Strive or thrive: Trends in gene expression in partially resistant pepper.

Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of during infection of pepper ( L.

Correction: Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape.

[This corrects the article DOI: 10.1371/journal.pcbi.

A real-world implementation of a nationwide, long-term monitoring program to assess the impact of agrochemicals and agricultural practices on biodiversity.

Biodiversity has undergone a major decline throughout recent decades, particularly in farmland. Agricultural practices are recognized to be an important pressure on farmland biodiversity, and pesticides are suspected to be one of the main causes of this decline in biodiversity. As part of the national plan for reduction of pesticides use (Ecophyto), the French ministry of agriculture launched the 500 ENI (nonintended effects) monitoring program in 2012 in order to assess the unintended effects of agricultural practices, including pesticide use, on biodiversity represented by several taxonomic groups of interest for farmers.

Stochastic models support rapid peopling of Late Pleistocene Sahul.

The peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers.

Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits.

Most molecularly characterized plant resistance genes (R genes) belong to the nucleotide-binding-site-leucine-rich-repeat (NLR) receptor family and are prone to duplication and transposition with high sequence diversity. In this family, the Vat gene in melon is one of the few R genes known for conferring resistance to insect, i.e.

Spatial Distribution Patterns of (Hemiptera, Coccidae) and of the Ampelovirus GLRaV-1 and the Vitivirus GVA in a Commercial Vineyard.

Distribution patterns of the European fruit lecanium (Bouché) and of grapevine leafroll-associated virus-1 (GLRaV-1) and grapevine virus A (GVA) were monitored from 2003 to 2015 in a Riesling vine plot in the northeast of France. Virus spread was compared between two periods: 2003-2008 and 2009-2014. The percentage of infected vines increased from 54 to 78% for GLRaV-1 and from 14 to 26% for GVA.

Ecological Specialization and Rarity of Arable Weeds: Insights from a Comprehensive Survey in France.

The definition of "arable weeds" remains contentious. Although much attention has been devoted to specialized, segetal weeds, many taxa found in arable fields also commonly occur in other habitats. The extent to which adjacent habitats are favorable to the weed flora and act as potential sources of colonizers in arable fields remains unclear.

Climate-human interaction associated with southeast Australian megafauna extinction patterns.

The mechanisms leading to megafauna (>44 kg) extinctions in Late Pleistocene (126,000-12,000 years ago) Australia are highly contested because standard chronological analyses rely on scarce data of varying quality and ignore spatial complexity. Relevant archaeological and palaeontological records are most often also biased by differential preservation resulting in under-representated older events. Chronological analyses have attributed megafaunal extinctions to climate change, humans, or a combination of the two, but rarely consider spatial variation in extinction patterns, initial human appearance trajectories, and palaeoclimate change together.

Arthropods life cycle and temperature: Beyond isomorphy hypothesis.

In poikilotherms, developmental time and adult lifespan are biological traits driven by temperature although their underlying physiological mechanisms differ. The developmental theory of ageing predicts a positive correlation between these two traits without confirming a genetic or causal relationship. The developmental rate isomorphy hypothesis established that the proportionality in the duration of each pre-imaginal stage with respect to total developmental time does not vary with temperature.

Atmosphere-soil carbon transfer as a function of soil depth.

The exchange of carbon between soil organic carbon (SOC) and the atmosphere affects the climate and-because of the importance of organic matter to soil fertility-agricultural productivity. The dynamics of topsoil carbon has been relatively well quantified, but half of the soil carbon is located in deeper soil layers (below 30 centimetres), and many questions remain regarding the exchange of this deep carbon with the atmosphere. This knowledge gap restricts soil carbon management policies and limits global carbon models.

Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape.

Characterising the spatio-temporal dynamics of pathogens in natura is key to ensuring their efficient prevention and control. However, it is notoriously difficult to estimate dispersal parameters at scales that are relevant to real epidemics. Epidemiological surveys can provide informative data, but parameter estimation can be hampered when the timing of the epidemiological events is uncertain, and in the presence of interactions between disease spread, surveillance, and control.

Domestication rewired gene expression and nucleotide diversity patterns in tomato.

Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication.

Herbicides do not ensure for higher wheat yield, but eliminate rare plant species.

