Asymptomatic oral carriage of Candida species in HIV-infected patients in the highly active antiretroviral therapy era

Oropharyngeal candidiasis is the most common opportunistic fungal infection in individuals infected with human immunodeficiency virus. CD4+ lymphocytes count and the quantification of viral RNA in blood plasma have been found to be the main markers of HIV disease progression. The present study was conducted to evaluate Candida sp. diversity in the oral cavity of HIV-infected patients and to determine whether there was association of CD4+ cell count and viral load with asymptomatic oral Candida carriage. Out of 99 HIV-positive patients studied, 62 (62.6%) had positive culture for Candida (oral carriage) and 37 patients (37.4%) had Candida negative culture (no oral carriage). The etiologic agents most common were C. albicans and C. tropicalis. The range of CD4+ was 6-2305 cells/mm³ in colonized patients and 3-839 cells/mm³ for non-colonized patients, while the viral load was 60-90016 copies/mL for colonized patients and 75-110488 copies/mL for non colonized patients. The viral load was undetectable in 15 colonized patients and in 12 non colonized patients. Our results showed that there was no significant difference of the variables CD4+ cell count and viral load between oral candida carriage and no oral candida carriage patients.

Brazilian mosquito (Diptera: Culicidae) fauna: I. Anopheles species from Porto Velho, Rondônia state, western Amazon, Brazil

This study contributes to knowledge of Anopheles species, including vectors of Plasmodium from the western Brazilian Amazon in Porto Velho, Rondônia State. The sampling area has undergone substantial environmental changes as a consequence of agricultural and hydroelectric projects, which have caused intensive deforestation and favored habitats for some mosquito species. The purpose of this study was to diagnose the occurrence of anopheline species from collections in three locations along an electric-power transmission line. Each locality was sampled three times from 2010 to 2011. The principal adult mosquitoes captured in Shannon trap were Anopheles darlingi, An. triannulatus, An. nuneztovari l.s., An.gilesi and An. costai. In addition, larvae were collected in ground breeding sites for Anopheles braziliensis, An. triannulatus, An. darlingi, An. deaneorum, An. marajoara, An. peryassui, An. nuneztovari l.s. and An. oswaldoi-konderi. Anopheles darlingi was the most common mosquito in the region. We discuss Culicidae systematics, fauna distribution, and aspects of malaria in altered habitats of the western Amazon.

SEROLOGICAL SURVEY OF Ehrlichia SPECIES IN DOGS, HORSES AND HUMANS: ZOONOTIC SCENERY IN A RURAL SETTLEMENT FROM SOUTHERN BRAZIL

SUMMARY The aims of this study were to determine the seroprevalence of Ehrlichia spp. and risk factors for exposure in a restricted population of dogs, horses, and humans highly exposed to tick bites in a Brazilian rural settlement using a commercial ELISA rapid test and two indirect immunofluorescent assays (IFA) with E. canis and E. chaffeensis crude antigens. Serum samples from 132 dogs, 16 horses and 100 humans were used. Fifty-six out of 132 (42.4%) dogs were seropositive for E. canis. Dogs > one year were more likely to be seropositive for E. canis than dogs ≤ one year (p = 0.0051). Ten/16 (62.5%) and 8/16 (50%) horses were seropositive by the commercial ELISA and IFA, respectively. Five out of 100 (5%) humans were seropositive for E. canis and E. chaffeensis. Rhipicephalus sanguineus (n = 291, 97.98%) on dogs and Amblyomma cajennense (n = 25, 96.15%) on horses were the most common ticks found. In conclusion, anti-Ehrlichia spp. antibodies were found in horses; however, the lack of a molecular characterization precludes any conclusion regarding the agent involved. Additionally, the higher seroprevalence of E. canis in dogs and the evidence of anti-Ehrlichia spp. antibodies in humans suggest that human cases of ehrlichiosis in Brazil might be caused by E. canis, or other closely related species.

