Determining species tree topologies from clade probabilities under the coalescent

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy consensus algorithm, which consecutively accepts the most probable clades compatible with previously accepted clades, can be used for this second stage, this method is known to be statistically inconsistent under the multispecies coalescent model. This raises the question of whether it is theoretically possible to reconstruct the species tree from known probabilities of clades on gene trees. We investigate clade probabilities arising from the multispecies coalescent model, with an eye toward identifying features of the species tree. Clades on gene trees with probability greater than 1/3 are shown to reflect clades on the species tree, while those with smaller probabilities may not. Linear invariants of clade probabilities are studied both computationally and theoretically, with certain linear invariants giving insight into the clade structure of the species tree. For species trees with generic edge lengths, these invariants can be used to identify the species tree topology. These theoretical results both confirm that clade probabilities contain full information on the species tree topology and suggest future directions of study for developing statistically consistent inference methods from clade frequencies on gene trees.Comment: 25 pages, 2 figure

Determining the Complex Refractive Index of Materials in the Far-Infrared from Terahertz Time-Domain Data

Terahertz time‐domain spectroscopy is a well‐established technique to study the far‐infrared electromagnetic response of materials. Measurements are broadband, fast, and performed at room temperature. Moreover, compact systems are nowadays commercially available, which can be operated by nonspecialist staff. Thanks to the determination of the amplitude and phase of the recorded signals, both refractive index and absorption coefficient of the sample material can be obtained. However, determining these electromagnetic parameters should be performed cautiously when samples are more or less transparent. In this chapter, we explain how to extract the material parameters from terahertz time‐domain data. We list the main sources of error, and their contribution to uncertainties. We give rules to select the most adapted technique for an optimized characterization, depending on the transparency of the samples, and address the case of samples with strong absorption peaks or exhibiting scattering

Histopathology of Fusarium wilt of staghorn sumac (Rhus typhina) caused by Fusarium oxysporum f. sp. callistephi race 3. I. Modes of tissue colonization and pathogen peculiarities

Light and transmission electron microscope studies of naturally infected or inoculated staghorn sumac plants by Fusarium oxysporum f. sp. callistephi race 3 are reported. Diverse extrinsic material (including latex in some instances) or elements occurred in vessel lumina. Some of this material labelled for pectin, often in association with tyloses, as did other opaque matter in paratracheal cells, related to alterations of their protective layer. Pronounced alterations of pit membranes of bordered pits occurred, with their outer portions disrupted into bodies of opaque matter, strongly labelled for cellulose, and their middle portions as unlabelled shreds. Similarly labelled opaque bodies occasionally occurred on vessel walls and lumina. Direct penetration of host cell secondary walls by the pathogen occurred, but these were degraded to any extent only following intramural invasion. Vessel walls, at all stages of infection, were lined with variously structured matter: in their thinnest forms, by single or paired, equidistant or widely spaced opaque bands, and in their thickest forms as alternating opaque and less opaque layers. Other thin elements, often enclosing opaque material, vesicular structures, or occasionally particles of ribosomal appearance were also delineated by similar but frequently infolded bands. These elements were sometimes observed to be confluent with fungal cells and to label for chitin. Many fungal elements were bound by only a thin or defective lucent wall layer, practically unlabelled for chitin, or by a locally thickened, labelled one; labelling for this substrate was also frequently associated with the fungal cell outer opaque wall layer or with some outer extracellular matter. Fine filamentous structures, connected to fungal cells, to the vessel lining matter, and to these other elements, extended into host walls. The lining itself generally did not label for cellulose or chitin. These observations are discussed in comparison with similar observations made regarding other wilt diseases that we have studied.Nous rapportons des observations microscopiques et ultrastructurales de l’infection par le F. oxysporum f. sp. callistephi race 3 de plants de vinaigrier inoculés ou infectés naturellement. Des structures ou du matériel étrangers aux éléments vasculaires ont été illustrés. Ce matériel ainsi que la matière liée à l’altération de la couche dite protectrice des cellules de parenchyme se sont marqués pour la pectine. Des corps opaques apposés aux parois des vaisseaux, présents dans leur lumière ou dans les cellules de parenchyme voisines, ont réagi pour la cellulose. La partie mitoyenne des membranes de ponctuation aréolées était altérée en lambeaux non marqués pour la cellulose et leur partie externe en corps opaques marqués. La pénétration des parois secondaires des cellules hôtes par le champignon a eu lieu, mais ces parois étaient fortement altérées seulement une fois colonisées de façon intralamellaire. Les parois vasculaires, à tous les stades de la maladie, étaient recouvertes de matière étrangère : dans les cas les plus prononcés, de couches de diverses épaisseurs, formées de strates d’opacité différente, et, dans leur plus simple expression, de lamelles opaques, simples ou jumelées mais souvent divergentes; des éléments, encadrés de lamelles semblables et souvent incurvées, et contenant de la matière opaque, des structures vésiculaires ou occasionnellement des particules semblables à des ribosomes garnissaient également les parois vasculaires. Ces éléments, inégalement marqués pour la chitine, étaient à l’occasion liés à des cellules du champignon. La couche translucide de ces cellules était souvent mince ou absente, pratiquement non marquée pour ce substrat, ou localement épaissie et alors fortement marquée, comme aussi occasionnellement leur couche pariétale externe et la matière extracellulaire semblable. Des structures filamenteuses rattachées aux cellules du champignon, comme au recouvrement des parois vasculaires et aux autres éléments, piquaient les parois cellulaires de l’hôte. Ces recouvrements ne se sont généralement pas marqués pour la cellulose ou la chitine. Ces observations se comparent avantageusement à celles concernant les autres maladies à flétrissement que nous avons étudiées

