Do stacked species distribution models reflect altitudinal diversity patterns?

The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed.

Genetic diversity in caribou linked to past and future climate change

Climate-driven range fluctuations during the Pleistocene have continuously reshaped species distribution leading to populations of contrasting genetic diversity. Contemporary climate change is similarly influencing species distribution and population structure, with important consequences for patterns of genetic diversity and species' evolutionary potential1. Yet few studies assess the impacts of global climatic changes on intraspecific genetic variation2, 3, 4, 5. Here, combining analyses of molecular data with time series of predicted species distributions and a model of diffusion through time over the past 21 kyr, we unravel caribou response to past and future climate changes across its entire Holarctic distribution. We found that genetic diversity is geographically structured with two main caribou lineages, one originating from and confined to Northeastern America, the other originating from Euro-Beringia but also currently distributed in western North America. Regions that remained climatically stable over the past 21 kyr maintained a high genetic diversity and are also predicted to experience higher climatic stability under future climate change scenarios. Our interdisciplinary approach, combining genetic data and spatial analyses of climatic stability (applicable to virtually any taxon), represents a significant advance in inferring how climate shapes genetic diversity and impacts genetic structure.

The Europeanisation of the measurement of diversity in education: a soft instrument of public policy

Faced with an increasing number of data and rankings, the author questions the roles of the different groups of actors who were originally involved in questioning the use of statistical indicators as a means of addressing issues of access to higher education. The comparison and nature of these international (UNESCO, OECD, EUROSTAT) and national (Germany, England, France, Switzerland) indicators in matters of inequalities of access to higher education question the tension between the discourses and the indicators they generate, and their recording at the national level. Who says what and with what consequences? What range of actors are involved in this process? What kind of power relations forms them? The author discusses how the issue of inequalities of access to higher education got on to the agendas of European organisations, identifies the policies that were defined, and sets them against an array of indicators, showing the discrepancy between the discourses and what the indicators reveal, the gap between the recommendations and the available tools. Why is there such a contrast? What are the mechanisms at work? Is it a technical or a political problem? What does this discrepancy reveal as far as national specificities within the construction of social inequalities are concerned?

Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps.

Abstract The giant hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as well as parts of North America. It has become a problematic species due to its ability to displace native flora and to cause public health hazards. Applying population genetics to species invasion can help reconstruct invasion history and may promote more efficient management practice. We thus analysed levels of genetic variation and population genetic structure of H. mantegazzianum in an invaded area of the western Swiss Alps as well as in its native range (the Caucasus), using eight nuclear microsatellite loci together with plastid DNA markers and sequences. On both nuclear and plastid genomes, native populations exhibited significantly higher levels of genetic diversity compared to invasive populations, confirming an important founder event during the invasion process. Invasive populations were also significantly more differentiated than native populations. Bayesian clustering analysis identified five clusters in the native range that corresponded to geographically and ecologically separated groups. In the invaded range, 10 clusters occurred. Unlike native populations, invasive clusters were characterized by a mosaic pattern in the landscape, possibly caused by anthropogenic dispersal of the species via roads and direct collection for ornamental purposes. Lastly, our analyses revealed four main divergent groups in the western Swiss Alps, likely as a consequence of multiple independent establishments of H. mantegazzianum.

European genetic diversity and susceptibility to pathogens.

Infectious diseases, both in their endemic and epidemic forms, have shaped the human genome. Ecology has also contributed to geographically constrained pressures on human populations. There are now multiple examples of population-specific genetic variants that modulate susceptibility to infection - several of which have been observed solely in Europeans. The pathogen genome also mutates and adapts to individuals and common alleles in populations. The current understanding has benefited from genome-wide association studies as well as from rapid progress in the genetic characterization of Mendelian immunodeficiencies that are defined by susceptibility to specific pathogens. It is expected that current efforts to characterize rare human genetic variants will contribute to the understanding of severe manifestations of common infections in European and other human groups.

Influence of biocontrol strain Pseudomonas fluorescens CHA0 and its antibiotic overproducing derivative on the diversity of root colonizing pseudomonads