Weed control is generally considered to be essential for crop production and herbicides have become the main method used for weed control in developed countries. However, concerns about harmful environmental consequences have led to strong pressure on farmers to reduce the use of herbicides. As food demand is forecast to increase by 50% over the next century, an in-depth quantitative analysis of crop yields, weeds and herbicides is required to balance economic and environmental issues.

High rates of gene flow by pollen and seed in oak populations across Europe.

Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q.

A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data.

The accurate identification of the route of transmission taken by an infectious agent through a host population is critical to understanding its epidemiology and informing measures for its control. However, reconstruction of transmission routes during an epidemic is often an underdetermined problem: data about the location and timings of infections can be incomplete, inaccurate, and compatible with a large number of different transmission scenarios. For fast-evolving pathogens like RNA viruses, inference can be strengthened by using genetic data, nowadays easily and affordably generated.

Asymmetrical over-infection as a process of plant virus emergence.

Disentangling the role of epidemiological factors in plant pathogen emergences is a prerequisite to identify the most likely future invaders. An example of emergence was recently observed in France: in 10 years, "classic" (CL) strains of Watermelon mosaic virus (WMV) were displaced at a regional scale by newly introduced "emerging" (EM) strains. Here we analyse a 3 years dataset describing the co-dynamics of CL and EM strains at field scale using state-space models estimating jointly: (i) probabilities of primary and secondary infection and (ii) probabilities of over-infecting with a CL [EM] strain a plant already infected with an EM [CL] strain.

The relationship between mutation frequency and replication strategy in positive-sense single-stranded RNA viruses.

For positive-sense single-stranded RNA virus genomes, there is a trade-off between the mutually exclusive tasks of transcription, translation and encapsidation. The replication strategy that maximizes the intracellular growth rate of the virus requires iterative genome transcription from positive to negative, and back to positive sense. However, RNA viruses experience high mutation rates, and the proportion of genomes with lethal mutations increases with the number of replication cycles.

Identifying risk factors for European stone fruit yellows from a survey.

ABSTRACT European stone fruit yellows (ESFY) is becoming a major economic problem for Prunus growers in Europe. The causal agent ("Candidatus Phytoplasma prunorum") and its vector (Cacopsylla pruni) have been identified, but the present knowledge of the risk factors for this disease relies, at best, on specific experiments. To assess the relative significance of several factors correlated with ESFY incidence in the field, an exhaustive survey was performed on apricot and Japanese plum orchards in the Crau plain (France).

Autoinfection in wheat leaf rust epidemics.

Autoinfection (within-host inoculum transmission) allows plant pathogens locally to increase their density on an infected host. Estimating autoinfection is of particular importance in understanding epidemic development in host mixtures. More generally, autoinfection influences the rate of host colonization by the pathogen, as well as pathogen evolution.

Different mutations in the genome-linked protein VPg of potato virus Y confer virulence on the pvr2(3) resistance in pepper.

Five different amino acid substitutions in the VPg of Potato virus Y were shown to be independently responsible for virulence toward pvr2(3) resistance gene of pepper. A consequence of these multiple mutations toward virulence involving single nucleotide substitutions is a particularly high frequency of resistance breaking (37% of inoculated plants from the first inoculation) and suggests a potentially low durability of pvr2(3) resistance. These five mutants were observed with significantly different frequencies, one of them being overrepresented.

Prevalence of multidrug resistant (MDR) Salmonella in bovine dairy herds in western France.

As a part of our effort in quantitative risk analysis of food-borne diseases, we carried out an epidemiologic study to estimate the prevalence of multidrug resistant (MDR) Salmonella in dairy herds situated in western France. The study population consisted of 489 farms in the region and manure or slurry was sampled from these operations and tested for the Salmonella spp. All strains isolated during the study were serotyped and tested for their antimicrobial susceptibility.

Modelling the interactions between phenology and insecticide resistance genes in the codling moth Cydia pomonella.

In the codling moth Cydia pomonella (L), insecticide resistance genes have been associated with pleiotropic effects affecting phenology. In this paper, we investigated whether an increase in the frequency of insecticide resistance in field populations of C pomonella was likely to entail significant divergences in the temporal occurrence of both susceptible and insecticide-resistant individuals. For this purpose, we built a phenological model that provided suitable predictions of the distinct and diverging seasonal evolutions of populations of a susceptible and two insecticide-resistant (at two and three loci) homozygous genotypes of C pomonella.