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Most vulnerable individuals are particularly affected by the COVID-19 pandemic. This study takes place in a large city in France. The aim of this study is to describe the mobility of the homeless population at the beginning of the health crisis and to analyze its impact in terms of COVID-19 prevalence. From June to August 2020 and September to December 2020, 1272 homeless people were invited to be tested for SARS-CoV-2 antibodies and virus and complete questionnaires. Our data show that homeless populations are sociologically different depending on where they live. We show that people that were living on the street were most likely to be relocated to emergency shelters than other inhabitants. Some neighborhoods are points of attraction for homeless people in the city while others emptied during the health crisis, which had consequences for virus circulation. People with a greater number of different dwellings reported became more infected. This first study of the mobility and epidemiology of homeless people in the time of the pandemic provides unique information about mobility mapping, sociological factors of this mobility, mobility at different scales, and epidemiological consequences. We suggest that homeless policies need to be radically transformed since the actual model exposes people to infection in emergency.

For most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population, the local environment, and immunity. Phylogeographic approaches are currently unable to disentangle the relative effects of these competing factors. We develop a spatiotemporally structured phylogenetic framework that addresses these limitations by considering individual transmission events, reconstructed across spatial scales. We apply it to geocoded dengue virus sequences from Thailand (N = 726 over 18 years). We find infected individuals spend 96% of their time in their home community compared to 76% for the susceptible population (mainly children) and 42% for adults. Dynamic pockets of local immunity make transmission more likely in places with high heterotypic immunity and less likely where high homotypic immunity exists. Age-dependent mixing of individuals and vector distributions are not important in determining spread. This approach provides previously unknown insights into one of the most complex disease systems known and will be applicable to other pathogens., Phylogeographic analyses can provide broad descriptions of the spread of pathogens between populations, but are limited by incomplete sampling. Here, the authors develop an inference framework that reconstructs sequential transmission events and use it to characterise dynamics of dengue in Thailand.

International audience; Social systems are major drivers of population structure and gene flow, with important effects on dynamics and dispersal of associated populations of parasites. Among bats, the common vampire bat (Desmodus rotundus) has likely one of the most complex social structures. Using autosomal and mitochondrial markers on vampires from Mexico, French Guiana, and North Brazil, from both roosting and foraging areas, we observed an isolation by distance at the wider scale and lower but significant differentiation between closer populations (

International audience; Wild populations are facing rapid and sometimes extreme environmental changes that are currently exacerbated by pressing human activities. A major scientific endeavor is to reveal the evolutionary processes allowing wild populations to generate adaptive responses to these rapid and drastic environmental changes. In the recent decades, the accumulation of empirical data as well as the development of new theories and molecular tools have largely improved our ability to tackle such a major question. In particular, there is now growing evidence that evolutionary processes (gene flow, drift, mutation, and natural selection) interact in sometimes complex ways to shape the rapid responses of organisms to changing environments, and this can lead to unexpected feedback between evolutionary and ecological dynamics. These rapid responses are sustained by genetic determinants in addition to alternative inheritance systems, including those that are epigenetically controlled. Revealing these underlying molecular mechanisms of adaptation may change the way wild populations are managed and conserved.

International audience; Africa is one of the endemic regions of HBV infection. In particular, genotype E is highly endemic in most of sub-Saharan Africa such as West African countries where it represents more than 90% of total infections. Madagascar, which is classified as a high endemic area for HBV and where the most prevalent genotype is E, might play a relevant role in the dispersion of this genotype due to its crucial position in the Indian Ocean. The aim of this study was to investigate the origin, population dynamics, and circulation of HBV-E genotype in Madagascar through high-resolution phylogenetic and phylodynamic approaches. The phylogenetic tree indicated that Malagasy isolates were intermixed and closely related with sequences mostly from West African countries. The Bayesian tree highlighted three statistically supported clusters of Malagasy strains which dated back to the years 1981 (95% HPD: 1971-1992), 1986 (95% HPD: 1974-1996), and 1989 (95% HPD: 1974-2001). Population dynamics analysis showed an exponential increase in the number of HBV-E infections approximately from the year 1975 until 2000s. The migration analysis was also performed and a dynamic pattern of gene flow was identified. In conclusion, this study confirms previous observation of HBV-E circulation in Africa and expands these findings at Madagascar demonstrating its recent introduction, and highlighting the role of the African countries in the spread of HBV-E genotype. Further studies on molecular epidemiology of HBV genotype E are needed to clarify the evolutionary history of this genotype.

Streptococcus pneumoniae serotype 3 remains a significant cause of morbidity and mortality worldwide, despite inclusion in the 13-valent pneumococcal conjugate vaccine (PCV13). Serotype 3 increased in carriage since the implementation of PCV13 in the USA, while invasive disease rates remain unchanged. We investigated the persistence of serotype 3 in carriage and disease, through genomic analyses of a global sample of 301 serotype 3 isolates of the Netherlands3–31 (PMEN31) clone CC180, combined with associated patient data and PCV utilization among countries of isolate collection. We assessed phenotypic variation between dominant clades in capsule charge (zeta potential), capsular polysaccharide shedding, and susceptibility to opsonophagocytic killing, which have previously been associated with carriage duration, invasiveness, and vaccine escape. We identified a recent shift in the CC180 population attributed to a lineage termed Clade II, which was estimated by Bayesian coalescent analysis to have first appeared in 1968 [95% HPD: 1939–1989] and increased in prevalence and effective population size thereafter. Clade II isolates are divergent from the pre-PCV13 serotype 3 population in non-capsular antigenic composition, competence, and antibiotic susceptibility, the last of which resulting from the acquisition of a Tn916-like conjugative transposon. Differences in recombination rates among clades correlated with variations in the ATP-binding subunit of Clp protease, as well as amino acid substitutions in the comCDE operon. Opsonophagocytic killing assays elucidated the low observed efficacy of PCV13 against serotype 3. Variation in PCV13 use among sampled countries was not independently correlated with the CC180 population shift; therefore, genotypic and phenotypic differences in protein antigens and, in particular, antibiotic resistance may have contributed to the increase of Clade II. Our analysis emphasizes the need for routine, representative sampling of isolates from disperse geographic regions, including historically under-sampled areas. We also highlight the value of genomics in resolving antigenic and epidemiological variations within a serotype, which may have implications for future vaccine development., Author summary Streptococcus pneumoniae is a leading cause of bacterial pneumoniae, meningitis, and otitis media. Despite its inclusion in the most recent pneumococcal conjugate vaccine, PCV13, serotype 3 remains epidemiologically important globally. We investigated the persistence of serotype 3 using whole-genome sequencing data from 301 isolates collected among 24 countries from 1993–2014. Through phylogenetic analysis, we identified three distinct lineages within a single clonal complex, CC180, and found one that has recently emerged and grown in prevalence. We then compared genomic difference among lineages as well as variations in pneumococcal vaccine use among sampled countries. We found that the recently emerged lineage, termed Clade II, has a higher prevalence of antibiotic resistance compared to other lineages, diverse surface protein antigens, and a higher rate of recombination, a process by which bacteria can uptake and incorporate genetic material from its surroundings. Differences in vaccine use among sampled countries did not appear to be associated with the emergence of Clade II. We highlight the need for routine, representative sampling of bacterial isolates from diverse geographic areas and show the utility of genomic data in resolving epidemiological differences within a pathogen population.

