The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferasesare enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci.

46The repeated evolution of herbicide resistance has been cited as an example of genetic 47 parallelism, wherein separate species or genetic lineages utilize the same genetic solution in 48 response to selection. However, most studies that investigate the genetic basis of herbicide 49 resistance examine the potential for changes in the protein targeted by the herbicide rather than 50 considering genome-wide changes. We used a population genomics screen and targeted 51 exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the 52 common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the 53 repeated evolution of resistance across replicate resistant populations. We found no evidence 54for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target 55protein, that were associated with resistance, and instead identified five genomic regions that 56show evidence of selection. Within these regions, genes involved in herbicide detoxification--57 cytochrome P450s, ABC transporters, and glycosyltransferases--are enriched and exhibit signs 58 of selective sweeps. One region under selection shows parallel changes across all assayed 59 resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears 60 likely that the physiological mechanism of resistance in this species is likely the same among 61 resistant populations, we find patterns of both similar and divergent selection across separate 62 resistant populations at particular loci.

The adaptation of weedy plants to herbicide is both a significant problem in agriculture and a model for the study of rapid adaptation under regimes of strong selection. Despite recent advances in our understanding of simple genetic changes that lead to resistance, a significant gap remains in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance over time. Here, we perform a multi-level analysis involving whole genome sequencing and assembly, resequencing, and gene expression analysis to both uncover putative loci involved in nontarget herbicide resistance and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification, stress sensing, and alterations in the shikimate acid pathway to be under selection, and confirmed that detoxification is responsible for glyphosate resistance using a functional assay. Furthermore, we found interchromosomal linkage disequilibrium (ILD), most likely associated with epistatic selection, to influence NTSR loci found on separate chromosomes thus potentially mediating resistance through generations. Additionally, by combining the selection screen, differential expression, and LD analysis, we identified fitness cost loci that are strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work strongly suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are maintained through generations via ILD and that the fitness cost associated with resistance in this species is a by-product of genetic-hitchhiking.

Summary The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide‐resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget‐site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by‐product of genetic hitchhiking.