Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)?

Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies.

Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations.

Major climatic and geological events but also population history (secondary contacts) have generated cycles of population isolation and connection of long and short periods. Recent empirical and theoretical studies suggest that fast evolutionary processes might be triggered by such events, as commonly illustrated in ecology by the adaptive radiation of cichlid fishes (isolation and reconnection of lakes and watersheds) and in epidemiology by the fast adaptation of the influenza virus (isolation and reconnection in hosts). We test whether cyclic population isolation and connection provide the raw material (standing genetic variation) for species evolution and diversification. Our analytical results demonstrate that population isolation and connection can provide, to populations, a high excess of genetic diversity compared with what is expected at equilibrium. This excess is either cyclic (high allele turnover) or cumulates with time depending on the duration of the isolation and the connection periods and the mutation rate. We show that diversification rates of animal clades are associated with specific periods of climatic cycles in the Quaternary. We finally discuss the importance of our results for macroevolutionary patterns and for the inference of population history from genomic data.

Genetic diversity and host plant preferences revealed by simple sequence repeat and mitochondrial markers in a population of the arbuscular mycorrhizal fungus Glomus intraradices.

Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants that improve plant nutrient acquisition and promote plant diversity. Although within-species genetic differences among AMF have been shown to differentially affect plant growth, very little is actually known about the degree of genetic diversity in AMF populations. This is largely because of difficulties in isolation and cultivation of the fungi in a clean system allowing reliable genotyping to be performed. A population of the arbuscular mycorrhizal fungus Glomus intraradices growing in an in vitro cultivation system was studied using newly developed simple sequence repeat (SSR), nuclear gene intron and mitochondrial ribosomal gene intron markers. The markers revealed a strong differentiation at the nuclear and mitochondrial level among isolates. Genotypes were nonrandomly distributed among four plots showing genetic subdivisions in the field. Meanwhile, identical genotypes were found in geographically distant locations. AMF genotypes showed significant preferences to different host plant species (Glycine max, Helianthus annuus and Allium porrum) used before the fungal in vitro culture establishment. Host plants in a field could provide a heterogeneous environment favouring certain genotypes. Such preferences may partly explain within-population patterns of genetic diversity.

Use of an isothermal microcalorimetry assay to characterize microbial oxalotrophic activity

Isothermal microcalorimetry (IMC) has been used in the past to monitor metabolic activities in living systems. A few studies have used it on ecological research. In this study, IMC was used to monitor oxalotrophic activity, a widespread bacterial metabolism found in the environment, and particularly in soils. Six model strains were inoculated in solid angle media with K-oxalate as the sole carbon source. Cupriavidus oxalaticus, Cupriavidus necator, and Streptomyces violaceoruber presented the highest activity (91, 40, and 55 μW, respectively) and a maximum growth rate (μmax h(-1) ) of 0.264, 0.185, and 0.199, respectively, among the strains tested. These three strains were selected to test the incidence of different oxalate sources (Ca, Cu, and Fe-oxalate salts) in the metabolic activity. The highest activity was obtained in Ca-oxalate for C. oxalaticus. Similar experiments were carried out with a model soil to test whether this approach can be used to measure oxalotrophic activity in field samples. Although measuring oxalotrophic activity in a soil was challenging, there was a clear effect of the amendment with oxalate on the metabolic activity measured in soil. The correlation between heat flow and growth suggests that IMC analysis is a powerful method to monitor bacterial oxalotrophic activity

Parallel changes in genetic diversity and species diversity following a natural disturbance.

We examined the spatial and temporal variation of species diversity and genetic diversity in a metacommunity comprising 16 species of freshwater gastropods. We monitored species abundance at five localities of the Ain river floodplain in southeastern France, over a period of four years. Using 190 AFLP loci, we monitored the genetic diversity of Radix balthica, one of the most abundant gastropod species of the metacommunity, twice during that period. An exceptionally intense drought occurred during the last two years and differentially affected the study sites. This allowed us to test the effect of natural disturbances on changes in both genetic and species diversity. Overall, local (alpha) diversity declined as reflected by lower values of gene diversity H(S) and evenness. In parallel, the among-sites (beta) diversity increased at both the genetic (F(ST)) and species (F(STC)) levels. These results suggest that disturbances can lead to similar changes in genetic and community structure through the combined effects of selective and neutral processes.

Exhaustion of bacteria-specific CD4 T cells and microbial translocation in common variable immunodeficiency disorders.

