # Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking

[https://doi.org/10.5061/dryad.xd2547dpv](https://doi.org/10.5061/dryad.xd2547dpv)

### Change log

Sept 2024: Added file (Orchard2021_Founders.csv) with specific inbred line names used to found this experiment).

Nov 2024: Upload of .vcf file containing sequence variant information for inbred reference panel used in this study.

Dec 2024: Added t1_11.SigSites.csv, containing SNPs identified via GLM across all replicates from time point 1 to 11 (summer to fall transition) of the experiment (FDR < 0.05; effect size > 2%).

## Description of the data and file structure

The two attached '.RData' files contain sample and allele frequency data used in the analysis of Bitter et al. 2024 (10.1038/s41586-024-07834-x). These data were derived from sequencing data provided on NCBI (PRJNA1031645) and generated via code provided at [https://github.com/MarkCBitter/DrosophilaMesocosm21\\_Fluc...