Molecular identification and antifungal susceptibility profiles of Candida parapsilosis complex species isolated from culture collection of clinical samples

AbstractINTRODUCTION:Candida parapsilosis is a common yeast species found in cases of onychomycosis and candidemia associated with infected intravascular devices. In this study, we differentiated Candida parapsilosis sensu stricto, Candida orthopsilosis , and Candida metapsilosis from a culture collection containing blood and subungual scraping samples. Furthermore, we assessed the in vitro antifungal susceptibility of these species to fluconazole, itraconazole, voriconazole, posaconazole, amphotericin B, and caspofungin.METHODS:Differentiation of C. parapsilosis complex species was performed by amplification of the secondary alcohol dehydrogenase (SADH) gene and digestion by the restriction enzyme Ban I. All isolates were evaluated for the determination of minimal inhibitory concentrations using Etest, a method for antifungal susceptibility testing.RESULTS:Among the 87 isolates, 78 (89.7%) were identified as C. parapsilosis sensu stricto , five (5.7%) were identified as C. orthopsilosis , and four (4.6%) were identified as C. metapsilosis . Analysis of antifungal susceptibility showed that C. parapsilosis sensu strictoisolates were less susceptible to amphotericin B and itraconazole. One C. parapsilosis sensu stricto isolate was resistant to amphotericin B and itraconazole. Moreover, 10.2% of C. parapsilosis sensu stricto isolates were resistant to caspofungin. Two C. parapsilosis sensu strictoisolates and one C. metapsilosis isolate were susceptible to fluconazole in a dose-dependent manner.CONCLUSIONS:We reported the first molecular identification of C. parapsilosiscomplex species in State of Goiás, Brazil. Additionally, we showed that although the three species exhibited differences in antifungal susceptibility profiles, the primary susceptibility of this species was to caspofungin.

Evidence for inter- and intra-species biofilm formation variability among a small group of coagulase-negative staphylococci

Coagulase-negative staphylococci (CoNS) are common bacterial colonisers of the human skin. They are often involved in nosocomial infections due to biofilm formation in indwelling medical devices. While biofilm formation has been extensively studied in Staphylococcus epidermidis, little is known regarding other CoNS species. Here, biofilms from six different CoNS species were characterised in terms of biofilm composition and architecture. Interestingly, the ability to form a thick biofilm was not associated with any particular species, and high variability on biofilm accumulation was found within the same species. Cell viability assays also revealed different proportions of live and dead cells within biofilms formed by different species, although this parameter was particularly similar at the intra-species level. On the other hand, biofilm disruption assays demonstrated important inter- and intra-species differences regarding extracellular matrix composition. Lastly, confocal laser scanning microscopy (CLSM) experiments confirmed this variability, highlighting important differences and common features of CoNS biofilms. We hypothesised that the biofilm formation heterogeneity observed was rather associated with biofilm matrix composition than with cells themselves. Additionally, our results indicate that polysaccharides, DNA and proteins are fundamental pieces in the process of CoNS biofilm formation.

Density, size and distribution of stomata in 35 rainforest tree species in Central Amazonia

Stomata are turgor-operated valves that control water loss and CO2 uptake during photosynthesis, and thereby water relation and plant biomass accumulation is closely related to stomatal functioning. The aims of this work were to document how stomata are distributed on the leaf surface and to determine if there is any significant variation in stomatal characteristics among Amazonian tree species, and finally to study the relationship between stomatal density (S D) and tree height. Thirty five trees (>17 m tall) of different species were selected. Stomatal type, density (S D), size (S S) and stomatal distribution on the leaf surface were determined using nail polish imprints taken from both leaf surfaces. Irrespective of tree species, stomata were located only on the abaxial surface (hypostomaty), with large variation in both S D and S S among species. S D ranged from 110 mm-2 in Neea altissima to 846 mm-2 in Qualea acuminata. However, in most species S D ranges between 271 and 543 mm-2, with a negative relationship between S D and S S. We also found a positive relationship between S D and tree height (r² = 0.14, p < 0.01), but no correlation was found between S D and leaf thickness. The most common stomatal type was anomocytic (37%), followed by paracytic (26%) and anisocytic (11%). We conclude that in Amazonian tree species, stomatal distribution on the leaf surface is a response most likely dependent on the genetic background of every species, rather than a reaction to environmental changes, and that somehow S D is influenced by environmental factors dependent on tree height.

