Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea

Meeting Report on the Symposium "Evolutionary Applications" at the 3rd Joint Congress on Evolutionary Biology

The symposium "Evolutionary Applications" took place on June 28, 2024 in the virtual part of the 3rd Joint Congress on Evolutionary Biology. It was contributed to the conference by the European Society for Evolutionary Biology (ESEB). The symposium highlighted research on evolutionary biology applied to address questions and contemporary problems in medicine and public health, conservation biology, and food production and agriculture. Each of the six talks covered a different application and a different organism: domestication of cheese-making fungi, restoration of long-lived bird populations, evolution of herbicide resistance, coral reef conservation, gene drive systems targeting Malaria vectors, and antibiotic resistance evolution in bacteria. By including speakers who are active in a consortium or work in an NGO, the symposium also showed how to make the step from scientific findings to practical application. The symposium furthermore featured a range of scientific methods, ranging from genomic analyses and mathematical modeling to laboratory evolution and field experiments. Speakers from across 15 time zones highlighted the potential of virtual symposia to foster global collaboration in evolutionary biology.

Herbicidal interference: glyphosate drives both the ecology and evolution of plant-herbivore interactions

The coevolution of plants and their insect herbivores reflects eco-evolutionary dynamics at work - ecological interactions influence adaptive traits, which feed back to shape the broader ecological community. However, novel anthropogenic stressors like herbicide, which are strong selective agents, can disrupt these dynamics. Little is known about how the evolution of herbicide resistance may impact plant-herbivore interactions. We performed a common garden field experiment using Ipomoea purpurea (common morning glory) and the herbicide glyphosate (Roundup) to investigate the ecological effects of herbicide exposure on insect herbivory patterns and assess the potential evolutionary consequences. We find that plants treated with glyphosate experienced higher levels of herbivory and altered chewing herbivory damage patterns. Additionally, we found that glyphosate resistance is positively associated with herbivory resistance, and uncovered positive selection for increased glyphosate resistance, suggesting that selection for increased glyphosate resistance has the potential to lead to increased herbivory resistance. Positive selection for glyphosate resistance, coupled with the detection of genetic variation for this trait, suggests there is potential for glyphosate resistance - and herbivory resistance via hitchhiking - to further evolve. Our results show that herbicides cannot just influence, but potentially drive the eco-evolutionary dynamics of plant-herbivore interactions.

Early growth, development and allometry of glyphosate-resistant and susceptible Amaranthus palmeri in response to current and elevated temperature and CO2

This study aimed to evaluate the influence of CO2 and temperature on glyphosate-resistant and susceptible biotypes of Amaranthus palmeri (Palmer amaranth) in terms of morphological development. Height (cm), stem diameter (cm), leaf area (cm2), number of leaves, leaf, stem, and root dry matter, plant volume (m3), as well as shoot-to-root allometry were evaluated. The Palmer amaranth biotypes were grown under four different scenarios: 1-low temperature (23/33 °C) and CO2 (410 ± 25 ppm); 2-low temperature (23/33 °C) and high CO2 (750 ± 25 ppm); 3-high temperature (26/36 °C) and low CO2 (410 ± 25 ppm); and 4-high temperature (26/36 °C) and CO2 (750 ± 25 ppm). Between CO2 and temperature, the majority of differences observed were driven by CO2 levels. Palmer amaranth grown under 750 ppm of CO2 was 15.5% taller, displayed 10% more leaf area (cm2), 18% more stem dry matter, and had a 28.4% increase in volume (m3) compared to 410 ppm of CO2. GA2017 and GA2020 were 18% and 15.5% shorter, respectively. The number of leaves was 27% greater for GA2005. Plant volume decreased in GA2017 (35.6%) and GA2020 (23.8%). The shoot-to-root ratio was isomeric, except at 14 and 21 DAT, where an allometric growth towards shoot development was significant. Palmer amaranth biotypes responded differently to elevated CO2, and the impacts of temperature need further investigation on weed physiology. Thus, environmental and genetic background may affect the response of glyphosate-resistant and susceptible populations to climate change scenarios.

Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

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.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Dissecting weed adaptation: Fitness and trait correlations in herbicide-resistant Alopecurus myosuroides

BACKGROUND

Unravelling the genetic architecture of non-target-site resistance (NTSR) traits in weed populations can inform questions about the inheritance, trade-offs and fitness costs associated with these traits. Classical quantitative genetics approaches allow study of the genetic architecture of polygenic traits even where the genetic basis of adaptation remains unknown. These approaches have the potential to overcome some of the limitations of previous studies into the genetics and fitness of NTSR.

RESULTS

Using a quantitative genetic analysis of 400 pedigreed Alopecurus myosuroides seed families from nine field-collected populations, we found strong heritability for resistance to the acetolactate synthase and acetyl CoA carboxylase inhibitors (h²  = 0.731 and 0.938, respectively), and evidence for shared additive genetic variance for resistance to these two different herbicide modes of action, r_g  = 0.34 (survival), 0.38 (biomass). We find no evidence for genetic correlations between life-history traits and herbicide resistance, indicating that resistance to these two modes of action is not associated with large fitness costs in blackgrass. We do, however, demonstrate that phenotypic variation in plant flowering characteristics is heritable, h²  = 0.213 (flower height), 0.529 (flower head number), 0.449 (time to flowering) and 0.372 (time to seed shed), demonstrating the potential for adaptation to other nonchemical management practices (e.g. mowing of flowering heads) now being adopted for blackgrass control.

CONCLUSION

These results highlight that quantitative genetics can provide important insight into the inheritance and genetic architecture of NTSR, and can be used alongside emerging molecular techniques to better understand the evolutionary and fitness landscape of herbicide resistance. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Does seed mass drive interspecies variation in the effect of management practices on weed demography?

Optimizing the effect of management practices on weed population dynamics is challenging due to the difficulties in inferring demographic parameters in seed banks and their response to disturbance. Here, we used a long-term plant survey between 2006 and 2012 in 46 French vineyards and quantified the effects of management practices (tillage, mowing, and herbicide) on colonization, germination, and seed survival of 30 weed species in relation to their seed mass. To do so, we used a recent statistical approach to reliably estimate demographic parameters for plant populations with a seed bank using time series of presence-absence data, which we extended to account for interspecies variation in the effects of management practices on demographic parameters. Our main finding was that when the level of disturbance increased (i.e., in plots with a higher number of herbicides, tillage, or mowing treatments), colonization success and survival in large-seeded species increased faster than in small-seeded species. High disturbance through tillage increased survival in the seed bank of species with high seed mass. The application of herbicides increased germination, survival, and colonization probabilities of species with high seed mass. Mowing, representing habitats more competitive for light, increased the survival of species with high seed mass. Overall, the strong relationships between the effects of management practices and seed mass provide an indicator for predicting the dynamics of weed communities under disturbance.

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

Fate and adaptive plasticity of heterogeneous resistant population of Echinochloa colona in response to glyphosate

Understanding the fate of heterogenous herbicide resistant weed populations in response to management practices can help towards overcoming the resistance issues. We selected one pair of susceptible (S) and resistant (R) phenotypes (2B21-R vs 2B21-S and 2B37-R vs 2B37-S) separately from two glyphosate resistant heterogeneous populations (2B21 and 2B37) of Echinochloa colona and their fate and adaptive plasticity were evaluated after glyphosate application. Our study revealed the glyphosate concentration required to cause a 50% plant mortality (LD50) was 1187, 200, 3064, and 192 g a. e. ha-1 for the four phenotypes 2B21-R, 2B21-S, 2B37-R, and 2B37-S respectively. Both S phenotypes accumulated more biomass than the R phenotypes at the lower application rates (34 and 67.5 g a. e. ha-1) of glyphosate. However, the R phenotypes generally produced more biomass at rates of glyphosate higher than 100 g a. e. ha-1 throughout the growth period. Plants from the R phenotypes of 2B21 and 2B37 generated 32% and 38% fewer spikesplant-1 than their respective S counterparts in the absence of glyphosate respectively. The spike and seed numbersplant-1 significantly higher in R than S phenotypes at increased rates of glyphosate and these relationships were significant. Our research suggests that glyphosate-resistant E. colona plants will be less fit than susceptible plants (from the same population) in the absence of glyphosate. But in the presence of glyphosate, the R plants may eventually dominate in the field. The use of glyphosate is widespread in field, would favour the selection towards resistant individuals.

