Rapid weed adaptation and range expansion in response to agriculture over the past two centuries

Multiple Origins or Widespread Gene Flow in Agricultural Fields? Regional Population Genomics of Herbicide Resistance in Bromus tectorum

The repeated evolution of herbicide resistance in agriculture provides an unprecedented opportunity to understand how organisms rapidly respond to strong anthropogenic-driven selection pressure. We recently identified agricultural populations of the grass species Bromus tectorum L. with resistance to multiple herbicides. To understand the evolutionary origins and spread of resistance, we investigated the resistance mechanisms to acetolactate synthase (ALS) inhibitors and photosystem II inhibitors, two widely used herbicide modes of action, in 49 B. tectorum populations. We assessed the genetic diversity, structure and relatedness in a subset of 21 populations. Resistance to ALS inhibitors was associated with multiple nonsynonymous mutations in ALS, the target site gene, despite the relatively small geographic region where populations originated, suggesting ALS inhibitor resistance evolution occurred multiple times in the region. We also found evidence that mechanisms not related to the target site evolved and were common in the populations studied. Resistance to photosystem II inhibitors was confirmed in two populations and was conferred by nonsynonymous mutations in the plastid gene psbA. Population genomics analyses suggested that ALS resistance in most populations, at the nucleotide level, spread via gene flow, except for one population where we found evidence that Pro-197-His mutations may have evolved in three separate events. Our results suggest that both gene flow via pollen and/or seed dispersal and multiple local evolutionary events were involved in the spread of herbicide-resistant B. tectorum. Our results provide an empirical example of the rapid repeated evolution of a trait under strong anthropogenic selection and elucidate the evolutionary origins of herbicide resistance in a plant species of agricultural importance.

Resistance to the herbicides haloxyfop and iodosulfuron is common in commercial ryegrass (Lolium) seed lines

BACKGROUND

Ryegrass (Lolium spp.) is a key forage providing a $14 billion contribution to New Zealand's gross domestic product (GDP). However, ryegrass can also act as a weed and evolve resistance to herbicides used for its control. Farmers suspected that imported seed might contribute to resistance issues. Herbicide resistance frequencies were investigated in commercial ryegrass seed lines intended for multiplication in New Zealand. Samples from 56 basic seed lots and 52 unique cultivars sourced from regions including New Zealand, United States, Europe and Japan were planted in field trials. Seedlings were then sprayed with three common herbicides: glyphosate, iodosulfuron, and haloxyfop. Surviving plants were retested to confirm resistance.

RESULTS

Resistance to haloxyfop and or iodosulfuron was detected in 79% of seed lines. However, frequencies were not significantly higher in imported lines (from United States and Europe) compared with New Zealand lines. Resistance was detected at frequencies between 0.00112% and 10% for haloxyfop and between 0.00212% and 14.28% for iodosulfuron Resistance to glyphosate was not found. There was no significant difference between the resistance detected in seed samples sourced from different seed companies.

CONCLUSIONS

It was found that 63% of resistant lines had resistance frequencies rarer than 0.1%, but this is potentially problematic considering typical sowing rates. Imported versus domestic seed sources were not significantly different; they pose similar levels of resistance risk to farmers. Lolium multiflorum had a higher resistance frequency compared to Lolium perenne (although only six L. multiflorum lots were evaluated). Breeders should screen progeny of early crosses for herbicide resistance. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Using weedy traits in crops as part of a new green revolution

Crop production faces major challenges, including climate change, biodiversity loss, and global food insecurity, with the need to produce more food under increasingly difficult climatic conditions without negatively impacting ecosystems. Weeds are plants that have adapted to cropping systems despite intensive management efforts over centuries. We propose that weeds possess novel and useful sources of genetic variation that can be used to improve crops for abiotic and biotic stress tolerance. We discuss the potential advantages and disadvantages associated with this approach and outline the interdisciplinary research that will be necessary to successfully identify and utilize this genetic diversity to improve crops. Although the concept of utilizing weedy traits in crops has been put forward previously, recent advances in weed genomics resources, bioinformatics tools to identify the genetic basis of adaptive traits, and genome editing methods now combine to make this approach more feasible.

