Data analysis
Because ants are colonial organisms and the presence of multiple individuals in a single trap likely represents individuals from a single colony, only the presence or absence of each ant species was quantified in each Winkler sack (frequency of occurrence ranging from zero to 10 in each patch). For each patch, we created a patch × species matrix (26 rows × 251 columns) filled with species occurrence frequencies in Winkler extractors. These data were used to estimate the occupancy and detection of individual species in each patch and the effect of predictor variables (patch and landscape area, connectivity, and cattle presence) on species detection and occupancy. Because true presence (occupancy) of individual species in patches determines community-level patterns (e.g. species richness), we indirectly estimated the effects of the covariates on local ant diversity (alpha), and on the composition of ant species (beta-diversity) through their effects on individual species occupancy. If all species were perfectly detected, this approach would provide the same results as regression models directly associating species diversity with predictor variables.
Occupancy models require a hierarchical structure for data sampling and organization. In our study, we estimated species occupancy at the patch level (higher level) and used replication within patches (Winkler extractions; lower level) to estimate detection probabilities. It is important to acknowledge that at the replication scale (within a patch), detection can be influenced by various factors, such as species rarity, aggregation patterns, and behaviour (Iknayan et al. , 2014). Therefore, differences in detectability among patches are not solely attributable to sampling limitations but also reflect biological processes.
Similar to other studies using occupancy models with temporal bird surveys (Guillera‐Arroita et al. 2018) or camera traps for mammals (Van der Weyde 2018), which do not incorporate covariates at the replication level, our model assumes that all Winkler extractions within a patch (but not among patches or species) have a similar probability of capturing a given species. This assumption is reasonable considering that leaf-litter ants have a limited foraging range (Hölldobler and Wilson 1990) and that the similarity between neighbouring extractions as close as 5 meters apart is extremely low (Fisher et al. 1990).