Evaluation of fish pots as a feasible fishing method in Irish waters, with specific reference to the physiological effects of common and alternate pots on the lesser spotted dogfish (Scyliorhinus canicula).

Finfish pots have emerged as a “responsible” gear, when used in combination with conservational and technical measures to sustain fisheries. Previous trials in Irish waters have offered no published reported data and so three designs tested in the current study provide new information on this gear. The most successful traps in terms of fish catch were rigid steel framed rectangular pots used to target Conger eel. Although commercial yield was low (0.2 per trap haul), potential existed for a viable pot fishery. Deployment and storage of Norwegian floating pots was conducted with relative ease but performance in the water was poor resulting in loss of gear. Catch returns were notable even though effort was restricted as mega-faunal by-catch was a problem, which lead to ending this trial. From these initial trials it was evident that catch rates were low compared to established Norwegian fisheries (3.6 cod per pot), which resulted in the utilisation of pots, already established in the crustacean fishery, to find species readily accessible to pot capture. Although fished and designed differently, these gears provided an opportunity to establish the benefits of pot fishing to fish quality and to determine the effects on by-catch. The fishing effects of three catching methods (pots, angling and trawl) and the effects of air exposure on the physiological status of a common by-catch, the lesser spotted dogfish Scyliorhinus canícula (L.) were examined using a range of physiological biomarkers (plasma catecholamine, glucose, lactate, muscle pH and muscle lactate). Physiological responses of fish to an emersion stress regime resulted in a significant metabolic disturbance in groups, but may not have weakened the overall health of these fish, as signified in the revival of some metabolites. Plasma glucose and lactate concentrations did not however recovery to baseline levels indicating that to achieve an accurate profile, responses should be determined by a suite of biomarkers. Responses did not demonstrate that samples from the pots were significantly less stressed than for the other two methods; angling and trawling, which are in contrast to many other studies. Employment of finfish potting therefore in Irish waters needs further consideration before further promotion as a more responsible method to supplement or replace established techniques.

An assessment of biological and population parameters of the Common whelk, Buccinum undatum (L.) in the region of the North West Irish whelk fishery

The Common whelk, Buccinum undatum (L.) is a conspicuous benthic scavenger in Irish waters, and is a valuable fisheries resource in South East Ireland. B. undatum is fished in many parts of its range, and previous studies have shown that certain life history parameters, which vary with location, make this species vulnerable to overexploitation. This makes research into each exploited stock essential to ensure sustainable fisheries management of the species. In 2003, interest in B. undatum as a complementary species in the inshore fishery east of the Inishowen Peninsula, North West Ireland, initiated investigation into fisheries related biological and population aspects of the species in this region. The current study presents estimates of spatial variation and density of the stock, size at age and growth rates, size and age at onset of sexual maturity, and timing of reproductive events in the region of the North West Irish whelk fishery for the period of June 2003 to May 2004. Analysis of variance of the total shell length of whelk landings to the fishery was conducted over spatial scales of fishing pot, fishing string and landings to vessels. Landings varied significantly in shell length at the spatial scale at which whelks are attracted to baited pots, but did not vary significantly over larger spatial scales. Depletion estimates of stock density from fisheries derived Catch per Unit Effort data and a mark re-capture experiment estimate 0.134 - 0.227 whelks per m2. Two independent methods of age determination found similar growth logistics functions for B. undatum.Modal analysis of length frequency distribution of landings to the fishery estimated symptotic length, Leo = 151.64 mm and Brody growth coefficient, K = 0.04. Analysis of the striae in individual opercula, where each stria was found to represent annual growth, estimated Loo = 137.73 mm and K = 0.12. Common whelks in the region of the North West Irish whelk fishery grow slowly and are long-lived, with 19 opercula striae recorded in one individual. Onset of sexual maturity is late, and no sex-specific differences in size or age at maturity were determined in the present study. Males were found to achieve sexual maturity at 83.30 ± 10.77 mm, and 8.9 - 11.1 years of age, and females at 82.62 ± 10.68 mm and 8.8 to 11.1 years of age. Systematic observations of reproductive events, including histological changes to the female ovary and male testis, and changes in the size and mass of body components, suggest that breeding occurred between the autumn and winter months of October and December 2003. Biological aspects of B. undatum in the study region are compared with previous studies from other regions, and discussed in relation to sustainable management of the fishery.