With escalating urbanization, the environmental, demographic, and socio-economic heterogeneity of urban landscapes poses a challenge to mathematical models for the transmission of vector-borne infections. Classical coupled vector–human models typically assume that mosquito abundance is either independent from, or proportional to, human population density, implying a decreasing force of infection, or per capita infection rate with host number. We question these assumptions by introducing an explicit dependence between host and vector densities through different recruitment functions, whose dynamical consequences we examine in a modified model formulation. Contrasting patterns in the force of infection are demonstrated, including in particular increasing trends when recruitment grows sufficiently fast with human density. Interaction of these patterns with seasonality in temperature can give rise to pronounced differences in timing, relative peak sizes, and duration of epidemics. These proposed dependencies explain empirical dengue risk patterns observed in the city of Delhi where socio-economic status has an impact on both human and mosquito densities. These observed risk trends with host density are inconsistent with current standard models. A better understanding of the connection between vector recruitment and host density is needed to address the population dynamics of mosquito-transmitted infections in urban landscapes.

The distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains to be fully characterized. We addressed this question, by generating 300 high-coverage exome sequences from various populations of rainforest hunter-gatherers and neighboring farmers from the western and eastern parts of the central African equatorial rainforest. We show here, by model-based demographic inference, that the effective population size of African populations remained fairly constant until recent millennia, during which the populations of rainforest hunter-gatherers have experienced a ~75% collapse and those of farmers a mild expansion, accompanied by a marked increase in gene flow between them. Despite these contrasting demographic patterns, African populations display limited differences in the estimated distribution of fitness effects of new nonsynonymous mutations, consistent with purifying selection against deleterious alleles of similar efficiency in the different populations. This situation contrasts with that we detect in Europeans, which are subject to weaker purifying selection than African populations. Furthermore, the per-individual mutation load of rainforest hunter-gatherers was found to be similar to that of farmers, under both additive and recessive modes of inheritance. Together, our results indicate that differences in the subsistence patterns and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.

Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans , a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans . Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia. IMPORTANCE This phylogenetic study of the bat white-nose syndrome agent, P. destructans , uses genomics to elucidate evolutionary relationships among populations of the fungal pathogen to understand the epizoology of this biological invasion. We analyze hypervariable and abundant genetic characters (microsatellites and genomic SNPs, respectively) to reveal previously uncharacterized diversity among populations of the pathogen from North America and Eurasia. We present new evidence supporting recent introduction of the fungus to North America from a diverse Eurasian population, with limited increase in genetic variation in North America since that introduction.

International audience; From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their history of admixture and natural selection remains largely undefined. Here, we studied the genome-wide diversity of the African-descent Makranis, who reside on the Arabian Sea coast of Pakistan, as well that of four neighboring Pakistani populations , to investigate the genetic legacy, population dynamics, and tempo of the Indian Ocean slave trade. We show that the Makranis are the result of an admixture event between local Baluch tribes and Bantu-speaking populations from eastern or southeastern Africa; we dated this event to $300 years ago during the Omani Empire domination. Levels of parental relatedness, measured through runs of ho-mozygosity, were found to be similar across Pakistani populations, suggesting that the Makranis rapidly adopted the traditional practice of endogamous marriages. Finally, we searched for signatures of post-admixture selection at traits evolving under positive selection, including skin color, lactase persistence, and resistance to malaria. We demonstrate that the African-specific Duffy-null blood group-believed to confer resistance against Plasmodium vivax infection-was recently introduced to Pakistan through the slave trade and evolved adaptively in this P. vivax malaria-endemic region. Our study reconstructs the genetic and adaptive history of a neglected episode of the African Diaspora and illustrates the impact of recent admixture on the diffusion of adaptive traits across human populations.

International audience; Many species have suffered large population declines due to the anthropogenic influence on ecosystems. Understanding historical population trends is essential for informing best efforts to preserve species. We propose a new method to reconstruct the past structure of a regional species pool, based on historical naturalist literature. Qualitative information collected from annotated checklists and reports can be relevant to identify major long-term community changes. We reviewed ornithological literature on the Camargue, the largest wetland in France. We reconstructed the entire breeding bird community from 1830 to 2009 and translated historical data into semi-quantitative data. This data permitted a calculation of a Community Commonness Index to measure the average level of abundance of species in a community. The Community Specialization and Community Temperature Indices were used to evaluate the potential long-term impact of land-use and climate changes on the composition of the regional bird species pool. We found a decrease in average abundance and specialization between 1950 and 1989, suggesting that changes in land-use negatively impacted the structure and composition of the local bird community by reducing species abundance and removing habitat-specialists (e.g. Southern Grey Shrike, Greater Shorttoed Lark). These results are likely to be linked with a major loss of natural habitats in the Camargue between 1942 and 1984 when natural areas and traditional farmland were converted into intensive cultivated lands. We also found fluctuations among species with high versus low temperature preference. However, long-term effects of climate change on the bird community might be blurred by the impact of land-use changes. Overall, our results contrast with those obtained from well-monitored colonial waterbirds showing long-term increases. Our results plead for a more regular use of historical naturalist data when examining long-term changes in species communities as they allow the establishment of an older temporal point of reference and consideration of species not covered by traditional monitoring schemes.

