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.

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.

Interspecific variation in resistance and tolerance to herbicide drift reveals potential consequences for plant community co-flowering interactions and structure at the agro-eco interface.

BACKGROUND AND AIMS: When plant communities are exposed to herbicide 'drift', wherein particles containing the active ingredient travel off-target, interspecific variation in resistance or tolerance may scale up to affect community dynamics. In turn, these alterations could threaten the diversity and stability of agro-ecosystems. We investigated the effects of herbicide drift on the growth and reproduction of 25 wild plant species to make predictions about the consequences of drift exposure on plant-plant interactions and the broader ecological community. METHODS: We exposed potted plants from species that commonly occur in agricultural areas to a drift-level dose of the widely used herbicide dicamba or a control solution in the glasshouse. We evaluated species-level variation in resistance and tolerance for vegetative and floral traits. We assessed community-level impacts of drift by comparing the species evenness and flowering networks of glasshouse synthetic communities comprised of drift-exposed and control plants. KEY RESULTS: Species varied significantly in resistance and tolerance to dicamba drift: some were negatively impacted while others showed overcompensatory responses. Species also differed in the way they deployed flowers over time following drift exposure. While drift had negligible effects on community evenness based on vegetative biomass, it caused salient differences in the structure of co-flowering networks within communities. Drift reduced the degree and intensity of flowering overlap among species, altered the composition of groups of species that were more likely to co-flower with each other than with others and shifted species roles (e.g. from dominant to inferior floral producers, and vice versa). CONCLUSIONS: These results demonstrate that even low levels of herbicide exposure can significantly alter plant growth and reproduction, particularly flowering phenology. If field-grown plants respond similarly, then these changes would probably impact plant-plant competitive dynamics and potentially plant-pollinator interactions occurring within plant communities at the agro-ecological interface.

Below-ground competition favors character convergence but not character displacement in root traits.

Character displacement can play a major role in species ecology and evolution; however, research testing whether character displacement can influence the evolution of root traits in plant systems remains scarce in the literature. Here we investigated the potential that character displacement may influence the evolution of root traits using two closely related morning glory species, Ipomoea purpurea and Ipomoea hederacea. We performed a field experiment where we grew the common morning glory, I. purpurea, in the presence and absence of competition from I. hederacea and examined the potential that the process of character displacement could influence the evolution of root traits. We found maternal line variation in root phenotypes and evidence that below-ground competition acts as an agent of selection on these traits. Our test of character displacement, however, showed evidence of character convergence on our measure of root architecture rather than displacement. These results suggest that plants may be constrained by their local environments to express a phenotype that enhances fitness. Therefore, the conditions of the competitive environment experienced by a plant may influence the potential for character convergence or displacement to influence the evolution of root traits.

Herbicides as anthropogenic drivers of eco-evo feedbacks in plant communities at the agro-ecological interface.

Herbicides act as human-mediated novel selective agents and community disruptors, yet their full effects on eco-evolutionary dynamics in natural communities have only begun to be appreciated. Here, we synthesize how herbicide exposures can result in dramatic phenotypic and compositional shifts within communities at the agro-ecological interface and how these in turn affect species interactions and drive plant (and plant-associates') evolution in ways that can feedback to continue to affect the ecology and ecosystem functions of these assemblages. We advocate a holistic approach to understanding these dynamics that includes plastic changes and plant community transformations and also extends beyond this single trophic level targeted by herbicides to the effects on nontarget plant-associated organisms and their potential to evolve, thereby embracing the complexity of these real-world systems. We make explicit recommendations for future research to achieve this goal and specifically address impacts of ecology on evolution, evolution on ecology and their feedbacks so that we can gain a more predictive view of the fates of herbicide-impacted communities.

Variable inbreeding depression may explain associations between the mating system and herbicide resistance in the common morning glory.

Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea artificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field, and paired this work with an examination of gene expression changes. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to nonselected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs. outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.

Belowground Competition Can Influence the Evolution of Root Traits.

