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Jose Castresana - One of the best experts on this subject based on the ideXlab platform.

  • Quantitative analysis of connectivity in populations of a semi-Aquatic Mammal using kinship categories and network assortativity.
    Molecular ecology resources, 2019
    Co-Authors: Lídia Escoda, Angel Fernández-gonzález, Jose Castresana
    Abstract:

    Analysing the impact of anthropogenic and natural river barriers on the dispersal of Aquatic and semi-Aquatic species may be critical for their conservation. Knowledge of kinship relationships between individuals and reconstructions of pedigrees obtained using genomic data can be extremely useful, not only for studying the social organization of animals, but also inferring contemporary dispersal and quantifying the effect of specific barriers on current connectivity. In this study, we used kinship data to analyse connectivity patterns in a small semi-Aquatic Mammal, the Pyrenean desman (Galemys pyrenaicus), in an area comprising two river systems with close headwaters and dams of various heights and types. Using a large SNP dataset from 70 specimens, we obtained kinship categories and reconstructed pedigrees. To quantify the barrier effect of specific obstacles, we built kinship networks and devised a method based on the assortativity coefficient, which measures the proportion between observed and expected kinship relationships across a barrier. The estimation of this parameter enabled us to infer that the most important barrier in the area was the watershed divide between the rivers, followed by a dam on one of the rivers. Other barriers did not significantly reduce the expected number of kinship relationships across them. This strategy and the information obtained with it may be crucial in determining the most important connectivity problems in an area and help develop conservation plans aimed at improving genetic exchange between populations of threatened species.

  • Evolutionary history of the endemic water shrew Neomys anomalus: Recurrent phylogeographic patterns in semi-Aquatic Mammals of the Iberian Peninsula.
    Ecology and evolution, 2018
    Co-Authors: Marina Querejeta, Jose Castresana
    Abstract:

    The Cabrera's water shrew (Neomys anomalus) is a small semi-Aquatic Mammal whose taxonomic status was recently elevated from subspecies to species; as a consequence of this change, this species is now endemic to the Iberian Peninsula. In this study, we looked at its evolutionary history by combining phylogeography, the spatial distribution of genetic diversity, and species distribution modeling. To perform these analyses, we used noninvasive samples collected across the species distribution range and sequenced partial mitochondrial cytochrome b and D-loop genes. Maximum-likelihood and Bayesian phylogenetic trees derived from these sequences indicated that N. anomalus is divided into two main phylogroups that correlate strongly with geography, with two contact zones between the groups that showed limited spatial mixing between them. River basins were responsible for only a small percentage of the structure of the genetic diversity of this species despite its riparian habitat. The nucleotide diversity variation map showed the highest genetic diversity to be in the north of the Iberian Peninsula. Finally, species distribution modeling allowed the inference of an optimal area during the Last Interglacial in the north of the Iberian Peninsula, and multiple glacial refugia during the Last Glacial Maximum. The phylogeographic pattern of N. anomalus is strikingly similar to that of another semi-Aquatic Iberian Mammal, the Pyrenean desman (Galemys pyrenaicus), revealing how Pleistocene glaciations could have had equivalent effects on species of similar ecology and distribution. This phylogeographic structure is consistent with N. anomalus having been isolated for long periods in multiple glacial refugia within the Iberian Peninsula, in agreement with the "refugia-within-refugia" hypothesis, and further supporting its status as a distinct species.