International audience; Today, we are witnessing changes in the spatial distribution and abundance of many species, including ticks and their associated pathogens. Evidence that these changes are primarily due to climate change, habitat modifications, and the globalisation of human activities are accumulating. Changes in the distribution of ticks and their invasion into new regions can have numerous consequences including modifications in their ecological characteristics and those of endemic species, impacts on the dynamics of local host populations and the emergence of human and livestock disease. Here, we review the principal causes for distributional shifts in tick populations and their consequences in terms of the ecological attributes of the species in question (i.e. phenotypic and genetic responses), pathogen transmission and disease epidemiology. We also describe different methodological approaches currently used to assess and predict such changes and their consequences. We finish with a discussion of new research avenues to develop in order to improve our understanding of these host-vector-pathogen interactions in the context of a changing world.

International audience; Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways because of adaptation to their environment. Here, we introduced ancestry distribution models, that is, statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic admixture instead of species occurrence data. Using multi-locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25 to 4 °C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of movement in a north-east direction was predicted, the magnitude of displacement was species-specific. For a temperature increase of 2 °C, contact zones were predicted to move by 92 km on average (minimum of 5 km, maximum of 212 km) and by 188 km for an increase of 4 °C (minimum of 11 km, maximum of 393 km). Intra-specific turnover-measuring the extent of change in global population genetic structure-was generally found to be moderate for 2 °C of temperature warming. For 4 °C of warming, however, the models indicated substantial intra-specific turnover for ten species. These results illustrate that, in spite of unavoidable simplifications, ancestry distribution models open new perspectives to forecast population genetic changes within species and complement more traditional distribution-based approaches.

According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of carrot (Daucus carota L. ssp. sativus). The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean pi (sil) = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F (ST) = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r (2) = 0.635) within the 700-1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.

In this study, we describe the landscape of human demographic expansions in Eurasia using a large continental Y chromosome and mitochondrial DNA dataset. Variation at these two uniparentally-inherited genetic systems retraces expansions that occurred in the past 60 ky, and shows a clear decrease of expansion ages from east to west Eurasia. To investigate the demographic events at the origin of this westward decrease of expansion ages, the estimated divergence ages between Eurasian populations are compared with the estimated expansion ages within each population. Both markers suggest that the demographic expansion diffused from east to west in Eurasia in a demic way, i.e., through migrations of individuals (and not just through diffusion of new technologies), highlighting the prominent role of eastern regions within Eurasia during Palaeolithic times.

International audience; Genome wide patterns of nucleotide diversity and recombination reveal considerable variation including hotspots. Some studies suggest that these patterns are primarily dictated by individual locus history related at a broader scale to the population demographic history. Because bottlenecks have occurred in the history of numerous species, we undertook a simulation approach to investigate their impact on the patterns of aggregation of polymorphic sites and linkage disequilibrium (LD). We developed a new index (Polymorphism Aggregation Index) to characterize this aggregation and showed that variation in the density of polymorphic sites results from an interplay between the bottleneck scenario and the recombination rate. Under particular conditions, aggregation is maximized and apparent mutation hotspots resulting in a 50-fold increase in polymorphic sites density can occur. In similar conditions, long distance LD can be detected.

International audience; The completion of the life cycle of Echinococcus multilocularis needs a spatial overlap between intermediate host species (voles) and definitive host (fox) faeces. Factors influencing the importance of this overlap were investigated in north eastern France. Kilometric transects were walked to collect fox faeces and to estimate vole relative densities through surface indices. Habitat and climatic conditions were the strongest predictors of the number of faeces collected, while vole densities had no predictive power. Densities of both Microtus sp. and fox faeces were higher in medium-height vegetation edge. The consequences of such results to understand local transmission processes and human exposure are discussed.

Accurate inferences on population genetics data require a sound underlying theoretical null model. Nearly nothing is known about the gene dynamics of organisms with complex life cycles precluding any biological interpretation of population genetics parameters. In this article, we used an infinite island model to derive the expectations of those parameters for the life cycle of a dioecious organism obligatorily alternating sexual and asexual reproductions as it is the case for schistosomes (plathyhelminth parasites). This model allowed us to investigate the effects of the degree of mixing among individuals coming from different subpopulations at each new generation (represented in the model by the migration rates before and after clonal reproductions) and the variance in the reproductive success of individuals during the clonal phase. We also consider the effects of different migration rates and degrees of clonal reproductive skew between male and female individuals. Results show that the variance in the reproductive success of clones is very important in shaping the distribution of the genetic variability both within and among subpopulations. Thus, higher variance in the reproductive success of clones generates heterozygous excesses within subpopulations and also increases genetic differentiation between them. Migration occurring before and after asexual reproduction has different effects on the patterns of F(IS) and F(ST). When males and females display different degrees of reproductive skew or migration rates, we observe differences in their respective population genetic structure. While results of the model apply to any organism alternating sexual and clonal reproductions (e.g. all parasitic trematodes, many plants, and all aphididae), we finally confront some of these theoretical expectations to empirical data from Schistosoma mansoni infecting Rattus rattus in Guadeloupe.

Several studies showed that surnames are good markers to infer patrilineal genetic structures of populations, both on regional and microregional scales. As a case study, the spatial patterns of the 9,929 most com- mon surnames of the Netherlands were analyzed by a clustering method called self-organizing maps (SOMs). The resulting clusters grouped surnames with a similar geographic distribution and origin. The analysis was shown to be in agreement with already known features of Dutch surnames, such as 1) the geographic distribution of some well-known locative suffixes, 2) historical census data, 3) the distribution of foreign surnames, and 4) polyphyletic surnames. Thus, these results validate the SOM clustering of surnames, and allow for the generali- zation of the technique. This method can be applied as a new strategy for a better Y-chromosome sampling design in retrospective population genetics studies, since the idenfication of surnames with a defined geographic origin enables the selection of the living descendants of those families settled, centuries ago, in a given area. In other words, it becomes possible to virtually sample the popu- lation as it was when surnames started to be in use. We show that, in a given location, the descendants of those individuals who inhabited the area at the time of origin of surnames can be as low as 20%. This finding suggests 1) the major role played by recent migrations that are likely to have distorted or even defaced ancient genetic patterns, and 2) that standard-designed samplings can hardly por- tray a reliable picture of the ancient Y-chromosome vari- ability of European populations. Am J Phys Anthropol 126:214 -228, 2005. © 2004 Wiley-Liss, Inc.

