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Charbonnel A.,Conservatoire dEspaces Naturels Midi Pyrenees | Charbonnel A.,CNRS Functional Ecology & Environment Laboratory | Buisson L.,CNRS Functional Ecology & Environment Laboratory | Biffi M.,CNRS Functional Ecology & Environment Laboratory | And 13 more authors.
Biological Conservation | Year: 2015

As freshwater habitats are among the most endangered, there is an urgent need to identify critical areas for conservation, especially those that are home to endangered species. The Pyrenean desman (. Galemys pyrenaicus) is a semi-aquatic mammal whose basic ecological requirements are largely unknown, hindering adequate conservation planning even though it is considered as a threatened species. Species distribution modelling is challenging for freshwater species. Indeed, the complexity of aquatic ecosystems (e.g., linear and hierarchical ordering) must be taken into account as well as imperfect sampling. High-quality and relevant hydrological descriptors should also be used. To understand the influence of environmental covariates on the occupancy and detection of the Pyrenean desman, we combine both a robust sign-survey data set (i.e. with genetic validation ensuring true presence information) and a hydrological model to simulate the flow regime across a whole catchment. Markovian site-occupancy analysis, taking into account sign detection and based on spatially adjacent replicates, indicated a positive influence of heterogeneity of substrate and shelters, and a negative influence of flow variability on Pyrenean desman detection. This valuable information should help to improve monitoring programs for this endangered species. Our results also highlighted a spatially clustered distribution and a positive influence of stream flow and number of tributaries on occupancy. Hence, modifications of flow regime (e.g. hydropower production, irrigation, climate change) and habitat fragmentation appear to be major threats for this species, altering the connectivity between tributaries and the mainstream river as well as between adjacent sub-catchments. © 2015 Elsevier Ltd.


Charbonnel A.,Conservatoire dEspaces Naturels Midi Pyrenees | Charbonnel A.,CNRS Functional Ecology & Environment Laboratory | D'Amico F.,University of Pau and Pays de l'Adour | Besnard A.,EPHE Paris | And 4 more authors.
Journal of Applied Ecology | Year: 2014

Occupancy estimates can inform biodiversity managers about the distribution of elusive species, such as the Pyrenean desman Galemys pyrenaicus, a small semi-aquatic mammal that lives along streams. Occupancy models rely on replication within a sampling site and provide estimates of the probability of detection. However, we still do not know how occupancy and detection estimates obtained from spatial vs. temporal replications differ or the appropriateness of using one or the other when cost and logistics make one approach prohibitive. Recently, the Markovian occupancy model has been developed to analyse adjacent spatial replicates and to test for spatial dependence between them. This model has already been applied to large and highly mobile mammals using trails, but never tested for any species with linear home ranges. We compared detection and occupancy estimates obtained from both temporal and spatial sampling designs that were subsequently organized into four data configurations (sites with both spatial and temporal replicates, adjacent spatial replicates only, temporal replicates only at the segment and site scales). From that, five occupancy models with different assumptions (the standard occupancy model, the standard multiscale model, the multiscale model with Markovian process for detection, the Markovian detection model and the Markovian occupancy model) were used. We also assessed which occupancy model was the most appropriate for each data configuration to determine whether it is necessary to incorporate correlation into models. We found that the estimated detection probabilities were relatively high (≥0·58) and similar when the same model was applied to each data configuration. Spatial replication weakly underestimated occupancy. But when using this design, the Markovian occupancy model was the most supported and minimized the underestimation of occupancy, highlighting a spatial dependence between adjacent replicates. Synthesis and applications. We show that a survey based on adjacent spatial replicates for a mammal living along linear features of the landscape is a good compromise between cost and occupancy estimates, while using the Markovian occupancy model to estimate detection and occupancy. Our finding may have wider applications for the monitoring of species especially when temporal replicates are difficult or unrealistic. Spatial design, for surveys based on sign detection, could thus be applied for species with linear home ranges or when surveys are constrained by linear habitats. We show that a survey based on adjacent spatial replicates for a mammal living along linear features of the landscape is a good compromise between cost and occupancy estimates, while using the Markovian occupancy model to estimate detection and occupancy. Our finding may have wider applications for the monitoring of species especially when temporal replicates are difficult or unrealistic. Spatial design, for surveys based on sign detection, could thus be applied for species with linear home ranges or when surveys are constrained by linear habitats. © 2014 British Ecological Society.


Charbonnel A.,Conservatoire dEspaces Naturels Midi Pyrenees | Charbonnel A.,CNRS Functional Ecology & Environment Laboratory | Laffaille P.,CNRS Functional Ecology & Environment Laboratory | Biffi M.,CNRS Functional Ecology & Environment Laboratory | And 7 more authors.
PLoS ONE | Year: 2016

Species distribution models (SDMs) are the main tool to predict global change impacts on species ranges. Climate change alone is frequently considered, but in freshwater ecosystems, hydrology is a key driver of the ecology of aquatic species. At large scale, hydrology is however rarely accounted for, owing to the lack of detailed stream flow data. In this study, we developed an integrated modelling approach to simulate stream flow using the hydrological Soil and Water Assessment Tool (SWAT). Simulated stream flow was subsequently included as an input variable in SDMs along with topographic, hydrographic, climatic and land-cover descriptors. SDMs were applied to two temporally-distinct surveys of the distribution of the endangered Pyrenean desman (Galemys pyrenaicus) in the French Pyrenees: A historical one conducted from 1985 to 1992 and a current one carried out between 2011 and 2013. The model calibrated on historical data was also forecasted onto the current period to assess its ability to describe the distributional change of the Pyrenean desman that has been modelled in the recent years. First, we found that hydrological and climatic variables were the ones influencing the most the distribution of this species for both periods, emphasizing the importance of taking into account hydrology when SDMs are applied to aquatic species. Secondly, our results highlighted a strong range contraction of the Pyrenean desman in the French Pyrenees over the last 25 years. Given that this range contraction was under-estimated when the historical model was forecasted onto current conditions, this finding suggests that other drivers may be interacting with climate, hydrology and land-use changes. Our results imply major concerns for the conservation of this endemic semi-aquatic mammal since changes in climate and hydrology are expected to become more intense in the future. © 2016 Charbonnel et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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