New species of Lopesia (Diptera, Cecidomyiidae) associated with Eichhornia azurea (Pontederiaceae) from Brazil

A new species of gall midge, Lopesia eichhorniae sp. nov. (Cecidomyiidae, Diptera), associated with rhizomes of Eichhornia azurea (Sw.) Kunth (Pontederiaceae) is described. This is the first record of Lopesia galls in this species of macrophyte, quite common in natural and artificial lakes in Southeast Brazil. Illustrations of the adults (male and female), pupa, larva, and gall of the new species are presented.

Ecomorphology and diet reflect the spatial segregation between two Siluriformes species inhabiting a stream of the Bodoquena Plateau, in Central Brazil

Pimelodella taenioptera Miranda Ribeiro, 1914 and Imparfinis schubarti (Gomes, 1956) are two of the most common fish species in Bodoquena Plateau streams, Paraguay basin. These species have benthic habits and subaquatical observations suggested that they present differentiation in their preference for mesohabitat types. Pimelodella taenioptera shows preference for slow waters, such as pools, while I. schubarti is associated to riffles. In this study we investigated if the known patterns of mesohabitat use of P. taenioptera and I. schubarti can be predict by their ecomorphological and trophic traits. We described the dietary habits and ecomorphological attributes of P. taenioptera and I. schubarti individuals, captured in the Parque Nacional da Serra da Bodoquena (PNSB), Mato Grosso do Sul state, central Brazil. Pimelodella taenioptera presented a more generalist diet, consuming a total of 23 different food items. Imparfinis schubarti have a diet based exclusively on aquatic insects. The ecomorphological analysis revealed that the species differed in relation to five morphological traits associated to habitat use (p <0.01). The results of this study reveal a clear functional dissimilarity between P. taenioptera and I. shubarti. The observed trophic and ecomorphological patterns are congruent with the known habitat use for these species and probably reflect the spatial and temporal variability on conditions and resources present in riffles and pools. Therefore, as expected, the morphological and feeding attributes represent predictive information related to mesohabitat use.

The life history of Hepatozoon leptodactyli (Lesage, 1908) Pessoa, 1970: a parasite of the common laboratory animal: the frog of the genus Leptodactylus

The main object of the present paper is to furnish a brief account to the knowledgement of Protozoa parasitic in common Brazilian frog of the genus Leptodactylus for general students in Zoology and for investigators that use this frog as a laboratory animal. Hepatozoon leptodactyli (Haemogregarina leptodactyli) was found in two species of frogs - Leptodactylus ocellatus and L. pentadactylus - in which develop schizogony whereas sporogony occurs in the leech Haementeria lutzi as was obtainded in experimental conditions. Intracellular forms have been found in peripheral circulation, chiefly in erythrocytes, but we have found them in leukocytes too. Tissue stages were found in frog, liver, lungs, spleen, gut, brain and heart. The occurence of hemogregarine in the Central Nervous System was recorded by Costa & al,(13) and Ball (2). Some cytochemical methods were employed in attempt to differentiate gametocytes from trophozoites in the peripheral blood and to characterize the cystic membrane as well. The speorogonic cycle was developed in only one specie of leech. A brief description of the parasite is given.