In the present study, we have investigated the functional profile of CD4 T cells from patients with common variable immunodeficiency (CVID), including production of cytokines and proliferation in response to bacteria and virus-derived antigens. We show that the functional impairment of CD4 T cells, including the reduced capacity to proliferate and to produce IFN-γ and IL-2, was restricted to bacteria-specific and not virus-specific CD4 T cells. High levels of endotoxins were found in the plasma of patients with CVID, suggesting that CD4 T cell dysfunction might be caused by bacterial translocation. Of note, endotoxemia was associated with significantly higher expression of programmed death 1 (PD-1) on CD4 T cells. The blockade of the PD-1-PD-L1/2 axis in vitro restored CD4 T cell proliferation capacity, thus indicating that PD-1 signaling negatively regulates CD4 T cell functions. Finally, we showed that intravenous immunoglobulin G (IVIG) treatment significantly reduced endotoxemia and the percentage of PD-1(+) CD4 T cells, and restored bacteria-specific CD4 T cell cytokine production and proliferation. In conclusion, the present study demonstrates that the CD4 T cell exhaustion and functional impairment observed in CVID patients is associated with bacterial translocation and that IVIG treatment resolves bacterial translocation and restores CD4 T cell functions.

Transforming personal experience and emotions through education to cultural diversity: an interplay between unicity and genericity

When subjects studied at school are close to societal discourses and to the students' social identities, when they have high emotional resonance, is it possible to enable the students to distance themselves from their emotions and personal experience, and to conceptualise them? Examining the relation between emotion and learning through the lens of socio-cultural psychology, the aim of our study was to shed light on "secondarisation" processes, that is, processes that transform personal experience and emotions into conceptualised forms of thinking. We analysed 85 video-recorded lessons in education for cultural diversity involving 12 teachers (of primary and secondary schools). Having identified episodes in which emotions were put into words or personal experience was reported, we analysed the use of pronouns (taken as indicators of secondarisation processes) and found a recurrent pattern: "the unicity-genericity routine". We illustrate the functioning of this routine with various excerpts taken from lessons in education for diversity taught in the classes of two teachers in primary school. The results show that the interplay between unicity and genericity works as a discursive resource for the development of secondarisation processes.

Cryptic diversity among Western Palearctic tree frogs: postglacial range expansion, range limits, and secondary contacts of three European tree frog lineages (Hyla arborea group).

We characterize divergence times, intraspecific diversity and distributions for recently recognized lineages within the Hyla arborea species group, based on mitochondrial and nuclear sequences from 160 localities spanning its whole distribution. Lineages of H. arborea, H. orientalis, H. molleri have at least Pliocene age, supporting species level divergence. The genetically uniform Iberian H. molleri, although largely isolated by the Pyrenees, is parapatric to H. arborea, with evidence for successful hybridization in a small Aquitanian corridor (southwestern France), where the distribution also overlaps with H. meridionalis. The genetically uniform H. arborea, spread from Crete to Brittany, exhibits molecular signatures of a postglacial range expansion. It meets different mtDNA clades of H. orientalis in NE-Greece, along the Carpathians, and in Poland along the Vistula River (there including hybridization). The East-European H. orientalis is strongly structured genetically. Five geographic mitochondrial clades are recognized, with a molecular signature of postglacial range expansions for the clade that reached the most northern latitudes. Hybridization with H. savignyi is suggested in southwestern Turkey. Thus, cryptic diversity in these Pliocene Hyla lineages covers three extremes: a genetically poor, quasi-Iberian endemic (H. molleri), a more uniform species distributed from the Balkans to Western Europe (H. arborea), and a well-structured Asia Minor-Eastern European species (H. orientalis).

Improved detection of microbial ureteral stent colonisation by sonication.

PURPOSE: The diagnosis of microbial ureteral stent colonisation (MUSC) is difficult, since routine diagnostic techniques do not accurately detect microorganisms embedded in biofilms. New methods may improve diagnostic yield and understanding the pathophysiology of MUSC. The aim of the present study was to evaluate the potential of sonication in the detection of MUSC and to identify risk factors for device colonisation. METHODS: Four hundred and eight polyurethane ureteral stents of 300 consecutive patients were prospectively evaluated. Conventional urine culture (CUC) was obtained prior to stent placement and device removal. Sonication was performed to dislodge adherent microorganisms. Data of patient sex and age, indwelling time and indication for stent placement were recorded. RESULTS: Sonicate-fluid culture detected MUSC in 36%. Ureteral stents inserted during urinary tract infection (UTI) were more frequently colonised (59%) compared to those placed in sterile urine (26%; P < 0.001). Female sex (P < 0.001) and continuous stenting (P < 0.005) were significant risk factors for MUSC; a similar trend was observed in patients older than 50 years (P = 0.16). MUSC and indwelling time were positively correlated (P < 0.005). MUSC was accompanied by positive CUC in 36%. Most commonly isolated microorganisms were Coagulase-negative staphylococci (18.3%), Enterococci (17.9%) and Enterobacteriaceae (16.9%). CONCLUSIONS: Sonication is a promising approach in the diagnosis of MUSC. Significant risk factors for MUSC are UTI at the time of stent insertion, female sex, continuous stenting and indwelling time. CUC is a poor predictor of MUSC. The clinical relevance of MUSC needs further evaluation to classify isolated microorganism properly as contaminants or pathogens.

