Spatial replicates as an alternative to temporal replicates for occupancy modelling when surveys are based on linear features of the landscape

Abstract

Summary1. 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 (≥0Á58) 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 *Correspondence author. E-mail: anais.charbonnel@espaces-naturels.fr Journal of Applied Ecology 2014Ecology , 51, 1425Ecology -1433Ecology doi: 10.1111Ecology /1365Ecology -2664 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.

Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods

“…Our sampling protocol meets the recommendations of Parry et al (2013) who found that repeating visits in a single site rather than enlarging the sampled area allowed better detection probabilities for the Eurasian otter. It is also in agreement with Charbonnel et al (2014) who obtained reasonable detection probabilities for G. pyrenaicus (0.58) in a survey of 100 m-long sections of rivers using temporal replicates. The search for faeces is a standard and effective protocol for detecting the presence of G. pyrenaicus (Charbonnel et al, 2014) and has also proven efficiency for N. fodiens (Aymerich and Gosálbez, 2004).…”

“…It is also in agreement with Charbonnel et al (2014) who obtained reasonable detection probabilities for G. pyrenaicus (0.58) in a survey of 100 m-long sections of rivers using temporal replicates. The search for faeces is a standard and effective protocol for detecting the presence of G. pyrenaicus (Charbonnel et al, 2014) and has also proven efficiency for N. fodiens (Aymerich and Gosálbez, 2004).…”

Substituting space for time: Empirical evaluation of spatial replication as a surrogate for temporal replication in occupancy modelling

“…To our knowledge, only two studies so far have directly compared estimates of occupancy and detection from temporal vs. spatial replicates using empirical data: Charbonnel et al. () with Pyrenean desmans Galemys pyrenaicus , and Whittington, Heuer, Hunt, Hebblewhite, and Lukacs () with a large mammal assemblage in Canada. While Charbonnel et al.…”

Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys

“…p  < 1) itself and covariates such as habitat and species abundance [36] cannot be controlled, other covariates, particularly temporal ones, can be. Our study showed these temporal covariates are important for determining detection probability and whether these are controlled before sampling via survey design or afterwards through modelling [37] is down to the objectives of the study [35] and the spatial pattern of species occurrence [7]. …”

“…With this in mind, it is likely that case-specific measures of detection probability need to be developed and applied [27], particularly where there is variation in breeding habitat but also where there are known differences in densities [36] or patterns of occurrence [7] or behaviour [39]. The use of a priori knowledge is essential for effective survey design [35], particularly for some species where sampling itself can violate the closure assumption through disturbance [40].…”