Connectivity loss in human dominated landscape: operational tools for the identification of suitable habitat patches and corridors on amphibian's population

International audienceLandscape connectivity is a key issue for biodiversity conservation. Many species have to refrain to move between scattered resources patches. This is particularly the case for the common frog, a widespread amphibian migrating between forest and aquatic habitats for breeding. Face to the growing need for maintaining connectivity between amphibians' habitat patches, the aim of this study is to provide a method based on habitat suitability modelling and graph theory to explore and analyze ecological networks. We first used the maximum entropy modelling with environmental variables based on forest patches distribution to predict habitat patches distribution. Then, with considerations about landscape permeability, we applied graph theory in order to highlight the main habitat patches influencing habitat availability and connectivity by the use of the software's Conefor Sensinode 2.2 and Guidos. The use of the JRC Forest/Non Forest European map for the characterisation of common frog terrestrial habitat distribution combined with the maximum entropy modelling gives promising results for the identification of habitat discontinuities within a regional perspective. This approach should provide an operational tool for the identification of the effects of landscape barriers and corridors on populations structure. Then, the method appears as a promising tool for landscape planning

Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

<p>Abstract</p> <p>Background</p> <p>The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, <it>i.e</it>. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (<it>Cichorium intybus </it>L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae.</p> <p>Findings</p> <p>Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from <it>Hin</it>dIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and <it>S</it>₂<it>S</it>₂for the <it>S</it>-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and <it>S</it>₁<it>S</it>₄. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers.</p> <p>Conclusions</p> <p>This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the <it>S</it>-locus in this Asteraceae species.</p

Connectivity and landscape patterns in human dominated landscape: a case study with the common frog Rana temporaria

International audienceLandscape connectivity is considered a key issue for biodiversity conservation and for the maintenance of natural ecosystems stability and integrity. Landscape connectivity defines the degree to which the landscape facilitates or impedes movement among resource patches. A wide range of methodological approaches can be involved in such studies. Spatial distribution analyses are common tools but can hardly integrate connectivity. We do here suggestions to apply graph theory and least cost path approaches in a specific application related to common frog habitats connectivity. Amphibian's life cycle involve seasonal migrations between terrestrial and aquatic habitats which constrain them to regularly cross an inhospitable fragmented landscape matrix. Thus, there is a growing need for maintaining and restoring landscape connectivity between their habitat patches. This is especially the case for the common frog Rana temporaria, a widespread amphibian in Europe occurring in various habitat types and migrating between forest and aquatic habitats for breeding. The aim of preliminary study is to explore a method based on habitat suitability modeling and graph theory in order to analyze an ecological network. In order to assess in which manner habitat patches distribution can affect landscape connectivity between ponds, we use both configuration and distributions of suitable forest patches as model inputs. The link between common frog occurrence and forest patches configuration and distribution is defined with a probabilistic model from sampled data and relevant indices. Especially, elevation, land use distribution, distances to forest patches, distance to rivers, and landscape indices computed from forest patches distribution were shown being the main significant environmental variables influencing habitat patches distribution. In our application, we obtained then a suitable habitat patches distribution map by the use of ponds occupancy location data and maximum entropy modelling. Then, we applied least cost path modelling and graph theory approach in order to highlight the connected ponds and their importance for regional connectivity. These results emphasize the potential of maximum entropy modelling, and graph theory approach for integrating connectivity in landscape planning. The quantification of landscape matrix permeability in relation with the common frog dispersion patterns appears as limited in order to quantify edge between nodes for the design of a graph integrating ponds as nodes for a regional perspective. Nevertheless, this method combined with the use of genetic markers may be useful to assess main barriers and corridors for the common frog from a regional to a local perspective for planning. In this context, the use of genetic distances could be considered as a good surrogate to the use of least cost path as edges in a graph theoretical approach for studying connectivity

Effets des patrons d'organisation spatiale du paysage sur l'habitat d'une espèce animale à gestion conservatoire : le cas de l'habitat de reproduction du tétras-lyre (Tetrao tetrix L.) dans un contexte d'expansion des aulnaies vertes (Alnus alnobetula (Ehrh.) C. Koch)