  • A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-Aquatic Mammal
    PloS one, 2018
    Co-Authors: Oliver Hawlitschek, Angel Fernández-gonzález, Alfonso Balmori-de La Puente, Jose Castresana
    Abstract:

    Metabarcoding allows the genetic analysis of pooled samples of various sources. It is becoming popular in the study of animal diet, especially because it allows the analysis of the composition of feces without the need of handling animals. In this work, we studied the diet of the Pyrenean desman (Galemys pyrenaicus), a small semi-Aquatic Mammal endemic to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes from feces using next-generation sequencing techniques. For the identification of assembled sequences, we employed a tree-based identification method that used a reference tree of sequences of freshwater organisms. The comparison of freshly collected fecal samples and older samples showed that fresh samples produced significantly more sequencing reads. They also rendered more operational taxonomical units (OTUs), but not significantly. Our analyses of 41 samples identified 224 OTUs corresponding to species of the reference tree. Ephemeroptera, Diptera excl. Chironomidae, and Chironomidae were the most highly represented groups in terms of reads as well as samples. Other groups of freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida, Coleoptera, Crustacea, and Annelida. Our results are largely in line with previous morphological and genetic studies on the diet of the Pyrenean desman, but allowed the identification of a higher diversity of OTUs in each sample. Additionally, the bioinformatic pipeline we developed for deep sequencing of fecal samples will enable the quantitative analysis of the diet of this and other species, which can be highly useful to determine their ecological requirements.

  • phylogeography and postglacial expansion of the endangered semi Aquatic Mammal galemys pyrenaicus
    BMC Evolutionary Biology, 2013
    Co-Authors: Javier Igea, Pere Aymerich, Angel Fernandezgonzalez, Jorge Gonzalezesteban, Asuncion Gomez, Rocio Alonso, Joaquim Gosalbez, Jose Castresana
    Abstract:

    Background Species with strict ecological requirements may provide new insights into the forces that shaped the geographic variation of genetic diversity. The Pyrenean desman, Galemys pyrenaicus, is a small semi-Aquatic Mammal that inhabits clean streams of the northern half of the Iberian Peninsula and is endangered in most of its geographic range, but its genetic structure is currently unknown. While the stringent ecological demands derived from its Aquatic habitat might have caused a partition of the genetic diversity among river basins, Pleistocene glaciations would have generated a genetic pattern related to glacial refugia.

Laëtitia Buisson - One of the best experts on this subject based on the ideXlab platform.

  • Can Recent Global Changes Explain the Dramatic Range Contraction of an Endangered Semi-Aquatic Mammal Species in the French Pyrenees?
    PloS one, 2016
    Co-Authors: Anaïs Charbonnel, Marjorie Biffi, Pascal Laffaille, Frédéric Blanc, Anthony Maire, Mélanie Némoz, José-miguel Sanchez-pérez, Sabine Sauvage, Laëtitia Buisson
    Abstract:

    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.

  • Integrating hydrological features and genetically validated occurrence data in occupancy modeling of an endemic and endangered semi-Aquatic Mammal species, Galemys pyrenaicus, in a Pyrenean catchment
    Biological Conservation, 2015
    Co-Authors: Anaïs Charbonnel, Marjorie Biffi, Frédéric Blanc, Laëtitia Buisson, Frank D'amico, Aurélien Besnard, Stéphane Aulagnier, François Gillet, Vincent Lacaze, Johan R. Michaux
    Abstract:

    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.

  • Spatial replicates as an alternative to temporal replicates for occupancy modelling when surveys are based on linear features of the landscape
    Journal of Applied Ecology, 2014
    Co-Authors: Anaïs Charbonnel, Frédéric Blanc, Mélanie Némoz, Laëtitia Buisson, Frank D'amico, Aurélien Besnard, Pascal Laffaille
    Abstract:

    1- 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. 2- 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. 3 - We found that the estimated detection probabilities were relatively high (≥0·58) and similar when the same model was applied to each data configuration. 4 - 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. 5 - 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.

Anaïs Charbonnel - One of the best experts on this subject based on the ideXlab platform.

  • Can Recent Global Changes Explain the Dramatic Range Contraction of an Endangered Semi-Aquatic Mammal Species in the French Pyrenees?
    PloS one, 2016
    Co-Authors: Anaïs Charbonnel, Marjorie Biffi, Pascal Laffaille, Frédéric Blanc, Anthony Maire, Mélanie Némoz, José-miguel Sanchez-pérez, Sabine Sauvage, Laëtitia Buisson
    Abstract:

    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.

