A new pear scab resistance gene Rvp1 from the European pear cultivar ‘Navara’ maps in a genomic region syntenic to an apple scab resistance gene cluster on linkage group 2

Scab, caused by the ascomycete fungus Venturia pirina, leads to severe damage on European pear varieties resulting in a loss of commercial value and requiring frequent use of fungicides. Identifying scab resistance genes, developing molecular markers linked to these genes and establishing marker-assisted selection would be an effective way to improve European pear breeding for scab resistance. Most of the European pear cultivars (Pyrus communis) are currently reported to be sensitive. The pear cultivar ‘Navara’ was shown to carry a major scab resistance gene whose phenotypic expression in seedling progenies was a typical stellate necrosis symptom. The resistance gene was called Rvp1, for resistance to V. pirina, and was mapped on linkage group 2 of the pear genome close to microsatellite marker CH02b10. This genomic region is known to carry a cluster of scab resistance genes in apple indicating a first functional synteny for scab resistance between apple and pear

Averaging bias correction for the future space-borne methane IPDA lidar mission MERLIN

The CNES (French Space Agency) and DLR (German Space Agency) project MERLIN is a future integrated path differential absorption (IPDA) lidar satellite mission that aims at measuring methane dry-air mixing ratio columns (XCH4) in order to improve surface flux estimates of this key greenhouse gas. To reach a 1&thinsp;% relative random error on XCH4 measurements, MERLIN signal processing performs an averaging of data over 50&thinsp;km along the satellite trajectory. This article discusses how to process this horizontal averaging in order to avoid the bias caused by the non-linearity of the measurement equation and measurements affected by random noise and horizontal geophysical variability. Three averaging schemes are presented: averaging of columns of XCH4, averaging of columns of differential absorption optical depth (DAOD) and averaging of signals. The three schemes are affected both by statistical and geophysical biases that are discussed and compared, and correction algorithms are developed for the three schemes. These algorithms are tested and their biases are compared on modelled scenes from real satellite data. To achieve the accuracy requirements that are limited to 0.2&thinsp;% relative systematic error (for a reference value of 1780&thinsp;ppb), we recommend performing the averaging of signals corrected from the statistical bias due to the measurement noise and from the geophysical bias mainly due to variations of methane optical depth and surface reflectivity along the averaging track. The proposed method is compliant with the mission relative systematic error requirements dedicated to averaging algorithms of 0.06&thinsp;% (±1&thinsp;ppb for XCH4 = 1780 ppb) for all tested scenes and all tested ground reflectivity values.</p

Balancing Selection at the Tomato RCR3 Guardee Gene Family Maintains Variation in Strength of Pathogen Defense

Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant-pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the''Guard-Hypothesis,'' R proteins (the ``guards'') can sense modification of target molecules in the host (the ``guardees'') by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the ``guardee-effector'' interface for pathogen recognition, natural selection acts on the ``guard-guardee'' interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen

Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum

Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are based on summarizing polymorphism data at multiple loci in two species using the joint site-frequency spectrum (JSFS). We have developed two improvements of these methods based on a more extensive use of the JSFS classes of polymorphisms for species with high intra-locus recombination rates. First, using a likelihood based method, we demonstrate that taking into account low-frequency polymorphisms shared between species significantly improves the joint estimation of the divergence time and gene flow between species. Second, we introduce a local linear regression algorithm that considerably reduces the computational time and allows for the estimation of unequal rates of gene flow between species. We also investigate which summary statistics from the JSFS allow the greatest estimation accuracy for divergence time and migration rates for low (around 10) and high (around 100) numbers of loci. Focusing on cases with low numbers of loci and high intra-locus recombination rates we show that our methods for the estimation of divergence time and migration rates are more precise than existing approaches

Judgments of length in the economics laboratory: Are there brains in choice?