Agricultural adaptation in the native North American weed waterhemp, Amaranthus tuberculatus (Amaranthaceae)

There is increasing interest in documenting adaptation of weedy plant species to agricultural ecosystems, beyond the evolution of herbicide resistance. Waterhemp (Amaranthus tuberculatus) is a native plant of the Midwestern U.S. that began infesting agricultural fields in the 20th century within the central portion of its range. We hypothesized that the vegetative growth and reproductive traits of waterhemp from this heavily infested central region provide differential fitness benefits in agricultural environments. We collected seeds from across the species' native range, representing regions with varying degrees of waterhemp infestation, and planted them together in common garden soybean plots. A 2010 common garden experiment was conducted within the range of agriculturally weedy waterhemp (in Missouri), and a 2011 common garden experiment was conducted outside of this range (in Ohio). Days to flowering and flowering plant height, mature plant size data (height, number of branches, and length of the longest branch), and above-ground biomass were measured to estimate relative fitness. In both common garden locations, plants from regions where waterhemp occurs as an agricultural weed - including those from the heavily infested Mississippi Valley region (Iowa, Illinois, and Missouri) and the less severely infested Plains region (Nebraska, Kansas, and Oklahoma) - had higher relative performance in almost all fitness-related measures than plants from the Northeast region (Ohio, Michigan, and Ontario), which had little to no agriculturally weedy waterhemp at the time of our study. Further analysis revealed that fewer days to flowering in the Northeast populations can be largely accounted for by latitude of origin, suggesting a strong genetic influence on this reproductive trait. These findings suggest intraspecific variation in agricultural adaptation in a native U.S. weed, and support the use of agricultural weeds to study adaptation.

StMADS11 Subfamily Gene PfMADS16 From Polypogon fugax Regulates Early Flowering and Seed Development

The evolution of herbicide resistance in weedy plants leads to various adaptation traits including flowering time and seed germination. In our previous studies, we found an association of the early flowering phenotype with the ACCase inhibitor herbicide resistance genotype in a population of Polypogon fugax. MADS-box transcription factors are known to play pivotal roles in regulating plant flowering time. In this study, a SHORT VEGETATIVE PHASE (SVP)-like gene, belonging to the StMADS11 subfamily in the MADS-box family, was cloned from the early flowering P. fugax population (referred to as PfMADS16) and resistant to the herbicide clodinafop- propargyl. Overexpression of the SVP-like gene PfMADS16 in Arabidopsis thaliana resulted in early flowering and seed abortion. This is consistent with the phenotypic characters of resistant P. fugax plants, but contrary to the conventional role of SVP-like genes that usually suppress flowering. In addition, down regulation of the seed formation gene AtKTN1 in flowers of PfMADS16 transgenic Arabidopsis plants indicates that PfMADS16 may be indirectly associated with seed viability. Furthermore, one protein (PfMADS2) from the APETALA1 (AP1) subfamily interacting with PfMADS16 in P. fugax was identified with relevance to flowering time regulation. These results suggest that the PfMADS16 gene is an early flowering regulation gene associated with seed formation and viability in resistant P. fugax population. Our study provides potential application of PfMADS16 for integrated weed management (such as genetic-based weed control strategies) aiming to reduce the soil weed seedbank.

Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed

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 glycosyltransferases-are 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.

Fitness of Herbicide-Resistant Weeds: Current Knowledge and Implications for Management

Herbicide resistance is the ultimate evidence of the extraordinary capacity of weeds to evolve under stressful conditions. Despite the extraordinary plant fitness advantage endowed by herbicide resistance mutations in agroecosystems under herbicide selection, resistance mutations are predicted to exhibit an adaptation cost (i.e., fitness cost), relative to the susceptible wild-type, in herbicide untreated conditions. Fitness costs associated with herbicide resistance mutations are not universal and their expression depends on the particular mutation, genetic background, dominance of the fitness cost, and environmental conditions. The detrimental effects of herbicide resistance mutations on plant fitness may arise as a direct impact on fitness-related traits and/or coevolution with changes in other life history traits that ultimately may lead to fitness costs under particular ecological conditions. This brings the idea that a “lower adaptive value” of herbicide resistance mutations represents an opportunity for the design of resistance management practices that could minimize the evolution of herbicide resistance. It is evident that the challenge for weed management practices aiming to control, minimize, or even reverse the frequency of resistance mutations in the agricultural landscape is to “create” those agroecological conditions that could expose, exploit, and exacerbate those life history and/or fitness traits affecting the evolution of herbicide resistance mutations. Ideally, resistance management should implement a wide range of cultural practices leading to environmentally mediated fitness costs associated with herbicide resistance mutations.

Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover?

The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide-resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide-resistant weeds in three broad areas - the genetic basis of adaptation, evolutionary constraints, experimental evolution - and similarly discuss questions left to be answered. I then develop how one would use herbicide-resistance evolution as a model for studying eco-evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide-resistant plants as models for addressing key questions within ecology and evolution.

Fitness costs associated with multiple resistance to dicamba and atrazine in Chenopodium album

Detrimental pleiotropic effects of resistance mutation(s) were observed for multiple-resistant phenotypes (resistant to both atrazine and dicamba). The multiple-resistant phenotypes had lower growth rates and less capacity for vegetative growth compared to the phenotypes only resistant to atrazine. The fitness costs that are conferred by herbicide resistance alleles can affect the rate of herbicide resistance evolution within populations. We evaluated the direct fitness costs involved with multiple resistance to dicamba and atrazine (R1 and R2) in Chenopodium album by comparing the performance of multiple-resistant phenotypes to those phenotypes that were only resistant to atrazine (S1 and S2). The R1 and R2 phenotypes were consistently shorter and produced less dry matter than the S1 and S2 phenotypes. The R1 and R2 phenotypes were shown to have lower relative growth rates (RGR) and net assimilation rates (NAR) than the S1 and S2 phenotypes at an early stage of growth. However, there was no significant difference in RGR between the R1 and R2 and, S1 and S2 phenotypes at a later stage of growth, though the R1 and R2 phenotypes still had a lower NAR at this later stage. Further investigations using a neighbouring crop competition approach showed that the R1 and R2 phenotypes were weaker competitors, and exhibited significantly less capacity for vegetative growth compared to the S1 and S2 phenotypes during competition. Overall, the results of this study revealed multiple- resistance to atrazine and dicamba endowed a significant fitness penalty to C. album, and it is possible that the frequency of multiple-resistant individuals would gradually decline once selection pressure from herbicides was discontinued.