  • Integrating hydrological features and genetically validated occurrence data in occupancy modeling of an endemic and endangered semi-Aquatic Mammal species, Galemys pyrenaicus, in a Pyrenean catchment
    Biological Conservation, 2015
    Co-Authors: Anaïs Charbonnel, Marjorie Biffi, Frédéric Blanc, Laëtitia Buisson, Frank D'amico, Aurélien Besnard, Stéphane Aulagnier, François Gillet, Vincent Lacaze, Johan R. Michaux
    Abstract:

    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.

  • Spatial replicates as an alternative to temporal replicates for occupancy modelling when surveys are based on linear features of the landscape
    Journal of Applied Ecology, 2014
    Co-Authors: Anaïs Charbonnel, Frédéric Blanc, Mélanie Némoz, Laëtitia Buisson, Frank D'amico, Aurélien Besnard, Pascal Laffaille
    Abstract:

    1- 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. 2- 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. 3 - We found that the estimated detection probabilities were relatively high (≥0·58) and similar when the same model was applied to each data configuration. 4 - 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. 5 - 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.

Anna Loy - One of the best experts on this subject based on the ideXlab platform.

  • why camera traps fail to detect a semi Aquatic Mammal activation devices as possible cause
    Wildlife Society Bulletin, 2015
    Co-Authors: Laura Lerone, Giuseppe M. Carpaneto, Anna Loy
    Abstract:

    Camera-trapping represents a powerful tool in wildlife research, particularly when dealing with elusive and rare species such as otters (Lutra spp.). Nevertheless, detection problems arise when trying to detect otters with camera traps. We hypothesized that the temperature difference between the otter emerging from the water and the environment was too low to be detected by the standard passive infrared sensors (PIR). During June–September of 2010 and 2011 in the Sangro River basin in central Italy, we designed and tested a new pressure trigger and compared its effectiveness with that of the standard PIR. Results are encouraging and suggest that the new trigger could be able to detect otters and other semi-Aquatic Mammals. © 2015 The Wildlife Society.

  • Why camera traps fail to detect a semi‐Aquatic Mammal: Activation devices as possible cause
    Wildlife Society Bulletin, 2015
    Co-Authors: Laura Lerone, Giuseppe M. Carpaneto, Anna Loy
    Abstract:

    Camera-trapping represents a powerful tool in wildlife research, particularly when dealing with elusive and rare species such as otters (Lutra spp.). Nevertheless, detection problems arise when trying to detect otters with camera traps. We hypothesized that the temperature difference between the otter emerging from the water and the environment was too low to be detected by the standard passive infrared sensors (PIR). During June–September of 2010 and 2011 in the Sangro River basin in central Italy, we designed and tested a new pressure trigger and compared its effectiveness with that of the standard PIR. Results are encouraging and suggest that the new trigger could be able to detect otters and other semi-Aquatic Mammals. © 2015 The Wildlife Society.

Carmen Rosa Garcia Davila - One of the best experts on this subject based on the ideXlab platform.

  • Detection of infection with Leptospira spp. in manatees (Trichechus inunguis) of the Peruvian Amazon
    Latin American Journal of Aquatic Mammals, 2015
    Co-Authors: Patrick Mathews Delgado, Nofre Sanchez Perea, Claudia Biffi Garcia, Carmen Rosa Garcia Davila
    Abstract:

    The Amazonian manatee ( Trichechus inunguis ) is an Aquatic Mammal (Family Trichechidae) that inhabits freshwater environments. It is endemic to the Amazon Basin, and occurs from Marajo Island (at the mouth of the Amazon River in Brazil) to the headwaters of the floodplain in Colombia, Peru and Ecuador. Little is known of the causes of death or the prevalence of zoonotic organisms in manatees from Peru; however, Leptospira spp. have been reported to cause mortalities in marine Mammals. Here we evaluated the presence of Leptospira spp. antibodies in Amazonian manatees. To our knowledge, this is the first report of presence of antibodies against Leptospira spp. in Aquatic Mammals maintained in captivity in the Peruvian Amazon.

