A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short‐time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.     

The Third Replicon of Members of the Burkholderia cepacia Complex,Plasmid pC3, Plays a Role in Stress Tolerance

The metabolically versatile Burkholderia cepacia complex (Bcc) occupies a variety of niches, including the plant rhizosphere and the cystic fibrosis lung (where it is often fatal to the patient). Bcc members have multipartite genomes, of which the third replicon, pC3 (previously chromosome 3), has been shown to be a nonessential megaplasmid which confers virulence and both antifungal and proteolytic activity on several strains. In this study, pC3 curing was extended to cover strains of 16 of the 17 members of the Bcc, and the phenotypes conferred by pC3 were determined. B. cenocepacia strains H111, MCO-3, and HI2424 were previously cured of pC3; however, this had not proved possible in the epidemic strain K56-2. Here, we investigated the mechanism of this unexpected stability and found that efficient toxin-antitoxin systems are responsible for maintaining pC3 of strain K56-2. Identification of these systems allowed neutralization of the toxins and the subsequent deletion of K56-2pC3. The cured strain was found to exhibit reduced antifungal activity and was attenuated in both the zebrafish and the Caenorhabditis elegans model of infection. We used a PCR screening method to examine the prevalence of pC3 within 110 Bcc isolates and found that this replicon was absent in only four cases, suggesting evolutionary fixation. It is shown that plasmid pC3 increases the resistance of B. cenocepacia H111 to various stresses (oxidative, osmotic, high-temperature, and chlorhexidine-induced stresses), explaining the prevalence of this replicon within the Bcc.     

Grain-dependent relationships between plant productivity and invertebrate species richness and biomass in calcareous grasslands

The relationships among productivity, species richness and consumer biomass are of fundamental importance for understanding determinants of biodiversity. These relationships may depend on grain size. We examined the relationships between productivity (above-ground phytomass) and plant species richness and between productivity and species richness and biomass of gastropods and grasshoppers using sampling units of different sizes (0.5, 2.75 and 23 m²) in nutrient-poor, calcareous grasslands in north-western Switzerland in two successive years. Species richness of forbs had a unimodal relationship with productivity in sampling units of 0.5 m² and was negatively correlated with productivity at the other two plot sizes in one year. In the other year, forb species richness tended to decrease with productivity in sampling units of 23 m². No similar relationship was found for grasses. Gastropod biomass had a unimodal relationship with productivity at 0.5 m² in the first year. Grasshopper species richness was correlated with forb species richness at plot sizes of 2.75 and 23 m². This study demonstrates that patterns detected between productivity and diversity and between productivity and biomass of consumers depend on the grain size used in the investigation and vary among years.Die Zusammenhänge zwischen Produktivität, Artenreichtum und Biomasse von Konsumenten sind wichtig, um zu verstehen, was Biodiversität beeinflußt. Diese Zusammenhänge können von der Größe der Untersuchungsfläche abhängig sein. Wir untersuchten während zwei aufeinanderfolgenden Jahren die Zusammenhänge zwischen Produktivität (oberirdische Pflanzenbiomasse) und Artenreichtum von Gefäßpflanzen, sowie zwischen Produktivität und Artenreichtum und Biomasse von Schnecken und Heuschrecken bezüglich dreier räumlicher Skalen (0,5, 2,75 und 23 m²) in Kalkmagerrasen in der Nordwestschweiz. Der Zusammenhang zwischen dem Artenreichtum von Kräutern und der Produktivität war unimodal in Flächeneinheiten von 0,5 m² und negativ in Flächeneinheiten von 2,75 und 23 m² im ersten Jahr und war tendenziell negativ in Flächeneinheiten von 23 m² im zweiten Jahr, während kein solcher Zusammenhang bei Gräsern gefunden wurde. Der Zusammenhang zwischen Produktivität und Biomasse von Schnecken war unimodal in Flächeneinheiten von 0,5 m² im ersten Jahr. Außerdem bestand ein Zusammenhang zwischen dem Artenreichtum von Kräutern und Heuschrecken in Flächeneinheiten von 2,75 und 23 m². Diese Arbeit zeigt, daß Zusammenhänge zwischen Produktivität und Diversität sowie zwischen Produktivität und Biomasse von Konsumenten von der Größe der Untersuchungsfläche abhängen und zwischen Jahren variieren.     

Articulations of Islamophobia: from the extreme to the mainstream?