Genetic diversity and population structure of ALS-resistant Amaranthus hybridus across Brazil's primary soybean-growing regions

BACKGROUND

Resistance to acetolactate synthase (ALS)-inhibiting herbicides has emerged in Amaranthus hybridus populations across Brazil's soybean-growing regions. To gain insights into the evolutionary origins and spread of resistance, this study (1) investigated the ALS inhibitor resistance mechanisms in nine A. hybridus populations and (2) assessed their genetic diversity, structure, and relatedness.

RESULTS

Resistance to the ALS inhibitor chlorimuron in A. hybridus was associated with two distinct target-site mutations: Trp-574-Leu and Asp-376-Glu. Population genetics revealed low levels of genetic diversity (HE = 0.00117 to 0.16019; π = 0.00126 to 0.17421) and inbreeding (FIS = 0.0015 to 0.13157). Principal component analysis differentiated A. hybridus by geographical region, while ADMIXTURE analysis revealed population structure with evidence of admixture between genetic clusters in three groups of populations.

CONCLUSION

The results suggest multiple local and independent evolutionary origins of resistance. The spread of resistance is primarily driven by local herbicide selection pressure and gene flow through seed dispersal. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Rational Redomestication for Future Agriculture

Modern agricultural practices rely on high-input, intensive cultivation of a few crop varieties with limited diversity, increasing the vulnerability of our agricultural systems to biotic and abiotic stresses and the effects of climate changes. This necessitates a paradigm shift toward a more sustainable agricultural model to ensure a stable and dependable food supply for the burgeoning global population. Leveraging knowledge from crop biology, genetics, and genomics, alongside state-of-the-art biotechnologies, rational redomestication has emerged as a targeted and knowledge-driven approach to crop innovation. This strategy aims to broaden the range of species available for agriculture, restore lost genetic diversity, and further improve existing domesticated crops. We summarize how diverse plants can be exploited in rational redomestication endeavors, including wild species, underutilized plants, and domesticated crops. Equipped with rational redomestication approaches, we propose different strategies to empower the fast and slow breeding systems distinguished by plant reproduction systems.

Discovery, Herbicidal Activity and Biosynthesis of a Novel Natural Tetramic Acid from Alternaria Species

The tetramic acid moiety is a pivotal structural unit in numerous natural products. As an analogue of the simplest tetramic acid compound tenuazonic acid (TeA), sec-pentyl-TeA (S-TeA) exhibits double herbicidal activity of TeA. Here, this work identifies S-TeA as a novel natural product synthesized by Alternaria alternata and three other filamentous fungi. Chiral analysis confirm the absolute configuration of natural S-TeA as (5S, 6S). Configuration-bioactivity studies reveal that natural (5S, 6S)-S-TeA is the eutomer and possesses the highest herbicidal activity among all tested diastereomers. Biosynthetic analyses demonstrate that threonine is the precursor to S-TeA, beginning with the production of 2-amino-3-methylhexanoic acid (AMHA) via eight enzymes from the branched-chain amino acid (BCAA) biosynthetic pathway, including threonine deaminase, 2-isopropylmalate synthase (IPMS), 3-isopropylmalate dehydratase (IPMDH), isopropylmalate dehydrogenase (ISMD), acetolactate synthase, ketol-acid reductoisomerase, dihydroxy acid dehydratase, and BCAA aminotransferase. Subsequently, AMHA undergoes acetylation and cyclization by non-ribosomal peptide synthetases to form S-TeA. Distinct differences in the biosynthetic pathways of S-TeA and TeA are identified. In vitro studies confirm the critical roles of three unique enzymes IPMS, IPMDH, and ISMD in S-TeA biosynthesis, which are absent in TeA biosynthesis. These findings provide a solid basis for developing S-TeA as a natural product herbicide.