Functional diversity decreases with temperature in high elevation ant fauna

1. Severe environmental conditions filter community species compositions, forming clines of functional diversity along environmental gradients. Here, the changes in functional diversity in ant assemblages with severe environmental conditions in the Swiss Alps were investigated. 2. Eight sites were sampled along an elevation gradient (1800-2550 m). The variation in functional diversity was analysed along an elevation gradient considering four traits: social structure (monogynous vs. polygynous), worker size, pupal development, and nest structure. 3. Ant species richness and functional diversity decreased with decreasing temperature. Species found in colder habitats tended to live in subterranean nests rather than in mounds and exhibit a polymorphism in queen number, either within or across populations. The phylogenetic diversity did not decrease at colder temperature: Formicinae and Myrmicinae occupied the full range of elevations investigated. 4. An insulation experiment indicated that mounds are more thermally insulated against the cold compared with soil. The absence of a mound-building ant from high elevations probably results from a reduction in the amount of vegetal materials provided by coniferous trees. 5. More severe abiotic conditions at higher elevations act as a filter on ant assemblages, directly through physiological tolerances to the abiotic conditions and indirectly as the vegetation necessary for nest building shifts with elevation.</list-item

Use of the frc gene as a molecular marker to characterize oxalate-oxidizing bacterial abundance and diversity structure in soil.

Oxalate catabolism, which can have both medical and environmental implications, is performed by phylogenetically diverse bacteria. The formyl-CoA-transferase gene was chosen as a molecular marker of the oxalotrophic function. Degenerated primers were deduced from an alignment of frc gene sequences available in databases. The specificity of primers was tested on a variety of frc-containing and frc-lacking bacteria. The frc-primers were then used to develop PCR-DGGE and real-time SybrGreen PCR assays in soils containing various amounts of oxalate. Some PCR products from pure cultures and from soil samples were cloned and sequenced. Data were used to generate a phylogenetic tree showing that environmental PCR products belonged to the target physiological group. The extent of diversity visualised on DGGE pattern was higher for soil samples containing carbonate resulting from oxalate catabolism. Moreover, the amount of frc gene copies in the investigated soils was detected in the range of 1.64x10(7) to 1.75x10(8)/g of dry soil under oxalogenic tree (representing 0.5 to 1.2% of total 16S rRNA gene copies), whereas the number of frc gene copies in the reference soil was 6.4x10(6) (or 0.2% of 16S rRNA gene copies). This indicates that oxalotrophic bacteria are numerous and widespread in soils and that a relationship exists between the presence of the oxalogenic trees Milicia excelsa and Afzelia africana and the relative abundance of oxalotrophic guilds in the total bacterial communities. This is obviously related to the accomplishment of the oxalate-carbonate pathway, which explains the alkalinization and calcium carbonate accumulation occurring below these trees in an otherwise acidic soil. The molecular tools developed in this study will allow in-depth understanding of the functional implication of these bacteria on carbonate accumulation as a way of atmospheric CO(2) sequestration.

Peak and persistent excess of genetic diversity following an abrupt migration increase.

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population's demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations.

Strain diversity of mycobacteria isolated from pulmonary tuberculosis patients at Debre Birhan Hospital, Ethiopia.

BACKGROUND: Ethiopia ranks seventh in the list of 22 high tuberculosis (TB) burden countries, with an incidence rate of 379 cases per 100 000 population for TB all forms. However, information on the genomic diversity of Mycobacterium tuberculosis in Ethiopia is limited. OBJECTIVE: To investigate the molecular characteristics of M. tuberculosis strains implicated in pulmonary TB in the study area. METHODS AND RESULTS: A cross-sectional study was conducted using socio-demographic, clinical and culture data combined with molecular typing analysis. The proportion of TB and M. tuberculosis isolates was not associated with risk factors (P > 0.05). Of 99 sputum samples, 80.8% were culture-positive. Speciation of isolates showed that 88.8% were M. tuberculosis. Further characterisation led to the identification of 27 different spoligotype patterns of M. tuberculosis; the most dominant shared types were SIT149, SIT53 and SIT54. Of the 27 strains, three strains were new and were reported to the SITVIT database. More than two thirds of the strains belonged to the Euro-American lineage. CONCLUSION: This study shows the presence of several clusters and new strains of M. tuberculosis circulating in pulmonary TB patients in the study area, suggesting recent transmission. Nationwide studies are recommended to map the population structure of M. tuberculosis and set control measures.