Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation,loss of sex and post-mating genetic incompatibilities

Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.     

Effects of clutch sizes and incubation stage on nest desertion in the female Common Eider Somateria mollissima nesting in the high Arctic

In bird species, one of the trade-offs between reproduction and survival appears in the parental decision to desert the nest. Nest desertion is modulated by several factors including clutch size. However, the incubation stage at which predation occurs is also an important factor. In this study, we examined whether nest desertion was linked to initial clutch size, partial clutch predation (final clutch size) and the incubation stage at which it happened in a capital breeder: the female common eider (Somateria mollissima) nesting in the high Arctic. The study was performed in Kongsfjorden in 2002 on the western coast of the Svalbard Archipelago (78°55′N, 20°07′E). We observed that nest desertion was higher when the initial clutch size was small. Also, females deserted their nests more during the first third of incubation than later. Thus, as incubation proceeded, nest desertion was less likely to occur even after egg reduction. Our results pointed out that this parental decision in female eiders seemed to depend on initial clutch size and on the date into incubation of clutch reduction. Sophie Bourgeon and Francois Criscuolo contributed equally to the work     

Pachyceras arenosum (Waagen) (Ammonitina,Pachyceratidae)du Callovien du Kutch: Nouvelles definition et position systematique

The revision of Waagen's figured specimens from Kutch (India) shows that “Stephanoceras arenosum” after being considered as a Macrocephalites and than as a Mayaites is really a Pachyceras. This species is morphologically very close to the microconch of Pachyceras la landeanum (d'ORBIGNY) from Lamberti zone (Upper Callovian) of Western Europ. Its validity and that of others species of this genus collected in India is discussed. Its importance for stratigraphical correlations between european and indo-malagasy provinces is pointed out.     

A simple and rapid one-time method to evaluate the non-acidic gas content from bioprocesses

This paper presents a rapid less than 2 min and low-cost method involving the use of alkali solution to capture the acidic gasses from a biogas, thereby providing an estimate of the percentage of non-acidic gasses. Such a method was mentioned in the literature but never fully described or optimized. After sampling an aliquot of gas from bioprocess, gas was injected in a sealed flask with a 3 M NaOH solution, and after equilibrium was obtained, the non-acidic gas volume was measured. The method was first calibrated with certified gasses with an accuracy observed between 98 and 105 %. Regarding the validation step, certified standard gas mixtures and nine biogas-laboratory batch reactors were used, the overall accuracy reported was 103 + 3 %. This rapid and low-cost method may either be used in laboratory conditions as a quick and low cost alternative to standard analysis equipment or in addition as a routine field control method used on full-scale plants.     

Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae)

Aim Vitis subg. Vitis provides an example of a plant disjunction occurring in the Northern Hemisphere. It shows broad morphological variation but is assumed to be a species complex with limited genetic differentiation. Based on a comprehensive sampling of taxa and polymorphism in both chloroplast and nuclear DNA, we assessed genetic variation within this subgenus. Our aims were to clarify the relationships among species and to examine their historical biogeography. Location Asia, Europe, North America. Methods We analysed a total of 30 species and putative hybrids from subgenus Vitis and examined the infra‐specific variation in some species. Polymorphism in chloroplast DNA was assessed in trnL and trnH–psbA–trnK sequences (c. 2170 bp) and in 15 microsatellite loci. We also obtained nuclear data for size variation at 24 microsatellite loci. Phylogenetic inference was performed with Bayesian analyses. A maximum parsimony network was constructed to depict the evolutionary relationships among haplotypes, and microsatellite data were also subjected to hierarchical clustering analysis using the Ward distance. In addition, we assessed size homoplasy by sequencing both chloroplast and nuclear microsatellite loci. Results Chloroplast polymorphisms resolved subgenus Vitis as a monophyletic group with limited genetic variation. The ancestral haplotypes were found in Eurasia. American taxa all harboured derived haplotypes. Most of them formed a monophyletic group that did not include Vitis californica. The four main haplotypes in Vitis vinifera corresponded to two different origins. Nuclear microsatellites indicated that genetic variation was especially large in North America. Asian species exhibited a lower level of nuclear divergence and the European V. vinifera corresponded to a differentiated nuclear lineage. Main conclusions We obtained some evidence that subgenus Vitis has an Asian origin and then dispersed to Europe and North America. Geographic separation was followed by diversification, presumably during the Pleistocene, resulting in phylogeographic patterns similar to other biota. In contrast to chloroplast DNA, nuclear DNA shows a larger than expected genetic variation. Our molecular data also highlight the need to re‐examine certain aspects of the current subgeneric classification.     