This article will examine the construction and functions of, as well as relationship between, the diverse and changing articulations of Islamophobia. The aim is to contribute to debates about the definition of Islamophobia, which have tended to be contextually specific, fixed and/or polarized between racism and religious prejudice, between extreme and mainstream, state and non-state versions or undifferentiated, and offer a more nuanced framework to: (a) delineate articulations of Islamophobia as opposed to precise types and categories; (b) highlight the porosity in the discourse between extreme articulations widely condemned in the mainstream, and normalized and insidious ones, which the former tend to render more acceptable in comparison; (c) map where these intersect in response to events, historical and political conditions and new ideological forces and imperatives and (d) compare these articulations of Islamophobia in two contexts, France and the US.     

CC2D1A is a regulator of ESCRT-III CHMP4B

Endosomal sorting complexes required for transport (ESCRTs) regulate diverse processes ranging from receptor sorting at endosomes to distinct steps in cell division and budding of some enveloped viruses. Common to all processes is the membrane recruitment of ESCRT-III that leads to membrane fission. Here, we show that CC2D1A is a novel regulator of ESCRT-III CHMP4B function. We demonstrate that CHMP4B interacts directly with CC2D1A and CC2D1B with nanomolar affinity by forming a 1:1 complex. Deletion mapping revealed a minimal CC2D1A-CHMP4B binding construct, which includes a short linear sequence within the third DM14 domain of CC2D1A. The CC2D1A binding site on CHMP4B was mapped to the N-terminal helical hairpin. Based on a crystal structure of the CHMP4B helical hairpin, two surface patches were identified that interfere with CC2D1A interaction as determined by surface plasmon resonance. Introducing these mutations into a C-terminal truncation of CHMP4B that exerts a potent dominant negative effect on human immunodeficiency virus type 1 budding revealed that one of the mutants lost this effect completely. This suggests that the identified CC2D1A binding surface might be required for CHMP4B polymerization, which is consistent with the finding that CC2D1A binding to CHMP4B prevents CHMP4B polymerization in vitro. Thus, CC2D1A might act as a negative regulator of CHMP4B function.     

Slow life history and rapid extreme flood: demographic mechanisms and their consequences on population viability in a threatened amphibian

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Approximate Bayesian Computation Untangles Signatures of Contemporary and Historical Hybridization between Two Endangered Species

Contemporary gene flow, when resumed after a period of isolation, can have crucial consequences for endangered species, as it can both increase the supply of adaptive alleles and erode local adaptation. Determining the history of gene flow and thus the importance of contemporary hybridization, however, is notoriously difficult. Here, we focus on two endangered plant species, Arabis nemorensis and A. sagittata, which hybridize naturally in a sympatric population located on the banks of the Rhine. Using reduced genome sequencing, we determined the phylogeography of the two taxa but report only a unique sympatric population. Molecular variation in chloroplast DNA indicated that A. sagittata is the principal receiver of gene flow. Applying classical D-statistics and its derivatives to whole-genome data of 35 accessions, we detect gene flow not only in the sympatric population but also among allopatric populations. Using an Approximate Bayesian computation approach, we identify the model that best describes the history of gene flow between these taxa. This model shows that low levels of gene flow have persisted long after speciation. Around 10 000 years ago, gene flow stopped and a period of complete isolation began. Eventually, a hotspot of contemporary hybridization was formed in the unique sympatric population. Occasional sympatry may have helped protect these lineages from extinction in spite of their extremely low diversity.     

Environmental metagenomics: An innovative resource for industrial biocatalysis

The current existing enzymes have been identified from cultivable micro-organisms, most frequently from bacteria. These bacterial biocatalytic capabilities have been widely used for biotransformations, resulting in the development of profitable industrial bioprocesses in the fields of feed and food processing, textiles, agro-chemistry, cosmetics, pharmaceuticals and fine chemistry. However, the originality of this bioresource is progressively drying up, while requests from industry for novel biocatalytic activities are increasing in the face of economic and environmental pressure. Metagenomics, through access to the huge reservoir of uncultivated bacteria which represents the majority of the present biodiversity, opens the door to new industrial sources of enzymes. Surmounting hurdles encountered with this technology (e.g. DNA extraction to obtain high quality DNA libraries with proper statistical representativity, setting up of relevant high throughput screenings assays, combining functional and genome-based identifications), gives unique opportunities to access novel biocatalysts that better fit with the required industrial specifications, thus providing new biocatalysis tool boxes.