Chromosome-Level Assemblies of the Allohexaploid Genomes of Conyza sumatrensis and Conyza bonariensis

Conyza sumatrensis and Conyza bonariensis are two important hexaploid weed species that impact crop production systems across the globe. Here, we report reference genome assemblies for both species. The sequenced accession of C. sumatrensis is resistant to multiple herbicides and was collected from the state of Paraná in Brazil, while the accession of C. bonariensis was collected from California, USA. Genomic long read data was used along with optical mapping data to assemble the C. sumatrensis genome into a single haplome at chromosome-level contiguity. The same approach was used along with chromatin contact mapping data to phase the haplotypes of C. bonariensis and generate two chromosome-level haplome assemblies. Subgenome-specific sequences were identified and used to classify the three subgenomes within each assembly. The assemblies are highly complete based on the presence of conserved single-copy orthologs and telomeres, and the size of these assemblies agrees with previous flow cytometry estimates. Full-length transcript sequencing along with gene models from other Asteraceae members was used to predict gene models within each assembly. The genomic resources reported here will be useful for investigations into evolutionary and ecological questions around weed invasion and management for these two species.

The genomic secrets of invasive plants

Genomics has revolutionised the study of invasive species, allowing evolutionary biologists to dissect mechanisms of invasion in unprecedented detail. Botanical research has played an important role in these advances, driving much of what we currently know about key determinants of invasion success (e.g. hybridisation, whole-genome duplication). Despite this, a comprehensive review of plant invasion genomics has been lacking. Here, we aim to address this gap, highlighting recent discoveries that have helped progress the field. For example, by leveraging genomics in natural and experimental populations, botanical research has confirmed the importance of large-effect standing variation during adaptation in invasive species. Further, genomic investigations of plants are increasingly revealing that large structural variants, as well as genetic changes induced by whole-genome duplication such as genomic redundancy or the breakdown of dosage-sensitive reproductive barriers, can play an important role during adaptive evolution of invaders. However, numerous questions remain, including when chromosomal inversions might help or hinder invasions, whether adaptive gene reuse is common during invasions, and whether epigenetically induced mutations can underpin the adaptive evolution of plasticity in invasive populations. We conclude by highlighting these and other outstanding questions that genomic studies of invasive plants are poised to help answer.

Museum genomics reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

Global patterns of population genetic variation through time offer a window into evolutionary processes that maintain diversity. Over time, lineages may expand or contract their distribution, causing turnover in population genetic composition. At individual loci, migration, drift, environmental change (among other processes) may affect allele frequencies. Museum specimens of widely distributed species offer a unique window into the genetics of understudied populations and changes over time. Here, we sequenced genomes of 130 herbarium specimens and 91 new field collections of Arabidopsis thaliana and combined these with published genomes. We sought a broader view of genomic diversity across the species, and to test if population genomic composition is changing through time. We documented extensive and previously uncharacterized diversity in a range of populations in Africa, populations that are under threat from anthropogenic climate change. Through time, we did not find dramatic changes in genomic composition of populations. Instead, we found a pattern of genetic change every 100 years of the same magnitude seen when comparing Eurasian populations that are 185 km apart, potentially due to a combination of drift and changing selection. We found only mixed signals of polygenic adaptation at phenology and physiology QTL. We did find that genes conserved across eudicots show altered levels of directional allele frequency change, potentially due to variable purifying and background selection. Our study highlights how museum specimens can reveal new dimensions of population diversity and show how wild populations are evolving in recent history.

