Lonsinger, R. C. 2022. Co-occurrence models fail to infer underlying patterns of avoidance and aggregation when closure is violated. Ecology and Evolution 7: e9104.
Advances in multi-species monitoring approaches have led to an increase in the use of multi-species occupancy analyses to assess patterns of co-occurrence among species, even when data were collected at spatial or temporal scales that likely violated the assumption that sites were closed to changes in occupancy state for the target species. Violating the closure assumption may lead to erroneous conclusions related to patterns of co-occurrence among species. Patterns of occurrence for two hypothetical species were simulated under patterns of avoidance, aggregation, or independence, when the closure assumption either was or was not met. Simulated populations were sampled at two levels (N = 250 or 100 sites) and two scales of temporal resolution for surveys. Sample data were analysed with conditional two-species occupancy models and performance was assessed by comparing the proportion of simulations recovering the true pattern of co-occurrence. Estimates of occupancy were unbiased when closure was met, but biased when closure violations occurred; bias increased when sample size was small and encounter histories were collapsed to a large-scale temporal resolution. When patterns of avoidance and aggregation were simulated, conditional two-species models tended to correctly find support for non-independence when closure was met and estimated species interaction factors aligned with predicted values. Models tended to incorrectly infer a pattern of independence when closure was violated and power to detect simulated patterns of avoidance or aggregation decreased with smaller sample size. Simulation results suggest that when the closure assumption is violated, occupancy-based models of co-occurrence often fail to detect underlying patterns of avoidance or aggregation and incorrectly identify a pattern of independence among species, which could have negative consequences for our understanding of species interactions and conservation efforts. When closure is not met, inferred patterns of independence from multi-species occupancy models should be interpreted cautiously. In contrast, when violations of the closure assumption likely occur, evidence of avoidance or aggregation is likely a conservative estimate of true pattern or interaction.