International audience; The rising incidence of emerging infectious diseases (EID) is mostly linked to biodiversity loss, changes in habitat use and increasing habitat fragmentation. Bats are linked to a growing number of EID but few studies have explored the factors of viral richness in bats. These may have implications for role of bats as potential reservoirs. We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. We performed the first comparative analysis testing the correlation of the fragmented geographical distribution (defined as the perimeter to area ratio) with viral richness in bats. Because of their potential effect, sampling effort, host body weight, ecological and behavioural traits such as roosting behaviour, migration and geographical range, were included into the analysis as variables. The results showed that the geographical distribution size, shape and host body weight have significant effects on viral richness in bats. Viral richness was higher in large-bodied bats which had larger and more fragmented distribution areas. Accumulation of viruses may be related to the historical expansion and contraction of bat species distribution range, with potentially strong effects of distribution edges on virus transmission. Two potential explanations may explain these results. A positive distribution edge effect on the abundance or distribution of some bat species could have facilitated host switches. Alternatively, parasitism could play a direct role in shaping the distribution range of hosts through host local extinction by virulent parasites. This study highlights the importance of considering the fragmentation of bat species geographical distribution in order to understand their role in the circulation of viruses in Africa.

International audience; Adaptive speciation with gene flow via the evolution of assortative mating has classically been studied in one of two different scenarios. First, speciation can occur if frequency-dependent competition in sympatry induces disruptive selection, leading to indirect selection for mating with similar phenotypes. Second, if a subpopulation is locally adapted to a specific environment, then there is indirect selection against hybridizing with maladapted immigrants. While both of these mechanisms have been modeled many times, the literature lacks models that allow direct comparisons between them. Here we incorporate both frequency-dependent competition and local adaptation into a single model and investigate whether and how they interact in driving speciation. We report two main results. First, we show that individually, the two mechanisms operate under separate conditions, hardly influencing each other when one of them alone is sufficient to drive speciation. Second, we also find that the two mechanisms can operate together, leading to a third speciation mode in which speciation is initiated by selection against maladapted migrants but completed by within-deme competition in a distinct second phase. While this third mode bears some similarity to classical reinforcement, it is considerably faster, and both newly formed species go on to coexist in sympatry.

Leprosy, a chronic human disease with potentially debilitating neurological consequences, results from infection with Mycobacterium leprae . This unculturable pathogen has undergone extensive reductive evolution, with half of its genome now occupied by pseudogenes. Using comparative genomics, we demonstrated that all extant cases of leprosy are attributable to a single clone whose dissemination worldwide can be retraced from analysis of very rare single-nucleotide polymorphisms. The disease seems to have originated in Eastern Africa or the Near East and spread with successive human migrations. Europeans or North Africans introduced leprosy into West Africa and the Americas within the past 500 years.

Parasites with complex life cycles are expected to manipulate the behaviour of their intermediate hosts (IHs), which increase their predation rate and facilitate the transmission to definitive hosts (DHs). This ability, however, is a double-edged sword when the parasite can also be transmitted vertically in the IH. In this situation, as the manipulation of the IH behaviour increases the IH death rate, it conflicts with vertical transmission, which requires healthy and reproducing IHs. The protozoan Toxoplasma gondii , a widespread pathogen, combines both trophic and vertical transmission strategies. Is parasite manipulation of host behaviour still adaptive in this situation? We model the evolution of the IH manipulation by T. gondii to study the conflict between these two routes of transmission under different epidemiological situations. Model outputs show that manipulation is particularly advantageous for virulent strains and in epidemic situations, and that different levels of manipulation may evolve depending on the sex of the IH and the transmission routes considered. These results may help to understand the variability of strain characteristics encountered for T. gondii and may extend to other trophically transmitted parasites.

[Departement_IRSTEA]Eaux [TR1_IRSTEA]BELCA; International audience; One of the main objectives of ecological risk assessment is to evaluate the effects of toxicants on ecologically relevant biological systems such as populations or communities. However, the effects of toxicants are commonly measured on selected subindividual or individual endpoints due to their specificity against chemical stressors. Introducing these effects into population models is a promising way to predict impacts on populations. The models currently employed are very simplistic, and their environmental relevance needs to be improved to establish the ecological relevance of hazard assessment. The present study with the gastropod Potamopyrgus antipodarum combines a field experimental approach with a modeling framework. It clarifies the role played by seasonal variability of life-history traits in the population's vulnerability to the alteration of individual performance, potentially due to toxic stress. The present study comprised 3 steps: 1) characterization of the seasonal variability in life-history traits of a local population over 1 yr by using in situ experiments on caged snails, coupled with a demographic follow-up; 2) development of a periodic matrix population model that visualizes the monthly variability of population dynamics; and 3) simulation of the demographic consequences of an alteration in life-history traits (i.e., fertility, juvenile, and adult survival). The results revealed that demographic impacts strongly depend on the season when alterations of individual performance occur. Model analysis showed that this seasonal variability in population vulnerability is strongly related to the phenology of the population. The authors emphasize that improving the realism of population models is a major objective for ecological risk assessment, and that taking into account species phenology in modeling approaches should be a priority.

International audience; Rats are major reservoirs of leptospirosis and considered as a main threat to biodiversity. A recent introduction of Rattus rattus to the island of Futuna (Western Polynesia) provided the opportunity to test if a possible change in species composition of rat populations would increase the risk of leptospirosis to humans. We trapped rodents on Wallis and Futuna and assessed Leptospira carriage in 357 rodents (Rattus norvegicus, R. rattus, Rattus exulans, and Mus domesticus) from 2008 to 2012. While Leptospira prevalence in rodents and the composition of rat populations on Futuna fluctuated with rainfall, the biomass of Leptospira-carrying rodents has been continuously rising from 2008 to 2012. Our results suggest that the introduction of R. rattus increases the risk to humans being infected with leptospirosis by rats.

Genetic assessment by spoligotyping of 565 Mycobacterium tuberculosis complex strains collected from the Western Region of Cameroon between 2004 and 2005 has confirmed the establishment of the “Cameroon family” as the leading cause of tuberculosis in 45.9% of cases and evidenced the rapid quasi extinction of Mycobacterium africanum , isolated in 3.3% of tuberculosis cases.