We design a choice experiment where the objects are valued according to only a single attribute with a continuous measure and we can observe the true preferences of subjects. However, subjects have an imperfect perception of their own preferences. Subjects are given a choice set involving several lines of various lengths and are told to select one of them. They strive to select the longest line because they are paid an amount that is increasing in the length of their selection. Subjects also make their choices while they are required to remember either a 6-digit number (high cognitive load) or a 1-digit number (low cognitive load). We find that subjects in the high load treatment make inferior line selections and perform worse searches. When we restrict attention to the set of viewed lines, we find evidence that subjects in the high load treatment make worse choices than subjects in the low load treatment. Therefore the low quality searches do not fully explain the low quality choices. Our results suggest that cognition affects choice, even in our idealized choice setting. We also find evidence of choice overload even when the choice set is small and the objects are simple. Further, our experimental design permits a multinomial discrete choice analysis on choice among single-attribute objects with an objective value. The results of our analysis suggest that the errors in our data are better described as having a Gumbel distribution rather than a normal distribution. Finally, we observe the effects of limited cognition, consistent with memory decay and attention

Investigating distribution of practice effects for the learning of foreign language verb morphology in the young learner classroom

Within limited-input language classrooms, understanding the effect of distribution of practice (spacing between practice) on learning is critical, yet evidence is conflicting and of limited relevance for young learners. For second language (L2) grammar learning, some studies reveal advantages for spacing of 7 days or more (Bird, 2010; Rogers, 2015), but others for shorter spacing (Suzuki, 2017). Further, little is known about the role of cognitive individual differences (e.g., language analytic ability) in mediating practice distribution effects for L2 grammatical knowledge development and retention (Suzuki & DeKeyser, 2017). To address this gap, this classroom-based study investigated whether distribution of practice and language analytic ability moderated the effectiveness of explicit, input-based grammar instruction for young first language (L1) English learners of French (aged 8 to 11). The study revealed minimal differences between longer (7-day) versus shorter (3.5-day) spacing of practice for learning an L2 French verb inflection subsystem, at either post- or delayed post-test. Minimal group-level gains and substantial within-group variation in performance at post-tests was observed. Accuracy of practice during training and language analytic ability were significantly associated with post-test performance under both practice schedules. These findings indicated that within an ecologically valid classroom context, differences in distribution of practice had limited impact on learner performance on our tests; rather, individual learner differences were more critical in moderating learning. This highlights the importance of considering individual learner differences in the development of resources and the potential of digital tools for dynamically adapting instruction to suit individuals

Oseltamivir–Resistant Pandemic H1N1/2009 Influenza Virus Possesses Lower Transmissibility and Fitness in Ferrets

The neuraminidase (NA) inhibitor oseltamivir offers an important immediate option for the control of influenza, and its clinical use has increased substantially during the recent H1N1 pandemic. In view of the high prevalence of oseltamivir-resistant seasonal H1N1 influenza viruses in 2007–2008, there is an urgent need to characterize the transmissibility and fitness of oseltamivir-resistant H1N1/2009 viruses, although resistant variants have been isolated at a low rate. Here we studied the transmissibility of a closely matched pair of pandemic H1N1/2009 clinical isolates, one oseltamivir-sensitive and one resistant, in the ferret model. The resistant H275Y mutant was derived from a patient on oseltamivir prophylaxis and was the first oseltamivir-resistant isolate of the pandemic virus. Full genome sequencing revealed that the pair of viruses differed only at NA amino acid position 275. We found that the oseltamivir-resistant H1N1/2009 virus was not transmitted efficiently in ferrets via respiratory droplets (0/2), while it retained efficient transmission via direct contact (2/2). The sensitive H1N1/2009 virus was efficiently transmitted via both routes (2/2 and 1/2, respectively). The wild-type H1N1/2009 and the resistant mutant appeared to cause a similar disease course in ferrets without apparent attenuation of clinical signs. We compared viral fitness within the host by co-infecting a ferret with oseltamivir-sensitive and -resistant H1N1/2009 viruses and found that the resistant virus showed less growth capability (fitness). The NA of the resistant virus showed reduced substrate-binding affinity and catalytic activity in vitro and delayed initial growth in MDCK and MDCK-SIAT1 cells. These findings may in part explain its less efficient transmission. The fact that the oseltamivir-resistant H1N1/2009 virus retained efficient transmission through direct contact underlines the necessity of continuous monitoring of drug resistance and characterization of possible evolving viral proteins during the pandemic