Evolution in Response to Management Increases Invasiveness Among Experimental Populations of Duckweed (Lemna minor)

Numerous management methods are deployed to try to mitigate the destructive impact of weedy and invasive populations. Yet, such management practices may cause these populations to inadvertently evolve in ways that have consequence on their invasiveness. To test this idea, we conducted a two-step field mesocosm experiment; we evolved genetically diverse populations of the duckweed Lemna minor to targeted removal management and then tested the impact of that evolution in replicated invasions into experimental resident communities. We found that evolution in response to management increased invasiveness compared to populations evolved without management. This evolution in response to management had little effect on the impact of the invader on the resident species. These results illustrate the potential eco-evolutionary consequences of management practices. Mitigating evolution to physical removal, in addition to pesticides, may be important to the long-term success of integrated pest management.

Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide

The mobilization of transposable elements is a potent source of mutations. In plants, several stransposable elements respond to external cues, fuelling the hypothesis that natural transposition can create environmentally sensitive alleles for adaptation. Here we report on the detailed characterization of a retrotransposon insertion within the first intron of the Arabidopsis floral-repressor gene FLOWERING LOCUS C (FLC) and the discovery of its role for adaptation. The insertion mutation augments the environmental sensitivity of FLC by affecting the balance between coding and non-coding transcripts in response to stress, thus expediting flowering. This balance is modulated by DNA methylation and orchestrated by IBM2, a factor involved in the processing of intronic heterochromatic sequences. The stress-sensitive allele of FLC has spread across populations subjected to recurrent chemical weeding, and we show that retrotransposon-driven acceleration of the life cycle represents a rapid response to herbicide application. Our work provides a compelling example of a transposable element-driven environmentally sensitive allele that confers an adaptive response in nature.

Population Genomic Scans for Natural Selection and Demography

Uncovering the fundamental processes that shape genomic variation in natural populations is a primary objective of population genetics. These processes include demographic effects such as past changes in effective population size or gene flow between structured populations. Furthermore, genomic variation is affected by selection on nonneutral genetic variants, for example, through the adaptation of beneficial alleles or balancing selection that maintains genetic variation. In this article, we discuss the characterization of these processes using population genetic models, and we review methods developed on the basis of these models to unravel the underlying processes from modern population genomic data sets. We briefly discuss the conditions in which these approaches can be used to infer demography or identify specific nonneutral genetic variants and cases in which caution is warranted. Moreover, we summarize the challenges of jointly inferring demography and selective processes that affect neutral variation genome-wide.

Environment-independent distribution of mutational effects emerges from microscopic epistasis

Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, in which the fitness effects of mutations scale with the fitness of the background genotype, can improve predictions, but how the environment modulates this scaling is unknown. We measured the fitness effects of ~100 insertion mutations in 42 strains of Saccharomyces cerevisiae in six laboratory environments and found that the global epistasis scaling is nearly invariant across environments. Instead, the environment tunes one global parameter, the background fitness at which most mutations switch sign. As a consequence, the distribution of mutational effects is predictable across genotypes and environments. Our results suggest that the effective dimensionality of genotype-to-phenotype maps across environments is surprisingly low.

Environment-independent distribution of mutational effects emerges from microscopic epistasis

Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, where the fitness effects of mutations scale with the fitness of the background genotype, can improve predictions, but how the environment modulates this scaling is unknown. We measured the fitness effects of ~100 insertion mutations in 42 strains of Saccharomyces cerevisiae in six laboratory environments and found that the global-epistasis scaling is nearly invariant across environments. Instead, the environment tunes one global parameter, the background fitness at which most mutations switch sign. As a consequence, the distribution of mutational effects is predictable across genotypes and environments. Our results suggest that the effective dimensionality of genotype-to-phenotype maps across environments is surprisingly low.