Ecology of sandflies (Diptera: Psychodidae) in a restricted focus of cutaneous leishmaniasis in Northern Venezuela: II. Species composition in relation to habitat, catching method and hour of catching

The ecology of phlebotomine sandflies in an endemic focus of cutaneous leishmaniasis in Northern Venezuela (San Esteban, Carabobo State) was investigated through a year-term study. Three different habitats: viz. a house, a pridomestic area and a sylvatic area, were covered and the species composition, the abundance and occurrence of each species were analyzed in relation to the habitats, catching methods and hour of catching. L. panamensis, L. gomezi and L. ovallesi are the species which bite man, although almost exclusively at night. All of them hide by day and are common in the sylvatic area. Moreover, L. panamensis and L. gomezi successfully approach the house and seem to settle in the peridomestic area. L. shannoni and L. olmeca bicolor also approach and accidentally bite man. L. trinidadensis, L. atroclavata and L. cayennensis are the common non-antrhopophilic species in the area.

Response of bat species to sylvo-pastoral abandonment

We assessed the effect of abandonment of sylvo-pastoral practices in chestnut orchards (Castanea sativa) on bats in southern Switzerland to determine practical recommendations for bat conservation. We compared bat species richness and foraging activities between traditionally managed and unmanaged chestnut orchards, testing the hypothesis that managed orchards provide better foraging opportunities and harbour more bat species. Echolocation calls of foraging bats were sampled simultaneously at paired sites of managed and unmanaged orchards using custom made recorders. Vegetation structure and aerial insect availability were sampled at the recording sites and used as explanatory variables in the model. In a paired sampling design, we found twice the number of bat species (12) and five times higher total foraging activity in the managed chestnut orchards compared to the unmanaged ones. Bat species with low flight manoeuvrability were 14 times more common in managed orchards, whereas bats with medium to high manoeuvrability were only 5 times more common than in abandoned orchards. The vegetation structure was less dense in managed orchards. However, management did not affect relative insect abundance. Bats primarily visited the most open orchards, free of undergrowth. As a result of restricted access into the overgrown forests, the abandonment of chestnut orchards leads to a decline in bat species richness and foraging activities. Continued management of chestnut orchards to maintain an open structure is important for the conservation of endangered bat species in the southern Swiss Alps.

Characterization of a Trypanosoma cruzi genomic fragment complementary to several species-specific mRNAs but different from the spliced leader sequence

We have isolated a clone of Trypanosoma cruzi genimic DNA, lambda 3b2-5, which contains sequences that are reiterated in the genome. Northtern blot analysis showed that clone 3b2-5 hybridizes to 1,200-5,000 bases different mRNA species. The number of mRNAs species hybridized to clone 3b2-5 exceeds its coding capacity showing that this clone carries sequences that are common to several mRNAs species and conserved in the poly A(+) RNA. These sequences are not homologous to the T. cruzi spliced leader sequence, since clone 3b2-5 hybridize to a synthetic 20 nucleotice complementary to the spliced leader sequence. Clone 3b2-5 does not hybridize to DNA and RNA from several genera of Trypanosomatidae and other Trypanosoma species indicating that it carries T. cruzi species-specific sequences.

Species distribution models for conservation-oriented studies in Switzerland : filling data and tools gaps