Non-target effects of biocontrol strains of Pseudomonas on the population of resident pseudomonads should be assessed prior to their large scale application in the environment. The rifampicin resistant bacterium P. fluorescens CHA0-Rif and its antibiotic overproducing derivative CHA0-Rif/pME3424 were introduced into soil microcosms and the population of resident pseudomonads colonizing cucumber roots was investigated after 10 and 52 days. Both CHA0-Rif and CHA0-Rif/pME3424 displaced a part of the resident pseudomonad population after 10 days. To investigate the population structure, utilization of 10 carbon sources and production of two exoenzymes was assessed for 5600 individual pseudomonad isolates and 1700 isolates were subjected to amplified ribosomal DNA restriction analysis of the spacer region (spacer-ARDRA). After 10 days, only the proportion of pseudomonads able to degrade -tryptophan was reduced in treatments inoculated with either biocontrol strain. In parallel the phenotypic diversity was reduced. These effects were only observed 10 days after inoculation, and they were similar for inoculation with CHA0-Rif and CHA0-Rif/pME3424. Changes in the population structure of resident pseudomonads on cucumber roots during plant growth were more pronounced than changes due to the inoculants. The inoculants did not affect the genotypic diversity detected with spacer-ARDRA, but the genotypic fingerprints corresponded only partially to the phenotypic profiles. Overall CHA0-Rif had a small and transient impact on the population of resident pseudomonads and the effect was essentially the same for the genetically engineered derivative CHA0-

Hidden diversity in honey bee gut symbionts detected by single-cell genomics.

Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera, presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi. For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification.

Ambiguous nucleotide calls from population-based sequencing of HIV-1 are a marker for viral diversity and the age of infection.

Background. The time passed since the infection of a human immunodeficiency virus (HIV)-infected individual (the age of infection) is an important but often only poorly known quantity. We assessed whether the fraction of ambiguous nucleotides obtained from bulk sequencing as done for genotypic resistance testing can serve as a proxy of this parameter. Methods. We correlated the age of infection and the fraction of ambiguous nucleotides in partial pol sequences of HIV-1 sampled before initiation of antiretroviral therapy (ART). Three groups of Swiss HIV Cohort Study participants were analyzed, for whom the age of infection was estimated on the basis of Bayesian back calculation (n = 3,307), seroconversion (n = 366), or diagnoses of primary HIV infection (n = 130). In addition, we studied 124 patients for whom longitudinal genotypic resistance testing was performed while they were still ART-naive. Results. We found that the fraction of ambiguous nucleotides increased with the age of infection with a rate of .2% per year within the first 8 years but thereafter with a decreasing rate. We show that this pattern is consistent with population-genetic models for realistic parameters. Finally, we show that, in this highly representative population, a fraction of ambiguous nucleotides of >.5% provides strong evidence against a recent infection event < 1 year prior to sampling (negative predictive value, 98.7%). Conclusions. These findings show that the fraction of ambiguous nucleotides is a useful marker for the age of infection.

Multiple introductions boosted genetic diversity in the invasive range of black cherry (Prunus serotina; Rosaceae).

BACKGROUND AND AIMS: Black cherry (Prunus serotina) is a North American tree that is rapidly invading European forests. This species was introduced first as an ornamental plant, then it was massively planted by foresters in many countries, but its origins and the process of invasion remain poorly documented. Based on a genetic survey of both native and invasive ranges, the invasion history of black cherry was investigated by identifying putative source populations and then assessing the importance of multiple introductions on the maintenance of gene diversity. METHODS: Genetic variability and structure of 23 populations from the invasive range and 22 populations from the native range were analysed using eight nuclear microsatellite loci and five chloroplast DNA regions. KEY RESULTS: Chloroplast DNA diversity suggests there were multiple introductions from a single geographic region (the north-eastern United States). A low reduction of genetic diversity was observed in the invasive range for both nuclear and plastid genomes. High propagule pressure including both the size and number of introductions shaped the genetic structure in Europe and boosted genetic diversity. Populations from Denmark, The Netherlands, Belgium and Germany showed high genetic diversity and low differentiation among populations, supporting the hypothesis that numerous introduction events, including multiple individuals and exchanges between sites, have taken place during two centuries of plantation. CONCLUSIONS: This study postulates that the invasive black cherry has originated from east of the Appalachian Mountains (mainly the Allegheny plateau) and its invasiveness in north-western Europe is mainly due to multiple introductions containing high numbers of individuals.

Cross-scale analysis of the region effect on vascular plant species diversity in southern and northern European mountain ranges.