Although root traits play a critical role in mediating plant-plant interactions and resource acquisition from the soil environment, research examining whether and how belowground competition can influence the evolution of root traits remains largely unexplored. Here we examine the possibility that root traits may evolve as a target of selection from interspecific competition using Ipomoea purpurea and I. hederacea, two closely related morning glory species that commonly co-occur in the United States, as a model system. We show that belowground competitive interactions between the two species can alter the pattern of selection on root traits in each species. Specifically, competition with I. purpurea changes the pattern of selection on root angle in I. hederacea, and competitive interactions with I. hederacea change the pattern of selection on root size in I. purpurea. However, we did not uncover evidence that intraspecific competition altered the pattern of selection on any root traits within I. hederacea. Overall, our results suggest that belowground competition between closely related species can influence the phenotypic evolution of root traits in natural populations. Our findings provide a microevolutionary perspective of how competitive belowground interactions may impact plant fitness, potentially leading to patterns of plant community structure.

The remarkable morphological diversity of leaf shape in sweet potato (Ipomoea batatas): the influence of genetics, environment, and G×E.

Leaf shape, a spectacularly diverse plant trait, varies across taxonomic levels, geography and in response to environmental differences. However, comprehensive intraspecific analyses of leaf shape variation across variable environments is surprisingly absent. Here, we performed a multilevel analysis of leaf shape using diverse accessions of sweet potato (Ipomoea batatas), and uncovered the role of genetics, environment, and G×E on this important trait. We examined leaf shape using a variety of morphometric analyses, and complement this with a transcriptomic survey to identify gene expression changes associated with shape variation. Additionally, we examined the role of genetics and environment on leaf shape by performing field studies in two geographically separate common gardens. We showed that extensive leaf shape variation exists within I. batatas, and identified promising candidate genes associated with this variation. Interestingly, when considering traditional measures, we found that genetic factors are largely responsible for most of leaf shape variation, but that the environment is highly influential when using more quantitative measures via leaf outlines. This extensive and multilevel examination of leaf shape shows an important role of genetics underlying a potentially important agronomic trait, and highlights that the environment can be a strong influence when using more quantitative measures of leaf shape.

The soil microbial community alters patterns of selection on flowering time and fitness-related traits in Ipomoea purpurea.

PREMISE: Plant flowering time plays an important role in plant fitness and thus evolutionary processes. Soil microbial communities are diverse and have a large impact, both positive and negative, on the host plant. However, owing to few available studies, how the soil microbial community may influence the evolutionary response of plant populations is not well understood. Here we sought to uncover whether belowground microbial communities act as an agent of selection on flowering and growth traits in the common morning glory, Ipomoea purpurea. METHODS: We performed a controlled greenhouse experiment in which genetic lines of I. purpurea were planted into either sterilized soils or in soils that were sterilized and inoculated with the microbial community from original field soil. We could thus directly test the influence of alterations to the microbial community on plant growth, flowering, and fitness and assess patterns of selection in both soil microbial environments. RESULTS: A more complex soil microbial community resulted in larger plants that produced more flowers. Selection strongly favored earlier flowering when plants were grown in the complex microbial environment than compared to sterilized soil. We also uncovered a pattern of negative correlational selection on growth rate and flowering time, indicating that selection favored different combinations of growth and flowering traits in the simplified versus complex soil community. CONCLUSIONS: Together, these results suggest the soil microbial community is a selective agent on flowering time and ultimately that soil microbial community influences important plant evolutionary processes.

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.

The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed.

Examining how the landscape may influence gene flow is at the forefront of understanding population differentiation and adaptation. Such understanding is crucial in light of ongoing environmental changes and the elevated risk of ecosystems alteration. In particular, knowledge of how humans may influence population structure is imperative to allow for informed decisions in management and conservation as well as to gain a better understanding of anthropogenic impacts on the interplay between gene flow, genetic drift, and selection. Here, we use genome-wide molecular markers to characterize the population genetic structure and connectivity of Ipomoea purpurea (Convolvulaceae), a noxious invasive weed. We, likewise, assess the interaction between natural and human-driven influences on genetic differentiation among populations. Our analyses find that human population density is an important predictor of pairwise population differentiation, suggesting that the agricultural and/or horticultural trade may be involved in maintaining some level of connectivity across distant agricultural fields. Climatic variation appears as an additional predictor of genetic connectivity in this species. We discuss the implications of these results and highlight future research needed to disentangle the mechanistic processes underlying population connectivity of weeds.