International audience; The bacterial and fungal communities associated with dandruff were investigated using culture-independent methodologies in the French subjects. The major bacterial and fungal species inhabiting the scalp subject's were identified by cloning and sequencing of the conserved ribosomal unit regions (16S for bacterial and 28S-ITS for fungal) and were further quantified by quantitative PCR. The two main bacterial species found on the scalp surface were Propionibacterium acnes and Staphylococcus epidermidis, while Malassezia restricta was the main fungal inhabitant. Dandruff was correlated with a higher incidence of M. restricta and S. epidermidis and a lower incidence of P. acnes compared to the control population (p

Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ∼ 150-fold, whereas the mutY mutations reduced the rate by ∼ 40–60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined.

International audience; Members of the Anopheles gambiae species complex are primary vectors of human malaria in Africa. Population heterogeneities for ecological and behavioral attributes expand and stabilize malaria transmission over space and time, and populations may change in response to vector control, urbanization and other factors. There is a need for approaches to comprehensively describe the structure and characteristics of a sympatric local mosquito population, because incomplete knowledge of vector population composition may hinder control efforts. To this end, we used a genome-wide custom SNP typing array to analyze a population collection from a single geographic region in West Africa. The combination of sample depth (n = 456) and marker density (n = 1536) unambiguously resolved population subgroups, which were also compared for their relative susceptibility to natural genotypes of Plasmodium falciparum malaria. The population subgroups display fluctuating patterns of differentiation or sharing across the genome. Analysis of linkage disequilibrium identified 19 new candidate genes for association with underlying population divergence between sister taxa, A. coluzzii (M-form) and A. gambiae (S-form).

International audience; Dispersal of organisms generates gene flow between populations. Identifying factors that influence dispersal will help predict how species will cope with rapid environmental change. We developed an innovative infrastructure, the Metatron, composed of 48 interconnected patches, designed for the study of terrestrial organism movement as a model for dispersal. Corridors between patches can be flexibly open or closed. Temperature, humidity and illuminance can be independently controlled within each patch. The modularity and adaptability of the Metatron provide the opportunity for robust experimental design for the study of 'meta-systems'. We describe a pilot experiment on populations of the butterfly Pieris brassicae and the lizard Zootoca vivipara in the Metatron. Both species survived and showed both disperser and resident phenotypes. The Metatron offers the opportunity to test theoretical models in spatial ecology.

Marked phenotypic variation characterizes isolates of Toxoplasma gondii, a ubiquitous zoonotic parasite that serves as an important experimental model for studying apicomplexan parasites. Progress in identifying the heritable basis for clinically and epidemiologically significant differences requires a robust system for describing and interpreting evolutionary subdivisions in this prevalent pathogen. To develop such a system, we have examined more than 950 isolates collected from around the world and genotyped them using three independent sets of polymorphic DNA markers, sampling 30 loci distributed across all nuclear chromosomes as well as the plastid genome. Our studies reveal a biphasic pattern consisting of regions in the Northern Hemisphere where a few, highly clonal and abundant lineages predominate; elsewhere, and especially in portions of South America are characterized by a diverse assemblage of less common genotypes that show greater evidence of recombination. Clustering methods were used to organize the marked genetic diversity of 138 unique genotypes into 15 haplogroups that collectively define six major clades. Analysis of gene flow indicates that a small number of ancestral lineages gave rise to the existing diversity through a process of limited admixture. Identification of reference strains for these major groups should facilitate future studies on comparative genomics and identification of genes that control important biological phenotypes including pathogenesis and transmission.

International audience; The cliff-edge hypothesis introduces the counterintuitive idea that the trait value associated with the maximum of an asymmetrical fitness function is not necessarily the value that is selected for if the trait shows variability in its phenotypic expression. We develop a model of population dynamics to show that, in such a system, the evolutionary stable strategy depends on both the shape of the fitness function around its maximum and the amount of phenotypic variance. The model provides quantitative predictions of the expected trait value distribution and provides an alternative quantity that should be maximized ("genotype fitness") instead of the classical fitness function ("phenotype fitness"). We test the model's predictions on three examples: (1) litter size in guinea pigs, (2) sexual selection in damselflies, and (3) the geometry of the human lung. In all three cases, the model's predictions give a closer match to empirical data than traditional optimization theory models. Our model can be extended to most ecological situations, and the evolutionary conditions for its application are expected to be common in nature.

International audience; 1. The assessment of species extinction risk has been well established for some time now. Assessing the potential for recovery in endangered species is however much more challenging, because complementary approaches are required to detect reliable signals of positive trends. 2. This study combines genetics, demography and behavioural data at three different time-scales to assess historical and recent population changes and evidence of reproductive synchrony in a small population of olive ridley sea turtle Lepidochelys olivacea. Lepidochelys is considered as the most extraordinary example of reproductive synchrony in reptiles, yet to date, it has only been reported in large populations. 3. Using Bayesian coalescent-based models on microsatellite nuclear DNA variability, we demonstrate that effective population size in olive ridleys nesting in French Guiana has dramatically declined by 99% over the last 20 centuries. This low current population size is further illustrated by the absence of genetic mitochondrial DNA diversity in the present nesting population. Yet, monitoring of nesting sites in French Guiana suggests a possible recovery of the population over the last decade. 4. Satellite telemetry shows that over the first 14 days of their 28-days inter-nesting interval, i.e. when eggs maturation is likely to occur, gravid females disperse over the continental shelf. They then gather together with a striking spatiotemporal consistency close to the nesting site, where they later emerge for their second nesting event. 5. Our results therefore suggest that reproductive synchrony also occurs in small populations. Olive ridleys may ensure this synchrony by adjusting the duration of the second half of their internesting interval prior to landing, possibly through social mediation. 6. Such reproductive synchrony may be related to the maintenance of some species-specific strategy despite former collapse and may contribute to the present population recovery. The gregarious behaviour of reproductive individuals close to shore where human-induced perturbations occur is however a cause for conservation concern for this still poorly known species.

