Early physiological responses of Abies alba and Rubus fruticosus to ungulate herbivory

For the last 50 years, Chamois (Rupicapra rupicapra) population exponentially increased in the French Alps. This herbivore faces a food shortage in the winter; its diet mainly includes woody species (Abies alba Mill.) and brambles (Rubus fruticosus). The physiological response following simulated herbivory of these two plants was assessed. More precisely, the effects of leaf clipping and ungulate saliva application on the epidermal flavonoids and chlorophyll contents were considered as an induced structural response. The chlorophyll fluorescence (Fv/Fm) was also measured to provide information on the photosynthesis status as an induced functional response. The non-invasive techniques used in this experiment highlighted an induced response, emerging during the days following the simulated herbivory. R. fruticosus was drastically affected, photosynthesis was disturbed (decreased Fv/Fm) and mortality began on day 5 reaching 100 % less than 1 week later. Physiological parameters were also affected in A. alba (slight decrease of Fv/Fm and lower content of flavonoids), but this species recovered and survived no matter what the stressing treatment was. These results did not point out an efficient repulsive-induced response of A. alba and R. fruticosus to herbivory. The existence of constitutive defences such as prickles (R. fruticosus) or low-digestible tannins (A. alba) is no more efficient to escape from ungulates consumption. Nevertheless, in spite of the increase of the ungulates exponential demography, these two plants do not face rarefaction problem in the French Alps. Thus, survival of A. alba stands is probably linked to the recovery ability of saplings, when R. fruticosus stands maintain themselves thanks to the strong resprouting capacity of this species.     

Phylogenetic alpha and beta diversities of butterfly communities correlate with climate in the western Swiss Alps

The observation of non‐random phylogenetic distribution of traits in communities provides evidence for niche‐based community assembly. Environment may influence the phylogenetic structure of communities because traits determining how species respond to prevailing conditions can be phylogenetically conserved. In this study, we investigate the variation of butterfly species richness and of phylogenetic α‐ and β‐diversities along temperature and plant species richness gradients. Our study indicates that butterfly richness is independently positively correlated to temperature and plant species richness in the study area. However, the variation of phylogenetic α‐ and β‐diversities is only correlated to temperature. The significant phylogenetic clustering at high elevation suggests that cold temperature filters butterfly lineages, leading to communities mostly composed of closely related species adapted to those climatic conditions. These results suggest that in colder and more severe conditions at high elevations deterministic processes and not purely stochastic events drive the assemblage of butterfly communities.     

Linking genetic and ecological differentiation in an ungulate with a circumpolar distribution

Genetic differentiation among populations may arise from the disruption of gene flow due to local adaptation to distinct environments and/or neutral accumulation of mutations and genetic drift resulted from geographical isolation. Quantifying the role of these processes in determining the genetic structure of natural populations remains challenging. Here, we analyze the relative contribution of isolation‐by‐resistance (IBR), isolation‐by‐environment (IBE), genetic drift and historical isolation in allopatry during Pleistocene glacial cycles on shaping patterns of genetic differentiation in caribou/reindeer populations Rangifer tarandus across the entire distribution range of the species. Our study integrates analyses at range‐wide and regional scales to partial out the effects of historical and contemporary isolation mechanisms. At the circumpolar scale, our results indicate that genetic differentiation is predominantly explained by IBR and historical isolation. At a regional scale, we found that IBR, IBE and population size significantly explained the spatial distribution of genetic variation among populations belonging to the Euro‐Beringian lineage within North America. In contrast, genetic differentiation among populations within the North American lineage was predominantly explained by IBR and population size, but not IBE. We also found discrepancies between genetic and ecotype designation across the Holarctic species distribution range. Overall, these results indicate that multiple isolating mechanisms have played roles in shaping the spatial distribution of genetic variation across the distribution range of a large mammal with high potential for gene flow. Considering multiple spatial scales and simultaneously testing a comprehensive suite of potential isolating mechanisms, our study contributes to understand the ecological and evolutionary processes underlying organism–landscape interactions.     

Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record

Foraminifera have one of the best known fossil records among the unicellular eukaryotes. However, the origin and phylogenetic relationships of the extant foraminiferal lineages are poorly understood. To test the current paleontological hypotheses on evolution of foraminifera, we sequenced about 1,000 base pairs from the 3' end of the small subunit rRNA gene (SSU rDNA) in 22 species representing all major taxonomic groups. Phylogenies were derived using neighbor- joining, maximum-parsimony, and maximum-likelihood methods. All analyses confirm the monophyletic origin of foraminifera. Evolutionary relationships within foraminifera inferred from rDNA sequences, however, depend on the method of tree building and on the choice of analyzed sites. In particular, the position of planktonic foraminifera shows important variations. We have shown that these changes result from the extremely high rate of rDNA evolution in this group. By comparing the number of substitutions with the divergence times inferred from the fossil record, we have estimated that the rate of rDNA evolution in planktonic foraminifera is 50 to 100 times faster than in some benthic foraminifera. The use of the maximum-likelihood method and limitation of analyzed sites to the most conserved parts of the SSU rRNA molecule render molecular and paleontological data generally congruent.      

Relationships between soil seed bank,vegetation and soil fertility along an urbanisation gradient

Questions: How does urbanisation influence soil mineral nitrogen stocks (nitrate and ammonium stocks) and what are the consequences of these modifications on the functional diversity of the herbaceous vegetation (vascular plants) and the seed bank? Location: Nine study sites were located on an urbanisation gradient in the city of Rennes, France. Methods: Three urbanisation levels were defined: urban areas (high grey/green ratio), suburban (medium grey/green ratio) and periurban (low grey/green ratio). For each urbanisation level, nitrates and ammonium stocks were quantified; the herbaceous vegetation was surveyed as well as the soil seed bank (using the seedling emergence method). Results: Nitrate concentration increased with urbanisation (the nitrate level in urban plots was twice the concentration in periurban ones) whereas the ammonium level was higher in periurban areas than in urban areas. In urban plots, the vegetation and the seed bank were more nitrophilous, whereas the nitrogen requirement was lower for periurban species. The relationship between the seed bank and the above‐ground vegetation was not significant. Conclusions: The higher nitrate concentration in the urban area appeared to be related to higher concentrations of atmospheric pollutants found in this area and lower ammonium levels may be related to the higher temperature in urban areas (leading to higher nitrification rates). The shift in the composition of the seed bank and vegetation appeared to be a consequence of higher nitrate stocks. The dissimilarity between the seed bank and vegetation may be caused by enhanced emergence of nitrophilous species in urban areas.     

Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus

Background  

Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult.     

Defining the healthy "core microbiome" of oral microbial communities

Background  

Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).     

Mitochondrial heteroplasmy and DNA barcoding in Hawaiian <Emphasis Type="Italic">Hylaeus</Emphasis> (<Emphasis Type="Italic">Nesoprosopis</Emphasis>) bees (Hymenoptera: Colletidae)

Background  

The past several years have seen a flurry of papers seeking to clarify the utility and limits of DNA barcoding, particularly in areas such as species discovery and paralogy due to nuclear pseudogenes. Heteroplasmy, the coexistence of multiple mitochondrial haplotypes in a single organism, has been cited as a potentially serious problem for DNA barcoding but its effect on identification accuracy has not been tested. In addition, few studies of barcoding have tested a large group of closely-related species with a well-established morphological taxonomy. In this study we examine both of these issues, by densely sampling the Hawaiian Hylaeus bee radiation.     

Temporally dynamic habitat suitability predicts genetic relatedness among caribou

Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its ability to explain the genetic relatedness among individuals. We assessed habitat selection using locations of collared individuals in migratory herds and static occurrences from sedentary groups. Connectivity models based on habitat use outperformed a baseline isolation-by-distance model in explaining genetic relatedness, suggesting that variations in landscape features such as snow, vegetation productivity and land use modulate connectivity among populations. Connectivity surfaces derived from habitat use were the best predictors of genetic relatedness. The relationship between connectivity surface and genetic relatedness varied in time and peaked during the rutting period. Landscape permeability in the period of mate searching is especially important to allow gene flow among populations. Our study highlights the importance of considering temporal variations in habitat selection for optimizing connectivity across heterogeneous landscape and counter habitat fragmentation.