SUMMARYSpecies distribution models (SDMs) represent nowadays an essential tool in the research fields of ecology and conservation biology. By combining observations of species occurrence or abundance with information on the environmental characteristic of the observation sites, they can provide information on the ecology of species, predict their distributions across the landscape or extrapolate them to other spatial or time frames. The advent of SDMs, supported by geographic information systems (GIS), new developments in statistical models and constantly increasing computational capacities, has revolutionized the way ecologists can comprehend species distributions in their environment. SDMs have brought the tool that allows describing species realized niches across a multivariate environmental space and predict their spatial distribution. Predictions, in the form of probabilistic maps showing the potential distribution of the species, are an irreplaceable mean to inform every single unit of a territory about its biodiversity potential. SDMs and the corresponding spatial predictions can be used to plan conservation actions for particular species, to design field surveys, to assess the risks related to the spread of invasive species, to select reserve locations and design reserve networks, and ultimately, to forecast distributional changes according to scenarios of climate and/or land use change.By assessing the effect of several factors on model performance and on the accuracy of spatial predictions, this thesis aims at improving techniques and data available for distribution modelling and at providing the best possible information to conservation managers to support their decisions and action plans for the conservation of biodiversity in Switzerland and beyond. Several monitoring programs have been put in place from the national to the global scale, and different sources of data now exist and start to be available to researchers who want to model species distribution. However, because of the lack of means, data are often not gathered at an appropriate resolution, are sampled only over limited areas, are not spatially explicit or do not provide a sound biological information. A typical example of this is data on 'habitat' (sensu biota). Even though this is essential information for an effective conservation planning, it often has to be approximated from land use, the closest available information. Moreover, data are often not sampled according to an established sampling design, which can lead to biased samples and consequently to spurious modelling results. Understanding the sources of variability linked to the different phases of the modelling process and their importance is crucial in order to evaluate the final distribution maps that are to be used for conservation purposes.The research presented in this thesis was essentially conducted within the framework of the Landspot Project, a project supported by the Swiss National Science Foundation. The main goal of the project was to assess the possible contribution of pre-modelled 'habitat' units to model the distribution of animal species, in particular butterfly species, across Switzerland. While pursuing this goal, different aspects of data quality, sampling design and modelling process were addressed and improved, and implications for conservation discussed. The main 'habitat' units considered in this thesis are grassland and forest communities of natural and anthropogenic origin as defined in the typology of habitats for Switzerland. These communities are mainly defined at the phytosociological level of the alliance. For the time being, no comprehensive map of such communities is available at the national scale and at fine resolution. As a first step, it was therefore necessary to create distribution models and maps for these communities across Switzerland and thus to gather and collect the necessary data. In order to reach this first objective, several new developments were necessary such as the definition of expert models, the classification of the Swiss territory in environmental domains, the design of an environmentally stratified sampling of the target vegetation units across Switzerland, the development of a database integrating a decision-support system assisting in the classification of the relevés, and the downscaling of the land use/cover data from 100 m to 25 m resolution.The main contributions of this thesis to the discipline of species distribution modelling (SDM) are assembled in four main scientific papers. In the first, published in Journal of Riogeography different issues related to the modelling process itself are investigated. First is assessed the effect of five different stepwise selection methods on model performance, stability and parsimony, using data of the forest inventory of State of Vaud. In the same paper are also assessed: the effect of weighting absences to ensure a prevalence of 0.5 prior to model calibration; the effect of limiting absences beyond the environmental envelope defined by presences; four different methods for incorporating spatial autocorrelation; and finally, the effect of integrating predictor interactions. Results allowed to specifically enhance the GRASP tool (Generalized Regression Analysis and Spatial Predictions) that now incorporates new selection methods and the possibility of dealing with interactions among predictors as well as spatial autocorrelation. The contribution of different sources of remotely sensed information to species distribution models