Background: The divergent glacial histories of southern and northern Europe affect present-day species diversity at coarse-grained scales in these two regions, but do these effects also penetrate to the more fine-grained scales of local communities?Methodology/Principal Findings: We carried out a cross-scale analysis to address this question for vascular plants in two mountain regions, the Alps in southern Europe and the Scandes in northern Europe, using environmentally paired vegetation plots in the two regions (n = 403 in each region) to quantify four diversity components: (i) total number of species occurring in a region (total gamma-diversity), (ii) number of species that could occur in a target plot after environmental filtering (habitat-specific gamma-diversity), (iii) pair-wise species compositional turnover between plots (plot-to-plot beta-diversity) and (iv) number of species present per plot (plot gamma-diversity). We found strong region effects on total gamma-diversity, habitat-specific gamma-diversity and plot-to-plot beta-diversity, with a greater diversity in the Alps even towards distances smaller than 50 m between plots. In contrast, there was a slightly greater plot alpha-diversity in the Scandes, but with a tendency towards contrasting region effects on high and low soil-acidity plots.Conclusions/Significance: We conclude that there are strong regional differences between coarse-grained (landscape- to regional-scale) diversity components of the flora in the Alps and the Scandes mountain ranges,but that these differences do not necessarily penetrate to the finest-grained (plot-scale) diversity component, at least not on acidic soils. Because different processes can lead to a similar pattern, we discuss the consistency of our results with Quaternary history and other divergent features between the two regions such as habitat connectivity, selection for vagility and environmental differences not accounted for in our analyses

Nestmate recognition and levels of aggression are not altered by changes in genetic diversity in a socially polymorphic ant

The ability to distinguish nestmates from foreign individuals is central to the functioning of insect societies. In ants, workers from multiple-queen colonies are often less aggressive than workers from single-queen ones. In line with this observation, it has been hypothesized that workers from multiple-queen colonies have less precise recognition abilities than workers from single-queen ones because their colonies contain genetically more diverse individuals, which results in a broader template of recognition cues. Here, we assessed the impact of social structure ( queen number) variation on nestmate recognition and aggression in a large population of the socially polymorphic ant Formica selysi. We staged unilateral aggression tests on the nest surface. Workers from single-and multiple-queen colonies had good nestmate recognition ability and did not differ significantly in their level of aggression towards foreign, immobilized workers ( cue-bearers). In particular, workers from multiple-queen colonies efficiently recognized non-nestmates despite the higher genetic diversity in their colony. Cue-bearers from single- and multiple-queen colonies elicited similar reactions. However, the level of aggression was higher between than within social forms, suggesting that workers detect a signal that is specific to the colony social structure. Finally, the level of aggression was not correlated with the genetic distance between colonies. Overall, we found no evidence for the hypothesis that the presence of multiple breeders in the same colony decreases recognition abilities and found no simple relationship between genetic diversity and aggression level. (c) 2007 The Association for the Study of Animal Behaviou

Trophic resource partitioning and competition between the two sibling bat species Myotis myotis and Myotis blythii

1. Niche theory predicts that the stable coexistence of species within a guild should be associated, if resources are limited, with a mechanism of resource partitioning. Using extensive data on diets, the present study attempts: (i) to test the hypothesis that, in sympatry, the interspecific overlap between the trophic niches of the sibling bat species Myotis myotis and M. blythii-which coexist intimately in their roosts-is effectively lower than the two intraspecific overlaps; (ii) to assess the role played by interspecific competition in resource partitioning through the study of trophic niche displacement between several sympatric and allopatric populations. 2. Diets were determined by the analysis of faecal samples collected in the field from individual bats captured in various geographical areas. Trophic niche overlaps were calculated monthly for all possible intraspecific and interspecific pairs of individuals from sympatric populations. Niche breadth was estimated from: (i) every faecal sample; (ii) all the faecal samples collected per month in a given population (geographical area). 3. In every population, the bulk of the diets of M. myotis and M. blythii consisted of, respectively, terrestrial (e.g. carabid beetles) and grass-dwelling (mostly bush crickets) prey. All intraspecific trophic niche overlaps were significantly greater than the interspecific one, except in Switzerland in May when both species exploited mass concentrations of cockchafers, a non-limiting food source. This clearcut partitioning of resources may allow the stable, intimate coexistence observed under sympatric conditions. 4. Relative proportions of ground-and grass-dwelling prey, as well as niche breadths (either individual or population), did not differ significantly between sympatry and allopatry, showing that, under allopatric conditions, niche expansion does not take place. This suggests that active interspecific competition is not the underlying mechanism responsible for the niche partitioning which is currently observed between M. myotis and M. blythii.

The Economies of Urban Diversity : Ruhr Area and Istanbul

The Economics of Urban Diversity explores ethnic and religious minorities in urban economies. In this exciting work, the contributors develop an integrative approach to urban diversity and economy by employing concepts from different studies and linking historical and contemporary analyses of economic, societal, demographic, and cultural development. Contributors from a variety of disciplines-geography, economics, history, sociology, anthropology, and planning-make for a transdisciplinary analysis of past and present migration-related economic and social issues, which helps to better understand the situation of ethnic and religious minorities in metropolitan areas today.