Agricultural adaptation of common waterhemp over the last two centuries

North America has seen one of the greatest increases in agricultural land use over the last two centuries, and in the latter half of the 20th century, intensification of agricultural practices. Native plants that predate this transition and that persist in the face of extreme human-mediated disturbance present a remarkable opportunity to learn about the evolutionary consequences of contemporary land use and input regimes. We studied the extent and tempo of agricultural adaptation in a native plant now pervasive in agricultural habitats, common waterhemp (Amaranthus tuberculatus), through sequencing paired samples from natural and agricultural environments from the present day and historical individuals spanning the last two centuries. Despite near panmixia among environments, numerous loci across the genome showed strong evidence of antagonistic selection. These loci, including alleles coding for resistance to herbicides, have increased in frequency by more than 20% in agricultural environments over the last ~150 years with nearly all such change occurring since the intensification of practices in the 1960s (s = 0.0267). Over the same period, we show a clear expansion of southwestern ancestry into the northeastern part of the range and particularly so in agricultural environments. Regions of the genome enriched for southwestern ancestry showed the strongest signals of agricultural selection, implying a strong link between demographic and selective contemporary change. The intensification of agriculture has thus had extensive evolutionary impacts on both genome-wide diversity and variation for fitness in this native plant, facilitating its success as a 21st-century agricultural weed