Controlling for imperfect detection is important for developing species distribution models (SDMs... more Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy-detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time-to-detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time-to-first detection conditional on occupancy in relation to local factors, using modified interval-censored exponential survival models. Posterior distributions of occupancy probabilities derived from the models were used to produce species distribution maps. Simulations indicated that the modified time-to-detection model provided unbiased parameter estimates despite interval-censoring. There was a tendency for spatial variation in detection rates to be primarily influenced by depth and, to a lesser extent, stream width. Species occupancies were consistently affected by stream order, elevation, and annual precipitation. Bayesian P-values and AUCs indicated that all models had adequate fit and high discrimination ability, respectively. Mapping of predicted occupancy probabilities showed widespread distribution by most species, but uncertainty was generally higher in tributaries and upper reaches. The interval-censored time-to-detection model provides a practical solution to model occupancy-detection when detections are recorded in time intervals. This modeling framework is useful for developing SDMs while controlling for variation in detection rates, as it uses simple data that can be readily collected by field ecologists.
The study of areas of sympatry of species with predominantly parapatric distributions may provide... more The study of areas of sympatry of species with predominantly parapatric distributions may provide valuable insights about the factors shaping species occurrence. This information is key in biogeography, evolutionary biology and conservation planning. In this study we model the distributions of two pairs of partially co-occurring amphibian species in the Iberian Peninsula: tree frogs (Hyla molleri and H. meridionalis), with 11% of the occupied area shared by both species; and midwife toads (Alytes obstetricans and A. cisternasii), which co-occur in 4% of the total occupied area. We obtained distribution data from the herpetological atlases of Portugal and Spain, consisting of presences and absences on UTM 10x10-km grid cells. We built generalized linear models of presence / absence for each species and for the co-occurrence of each species pair, using 24 potential predictor variables representative of Iberian physiography, climate and human activity. Variables were selected for each model using information and significance criteria. The models were rated using calibration and discrimination measures and were compared using non-parametric correlation analysis after accounting for spatial autocorrelation. Preliminary results show a negative correlation between environmental favourability for A. obstetricans and A. cisternasii, indicating environmental segregation of the two species. Among the tree frogs, there was a strong positive correlation between favourability for H. meridionalis and for its overlap with H. molleri – i.e., sympatry occurs mainly in areas favourable for H. meridionalis. These results provide clues to understand the evolutionary history of these species, including the evolution of reproductive isolation, and suggest that conservation efforts for tree frogs may be focused on the areas that are favourable for both species, whereas midwife toads will require specific measures tailored for each species.
This study approaches the destruction of temporary ponds in an intensified agricultural landscape... more This study approaches the destruction of temporary ponds in an intensified agricultural landscape and the alternative breeding habitats for the amphibian community. We used several surveys to model the ponds survival since 1991 until 2009. Ponds inside the irrigation perimeter have a significant lower survival probability then those outside. Ponds, agricultural reservoirs, streams, irrigation channels and ditches were sampled for amphibian larvae in four different periods of a breeding season. We used a hierarchical dynamic occupation model that accounts for different detection probabilities to compare the occupation of aquatic habitats during the different periods. Ponds were the
habitat with higher specific richness per site followed by streams and reservoirs. Ditches and irrigation channels, usually, only supports one species per site. All habitats, except for ponds, have high incidence of exotic predators (fish and crayfish), that explains, in part, the low specific richness of these sites. There’s
no alternative habitat for the disappearing ponds. The conservation of the remaining ponds is essential for conserving the amphibian community. It should seriously be taken into consideration the construction of new clusters of ponds
inside of the irrigation perimeter.
In farmland landscapes, amphibians often breed in artificial water bodies, which may offset at le... more In farmland landscapes, amphibians often breed in artificial water bodies, which may offset at least partly the loss of natural wetlands associated with agricultural intensification. It is possible, however, that artificial habitats provide conditions for a minor proportion of the regional species pool, benefiting just a few widespread generalists. We assessed these alternative views by documenting the decline of temporary ponds in a Mediterranean farmland landscape between 1991 and 2009, and by estimating the occupancy of natural (temporary ponds and streams) and artificial water bodies (farm ponds, irrigation channels and drainage ditches) by amphibians across the breeding season (February–June 2010). We used hierarchical Bayesian dynamic multi-species occupancy modelling to control for differences in detectability across species, sampling occasions and habitat types. Over two decades the farmland landscape lost 56% of its temporary ponds, of which 89.3% were destroyed through agricultural activities such as cultivation, conversion to permanent farm ponds, and drainage. The survival rate of ponds was lowest within an irrigated perimeter, and there was no positive effect of protection by a natural park. Estimated species richness per site was at least twice as high in temporary ponds as in the other habitat types. From the 10 amphibian species recorded, seven had the highest occupancy in temporary ponds, and were absent or occurred rarely in artificial habitats. Only a single generalist species was widespread in farm ponds and irrigation channels. The results suggest that artificial water bodies are unlikely to sustain populations of most amphibian species in Mediterranean intensive farmland. Conservation efforts should be directed at protecting the temporary ponds still remaining within the farmed landscape, and at restoring or creating new temporary ponds where these have been lost during the last decades.
