Polygenic adaptation from standing variation underlies rapid evolution under anthropogenic selection in an agricultural weed

Herbicide resistance is among the clearest examples of rapid adaptation to intense anthropogenic selection. Yet, how the evolutionary origins and genetic architecture of resistance shapes its tempo and mode of evolution remain incompletely resolved. Here, we address these questions in Alopecurus myosuroides (blackgrass), Europe’s most widespread and economically damaging herbicide-resistant weed. We present the first genome-wide analysis of herbicide resistance in natural blackgrass populations, uniquely combining historical and contemporary populations collected before and after the onset of intensive herbicide use. This temporal framework provides novel empirical access to pre-selection genetic variation, enabling reconstruction of the tempo and mode of both target-site (TSR) and non-target-site resistance (NTSR) evolution across space and time. TSR mutations were not found in pre-herbicide populations and evolved recently through repeated, largely independent origins across Europe. NTSR, in contrast, has a polygenic architecture and is associated with a cluster of glutathione S-transferases (GSTs) with signatures of copy number variation, and broader stress-response genes. Most NTSR-associated alleles were already segregating in historical populations, consistent with rapid adaptation from standing genetic variation. Moreover, resistance-associated loci show signatures consistent with positive selection predating herbicide use, suggesting these stress and detoxification pathways were historically maintained by prior ecological selection and subsequently recruited under herbicide pressure. Together, these findings demonstrate that herbicide resistance encompasses contrasting genetic routes, with polygenic NTSR evolving largely through selection on standing variation, offering broader insights into the evolutionary dynamics of rapid polygenic adaptation under novel anthropogenic selection.