Early Syllabic Segmentation of Fluent Speech by Infants Acquiring French

Word form segmentation abilities emerge during the first year of life, and it has been proposed that infants initially rely on two types of cues to extract words from fluent speech: Transitional Probabilities (TPs) and rhythmic units. The main goal of the present study was to use the behavioral method of the Headturn Preference Procedure (HPP) to investigate again rhythmic segmentation of syllabic units by French-learning infants at the onset of segmentation abilities (around 8 months) given repeated failure to find syllabic segmentation at such a young age. The second goal was to explore the interaction between the use of TPs and syllabic units for segmentation by French-learning infants. The rationale was that decreasing TP cues around target syllables embedded in bisyllabic words would block bisyllabic word segmentation and facilitate the observation of syllabic segmentation. In Experiments 1 and 2, infants were tested in a condition of moderate TP decrease; no evidence of either syllabic or bisyllabic word segmentation was found. In Experiment 3, infants were tested in a condition of more marked TP decrease, and a novelty syllabic segmentation effect was observed. Therefore, the present study first establishes early syllabic segmentation in French-learning infants, bringing support from a syllable-based language to the proposal that rhythmic units are used at the onset of segmentation abilities. Second, it confirms that French-learning infants are sensitive to TP cues. Third, it demonstrates that they are sensitive to the relative weight of TP and rhythmic cues, explaining why effects of syllabic segmentation are not observed in context of high TPs. These findings are discussed in relation to theories of word segmentation bootstrapping, and the larger debate about statistically- versus prosodically-based accounts of early language acquisition.     

Frailty in Old Age Is Associated with Decreased Interleukin-12/23 Production in Response to Toll-Like Receptor Ligation

Aging is associated with progressive alterations of immune functions, leading to higher susceptibility to bacterial and viral infections and reduced vaccine responses. Data concerning cytokine production in response to Toll-like receptor (TLR) ligands are highly variable in old people, reflecting the heterogeneity of the geriatric population. The aim of our study was to define the relative contribution of age and clinical status on TLR-induced interleukin (IL)-12p70 and IL-23 production as these cytokines play an important role in the protection against intracellular and extracellular pathogens, respectively. For this purpose, we recruited 100 subjects (aged 23–96 years) in the general population or hospitalized for chronic diseases. We collected information on clinical status (medical history, ongoing comorbidities, treatments and geriatric scales), biological parameters (biochemical and hematological tests, telomere length determination, cytomegalovirus serology). Whole blood samples were stimulated with a combination of TLR4 and TLR7/8 ligands. We performed univariate and stepwise backward multivariate analyses regression to define which set of clinical variables could be predictive for IL-12p70 and IL-23 production in these conditions. Our results indicated that age was not correlated with TLR-mediated IL-12p70 and IL-23 production. In contrast, poor nutritional status and frailty in subjects >75 years were associated with decreased IL-12p70 and IL-23 production. By intracytoplasmic staining, we confirmed that production of IL-12/23p40 by conventional dendritic cells (DCs) upon TLR ligation was decreased in frail patients. However, proportion of DCs and monocytes subsets, phenotypic maturation and proximal signaling events were found to be comparable in frail and healthy old subjects. These results suggest the importance of age-associated clinical parameters and not age by itself in the alteration of innate immune responses in old individuals and emphasis the importance of innate immune responses in the susceptibility of frail geriatric patients to infections.     

Modeling landscape structure constraints on species dispersal with a cellular automaton: Are there convergences with empirical data?

Landscapes are typically complex systems which do not necessarily allow performing large scale field experiments. A lot of studies hence analyzed correlations between landscape structure and species distribution. However, empirical data integrate a non-reducible part of contingency, which implies a major issue: the generalization of results. In such complex contexts, modeling can be useful since it allows isolating factors and it can play the role of reference for comparisons. In this perspective, we modeled plant species dispersal within a hedgerow network with a simple cellular automaton. In parallel we studied empirically plant species distribution in hedgerows to see whether both, results from the model and results from empirical data were convergent. Results showed that the cellular automaton was characterized by non-linear responses, corresponding to different levels of landscape constraints. Furthermore, convergences were found between the theoretical model and empirical data, in terms of differential responses of plant species to landscape structure, according to dispersal type and habitat specialization. Finally examining past landscape structure, the theoretical model and empirical data converged, demonstrating that past landscape patterns are particularly relevant in terms of statistical explanation of plant species distribution. We conclude that cellular automata were relevant formalizations of dispersal processes at the landscape level.     

Fish-AMAZBOL: a database on freshwater fishes of the Bolivian Amazon

The Bolivian part of the Amazon Basin contains a mega diverse and well-preserved fish fauna. Since the last decade, this fish fauna has received an increasing attention from scientists and the national authorities as fishes represent one of the most important sources of proteins for local human communities. However, this fish fauna still remains poorly documented. Here, we present a database for fishes from the Bolivian Amazon. To build the database, we conducted an extensive literature survey of native and non-native (exotic) fishes inhabiting all major sub-drainages of the Bolivian Amazon. The database, named Fish-AMAZBOL, contains species lists for 13 Amazonian hydrological units, covering 100% of the Bolivian Amazon and approximately 65% (722,137 km²) of the all territory. Fish-AMAZBOL includes 802 valid species, 12 of them being non-native, that have been checked for systematic reliability and consistency. To put this number in perspective, this represents around 14% of the all Neotropical ichthyofauna and around 6% of all strictly freshwater fishes inhabiting the planet. This database is currently the most comprehensive database of native and non-native fish species richness available so far for the Bolivian Amazon.