Alterations in Life-History Associated With Non-target-site Herbicide Resistance in Alopecurus myosuroides

The evolution of resistance to herbicides is a classic example of rapid contemporary adaptation in the face of a novel environmental stress. Evolutionary theory predicts that selection for resistance will be accompanied by fitness trade-offs in environments where the stress is absent. Alopecurus myosuroides, an autumn-germinating grass weed of cereal crops in North-West Europe, has evolved resistance to seven herbicide modes-of-action, making this an ideal species to examine the presence and magnitudes of such fitness costs. Here, we use two contrasting A. myosuroides phenotypes derived from a common genetic background, one with enhanced metabolism resistance to a commercial formulation of the sulfonylurea (ALS) actives mesosulfuron and iodosulfuron, and the other with susceptibility to these actives (S). Comparisons of plant establishment, growth, and reproductive potential were made under conditions of intraspecific competition, interspecific competition with wheat, and over a gradient of nitrogen deprivation. Herbicide dose response assays confirmed that the two lines had contrasting resistance phenotypes, with a 20-fold difference in resistance between them. Pleiotropic effects of resistance were observed during plant development, with R plants having a greater intraspecific competitive effect and longer tiller lengths than S plants during vegetative growth, but with S plants allocating proportionally more biomass to reproductive tissues during flowering. Direct evidence of a reproductive cost of resistance was evident in the nitrogen deprivation experiment with R plants producing 27% fewer seed heads per plant, and a corresponding 23% reduction in total seed head length. However, these direct effects of resistance on fecundity were not consistent across experiments. Our results demonstrate that a resistance phenotype based on enhanced herbicide metabolism has pleiotropic impacts on plant growth, development and resource partitioning but does not support the hypothesis that resistance is associated with a consistent reproductive fitness cost in this species. Given the continued difficulties associated with unequivocally detecting costs of herbicide resistance, we advocate future studies that adopt classical evolutionary quantitative genetics approaches to determine genetic correlations between resistance and fitness-related plant life history traits.

Herbicide resistance costs: what are we actually measuring and why?

Despite the considerable research efforts invested over the years to measure the fitness costs of herbicide resistance, these have rarely been used to inform a predictive theory about the fate of resistance once the herbicide is discontinued. One reason for this may be the reductive focus on relative fitness of two genotypes as a single measure of differential performance. Although the extent of variation in relative fitness between resistant and susceptible plants has not been assessed consistently, we know enough about plant physiology and ecology not to reduce it to a single fixed value. Research must therefore consider carefully the relevance of the experimental environment, the life stage and the choice of metric when measuring fitness-related traits. The reason most often given for measuring the cost of resistance, prediction of the impacts of management options on population dynamics, cannot be addressed using arbitrary components of fitness or a fixed value of relative fitness. To inform management options, the measurement of traits that capture the relevant processes and the main causes of their variation are required. With an emphasis on the benefit of field experiments measured over multiple time points and seasons, we highlight examples of studies that have made significant advances in this direction. © 2017 Society of Chemical Industry.

Different Mutations Endowing Resistance to Acetyl-CoA Carboxylase Inhibitors Results in Changes in Ecological Fitness of Lolium rigidum Populations

Various mutations altering the herbicide target site (TS), can lead to structural modifications that decrease binding efficiency and results in herbicide resistant weed. In most cases, such a mutation will be associated with ecological fitness penalty under herbicide free environmental conditions. Here we describe the effect of various mutations, endowing resistance to acetyl-CoA carboxylase (ACCase) inhibitors, on the ecological fitness penalty of Lolium rigidum populations. The TS resistant populations, MH (substitution of isoleucine 1781 to leucine) and NO (cysteine 2088 to arginine), were examined and compared to a sensitive population (AL). Grain weight (GW) characterization of individual plants from both MH and NO populations, showed that resistant individuals had significantly lower GW compared with sensitive ones. Under high temperatures, both TS resistant populations exhibited lower germination rate as compared with the sensitive (AL) population. Likewise, early vigor of plants from both TS resistant populations was significantly lower than the one measured in plants of the sensitive population. Under crop-weed intra-species competition, we found an opposite trend in the response of plants from different populations. Relatively to inter-population competition conditions, plants of MH population were less affected and presented higher reproduction abilities compared to plants from both AL and NO populations. On the basis of our results, a non-chemical approach can be taken to favor the sensitive individuals, eventually leading to a decline in resistant individuals in the population.