was also assessed. The second paper (to be submitted) explores the combined effects of sample size and data post-stratification on the accuracy of models using data on grassland distribution across Switzerland collected within the framework of the Landspot project and supplemented with other important vegetation databases. For the stratification of the data, different spatial frameworks were compared. In particular, environmental stratification by Swiss Environmental Domains was compared to geographical stratification either by biogeographic regions or political states (cantons). The third paper (to be submitted) assesses the contribution of pre- modelled vegetation communities to the modelling of fauna. It is a two-steps approach that combines the disciplines of community ecology and spatial ecology and integrates their corresponding concepts of habitat. First are modelled vegetation communities per se and then these 'habitat' units are used in order to model animal species habitat. A case study is presented with grassland communities and butterfly species. Different ways of integrating vegetation information in the models of butterfly distribution were also evaluated. Finally, a glimpse to climate change is given in the fourth paper, recently published in Ecological Modelling. This paper proposes a conceptual framework for analysing range shifts, namely a catalogue of the possible patterns of change in the distribution of a species along elevational or other environmental gradients and an improved quantitative methodology to identify and objectively describe these patterns. The methodology was developed using data from the Swiss national common breeding bird survey and the article presents results concerning the observed shifts in the elevational distribution of breeding birds in Switzerland.The overall objective of this thesis is to improve species distribution models as potential inputs for different conservation tools (e.g. red lists, ecological networks, risk assessment of the spread of invasive species, vulnerability assessment in the context of climate change). While no conservation issues or tools are directly tested in this thesis, the importance of the proposed improvements made in species distribution modelling is discussed in the context of the selection of reserve networks.RESUMELes modèles de distribution d'espèces (SDMs) représentent aujourd'hui un outil essentiel dans les domaines de recherche de l'écologie et de la biologie de la conservation. En combinant les observations de la présence des espèces ou de leur abondance avec des informations sur les caractéristiques environnementales des sites d'observation, ces modèles peuvent fournir des informations sur l'écologie des espèces, prédire leur distribution à travers le paysage ou l'extrapoler dans l'espace et le temps. Le déploiement des SDMs, soutenu par les systèmes d'information géographique (SIG), les nouveaux développements dans les modèles statistiques, ainsi que la constante augmentation des capacités de calcul, a révolutionné la façon dont les écologistes peuvent comprendre la distribution des espèces dans leur environnement. Les SDMs ont apporté l'outil qui permet de décrire la niche réalisée des espèces dans un espace environnemental multivarié et prédire leur distribution spatiale. Les prédictions, sous forme de carte probabilistes montrant la distribution potentielle de l'espèce, sont un moyen irremplaçable d'informer chaque unité du territoire de sa biodiversité potentielle. Les SDMs et les prédictions spatiales correspondantes peuvent être utilisés pour planifier des mesures de conservation pour des espèces particulières, pour concevoir des plans d'échantillonnage, pour évaluer les risques liés à la propagation d'espèces envahissantes, pour choisir l'emplacement de réserves et les mettre en réseau, et finalement, pour prévoir les changements de répartition en fonction de scénarios de changement climatique et/ou d'utilisation du sol. En évaluant l'effet de plusieurs facteurs sur la performance des modèles et sur la précision des prédictions spatiales, cette thèse vise à améliorer les techniques et les données disponibles pour la modélisation de la distribution des espèces et à fournir la meilleure information possible aux gestionnaires pour appuyer leurs décisions et leurs plans d'action pour la conservation de la biodiversité en Suisse et au-delà. Plusieurs programmes de surveillance ont été mis en place de l'échelle nationale à l'échelle globale, et différentes sources de données sont désormais disponibles pour les chercheurs qui veulent modéliser la distribution des espèces. Toutefois, en raison du manque de moyens, les données sont souvent collectées à une résolution inappropriée, sont échantillonnées sur des zones limitées, ne sont pas spatialement explicites ou ne fournissent pas une information écologique suffisante. Un exemple typique est fourni par les données sur 'l'habitat' (sensu biota). Même s'il s'agit d'une information essentielle pour des mesures de conservation efficaces, elle est souvent approximée par l'utilisation du sol, l'information qui s'en approche le plus. En outre, les données ne sont souvent pas échantillonnées selon un plan d'échantillonnage établi, ce qui biaise les échantillons et par conséquent les résultats de la modélisation. Comprendre les sources de variabilité liées aux différentes phases du processus de modélisation s'avère crucial afin d'évaluer l'utilisation des cartes de distribution prédites à des fins de conservation.La recherche