The role of adaptive evolution in the success of an agricultural weed, Helianthus annuus

If a weed is defined as a plant that is “growing where it is not wanted”, then agricultural weeds, or plants that invade and persist in cultivated fields, might be the epitome of weeds. Agricultural weeds have arisen repeatedly from wild plant species, often undergoing rapid evolution to escape eradication. While agricultural weeds thus represent an attractive opportunity to study evolutionary processes operating over short timescales, the genetic basis of local adaptation and, in cases of multiple independent weed origins, the factors influencing parallel evolution, they remain understudied. For my thesis work, I asked whether populations of common sunflower (Helianthus annuus) growing as agricultural weeds have adapted to the unique challenges posed by cultivated fields. In a common garden, I compared paired weedy and wild (i.e., non-agricultural) populations, collected over a latitudinal transect from Canada to Kansas, USA. Weedy populations grew faster and flowered earlier than wild populations, suggesting an evolutionary shift in life history strategy to prioritize growth and reproduction. One wild population from a wetland site showed the same pattern, indicating that wild sunflowers may face similar selection pressures in certain contexts. I then used whole genome resequencing to investigate the extent of parallel genetic differentiation between weedy and wild populations. Using two different metrics, a “cluster separation score” based on genetic distance matrices and FST, I identified a list of 148 differentiated genomic regions, though our analysis lacked power to distinguish true positives after correction for multiple testing, and therefore these regions are only suggestively linked to adaptation to the agricultural environment. Genes overlapping these regions were varied and included those involved in plant stress responses, flowering time genes and transporter genes linked to herbicide resistance. To connect phenotype to genotype, I conducted a genome-wide association analysis of glyphosate resistance, a trait likely critical for the success of weedy populations. At a glyphosate application rate of 0.5 kg a.e. ha-¹, or half the rate typically applied by a farmer, resistance segregated in the mapping population, with surviving plants (78.5%) showing a variety of symptoms. Mapping identified 68 SNPs suggestively associated with resistance, and three transporter proteins, among other genes.Science, Faculty ofBotany, Department ofGraduat