Background Rift Valley fever (RVF) is a vector-borne viral zoonosis of increasing global importance. RVF virus (RVFV) is transmitted either through exposure to infected animals or through bites from different species of infected mosquitoes, mainly of Aedes and Culex genera. These mosquitoes are very sensitive to environmental conditions, which may determine their presence, biology, and abundance. In East Africa, RVF outbreaks are known to be closely associated with heavy rainfall events, unlike in the semi-arid regions of West Africa where the drivers of RVF emergence remain poorly understood. The assumed importance of temporary ponds and rainfall temporal distribution therefore needs to be investigated. Methodology/Principal Findings A hydrological model is combined with a mosquito population model to predict the abundance of the two main mosquito species (Aedes vexans and Culex poicilipes) involved in RVFV transmission in Senegal. The study area is an agropastoral zone located in the Ferlo Valley, characterized by a dense network of temporary water ponds which constitute mosquito breeding sites. The hydrological model uses daily rainfall as input to simulate variations of pond surface areas. The mosquito population model is mechanistic, considers both aquatic and adult stages and is driven by pond dynamics. Once validated using hydrological and entomological field data, the model was used to simulate the abundance dynamics of the two mosquito species over a 43-year period (1961–2003). We analysed the predicted dynamics of mosquito populations with regards to the years of main outbreaks. The results showed that the main RVF outbreaks occurred during years with simultaneous high abundances of both species. Conclusion/Significance Our study provides for the first time a mechanistic insight on RVFV transmission in West Africa. It highlights the complementary roles of Aedes vexans and Culex poicilipes mosquitoes in virus transmission, and recommends the identification of rainfall patterns favourable for RVFV amplification., Author Summary Rift Valley fever (RVF) is a zoonotic disease that affects domestic livestock and humans. During inter-epizootic periods, the main infection mechanism is suspected to be through bites by infected mosquitoes, mainly of Aedes and Culex genera. In East Africa, RVF outbreaks are known to be closely associated with heavy rainfall events, unlike in the semi-arid regions of West Africa where the drivers of RVF emergence remain poorly understood. This study brings mechanistic insight to explain why reported RVF outbreaks in Northern Senegal cannot be correlated directly to rainfall. This is done through the use of a rainfall-driven model of RVF vector populations that combines a hydrological model to simulate daily water variations of mosquito breeding sites, with mosquito population models capable of reproducing the major trends in population dynamics of the two main vectors of RVF virus in Senegal, Ae. vexans and Cx. poicilipes. Results show that RVF occurs during years when both species are present simultaneously in high densities. Simulations of inter-annual variations in mosquito populations successfully explained the dates of RVF outbreaks observed between 1961 and 2003.

International audience; The cliff-edge hypothesis introduces the counterintuitive idea that the trait value associated with the maximum of an asymmetrical fitness function is not necessarily the value that is selected for if the trait shows variability in its phenotypic expression. We develop a model of population dynamics to show that, in such a system, the evolutionary stable strategy depends on both the shape of the fitness function around its maximum and the amount of phenotypic variance. The model provides quantitative predictions of the expected trait value distribution and provides an alternative quantity that should be maximized ("genotype fitness") instead of the classical fitness function ("phenotype fitness"). We test the model's predictions on three examples: (1) litter size in guinea pigs, (2) sexual selection in damselflies, and (3) the geometry of the human lung. In all three cases, the model's predictions give a closer match to empirical data than traditional optimization theory models. Our model can be extended to most ecological situations, and the evolutionary conditions for its application are expected to be common in nature.

International audience; Many zoonotic diseases are caused by rodent-borne viruses. Major fluctuations in the transmission of these viruses have been related to large changes in reservoir host population numbers due to external factors. However, the impact of the pathogen itself on the demography of its reservoir host is often overlooked. We investigated the impact of Puumala virus (PUUV) on survival and reproductive maturation probability of its reservoir host, the bank vole (Myodes glareolus). Three years (2004-06) of data from nine independent sites in southern Belgium were collected and analyzed with a capture-mark-recapture (CMR) method that includes statistical correction for the variation in capture probability of voles. A multistate model based on four states of reproductive activity and PUUV immunoglobulin G (IgG) antibody status was used to estimate survival and probability of transition from one reproductive or infection state to another. Although survival estimates for reproductively active voles were similar between infected and noninfected individuals, PUUV infection in reproductively inactive voles decreased mean monthly survival by 14%. PUUV infection was associated with a threefold increase in the probability of reproductive maturation in bank voles. Moreover, the probability of PUUV IgG seroconversion was three times higher for reproductively active voles compared to reproductively inactive voles. Our model indicates that PUUV infection may alter bank vole population dynamics by affecting both survival and maturation in its host. Additional studies, using CMR methodology with shorter time intervals between trapping sessions and possibly a longer duration, are needed to confirm these findings.

International audience; Complex phenotypes are often controlled by many interacting genes. One question emerging from such organization is how selection, acting at the phenotypic level, shapes the evolution of genes involved in regulatory networks controlling the phenotypes. We studied this issue through a matrix model of such networks. In a population submitted to selection, we simulated the evolution of a quantitative trait controlled by a set of loci that regulate each other through positive or negative interactions. Investigating several levels of selection intensity on the trait, we studied the evolution of regulation intensity between the genes and the evolution of the genetic diversity of those genes as an indirect measure of the strength of selection acting on them. We show that an increasing intensity of selection on the phenotype leads to an increased level of regulation between the loci. Moreover, we found that the genes responding more strongly to selection within the network were those evolving towards stronger regulatory action on the other genes and/or those that are the less regulated by the other genes. This observation is strongest for an intermediate level of selection. This may explain why several experimental studies have shown evidence of selection on regulatory genes inside gene networks.

International audience; The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.

International audience; 1. We assessed the relative influence of variability in recruitment age, dynamic reproductive investment (time-specific reproductive states) and frailty (unobserved differences in survival abilities across individuals) on survival in the black-legged kittiwake. Furthermore, we examined whether observed variability in survival trajectories was best explained by immediate reproductive investment, cumulative investment, or both. 2. Individuals that delayed recruitment (≥ age 7) suffered a higher mortality risk than early recruits (age 3), especially later in life, suggesting that recruitment age may be an indicator of individual quality. Although recruitment age helped explain variation in survival, time-varying reproductive investment had a more substantial influence. 3. The dichotomy of attempting to breed or not explained variability in survival across life better than other parameterizations of reproductive states such as clutch size, brood size or breeding success. In the kittiwake, the sinequanon condition to initiate reproduction is to hold a nest site, which is considered a very competitive activity. This might explain why attempting to breed is the key level of investment that affects survival, independent of the outcome (failure or success). 4. Interestingly, the more individuals cumulate reproductive attempts over life, the lower their mortality risk, indicating that breeding experience may be a good indicator of parental quality as well. In contrast, attempting to breed at time t increased the risk of mortality between t and t + 1. We thus detected an immediate trade-off between attempting to breed and survival in this population; however, the earlier individuals recruited, and the more breeding experience they accumulated, the smaller the cost. 5. Lastly, unobserved heterogeneity across individuals improved model fit more (1*3 times) than fixed and dynamic sources of observed heterogeneity in reproductive investment, demonstrating that it is critical to account for both sources of individual heterogeneity when studying survival trajectories. Only after simultaneously accounting for both sources of heterogeneity were we able to detect the 'cost' of immediate reproductive investment on survival and the 'benefit' of cumulative breeding attempts (experience), a proxy to individual quality.

