A high diversity of mechanisms endows ALS-inhibiting herbicide resistance in the invasive common ragweed (Ambrosia artemisiifolia L.).

Ambrosia artemisiifolia L. (common ragweed) is a globally invasive, allergenic, troublesome arable weed. ALS-inhibiting herbicides are broadly used in Europe to control ragweed in agricultural fields. Recently, ineffective treatments were reported in France. Target site resistance (TSR), the only resistance mechanism described so far for ragweed, was sought using high-throughput genotyping-by-sequencing in 213 field populations randomly sampled based on ragweed presence. Additionally, non-target site resistance (NTSR) was sought and its prevalence compared with that of TSR in 43 additional field populations where ALS inhibitor failure was reported, using herbicide sensitivity bioassay coupled with ALS gene Sanger sequencing. Resistance was identified in 46 populations and multiple, independent resistance evolution demonstrated across France. We revealed an unsuspected diversity of ALS alleles underlying resistance (9 amino-acid substitutions involved in TSR detected across 24 populations). Remarkably, NTSR was ragweed major type of resistance to ALS inhibitors. NTSR was present in 70.5% of the resistant plants and 74.1% of the fields harbouring resistance. A variety of NTSR mechanisms endowing different resistance patterns evolved across populations. Our study provides novel data on ragweed resistance to herbicides, and emphasises that local resistance management is as important as mitigating gene flow from populations where resistance has arisen.

Ragweeds and relatives: Molecular phylogenetics of Ambrosiinae (Asteraceae).

Ambrosiinae are one of the most distinct subtribes in the Heliantheae alliance (Asteraceae), mainly due to specialization toward wind pollination. Taxa of the subtribe are principally native to the Americas, although some species have attained a cosmopolitan distribution. Members of subtribe Engelmanniinae are considered close to Ambrosiinae, due to shared morphological traits. However, the placement of Ambrosiinae within the Heliantheae alliance has not yet been corroborated by phylogenetic analyses. In the present study, we test the circumscription of subtribe Ambrosiinae and examine relationships among its genera. We used sequence information from three plastid (psbA-trnH, trnQ-rps16 and trnL-F) and two nuclear (ITS and D35) marker regions. Phylogenetic inference analyses were conducted, applying Bayesian Inference (BI) and Maximum Likelihood (ML). Subtribe Ambrosiinae is found monophyletic or nearly so in all analyses. The genera Dugesia and Rojasianthe (previously considered part of subtribe Engelmanniinae) in some cases cluster together with Ambrosiinae; these genera are clearly not part of Engelmanniinae. Within Ambrosiinae, the genera Parthenium and Parthenice occupy basal positions, whereas members of the genus Ambrosia are the most derived representatives of the subtribe. Previous subdivision of Ambrosiinae into "Iveae" (members having androgynous capitula and free achenes) and "Ambrosieae" (genera with unisexual heads and achenes enclosed in burs) is not corroborated. Results also allow consideration of relationships among species and subgeneric groups within Parthenium, Iva, and Ambrosia.

Herbarium collection-based phylogenetics of the ragweeds (Ambrosia, Asteraceae).

Ambrosia (Asteraceae) is a taxonomically difficult genus of weedy, wind-pollinated plants with an apparent center of diversity in the Sonoran Desert of North America. Determining Ambrosia's evolutionary relationships has been the subject of much interest, with numerous studies using morphological characters, cytology, comparative phytochemistry, and chloroplast restriction site variation to produce conflicting accounts the relationships between Ambrosia species, as well as the classification of their close relatives in Franseria and Hymenoclea. To resolve undetermined intra-generic relationships within Ambrosia, we used DNA extracted from tissues obtained from seed banks and herbarium collections to generate multi-locus genetic data representing nearly all putative species, including four from South America. We performed Bayesian and Maximum-Likelihood phylogenetic analyses of six chloroplast-genome and two nuclear-genome markers, enabling us to infer monophyly for the genus, resolve major infra-generic species clusters, as well as to resolve open questions about the evolutionary relationships of several Ambrosia species and former members of Franseria. We also provide molecular data supporting the hypothesis that A. sandersonii formed through the hybridization of A. eriocentra and A. salsola. The topology of our chloroplast DNA phylogeny is almost entirely congruent with the most recent molecular work based on chloroplast restriction site variation of a much more limited sampling of 14 North American species of Ambrosia, although our improved sampling of global Ambrosia diversity enables us to draw additional conclusions. As our study is the first direct DNA sequence-based phylogenetic analyses of Ambrosia, we analyze the data in relation to previous taxonomic studies and discuss several instances of chloroplast/nuclear incongruence that leave the precise geographic center of origin of Ambrosia in question.

Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes.

Population genetic studies of nonmodel organisms frequently employ reduced representation library (RRL) methodologies, many of which rely on protocols in which genomic DNA is digested by one or more restriction enzymes. However, because high molecular weight DNA is recommended for these protocols, samples with degraded DNA are generally unsuitable for RRL methods. Given that ancient and historic specimens can provide key temporal perspectives to evolutionary questions, we explored how custom-designed RNA probes could enrich for RRL loci (Restriction Enzyme-Associated Loci baits, or REALbaits). Starting with genotyping-by-sequencing (GBS) data generated on modern common ragweed (Ambrosia artemisiifolia L.) specimens, we designed 20 000 RNA probes to target well-characterized genomic loci in herbarium voucher specimens dating from 1835 to 1913. Compared to shotgun sequencing, we observed enrichment of the targeted loci at 19- to 151-fold. Using our GBS capture pipeline on a data set of 38 herbarium samples, we discovered 22 813 SNPs, providing sufficient genomic resolution to distinguish geographic populations. For these samples, we found that dilution of REALbaits to 10% of their original concentration still yielded sufficient data for downstream analyses and that a sequencing depth of ~7m reads was sufficient to characterize most loci without wasting sequencing capacity. In addition, we observed that targeted loci had highly variable rates of success, which we primarily attribute to similarity between loci, a trait that ultimately interferes with unambiguous read mapping. Our findings can help researchers design capture experiments for RRL loci, thereby providing an efficient means to integrate samples with degraded DNA into existing RRL data sets.

Short ragweeds is highly cross-reactive with other ragweeds.

BACKGROUND: The most widespread ragweed (Ambrosia) species in North America are short ragweed (Ambrosia artemisiifolia; Amb a), giant ragweed (Ambrosia trifida; Amb t), and western ragweed (Ambrosia psilostachya; Amb p). Varied geographic distributions of ragweed species raise questions regarding the need for ragweed species-specific allergen immunotherapy. OBJECTIVE: To determine allergenic cross-reactivity among ragweed species by immunologic analyses of sera from subjects allergic to ragweed from North America and Europe. METHODS: Sera were collected from 452 subjects allergic to ragweed who participated in Amb a sublingual immunotherapy tablet clinical trials. All subjects had positive skin prick test and serum IgE against Amb a. Ragweed-specific IgE (pre treatment) and IgG4 (post treatment) were measured by ImmunoCAP. IgE inhibition studies among Amb a, Amb t, and Amb p were conducted. Using pooled sera from another ragweed-allergic population, IgE inhibition studies of 7 less widespread Ambrosia species also were conducted. RESULTS: A strong correlation between Amb a vs Amb p and Amb t serum IgE levels was observed. In the vast majority of pretreatment sera, Amb a inhibited Amb a, Amb p, and Amb t IgE reactivity by more than 90%. Strong correlations were observed between Amb a vs Amb p and Amb t post-treatment IgG4 levels. In pooled sera, Amb a extract inhibited the binding of serum IgE to all 10 ragweed species by 98%-100%. CONCLUSION: In a population of subjects allergic to Amb a, substantial allergenic cross-reactivity among Amb a, Amb p, and Amb t was demonstrated. These in vitro data suggest that an Amb a-based single-species ragweed allergen immunotherapy may be therapeutically active in patients exposed to diverse ragweed pollens. TRIAL REGISTRY: Clinicaltrials.gov, NCT00770315, NCT00783198, and NCT00330083.