  • DETECTION OF INFECTION WITH Toxoplasma gondii IN MANATEES (Trichechus inunguis) OF THE PERUVIAN AMAZON Detección de infección por Toxoplasma gondii en manatíes (Trichechus inunguis) de la Amazonía peruana
    Universidad Nacional de Colombia, 2013
    Co-Authors: Patrick Mathews Delgado, Nofre Sanchez Perea, Claudia Biffi Garcia, Jonh Paul Mathews Delgado, Antonio Francisco Malheiros, Carmen Rosa Garcia Davila
    Abstract:

    The Amazonian manatee (Trichechus inunguis) is an Aquatic Mammal that inhabits freshwater environments and is endemic to the Amazon Basin. The presence of Toxoplasma gondii antibodies was investigated in 19 manatees in one rescue unit in the northern region of Peru. Antibodies to T. gondii were detected in 12 (63.2 %) of 19 animals by using the modified agglutination test (titer, 1:25), and no association between sex and age of the animals and the presence of T. gondii antibodies was observed (p < 0.05). The results suggest a contamination by T. gondii oocysts in the Aquatic environment where these animals live.El manatí amazónico (Trichechus inunguis) es un mamífero acuático que habita en ambientes de agua dulce y es endémico de la cuenca del Amazonas. La presencia de Toxoplasma gondii se investigó en 19 manatíes, en una unidad de rescate en la región norte del Perú. Los anticuerpos contra T. gondii fueron detectados en 12 (63,2 %), de 19 animales mediante el uso de la prueba de aglutinación modificada (título, 1:25). No fue observada asociación entre el sexo y edad de los animales con la presencia de anticuerpos de T. gondii (p < 0,05). Los resultados sugieren la contaminación por ooquistes de T. gondii en el medio acuático donde viven estos animales

  • DETECTION OF INFECTION WITH Toxoplasma gondii IN MANATEES (Trichechus inunguis) OF THE PERUVIAN AMAZON
    2013
    Co-Authors: Patrick Mathews Delgado, Nofre Sanchez Perea, Claudia Biffi Garcia, Jonh Paul Mathews Delgado, Antonio Francisco Malheiros, Carmen Rosa Garcia Davila
    Abstract:

    The Amazonian manatee ( Trichechus inunguis ) is an Aquatic Mammal that inhabits  freshwater environments and is endemic to the Amazon Basin. The presence of Toxoplasma  gondii antibodies was investigated in 19 manatees in one rescue unit in the northern region  of Peru. Antibodies to T. gondii  were detected in 12 (63.2 %) of 19 animals by using the  modified agglutination test (titer, 1:25), and no association between sex and age of the  animals and the presence of T. gondii  antibodies was observed (p suggest a contamination by T. gondii  oocysts in the Aquatic environment where these  animals live.

  • DETECTION OF INFECTION WITH Toxoplasma gondii IN MANATEES (Trichechus inunguis) OF THE PERUVIAN AMAZON
    Universidad Nacional de Colombia, 2013
    Co-Authors: Patrick Mathews Delgado, Nofre Sanchez Perea, Claudia Biffi Garcia, Jonh Paul Mathews Delgado, Antonio Francisco Malheiros, Carmen Rosa Garcia Davila
    Abstract:

    The Amazonian manatee (Trichechus inunguis) is an Aquatic Mammal that inhabits freshwater environments and is endemic to the Amazon Basin. The presence of Toxoplasma gondii antibodies was investigated in 19 manatees in one rescue unit in the northern region of Peru. Antibodies to T. gondii were detected in 12 (63.2 %) of 19 animals by using the modified agglutination test (titer, 1:25), and no association between sex and age of the animals and the presence of T. gondii antibodies was observed (p < 0.05). The results suggest a contamination by T. gondii oocysts in the Aquatic environment where these animals live