International audience; Population subgroups of the African malaria vector Anopheles gambiae have not been comprehensively characterized owing to the lack of unbiased sampling methods. In the arid savanna zone of West Africa, where potential oviposition sites are scarce, widespread collection from larval pools in the peridomestic human habitat yielded a comprehensive genetic survey of local A. gambiae population subgroups, independent of adult resting behavior and ecological preference. A previously unknown subgroup of exophilic A. gambiae is sympatric with the known endophilic A. gambiae in this region. The exophilic subgroup is abundant, lacks differentiation into M and S molecular forms, and is highly susceptible to infection with wild Plasmodium falciparum. These findings might have implications for the epidemiology of malaria transmission and control.

International audience; In many socially monogamous animals, females engage in extrapair copulation (EPC), causing some broods to contain both within-pair and extrapair young (EPY). The proportion of all young that are EPY varies across populations and species. Because an EPC that does not result in EPY leaves no forensic trace, this variation in the proportion of EPY reflects both variation in the tendency to engage in EPC and variation in the extrapair fertilization (EPF) process across populations and species. We analyzed data on the distribution of EPY in broods of four passerines (blue tit, great tit, collared flycatcher, and pied flycatcher), with 18,564 genotyped nestlings from 2,346 broods in two to nine populations per species. Our Bayesian modeling approach estimated the underlying probability function of EPC (assumed to be a Poisson function) and conditional binomial EPF probability. We used an information theoretical approach to show that the expected distribution of EPC per female varies across populations but that EPF probabilities vary on the above-species level (tits vs. flycatchers). Hence, for these four passerines, our model suggests that the probability of an EPC mainly is determined by ecological (population-specific) conditions, whereas EPF probabilities reflect processes that are fixed above the species level.

P>Polyploidy promotes the restructuring of merged genomes within initial generations of resynthesized Brassica napus, possibly caused by homoeologous recombination at meiosis. However, little is known about the impact of the first confrontation of two genomes at the first meiosis which could lead to genome exchanges in progeny. Here, we assessed the role of the first meiosis in the genome instability of synthetic B. napus. We used three different newly resynthesized B. napus plants and established meiotic pairing frequencies for the A and C genomes. We genotyped the three corresponding progenies in a cross to a natural B. napus on the two homoeologous A1 and C1 chromosomes. Pairing at meiosis in a set of progenies with various rearrangements was scored. Here, we confirmed that the very first meiosis of resynthesized plants of B. napus acts as a genome blender, with many of the meiotic-driven genetic changes transmitted to the progenies, in proportions that depend significantly on the cytoplasm background inherited from the progenitors. We conclude that the first meiosis generates rearrangements on both genomes and promotes subsequent restructuring in further generations. Our study advances the knowledge on the timing of genetic changes and the mechanisms that may bias their transmission.

International audience; Many social animals live in stable groups, and it has been argued that kinship plays a major role in their group formation process. In this study we present the mathematical analysis of a recent model which uses kinship as a main factor to explain observed group patterns in a finite sample of individuals. We describe the average number of groups and the probability distribution of group sizes predicted by this model. Our method is based on the study of recursive equations underlying these quantities. We obtain asymptotic equivalents for probability distributions and moments as the sample size increases, and we exhibit power-law behaviours. Computer simulations are also utilized to measure the extent to which the asymptotic approximation can be applied with confidence.

Background With an Annual Parasite Incidence (API) of 132.1, in the high and moderate risks zones, the Maroni area of French Guiana has the second highest malaria incidence of South-America after Guyana (API = 183.54) and far above Brazil (API = 28.25). Malaria transmission is occurring despite strong medical assistance and active vector control, based on general WHO recommendations. This situation is generated by two main factors that are the social and cultural characteristics of this border area, where several ethnic groups are living, and the lack of understanding of transmission dynamics of the main mosquito vector, Anopheles darlingi. In this context, entomological data collected in two villages belonging to two different ethnic groups of the French border of the Maroni River, were retrospectively analysed to find out how the mosquito bionomics are related to the malaria transmission patterns. Methods Data were provided by human landing catches of mosquitoes carried out each month for two years in two villages belonging to two ethnic groups, the Amerindians Wayanas and the Aloukous of African origin. The mosquitoes were sorted by species, sex, date, hour and place of collection and processed for Plasmodium sp. parasite detection. The data were compiled to provide the following variables: human biting rates (HBR), parity rates (PR), numbers of infective bites (IB), entomological inoculation rates (EIR) and numbers of infected mosquitoes surviving enough to transmit (IMT). Spatial and temporal differences of variables between locations and during the night were tested by the Kruskall-Wallis analysis of variance to find out significant variations. Results The populations of the main mosquito vector An. darlingi showed significant variations in the spatial and temporal HBR/person/night and HBR/person/hour, IB/person/month and IB/person/hour, and IMT/village/night and IMT/village/hour. In the village of Loca (Aloukous), the IMT peaked from June to August with a very low transmission during the other months. The risks were higher during the first part of the night and an EIR of 10 infective bites per person and per year was estimated. In the village of Twenke (Wayanas), high level of transmission was reported all year with small peaks in March and October. The risk was higher during the second part of the night and an EIR of 5 infective bites per person and per year was estimated. Conclusion For the first time in the past 40 years, the mosquito bionomics was related to the malaria transmission patterns in French Guiana. The peak of malaria cases reported from August to October in the Maroni region is concomitant with the significant peak of An. darlingi IMT, reported from the village of Loca where transmission is higher. However, the persistent number of cases reported all year long may also be related to the transmission in the Amerindian villages. The An. darlingi bionomics for these two close populations were found significantly different and may explain why a uniform vector control method is inadequate. Following these findings, malaria prevention measures adapted to the local conditions are needed. Finally, the question of the presence of An. darlingi sub-species is raised.