Paving the way for invasive species: road type and the spread of common ragweed (Ambrosia artemisiifolia).

Roads function as prime habitats and corridors for invasive plant species. Yet despite the diversity of road types, there is little research on the influence of these types on the spread of invaders. Common ragweed (Ambrosia artemisiifolia), a plant producing large amounts of allergenic pollen, was selected as a species model for examining the impact of road type on the spread of invasive plants. We examined this relationship in an agricultural region of Quebec, Canada. We mapped plant distribution along different road types, and constructed a model of species presence. Common ragweed was found in almost all sampling sites located along regional (97%) and local paved (81%) roads. However, verges of unpaved local roads were rarely (13%) colonized by the plant. A model (53% of variance explained), constructed with only four variables (paved regional roads, paved local roads, recently mown road verges, forest cover), correctly predicted (success rate: 89%) the spatial distribution of common ragweed. Results support the hypothesis that attributes associated with paved roads strongly favour the spread of an opportunistic invasive plant species. Specifically, larger verges and greater disturbance associated with higher traffic volume create propitious conditions for common ragweed. To date, emphasis has been placed on controlling the plant in agricultural fields, even though roadsides are probably a much larger seed source. Strategies for controlling the weed along roads have only focused on major highways, even though the considerable populations along local roads also contribute to the production of pollen. Management prioritizations developed to control common ragweed are thus questionable.

Ambrosia: a new impending disaster for the israeli allergic population.

The pollen of Ambrosia (ragweed) is one of the major causes of pollen-induced allergy worldwide. This genus of plants has apparently evolved in North America but later spread into Europe and Asia. Flowering of the Ambrosias starts in mid-July and continues throughout the autumn and is a cause of major morbidity to allergic sensitized patients. The invasion of new species of Ambrosia into Israel is still in progress. Plants of Ambrosia artemisiifolia (American short ragweed), Ambrosia trifida (American giant ragweed), Ambrosia confertifolia, Ambrosia grayi and Ambrosia tenuifolia are increasingly found in Israel, mainly in the Hula valley in the eastern Galilee and near the Alexander River in the Sharon plain. From experience it is known that the time it takes to eradicate a new invasive species is limited. Action should be taken immediately or this new invasion will spread and cause a significantly increased burden of morbidity and increased health costs in Israel.

Twenty years of changes in spatial association and community structure among desert perennials.

I present results from analyses of 20 years of spatiotemporal dynamics in a desert perennial community. Plants were identified and mapped in a 1-ha permanent plot in Joshua Tree National Park (California, USA) in 1984. Plant size, mortality, and new seedlings were censused every five years through 2004. Two species, Ambrosia dumosa and Tetracoccus hallii, were dominant based on their relative abundance and ubiquitous distributions. Spatial analysis for distance indices (SADIE) identified regions of significantly high (patches) or low (gaps) densities. I used SADIE to test for (1) transience in the distribution of patches and gaps within species over time and (2) changes in juvenile-adult associations with conspecific adults and adults of the two dominant species over time. Plant performance was quantified in patches and gaps to determine plant responsiveness to local spatial associations. Species identity was found to influence associations between juveniles and adults. Juveniles of all species showed significant positive spatial associations with the dominant A. dumosa but not with T. hallii. The broad distribution of A. dumosa may increase the spatial extent of non-dominant species that are facilitated by this dominant. The spatial location of patches and gaps was generally consistent over time for adults but not juveniles. Observed variability in the locations of juvenile patches and gaps suggested that suitable locations for establishment were broad relative to occupied regions of the habitat, and that conditions for seed germination were independent of conditions for seedling survival. A dramatic change in spatial distributions and associations within and between species occurred after a major drought that influenced data from the final census. Positive associations between juveniles and adults of all species were found independent of previous associations and most species distributions contracted to areas that were previously characterized by low density. By linking performance to spatial distribution, results from this study offer a spatial context for plant-plant interactions within and among species. Community composition could be influenced both by individual species tolerances of abiotic conditions and by the competitive or facilitative interactions individuals exert over neighbors.

