Ecology, Biology, Environmental Impacts, and Management of an Agro-Environmental Weed Ageratum conyzoides.

Ageratum conyzoides L. (Billy goat weed; Asteraceae) is an annual herbaceous plant of American origin with a pantropical distribution. The plant has unique biological attributes and a raft of miscellaneous chemical compounds that render it a pharmacologically important herb. Despite its high medicinal value, the constant spread of the weed is noticeable and alarming. In many countries, the weed has severely invaded the natural, urban, and agroecosystems, thus presenting management challenges to natural resource professionals and farmers. Its interference with agricultural crops, grassland forbs, forest ground flora, and its ability to replace native plant species are of serious concern. Therefore, it is pertinent to monitor its continuous spread, its entry into new geographic regions, the extent of its impact, and the associated evolutionary changes. While management strategies should be improvised to control its spread and reduce its adverse impacts, the possible utilization of this noxious weed for pharmacological and agronomic purposes should also be explored. The objective of this review is to provide a detailed account of the global distribution, biological activities, ecological and environmental impacts, and strategies for the management of the agro-environmental weed A. conyzoides.

Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations.

Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 19 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size estimate of 8 x 107. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show extreme parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. Two such forces are intra- and inter-locus allelic interactions; we report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.

Agricultural Weed Assessment Calculator: An Australian Evaluation.

Weed risk assessment systems are used to estimate the potential weediness or invasiveness of introduced species in non-agricultural habitats. However, an equivalent system has not been developed for weed species that occur in agronomic cropland. Therefore, the Agricultural Weed Assessment Calculator (AWAC) was developed to quantify the present and potential future adverse impact of a weed species on crop production and profitability (threat analysis), thereby informing or directing research, development, and extension (RDE) investments or activities. AWAC comprises 10 questions related primarily to a weed's abundance and economic impact. Twenty weed species from across Australia were evaluated by AWAC using existing information and expert opinion, and rated as high, medium, or low for RDE prioritization based on total scores of 70 to 100, 40 to <70, or <40, respectively. Five species were rated as high (e.g., Lolium rigidum Gaud.), eight were rated as medium (e.g., Conyza spp.), and seven were rated as low (e.g., Rapistrum rugosum L.). Scores were consistent with the current state of knowledge of the species' impact on grain crop production in Australia. AWAC estimated the economic or agronomic threat of 20 major or minor agricultural weeds from across Australia. The next phase of development is the testing of AWAC by weed practitioners (e.g., agronomists, consultants, farmers) to verify its utility and robustness in accurately assessing these and additional weed species.

Something old, something new: Evolution of Colombian weedy rice (Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization.

Weedy rice (Oryza spp.) is a worldwide weed of domesticated rice (O. sativa), considered particularly problematic due to its strong competition with the crop, which leads to reduction in yields and harvest quality. Several studies have established multiple independent origins for weedy rice populations in the United States and various parts of Asia; however, the origins of weedy rice in South America have not been examined in a global context. We evaluated the genetic variation of weedy rice populations in Colombia, as well as the contributions of local wild Oryza species, local cultivated varieties, and exotic Oryza groups to the weed, using polymorphism generated by genotyping by sequencing (GBS). We found no evidence for genomic contributions from local wild Oryza species (O. glumaepatula, O. grandiglumis, O. latifolia, and O. alta) to Colombian weedy rice. Instead, Colombian weedy rice has evolved from local indica cultivars and has also likely been inadvertently imported as an exotic pest from the United States. Additionally, weeds comprising de novo admixture between these distinct weedy populations now represent a large proportion of genomic backgrounds in Colombian weedy rice. Our results underscore the impressive ability of weedy rice to evolve through multiple evolutionary pathways, including in situ de-domestication, range expansion, and hybridization.

Contrasting patterns of variation in weedy traits and unique crop features in divergent populations of US weedy rice (Oryza sativa sp.) in Arkansas and California.

