The genomic response to drought across spatiotemporal scales in Amaranthus tuberculatus

How genetic diversity responds to environmental change across spatiotemporal scales remains poorly understood despite its importance for species persistence in changing landscapes. Agricultural weeds offer ideal models for studying these adaptive dynamics as they rapidly evolve under both the intensive management practices designed to eliminate them and increasingly severe climate challenges such as drought. Here, we combine experimental and herbarium genomic approaches spanning within-generation to century-long timescales to understand how genome-wide variation responds to drought in Amaranthus tuberculatus . A history of divergent selection between two ancestral lineages is thought to play a role in this native species’ invasion into agriculture. A drought survival experiment on accessions from paired agricultural and natural populations across its native range revealed substantial phenotypic variation differentiated by habitat, geography, and ancestry. Ancestry mapping revealed 43 independent regions across nearly all chromosomes that confer protective effects under drought, demonstrate particularly rapid allele frequency changes, and exhibit duration-specific selection over the course of the imposed drought. Observation of allele frequencies across the past century reveal evidence for climate-dependent fluctuating selection governing the evolution of drought-associated loci. Selection favors drought alleles during hot/dry years and selects against them in cool/wet years—a pattern more evident in long-term trends than in shorter temporal intervals, suggestive of adaptive lag in rapidly changing environments. By combining short and long-term spatiotemporal data, we demonstrate that fluctuating selection has preserved the polygenic variation underlying drought tolerance, enabling ongoing adaptive responses to contemporary land-use and climate change.