présentée dans cette thèse a été essentiellement menée dans le cadre du projet Landspot, un projet soutenu par le Fond National Suisse pour la Recherche. L'objectif principal de ce projet était d'évaluer la contribution d'unités 'd'habitat' pré-modélisées pour modéliser la répartition des espèces animales, notamment de papillons, à travers la Suisse. Tout en poursuivant cet objectif, différents aspects touchant à la qualité des données, au plan d'échantillonnage et au processus de modélisation sont abordés et améliorés, et leurs implications pour la conservation des espèces discutées. Les principaux 'habitats' considérés dans cette thèse sont des communautés de prairie et de forêt d'origine naturelle et anthropique telles que définies dans la typologie des habitats de Suisse. Ces communautés sont principalement définies au niveau phytosociologique de l'alliance. Pour l'instant aucune carte de la distribution de ces communautés n'est disponible à l'échelle nationale et à résolution fine. Dans un premier temps, il a donc été nécessaire de créer des modèles de distribution de ces communautés à travers la Suisse et par conséquent de recueillir les données nécessaires. Afin d'atteindre ce premier objectif, plusieurs nouveaux développements ont été nécessaires, tels que la définition de modèles experts, la classification du territoire suisse en domaines environnementaux, la conception d'un échantillonnage environnementalement stratifié des unités de végétation cibles dans toute la Suisse, la création d'une base de données intégrant un système d'aide à la décision pour la classification des relevés, et le « downscaling » des données de couverture du sol de 100 m à 25 m de résolution. Les principales contributions de cette thèse à la discipline de la modélisation de la distribution d'espèces (SDM) sont rassemblées dans quatre articles scientifiques. Dans le premier article, publié dans le Journal of Biogeography, différentes questions liées au processus de modélisation sont étudiées en utilisant les données de l'inventaire forestier de l'Etat de Vaud. Tout d'abord sont évalués les effets de cinq méthodes de sélection pas-à-pas sur la performance, la stabilité et la parcimonie des modèles. Dans le même article sont également évalués: l'effet de la pondération des absences afin d'assurer une prévalence de 0.5 lors de la calibration du modèle; l'effet de limiter les absences au-delà de l'enveloppe définie par les présences; quatre méthodes différentes pour l'intégration de l'autocorrélation spatiale; et enfin, l'effet de l'intégration d'interactions entre facteurs. Les résultats présentés dans cet article ont permis d'améliorer l'outil GRASP qui intègre désonnais de nouvelles méthodes de sélection et la possibilité de traiter les interactions entre variables explicatives, ainsi que l'autocorrélation spatiale. La contribution de différentes sources de données issues de la télédétection a également été évaluée. Le deuxième article (en voie de soumission) explore les effets combinés de la taille de l'échantillon et de la post-stratification sur le la précision des modèles. Les données utilisées ici sont celles concernant la répartition des prairies de Suisse recueillies dans le cadre du projet Landspot et complétées par d'autres sources. Pour la stratification des données, différents cadres spatiaux ont été comparés. En particulier, la stratification environnementale par les domaines environnementaux de Suisse a été comparée à la stratification géographique par les régions biogéographiques ou par les cantons. Le troisième article (en voie de soumission) évalue la contribution de communautés végétales pré-modélisées à la modélisation de la faune. C'est une approche en deux étapes qui combine les disciplines de l'écologie des communautés et de l'écologie spatiale en intégrant leurs concepts de 'habitat' respectifs. Les communautés végétales sont modélisées d'abord, puis ces unités de 'habitat' sont utilisées pour modéliser les espèces animales. Une étude de cas est présentée avec des communautés prairiales et des espèces de papillons. Différentes façons d'intégrer l'information sur la végétation dans les modèles de répartition des papillons sont évaluées. Enfin, un clin d'oeil aux changements climatiques dans le dernier article, publié dans Ecological Modelling. Cet article propose un cadre conceptuel pour l'analyse des changements dans la distribution des espèces qui comprend notamment un catalogue des différentes formes possibles de changement le long d'un gradient d'élévation ou autre gradient environnemental, et une méthode quantitative améliorée pour identifier et décrire ces déplacements. Cette méthodologie a été développée en utilisant des données issues du monitoring des oiseaux nicheurs répandus et l'article présente les résultats concernant les déplacements observés dans la distribution altitudinale des oiseaux nicheurs en Suisse.L'objectif général de cette thèse est d'améliorer les modèles de distribution des espèces en tant que source d'information possible pour les différents outils de conservation (par exemple, listes rouges, réseaux écologiques, évaluation des risques de propagation d'espèces envahissantes, évaluation de la vulnérabilité des espèces dans le contexte de changement climatique). Bien que ces questions de conservation ne soient pas directement testées dans cette thèse, l'importance des améliorations proposées pour la modélisation de la distribution des espèces est discutée à la fin de ce travail dans le contexte de la sélection de réseaux de réserves.