Controlling for imperfect detection is important for developing species distribution models (SDMs... more Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy-detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time-to-detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time-to-first detection conditional on occupancy in relation to local factors, using modified interval-censored exponential survival models. Posterior distributions of occupancy probabilities derived from the models were used to produce species distribution maps. Simulations indicated that the modified time-to-detection model provided unbiased parameter estimates despite interval-censoring. There was a tendency for spatial variation in detection rates to be primarily influenced by depth and, to a lesser extent, stream width. Species occupancies were consistently affected by stream order, elevation, and annual precipitation. Bayesian P-values and AUCs indicated that all models had adequate fit and high discrimination ability, respectively. Mapping of predicted occupancy probabilities showed widespread distribution by most species, but uncertainty was generally higher in tributaries and upper reaches. The interval-censored time-to-detection model provides a practical solution to model occupancy-detection when detections are recorded in time intervals. This modeling framework is useful for developing SDMs while controlling for variation in detection rates, as it uses simple data that can be readily collected by field ecologists.
The study of areas of sympatry of species with predominantly parapatric distributions may provide... more The study of areas of sympatry of species with predominantly parapatric distributions may provide valuable insights about the factors shaping species occurrence. This information is key in biogeography, evolutionary biology and conservation planning. In this study we model the distributions of two pairs of partially co-occurring amphibian species in the Iberian Peninsula: tree frogs (Hyla molleri and H. meridionalis), with 11% of the occupied area shared by both species; and midwife toads (Alytes obstetricans and A. cisternasii), which co-occur in 4% of the total occupied area. We obtained distribution data from the herpetological atlases of Portugal and Spain, consisting of presences and absences on UTM 10x10-km grid cells. We built generalized linear models of presence / absence for each species and for the co-occurrence of each species pair, using 24 potential predictor variables representative of Iberian physiography, climate and human activity. Variables were selected for each model using information and significance criteria. The models were rated using calibration and discrimination measures and were compared using non-parametric correlation analysis after accounting for spatial autocorrelation. Preliminary results show a negative correlation between environmental favourability for A. obstetricans and A. cisternasii, indicating environmental segregation of the two species. Among the tree frogs, there was a strong positive correlation between favourability for H. meridionalis and for its overlap with H. molleri – i.e., sympatry occurs mainly in areas favourable for H. meridionalis. These results provide clues to understand the evolutionary history of these species, including the evolution of reproductive isolation, and suggest that conservation efforts for tree frogs may be focused on the areas that are favourable for both species, whereas midwife toads will require specific measures tailored for each species.
This study approaches the destruction of temporary ponds in an intensified agricultural landscape... more This study approaches the destruction of temporary ponds in an intensified agricultural landscape and the alternative breeding habitats for the amphibian community. We used several surveys to model the ponds survival since 1991 until 2009. Ponds inside the irrigation perimeter have a significant lower survival probability then those outside. Ponds, agricultural reservoirs, streams, irrigation channels and ditches were sampled for amphibian larvae in four different periods of a breeding season. We used a hierarchical dynamic occupation model that accounts for different detection probabilities to compare the occupation of aquatic habitats during the different periods. Ponds were the
habitat with higher specific richness per site followed by streams and reservoirs. Ditches and irrigation channels, usually, only supports one species per site. All habitats, except for ponds, have high incidence of exotic predators (fish and crayfish), that explains, in part, the low specific richness of these sites. There’s
no alternative habitat for the disappearing ponds. The conservation of the remaining ponds is essential for conserving the amphibian community. It should seriously be taken into consideration the construction of new clusters of ponds
inside of the irrigation perimeter.
In farmland landscapes, amphibians often breed in artificial water bodies, which may offset at le... more In farmland landscapes, amphibians often breed in artificial water bodies, which may offset at least partly the loss of natural wetlands associated with agricultural intensification. It is possible, however, that artificial habitats provide conditions for a minor proportion of the regional species pool, benefiting just a few widespread generalists. We assessed these alternative views by documenting the decline of temporary ponds in a Mediterranean farmland landscape between 1991 and 2009, and by estimating the occupancy of natural (temporary ponds and streams) and artificial water bodies (farm ponds, irrigation channels and drainage ditches) by amphibians across the breeding season (February–June 2010). We used hierarchical Bayesian dynamic multi-species occupancy modelling to control for differences in detectability across species, sampling occasions and habitat types. Over two decades the farmland landscape lost 56% of its temporary ponds, of which 89.3% were destroyed through agricultural activities such as cultivation, conversion to permanent farm ponds, and drainage. The survival rate of ponds was lowest within an irrigated perimeter, and there was no positive effect of protection by a natural park. Estimated species richness per site was at least twice as high in temporary ponds as in the other habitat types. From the 10 amphibian species recorded, seven had the highest occupancy in temporary ponds, and were absent or occurred rarely in artificial habitats. Only a single generalist species was widespread in farm ponds and irrigation channels. The results suggest that artificial water bodies are unlikely to sustain populations of most amphibian species in Mediterranean intensive farmland. Conservation efforts should be directed at protecting the temporary ponds still remaining within the farmed landscape, and at restoring or creating new temporary ponds where these have been lost during the last decades.
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habitat with higher specific richness per site followed by streams and reservoirs. Ditches and irrigation channels, usually, only supports one species per site. All habitats, except for ponds, have high incidence of exotic predators (fish and crayfish), that explains, in part, the low specific richness of these sites. There’s
no alternative habitat for the disappearing ponds. The conservation of the remaining ponds is essential for conserving the amphibian community. It should seriously be taken into consideration the construction of new clusters of ponds
inside of the irrigation perimeter.
habitat with higher specific richness per site followed by streams and reservoirs. Ditches and irrigation channels, usually, only supports one species per site. All habitats, except for ponds, have high incidence of exotic predators (fish and crayfish), that explains, in part, the low specific richness of these sites. There’s
no alternative habitat for the disappearing ponds. The conservation of the remaining ponds is essential for conserving the amphibian community. It should seriously be taken into consideration the construction of new clusters of ponds
inside of the irrigation perimeter.