In the Northern French Alps, black grouse (Tetrao tetrix L.) is threatened by landscape closing induced by the colonization of ligneous species on abandoned pastures. Among these species, green alder (Alnus alnobetula (Ehrh.) C. Koch) is a major concern for the conservation of black grouse reproduction habitat. Thus, it is necessary to get a better understanding of the effects of green alder spatial organization on black grouse occurrence in order to control these colonization at the local scale of action plans in favour of the reproduction habitat. This phD firstly focuses on bringing out that black grouse occurrence can be predicted by the means of spatialised indicators in relation to landscape structure induced by green alder. Indeed, presenceabsence data from a systematic sampling were combined with a landscape analysis of green alder spatial organisation. This allowed to assess the effect of some landscape indices on black grouse probability of presence by using logistic regression. Our main results showed that females are influenced by green alder whereas it is not the case for the males. Especially, green alder cover, green alder patches density and green alder total edge are significant predictors of females occurrence. Then, these three predictors were used for designing spatially explicit models describing the spatial occupation of black grouse females in relation to a green alder distribution map. Once the models prediction were validated, the more efficient and validated model appeared to be using green alder total edge and cover. More over, this model were combined to a green alder dynamic of colonization model by the use of a stochastic cellular automaton. By this way, we managed to simulate the evolution in time and space of female occurrence in relation to the evolution of landscape patterns induced by green alder. The demonstrated link between landscape patterns and black grouse females spatial occupation at a fine scale argues that the use of landscape pattern index in a spatially explicit model should allow to develop a tool for assessing action plans in favour of black grouse habitat conservation based on landscape ecology approach.Dans les Alpes du Nord françaises, les populations de tétras-lyre sont menacées par la fermeture du paysage induite par la colonisation d'espèces ligneuses sur les pâturages abandonnés. Parmi ces espèces, l'aulne vert est considérée comme une menace majeure pour la conservation de l'habitat de reproduction du galliforme. Dans ce contexte, il est nécessaire de mieux connaître les effets de l'organisation spatiale de l'aulne vert sur l'occurrence du tétras-lyre afin de mieux maîtriser cette dynamique d'embuissonnement à l'échelle d'une gestion locale de cet habitat de reproduction. Ainsi, cette thèse s'est attachée dans un premier temps à mettre en évidence que l'occurrence du galliforme peut être prédite à l'aide d'indicateurs spatialisés relatifs à la structure du paysage induite par la distribution de l'aulne vert sur une étendue occupée au sein de son habitat de reproduction. En effet, des données de présence-absence du galliforme issues d'un échantillonnage systématique ont été combinées à une analyse de l'organisation spatiale de l'aulne vert. Ceci a permis d'évaluer l'effet de certains indices paysagers sur la probabilité de présence du galliforme à l'aide de modèles de régression logistique. Nos résultats ont principalement montré que les poules de tétras-lyre sont sensibles à l'organisation spatiale de l'aulne vert alors que ce n'est pas le cas pour les coqs. Plus précisément, le taux de recouvrement de l'aulne vert, le nombre de patchs d'aulne vert et la somme des longueurs de lisières d'aulne vert sont apparus comme étant des prédicteurs significatifs de l'occurrence des poules.Ces trois prédicteurs ont ensuite été utilisés pour construire des modèles spatialement explicites décrivant l'occupation de l'espace par les poules en fonction d'une carte de distribution de l'aulne vert. Après validation des prédictions des modèles, le modèle le plus pertinent et le plus valide pour prédire l'occurrence des poules est celui utilisant la somme des longueurs de lisières associée au taux de recouvrement de l'aulne vert. D'autre part, ce modèle a été combiné à un modèle de simulation de l'expansion de l'aulne vert dans le temps et l'espace à l'aide d'un modèle à automate cellulaire stochastique. Ainsi, nous avons pu simuler l'évolution de la distribution de l'occurrence des poules en fonction de l'évolution des patrons d'organisation du paysage induite par l'expansion de l'aulne vert.La mise en évidence d'un lien entre des patrons paysagers et l'occupation de l'espace par les poules à une échelle fine suggère qu'intégrer des indices paysagers spatialisés dans un modèle spatial et temporel devrait permettre de développer un outil d'aide à la gestion locale de l'habitat du galliforme reposant sur une approche d'écologie du paysage

Mechanism of RNA cleavage catalyzed by sequence specific polyamide nucleic acid-neamine conjugate.

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