BACKGROUND: Weed evolution from crops involves changes in key traits, but it is unclear how genetic and phenotypic variation contribute to weed diversification and productivity. Weedy rice is a conspecific weed of rice (Oryza sativa) worldwide. We used principal component analysis and hierarchical clustering to understand how morphologically and evolutionarily distinct US weedy rice populations persist in rice fields in different locations under contrasting management regimes. Further, we used a representative subset of 15 sequence-tagged site fragments of expressed genes from global Oryza to assess genome-wide sequence variation among populations. RESULTS: Crop hull color and crop-overlapping maturity dates plus awns, seed (panicle) shattering (> 50%), pigmented pericarp and stature variation (30.2% of total phenotypic variance) characterize genetically less diverse California weedy rice. By contrast, wild-like hull color, seed shattering (> 50%) and stature differences (55.8% of total phenotypic variance) typify genetically diverse weedy rice ecotypes in Arkansas. CONCLUSION: Recent de-domestication of weedy species - such as in California weedy rice - can involve trait combinations indistinguishable from the crop. This underscores the need for strict seed certification with genetic monitoring and proactive field inspection to prevent proliferation of weedy plant types. In established populations, tillage practice may affect weed diversity and persistence over time. © 2017 Society of Chemical Industry.

Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicate potential for spread of herbicide resistance via gene flow.

Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggest the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne.

Population genetics and origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus; Amaranthaceae).

UNLABELLED: • PREMISE OF THE STUDY: The evolution of invasiveness has been extensively studied in natural ecosystems; however, far less is known about the evolution of agricultural invasiveness, despite the major economic impact of weeds on crop productivity. Examining the population structure of recently arisen weeds can provide insights into evolutionary avenues to invasion of agroecosystems. Weeds that originate from wild plants are the most common yet least frequently studied type of agricultural invasive. Here we address several questions about the origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus), which invaded corn and soy fields in the midwestern United States in the 20th century.• METHODS: We genotyped 38 populations from across the species range with 10 microsatellite markers and used these data to assess genetic diversity and population structure within and outside the geographical region where waterhemp is agriculturally problematic.• KEY RESULTS: We found evidence for two ancestral genetic lineages in our data, supporting the hypothesis that A. tuberculatus was diverging into two evolutionary lineages prior to the 20th century. However, we found no support for the hypothesis that agricultural weed populations arose from admixture of these two lineages after secondary contact. Our data suggest that eastward movement of the western genetic lineage, facilitated by changing agricultural practices, is the source of the agricultural invasion of waterhemp.• CONCLUSIONS: This research demonstrates that agricultural invasion by native, wild plant species can proceed via different evolutionary trajectories from weeds related to domesticated plants, which has implications for evolutionary biology and weed control.

Evolution and spread of glyphosate resistance in Conyza canadensis in California.

Recent increases in glyphosate use in perennial crops of California, USA, are hypothesized to have led to an increase in selection and evolution of resistance to the herbicide in Conyza canadensis populations. To gain insight into the evolutionary origins and spread of resistance and to inform glyphosate resistance management strategies, we investigated the geographical distribution of glyphosate resistance in C. canadensis across and surrounding the Central Valley, its spatial relationship to groundwater protection areas (GWPA), and the genetic diversity and population structure and history using microsatellite markers. Frequencies of resistant individuals in 42 sampled populations were positively correlated with the size of GWPA within counties. Analyses of population genetic structure also supported spread of resistance in these areas. Bayesian clustering and approximate Bayesian computation (ABC) analyses revealed multiple independent origins of resistance within the Central Valley. Based on parameter estimation in the ABC analyses, resistant genotypes underwent expansion after glyphosate use began in agriculture, but many years before it was detected. Thus, diversity in weed control practices prior to herbicide regulation in GWPA probably kept resistance frequencies low. Regionally coordinated efforts to reduce seed dispersal and selection pressure are needed to manage glyphosate resistance in C. canadensis.