International audience; Plague affects mainly the rural areas in the central highlands of Madagascar. Rattus rattus is the main rodent host of Yersinia pestis in these localities. Since the introduction of plague, endemic foci have continued to expand, and spatiotemporal variability in the distribution of human plague has been observed. To assess the movements of R. rattus and evaluate the risk of dispersion of the disease, a field study at the scale of the habitats (houses, hedges of sisals, and rice fields) in the plague villages was carried out during high and low seasons of plague transmission to humans. The systemic oral marker Rhodamine B was used to follow rats' movements. Baits were placed in different habitats, and trapping success was carried out once a month for 3 months after the bait distribution. Plague indicators (reservoirs' abundance, flea index, Y. pestis prevalence in fleas, and Y. pestis antibody prevalence in rats) were determined. The highest abundance of rats and marking efficiency were observed in the sisal hedges and the rice fields. Marked rats were captured most commonly near the points where baits were initially placed. The main movements of rats were observed between the houses and sisal hedges. Major differences were observed between the seasons of high and low plague transmission. During the season of low plague transmission, rats were more abundant in the sisal hedges and rice fields, with rats moving from the houses to the rice fields. During the high plague transmission season, rats moved from the hedges of sisal to the rice fields. Important indicators of vector abundance and plague transmission were higher during the high plague transmission season. The three study habitats were the risk areas for plague transmission, but the risk appeared highest in the houses and sisals. Rats' movements according to the season were likely directed by the availability of food.

International audience; Over the last 20 years, a number of epidemiological studies on Alzheimer's disease (AD) have been conducted on large cohorts providing databases for studying the disease frequency, and leading to a more global overview of AD risk factors. However, precise identification of factors which potentiate or delay the pathological process of the disease is still incomplete. One of the major problems comes from difficulties for defining the cases and obtaining good clinical diagnoses in population-based studies. Moreover, it is difficult to determine the chronology of exposure-disease relationships whatever the factors studied: vascular factors, life habits (dietary habits, physical, social or intellectual activities...). Which life-course period is important for proposing interventions to modify these factors remains a central question. The longer follow-up of large cohorts and a better knowledge of potential risk factors constitute a research priority if we want to prevent efficiently AD in the near future.

E-mail: jjrobledo@gmail.com; International audience; The estimation of recent gene immigration is fundamental to a wide range of evolutionary and conservation studies. In a risk assessment context, gene flow estimation procedures are needed that are both accurate and readily amenable to formal evaluation of statistical uncertainty. However, genetic methods for estimating recent migration rates that are specific and have been thoroughly evaluated are scarce. Here we use an original and straightforward maximum-likelihood method to estimate recent uniparental gametic immigration from non-local plantations into an endangered population of the Iberian relict pine variety Pinus sylvestris var. nevadensis D. H. Christ. Our approach is not intended to ascertain population membership of individuals, but rather to obtain accurate immigration rate estimates with reliable confidence limits. We found very high (approximately 40%) pollen introgression at the seed-crop level into the Scots pine relict, and substantial (10-15%) male gametic introgression among naturally regenerated recruits. Using numerical simulation, we show that our method yields uniparental gametic immigration estimates that are expected to be virtually unbiased and usually accurate under our sampling conditions. Among four tested methods to estimate the confidence intervals for immigration estimates, the profile-likelihood method was the best, as it outperformed bootstrapping procedures and yielded coverage close to nominal limits under different sample sizes and migration rates. This study presents a method by which researchers can facilitate decision making within a gene flow risk assessment context.

International audience; Mouse-baited traps were used to assess the longevity and dispersal of male and female Aedes albopictus by mark-release-recapture at two sites on La Réunion Island. Recapture rate was high, and mosquitoes of both sexes appeared up to 23 d after release. A daily survival probability of approximately 0.95 for males and females, far higher than expected, was estimated from these results. There was evidence that both sexes prefer to follow corridors of vegetation rather than crossing open spaces. Populations of wild mosquitoes had parous and insemination rates indicative of a young population. These results are relevant to future attempts to control this species by sterile insect technology.

The selection of suitable field sites for integrated control of Anopheles mosquitoes using the sterile insect technique (SIT) requires consideration of the full gamut of factors facing most proposed control strategies, but four criteria identify an ideal site: 1) a single malaria vector, 2) an unstructured, relatively low density target population, 3) isolation of the target population and 4) actual or potential malaria incidence. Such a site can exist in a diverse range of situations or can be created. Two contrasting SIT field sites are examined here: the desert-flanked Dongola Reach of the Nile River in Northern State, Sudan, where malaria is endemic, and the island of La Reunion, where autochthonous malaria is rare but risk is persistent. The single malaria-transmitting vector at both sites is Anopheles arabiensis. In Sudan, the target area is a narrow 500 km corridor stretching from the rocky terrain at the Fourth Cataract - just above the new Merowe Dam, to the northernmost edge of the species range, close to Egypt. Vector distribution and temporal changes in density depend on the Nile level, ambient temperature and human activities. On La Reunion, the An. arabiensis population is coastal, limited and divided into three areas by altitude and exposure to the trade winds on the east coast. Mosquito vectors for other diseases are an issue at both sites, but of primary importance on La Reunion due to the recent chikungunya epidemic. The similarities and differences between these two sites in terms of suitability are discussed in the context of area-wide integrated vector management incorporating the SIT.

Transmission and persistence of avian influenza viruses (AIV) among wildlife remains an unresolved issue because it depends both on the ecology of the host (e.g. population density, migration) and on the environment (e.g. AIV persistence in water). We have developed a mathematical model that accounts for both AIV epidemics and bird community dynamics. The model is parameterized using bird counts and AN prevalence data. Results suggest that the transmission patterns driving the dynamics of infection at our study site (Camargue, South of France) involved both a density-dependent and a water-borne transmission processes. Water-borne transmission is, however, the main determinant of the disease dynamics and observed prevalence level. This pattern of transmission highlights the importance of the persistence of viral particles in water in AN dynamics in wild birds. Crown Copyright (C) 2009 Published by Elsevier B.V.. All rights reserved.