Biotic interactions promote local adaptation to soil in plants

Although different ecological factors shape adaptative evolution in natural habitats, we know little about how their interactions impact local adaptation. Here we used eight generations of experimental evolution with outcrossing Brassica rapa plants as a model system, in eight treatment groups that varied in soil type, herbivory (with/without aphids), and pollination mode (hand- or bumblebee-pollination), to study how biotic interactions affect local adaptation to soil. First, we show that several plant traits evolved in response to biotic interactions in a soil-specific way. Second, using a reciprocal transplant experiment, we demonstrate that significant local adaptation to soil-type evolved in the "number of open flowers", a trait used as a fitness proxy, but only in plants that evolved with herbivory and bee pollination. Whole genome re-sequencing of experimental lines revealed that biotic interactions caused a 10-fold increase in the number of SNPs across the genome with significant allele frequency change, and that alleles with opposite allele frequency change in different soil types (antagonistic pleiotropy) were most common in plants with an evolutionary history of herbivory and bee pollination. Our results demonstrate that the interaction with mutualists and antagonists can facilitate local adaptation to soil type through antagonistic pleiotropy.

The double life of trichomes: understanding their dual role in herbivory and herbicide resistance

Understanding the evolutionary forces that maintain phenotypic variation in ecologically relevant traits has long been one of the central goals of evolutionary ecology. While the maintenance of variation in plant defense is most often hypothesized to be due to trait trade-offs or spatiotemporal variation in herbivore abundance, the role that heterogeneous selective agents may play on the maintenance of variation in plant defense is less examined. Trichomes are hair-like appendages on plant surfaces that can defend against multiple damaging agents such as pathogens, herbivores, and UV radiation. It is currently unknown however if conflicting selection from such heterogeneous agents of damage may act to maintain the variation observed in trichome traits. Here, we assess whether trichomes serve as an herbicide resistance trait and how it coincides with the conventionally studied defensive strategy of herbivory resistance. In a series of experiments, we exposed the annual invasive velvetleaf (Abutilon theophrasti) to glyphosate (active ingredient in "Roundup") to investigate whether trichome traits (type and density) are linked to herbicide resistance and to test whether herbicide influences selection on plant trichomes. We found that an increased proportion of branched trichomes positively impacted herbicide resistance and chewing herbivory resistance. We also found evidence that glyphosate imposes positive selection on branched trichomes in velvetleaf. Overall, our results indicate that branched trichomes can contribute to both herbicide and herbivory resistance, serving a concordant rather than conflicting role to reduce plant injury. Our findings further suggest that novel anthropogenic agents of selection can alter the composition of plant defense traits, potentially impacting trait-mediated interactions among external stressors.

Current status of community resources and priorities for weed genomics research

Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.

Weed biology and management in the multi-omics era: Progress and perspectives

Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.

Rapid adaptation of Viola arvensis to pollinator declines

This article is a Commentary on Acoca‐Pidolle et al. (2023), 242: 717–726.

The effects of microplastics on crop variation depend on polymer types and their interactions with soil nutrient availability and weed competition

Microplastics pollution of agricultural soil is a global environmental concern because of its potential risk to food security and human health. Although many studies have tested the direct effects of microplastics on growth of Eruca sativa Mill., little is known about whether these effects are regulated by fertilization and weed competition in field management practices. Here, we performed a greenhouse experiment growing E. sativa as target species in a three-factorial design with two levels of fertilization (low versus. high), two levels of weed competition treatments (weed competition versus no weed competition) and five levels of microplastic treatments (no microplastics, Polybutylene adipate-co-terephthalate [PBAT], Polybutylene succinate [PBS], Polycaprolactone [PCL] or Polypropylene [PP]). Compared to the soil without microplastics, PBS and PCL reduced aboveground biomass and leaf number of the E. sativa. PBS also resulted in increased root allocation and thicker roots in E. sativa. In addition, fertilization significantly mitigated the negative effects of PBS and PCL on aboveground biomass of E. sativa, but weed competition significantly promoted these effects. Although fertilization alleviated the negative effect of PBS on aboveground biomass, such alleviation became weaker under weed competition than when E. sativa grew alone. The results indicate that the effects of specific polymer types on E. sativa growth could be regulated by fertilization, weed management, and even their interactions. Therefore, reasonable on-farm management practices may help in mitigating the negative effects of microplastics pollution on E. sativa growth in agricultural fields.

