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Data from: Beyond fixation: Persistent genetic variation under intense selection

Arnold, Kenneth1; Greenspan, Zachary2; Robinson, Ryan1; Pupo, Anastasia3; Chavarin, Valeria4; Chang, Kevin2; Cannell, Corrina2; Qi, Miao2; Mueller, Laurence2; Rose, Michael2; Phillips, Mark1

Published Jul 17, 2026 on Dryad. https://doi.org/10.5061/dryad.tdz08kqdc

Data files

Jul 17, 2026 version files 904.31 MB

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Abstract

Understanding how and why genetic variation is maintained under sustained selection remains a central question in evolutionary genetics. Experimental evolution shows that adaptation in sexually reproducing populations is often highly polygenic, proceeding through coordinated, genome-wide allele frequency shifts from standing variation rather than classic hard sweeps. Recent explanations emphasize highly polygenic architectures, optimizing selection, and genetic redundancy, which can slow fixation by distributing selection across many loci during adaptation. However, observations from long-term selection experiments reveal a pattern these frameworks do not fully explain: substantial genetic variation persists after hundreds of generations of intense directional selection in constant environments. Here, we use long-term experimental evolution in Drosophila melanogaster to test whether balancing selection actively maintains genetic variation under strong life-history selection and preserves evolutionary reversibility. Populations subjected to selection for accelerated or delayed reproduction for hundreds of generations were shifted to the opposing regime, imposing age-structured fitness trade-offs. Notably, selection for early reproduction is associated with substantial loss of genetic variation, providing a stringent test of whether standing variation is truly depleted. Following reciprocal shifts, populations showed rapid phenotypic convergence toward the target regime. At the genomic level, allele-frequency trajectories were strongly antiparallel and highly repeatable across replicates, revealing coordinated polygenic responses. Relaxing long-standing early-life selection produced a pronounced rebound in genome-wide heterozygosity. Deep sequencing uncovered ultra-rare alleles at sites appearing fixed under standard coverage, indicating that low-frequency functional variation persists below detection thresholds. These results suggest that substantial genetic variation can persist under intense directional selection and be rapidly redeployed when selection reverses, consistent with widespread balancing selection.