Estimation of pollen and seed production of common ragweed in France.

Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed of field crops and human-disturbed habitats in Europe. As well as in its natural range (North America), common ragweed is a threat to human health due to its abundant allergenic pollen release. Most studies have been focused on airborne pollen monitoring, but to date, no data have been available on precise individual plant pollen and seed production related to plant traits growing in natural environment and on their corresponding source of variation. The aim of this study was to evaluate pollen and seed production of common ragweed plants in several populations in France. Seasonal pollen production per plant ranged from 100 million to 3 billion and seed production from 346 to 6,114, depending on plant size and habitat. Common ragweed plants developing in field crops produced more pollens and seeds than those growing in other habitats. Pollen and seed production was closely related to plant volume and biomass, thus providing a means of estimating potential pollen and seed production in given target areas. Such biological data could be integrated into population management strategies or into airborne pollen modelling.

Giant ragweed specific immunotherapy is not effective in a proportion of patients sensitized to short ragweed: analysis of the allergenic differences between short and giant ragweed.

BACKGROUND: Short ragweed and giant ragweed pollen allergens are considered largely cross-reactive, and it is generally believed that 1 species is sufficient for skin testing and immunotherapy. However, in the area north of Milan (a zone widely invaded only by short ragweed), about 50% of patients submitted to injection specific immunotherapy with giant ragweed showed little or no clinical response, but showed an excellent outcome if they were shifted to short ragweed specific immunotherapy. OBJECTIVE: To investigate allergenic differences between short and giant ragweed. METHODS: IgE reactivity to short ragweed of sera from 16 patients allergic to ragweed was assessed by immunoblot before and after absorption with short and giant ragweed. Moreover, 41 ragweed-monosensitive patients underwent skin prick test with both ragweed species. RESULTS: In several cases, preabsorption of sera with giant ragweed extract was unable to inhibit IgE reactivity fully against both a 43-kd allergen and other allergens at different molecular weights in short ragweed. On skin prick test, short ragweed induced larger wheals than giant ragweed in the majority of patients, and 6 of 41 (15%) patients were strongly short ragweed-positive but giant ragweed-negative. The immunoblot with the serum from 1 of these subjects showed a strong IgE reactivity to short ragweed at about 43 kd in the absence of any reactivity to giant ragweed. CONCLUSION: Short and giant ragweed are not allergenically equivalent. Allergenic differences involve both the major allergens Amb a 1-2/Amb t 1-2 and some minor allergens. In patients allergic to ragweed, both diagnosis in vivo and immunotherapy should always be performed by using the ragweed species present in that specific geographic area.

[Ambrosia, Franseria, Xanthium from the Bonaparte Herbarium]. / Ambrosia, Franseria, Xanthium de l'herbier Bonaparte.

Recently, French Association for Ragweed Study (AFEDA) founders published, in French, a book "Ambrosia, ragweed, biological pollutants". This association was founded in 1982. The authors referred to Bonaparte Herbarium set up in the Université Claude-Bernard Lyon 1. This herbarium is ranking second in France and seventh in the world. There were three aims for this work: to set up, for this herbarium, a complete list of different species of Ambrosia, Franseria and their pollen grains and to study with them Xanthium whose pollen grains look like Ambrosia, to establish a chronological order for Ambrosia that were collected in Europe and in some countries of the New World, to compare some pollen grains of Ambrosia and Xanthium (scanning electronic microscope). Good state plants in spite of about a century of conservation could be selected. They were photographied and some pollens so. The consultation of this herbarium brought a better morphological knowledge of different species of Ambrosia, Franseria and Xanthium, (plants and pollen grains). The authors were able to broadcast this knowledge to scientists and interested public through their book.