The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change

Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.

Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus

Genome size variation, largely driven by repeat content, is poorly understood within and among populations, limiting our understanding of its significance for adaptation. Here we characterize intraspecific variation in genome size and repeat content across 186 individuals of Amaranthus tuberculatus, a ubiquitous native weed that shows flowering time adaptation to climate across its range and in response to agriculture. Sequence-based genome size estimates vary by up to 20% across individuals, consistent with the considerable variability in the abundance of transposable elements, unknown repeats, and rDNAs across individuals. The additive effect of this variation has important phenotypic consequences-individuals with more repeats, and thus larger genomes, show slower flowering times and growth rates. However, compared to newly-characterized gene copy number and polygenic nucleotide changes underlying variation in flowering time, we show that genome size is a marginal contributor. Differences in flowering time are reflected by genome size variation across sexes and marginally, habitats, while polygenic variation and a gene copy number variant within the ATP synthesis pathway show consistently stronger environmental clines than genome size. Repeat content nonetheless shows non-neutral distributions across the genome, and across latitudinal and environmental gradients, demonstrating the numerous governing processes that in turn influence quantitative genetic variation for phenotypes key to plant adaptation.

Temporal collections to study invasion biology

Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.

Resurrected seeds from herbarium specimens reveal rapid evolution of drought resistance in a selfing annual

PREMISE

Increased aridity and drought associated with climate change are exerting unprecedented selection pressures on plant populations. Whether populations can rapidly adapt, and which life history traits might confer increased fitness under drought, remain outstanding questions.

METHODS

We utilized a resurrection ecology approach, leveraging dormant seeds from herbarium collections to assess whether populations of Plantago patagonica from the semi-arid Colorado Plateau have rapidly evolved in response to approximately ten years of intense drought in the region. We quantified multiple traits associated with drought escape and drought resistance and assessed the survival of ancestors and descendants under simulated drought.

RESULTS

Descendant populations displayed a significant shift in resource allocation, in which they invested less in reproductive tissues and relatively more in both above- and below-ground vegetative tissues. Plants with greater leaf biomass survived longer under terminal drought; moreover, even after accounting for the effect of increased leaf biomass, descendant seedlings survived drought longer than their ancestors.

CONCLUSIONS

Our results document rapid adaptive evolution in response to climate change in a selfing annual and suggest that shifts in tissue allocation strategies may underlie adaptive responses to drought in arid or semi-arid environments. This work also illustrates a novel approach, documenting that under specific circumstances, seeds from herbarium specimens may provide an untapped source of dormant propagules for future resurrection experiments.

Ancient DNA genomics and the renaissance of herbaria

Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.

The role of intraspecific crop-weed hybridization in the evolution of weediness and invasiveness: Cultivated and weedy radish (Raphanus sativus) as a case study

PREMISE

The phenotype of hybrids between a crop and its wild or weed counterpart is usually intermediate and maladapted compared to that of their parents; however, hybridization has sometimes been associated with increased fitness, potentially leading to enhanced weediness and invasiveness. Since the ecological context and maternal genetic effects may affect hybrid fitness, they could influence the evolutionary outcomes of hybridization. Here, we evaluated the performance of first-generation crop-weed hybrids of Raphanus sativus and their parents in two contrasting ecological conditions.

METHODS

Using experimental hybridization and outdoor common garden experiments, we assessed differences in time to flowering, survival to maturity, plant biomass, and reproductive components between bidirectional crop-weed hybrids and their parents in agrestal (wheat cultivation, fertilization, weeding) and ruderal (human-disturbed, uncultivated area) conditions over 2 years.