Les complémentarités institutionnelles du modèle québécois de développement

Si le fonctionnement de l’économie québécoise poursuit principalement une logique libérale en raison de sa forte intégration continentale, divers facteurs historiques et culturels ont amené l’État du Québec à intervenir plus largement dans l’économie et à promouvoir un partage des fonctions de régulation avec certains groupes constitués de la société civile. À partir de la théorie des complémentarités institutionnelles, la présente étude cherche à alimenter le débat sur l’avenir du modèle québécois de développement. Refusant une approche manichéenne, cette étude repose sur l’hypothèse selon laquelle la performance économique du modèle québécois de développement serait fonction du degré d’intégration entre les institutions du libre marché et les institutions favorisant la redistribution des richesses et la participation citoyenne à la gouverne.The Quebec economy essentially operates within a liberal framework, due to its strong continental integration. However, various historical and cultural factors have led the Province of Quebec to intervene more in its economy and to promote the sharing of regulatory functions with certain civil society groups. Based on the theory of institutional complementarity, this study aims to contribute to the debate on the future of the Quebec development model. Rather than taking a Manichean approach, the study supports the hypothesis that the economic performance of the Quebec development model depends on the degree of integration between the free market institutions and the institutions that promote the redistribution of wealth and citizen participation in governance

Infrared supercontinuum generated in concatenated InF3 and As2Se3 fibers

We report on infrared supercontinuum (SC) generation through subsequent nonlinear propagation in concatenated step-index fluoride and As2Se3 fiber. These fibers were pumped by an all-fiber laser source based on an erbium amplifier followed by a thulium power amplifier. ZBLAN and InF3 fibers were compared for the concatenated scheme. The broadest SC produced was achieved by optimizing the length of the InF3 fiber. This arrangement allowed the generation of 200 mW infrared SC with high spectral flatness and spanning from 1.4 μm to 6.4 μm

Identification and characterization of the Non-race specific Disease Resistance 1 (NDR1) orthologous protein in coffee

<p>Abstract</p> <p>Background</p> <p>Leaf rust, which is caused by the fungus <it>Hemileia vastatrix </it>(Pucciniales), is a devastating disease that affects coffee plants (<it>Coffea arabica </it>L.). Disadvantages that are associated with currently developed phytoprotection approaches have recently led to the search for alternative strategies. These include genetic manipulations that constitutively activate disease resistance signaling pathways. However, molecular actors of such pathways still remain unknown in <it>C. arabica</it>. In this study, we have isolated and characterized the coffee <it>NDR1 </it>gene, whose <it>Arabidopsis </it>ortholog is a well-known master regulator of the hypersensitive response that is dependent on coiled-coil type R-proteins.</p> <p>Results</p> <p>Two highly homologous cDNAs coding for putative NDR1 proteins were identified and cloned from leaves of coffee plants. One of the candidate coding sequences was then expressed in the <it>Arabidopsis </it>knock-out null mutant <it>ndr1-1</it>. Upon a challenge with a specific strain of the bacterium <it>Pseudomonas syringae </it>(DC3000::<it>AvrRpt2</it>), analysis of both macroscopic symptoms and <it>in planta </it>microbial growth showed that the coffee cDNA was able to restore the resistance phenotype in the mutant genetic background. Thus, the cDNA was dubbed <it>CaNDR1a </it>(standing for <it>Coffea arabica Non-race specific Disease Resistance 1a</it>). Finally, biochemical and microscopy data were obtained that strongly suggest the mechanistic conservation of the <it>NDR1</it>-driven function within coffee and <it>Arabidopsis </it>plants. Using a transient expression system, it was indeed shown that the CaNDR1a protein, like its <it>Arabidopsis </it>counterpart, is localized to the plasma membrane, where it is possibly tethered by means of a GPI anchor.</p> <p>Conclusions</p> <p>Our data provide molecular and genetic evidence for the identification of a novel functional <it>NDR1 </it>homolog in plants. As a key regulator initiating hypersensitive signalling pathways, <it>CaNDR1 </it>gene(s) might be target(s) of choice for manipulating the coffee innate immune system and achieving broad spectrum resistance to pathogens. Given the potential conservation of <it>NDR1</it>-dependent defense mechanisms between <it>Arabidopsis </it>and coffee plants, our work also suggests new ways to isolate the as-yet-unidentified <it>R</it>-gene(s) responsible for resistance to <it>H. vastatrix</it>.</p