Natural and Anthropogenic Influences on the Mating System of the Common Morning Glory.

Evolutionary biologists remain puzzled by the often dramatic variation of mating strategies within single species. Of particular interest is the extent to which environmental conditions shape patterns of variation of mating system components within mixed mating species, and how widespread anthropogenic manipulations may influence these associations. Here, we address this question in the common morning glory (Ipomoea purpurea) by combining a dataset of floral traits, estimates of the mating system, and relevant environmental factors compiled for 22 populations of this species distributed along a wide range of environments from the Southeastern and Midwestern United States. We identify a disparate set of environmental factors to influence population-level variation in selfing, inbreeding, and flower morphology. Although floral traits are primarily associated with climatic variation, the outcrossing rate and inbreeding coefficient are primarily influenced by the level of herbicide resistance. Furthermore, we find that populations with higher levels of herbicide resistance exhibit a stronger correlation between mating system-floral traits and mating system estimates (outcrossing rate and inbreeding coefficient). Altogether, these results demonstrate the dominant role that herbicide application plays in the determination of I. purpurea's mating system, and more generally uncover the complex and unforeseen evolutionary consequences of anthropogenic manipulations in natural systems.

Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory.

Human-mediated selection can strongly influence the evolutionary response of natural organisms within ecological timescales. But what traits allow for, or even facilitate, adaptation to the strong selection humans impose on natural systems? Using a combination of laboratory and greenhouse studies of 32 natural populations of the common agricultural weed, Ipomoea purpurea, we show that herbicide-resistant populations self-fertilise more than susceptible populations. We likewise show that anther-stigma distance, a floral trait associated with self-fertilisation in this species, exhibits a nonlinear relationship with resistance such that the most and least resistant populations exhibit lower anther-stigma separation compared to populations with moderate levels of resistance. Overall, our results extend the general finding that plant mating can be impacted by human-mediated agents of selection to that of the extreme selection of the agricultural system. This work highlights the influence of human-mediated selection on rapid responses of natural populations that can lead to unexpected long-term evolutionary consequences.

Phylotranscriptomic analysis of the origin and early diversification of land plants.

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea.

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that these bottlenecks may have occurred prior to 2003. A greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. However, populations differed significantly between sampling years for resistance: some populations maintained high resistance between the sampling years whereas others exhibited increased or decreased resistance. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We probably uncovered only modest increases in resistance on average between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that nonresistant migrants germinate from the seed bank.

How weeds emerge: a taxonomic and trait-based examination using United States data.

Weeds can cause great economic and ecological harm to ecosystems. Despite their importance, comparisons of the taxonomy and traits of successful weeds often focus on a few specific comparisons - for example, introduced versus native weeds. We used publicly available inventories of US plant species to make comprehensive comparisons of the factors that underlie weediness. We quantitatively examined taxonomy to determine if certain genera are overrepresented by introduced, weedy or herbicide-resistant species, and we compared phenotypic traits of weeds to those of nonweeds, whether introduced or native. We uncovered genera that have more weeds and introduced species than expected by chance and plant families that have more herbicide-resistant species than expected by chance. Certain traits, generally related to fast reproduction, were more likely to be associated with weedy plants regardless of species' origins. We also found stress tolerance traits associated with either native or introduced weeds compared with native or introduced nonweeds. Weeds and introduced species have significantly smaller genomes than nonweeds and native species. These results support trends for weedy plants reported from other floras, suggest that native and introduced weeds have different stress adaptations, and provide a comprehensive survey of trends across weeds within the USA.