RESULTS

Crop, weeds, and bidirectional hybrids overlapped at least partially during the flowering period, indicating a high probability of gene flow. Hybrids survived to maturity at rates at least as successful as their parents and had higher plant biomass and fecundity, which resulted in higher fitness compared to their parents in both environments, without any differences associated with the direction of the hybridization.

CONCLUSIONS

Intraspecific crop-weed hybridization, regardless of the cross direction, has the potential to promote weediness in weedy R. sativus in agrestal and ruderal environments, increasing the chances for introgression of crop alleles into weed populations. This is the first report of intraspecific crop-weed hybridization in R. sativus.

Convergent Adaptation of Multiple Herbicide Resistance to Auxin Mimics and ALS- and EPSPS-Inhibitors in Brassica rapa from North and South America

Herbicide-resistant weeds have been identified and recorded on every continent where croplands are available. Despite the diversity of weed communities, it is of interest how selection has led to the same consequences in distant regions. Brassica rapa is a widespread naturalized weed that is found throughout temperate North and South America, and it is a frequent weed among winter cereal crops in Argentina and in Mexico. Broadleaf weed control is based on glyphosate that is used prior to sowing and sulfonylureas or mimic auxin herbicides that are used once the weeds have already emerged. This study was aimed at determining whether a convergent phenotypic adaptation to multiple herbicides had occurred in B. rapa populations from Mexico and Argentina by comparing the herbicide sensitivity to inhibitors of the acetolactate synthase (ALS), 5-enolpyruvylshikimate-3-phosphate (EPSPS), and auxin mimics. Five B. rapa populations were analyzed from seeds collected in wheat fields in Argentina (Ar1 and Ar2) and barley fields in Mexico (Mx1, Mx2 and MxS). Mx1, Mx2, and Ar1 populations presented multiple resistance to ALS- and EPSPS-inhibitors and to auxin mimics (2,4-D, MCPA, and fluroxypyr), while the Ar2 population showed resistance only to ALS-inhibitors and glyphosate. Resistance factors ranged from 947 to 4069 for tribenuron-methyl, from 1.5 to 9.4 for 2,4-D, and from 2.7 to 42 for glyphosate. These were consistent with ALS activity, ethylene production, and shikimate accumulation analyses in response to tribenuron-methyl, 2,4-D, and glyphosate, respectively. These results fully support the evolution of the multiple- and cross-herbicide resistance to glyphosate, ALS-inhibitors, and auxinic herbicides in B. rapa populations from Mexico and Argentina.

A lack of population structure characterizes the invasive Lonicera japonica in West Virginia and across eastern North America

Invasive plant species cause massive ecosystem damage globally, yet represent powerful case studies in population genetics and rapid adaptation to new habitats. The availability of digitized herbarium collections data, and the ubiquity of invasive species across the landscape make them highly accessible for studies of invasion history and population dynamics associated with their introduction, establishment, spread, and ecological interactions. Here we focus on Lonicera japonica, one of the most damaging invasive vine species in North America. We leveraged digitized collections data and contemporary field collections to reconstruct the invasion history and characterize patterns of genomic variation in the eastern USA, using a straightforward method for generating nucleotide polymorphism data and a recently published, chromosome-level genome for the species. We found an overall lack of population structure among sites in northern West Virginia, USA, as well as across sites in the central and eastern USA. Heterozygosity and population differentiation were both low based on Fst, analysis of molecular variance, principal components analysis, and cluster-based analyses. We also found evidence of high inbreeding coefficients and significant linkage disequilibrium, in line with the ability of this otherwise outcrossing, perennial species to propagate vegetatively. Our findings corroborate earlier studies based on allozyme data, and suggest that intentional, human-assisted spread explains the lack of population structure, as this species was planted for erosion control and as an ornamental, escaping cultivation repeatedly across the USA. Finally, we discuss how plant invasion genomics can be incorporated into experiential undergraduate education as a way to integrate teaching and research.