Functional Annotation of the Ophiostoma novo-ulmi Genome: Insights into the Phytopathogenicity of the Fungal Agent of Dutch Elm Disease

International audienceThe ascomycete fungus Ophiostoma novo-ulmi is responsible for the pandemic of Dutch elm disease that has been ravaging Europe and North America for 50 years. We proceeded to annotate the genome of the O. novo-ulmi strain H327 that was sequenced in 2012. The 31.784-Mb nuclear genome (50.1% GC) is organized into 8 chromosomes containing a total of 8,640 protein-coding genes that we validated with RNA sequencing analysis. Approximately 53% of these genes have their closest match to Grosmannia clavigera kw1407, followed by 36% in other close Sordariomycetes, 5% in other Pezizomycotina, and surprisingly few (5%) orphans. A relatively small portion (~3.4%) of the genome is occupied by repeat sequences; however, the mechanism of repeat-induced point mutation appears active in this genome. Approximately 76% of the proteins could be assigned functions using Gene Ontology analysis; we identified 311 carbohydrate-active enzymes, 48 cytochrome P450s, and 1,731 proteins potentially involved in pathogen– host interaction, along with 7 clusters of fungal secondary metabolites. Complementary mating-type locus sequencing, mating tests, and culturing in the presence of elm terpenes were conducted. Our analysis identified a specific genetic arsenal impacting the sexual and vegetative growth, phytopathogenicity, and signaling/plant–defense–degradation relationship between O. novo-ulmi and its elm host and insect vectors. Introduction During the last centuries, increased movements of people and goods across countries and continents have favored the emergence and global spread of plant pathogens, insect pests, and invasive weeds which have substantially altered the landscape of several parts of the world. One well-documented example is Dutch elm disease (DED), the most destructive disease of elms. It has been estimated that over 1 billion mature elms were killed by two successive pandemics since the early 1900s (Paoletti et al. 2005). The first pandemic, which prompted initial investigations by Dutch scientists shortly after the First World War (Holmes and Heybroek 1990), was caused by the ascomycete fungus Ophiostoma ulmi (Buisman) Nannf. As it spread relentlessly over Western Europe and, a few decade

Complexities underlying the breeding and deployment of Dutch elm disease resistant elms

Dutch elm disease (DED) is a vascular wilt disease caused by the pathogens Ophiostoma ulmi and Ophiostoma novo-ulmi with multiple ecological phases including pathogenic (xylem), saprotrophic (bark) and vector (beetle flight and beetle feeding wound) phases. Due to the two DED pandemics during the twentieth century the use of elms in landscape and forest restoration has declined significantly. However new initiatives for elm breeding and restoration are now underway in Europe and North America. Here we discuss complexities in the DED 'system' that can lead to unintended consequences during elm breeding and some of the wider options for obtaining durability or 'field resistance' in released material, including (1) the phenotypic plasticity of disease levels in resistant cultivars infected by O. novo-ulmi; (2) shortcomings in test methods when selecting for resistance; (3) the implications of rapid evolutionary changes in current O. novo-ulmi populations for the choice of pathogen inoculum when screening; (4) the possibility of using active resistance to the pathogen in the beetle feeding wound, and low attractiveness of elm cultivars to feeding beetles, in addition to resistance in the xylem; (5) the risk that genes from susceptible and exotic elms be introgressed into resistant cultivars; (6) risks posed by unintentional changes in the host microbiome; and (7) the biosecurity risks posed by resistant elm deployment. In addition, attention needs to be paid to the disease pressures within which resistant elms will be released. In the future, biotechnology may further enhance our understanding of the various resistance processes in elms and our potential to deploy trees with highly durable resistance in elm restoration. Hopefully the different elm resistance processes will prove to be largely under durable, additive, multigenic control. Elm breeding programmes cannot afford to get into the host-pathogen arms races that characterise some agricultural host-pathogen systems

Innovation in Physician Remuneration in France: What Lessons for Canada?

During the past decade, France has experienced two major reforms in remuneration models for general practitioners who work outside public healthcare organizations: Remuneration for Public Health Objectives (Rémunération sur Objectifs de Santé Publique—ROSP) and Experiments with New Models of Remuneration (Expérimentations desNouveaux Modes de Rémunération—ENMR). These two initiatives introduced payments based on performance in the areas of quality of care, organization of services and multidisciplinary practice. In the first model, individual physicians receive incentives for preventive practices, use of generics and improvements in work organization. In the second model, incentives are provided to multi-professional practice groups to foster interdisciplinary collaboration and patient involvement. While French general practitioners accustomed to fee-for-service remuneration were at first reluctant to accept a mixed remuneration model, they eventually came to embrace it. The ROSP has significantly improved targeted areas of practice, although it has had less impact on preventive practices than on use of generics and work organization. The ENMR has helped formalize inter-professional relationships in primary care and has thus contributed to team integration. These "experiments" suggest that a deliberate distinction between changes to individual physician payment and changes to how multi-professional practice groups are paid and practice may be a good starting point when introducing financial incentives to enable benefits and avoid negative consequences