Evolution Tracks Multiple Timescales at Once

Abstract

Adaptation is often modeled as an immediate response to the environment currently experienced, yet we demonstrate that past conditions can continue to shape future genomic change, independent of the present environment. Using seven years of longitudinal genomic, environmental, and phenotypic data from a wild Drosophila melanogaster population, spanning more than 75 generations, we identify two genomically independent temporal modes of adaptation: a concurrent mode, tracking the current environment, and a lagged mode, carrying the imprint of a prior period forward. Despite acting on largely distinct genetic variants, both modes converge on shared neural and developmental pathways, most strongly in genes with broad phenotypic effects, suggesting that the circuitry linking environmental sensing to behavior is a recurring target of multi-temporal selection. These results show that adaptation can proceed simultaneously across distinct timescales, a pattern that may be widespread wherever selection recurs in structured, predictable ways.