Optimal inventorying and monitoring of taxonomic, phylogenetic and functional diversity

Comparable data are essential to understand patterns of biodiversity. Inventorying communities and assemblages requires comprehensive sampling, whereas monitoring focuses on as few components as possible to detect change. Quantifying species, their evolutionary history, and their interactions requires studying changes in taxonomic (TD), phylogenetic (PD), and functional diversity (FD). Here, we propose a method to optimize sampling protocols for inventorying and monitoring communities and assemblages across these three diversity dimensions while considering sampling costs. We used an Iberian spider and an Amazonian bat as two case studies. The optimal combination of inventorying and monitoring methods required optimizing the accumulation curve of α-diversity and minimizing the difference (bias) between sampled and estimated β-diversity, respectively. For the Iberian spider, the optimal combination of TD, PD, and FD allowed sampling at least 50% of the estimated diversity in 24 person-hours of fieldwork. The optimal combination of 6 person-hours achieved less than 8% bias for all dimensions. For Amazonian bats, surveying all 12 sites with mist nets and 0 or 1 acoustic recorder was the optimal combination for almost all diversity types, achieving more than 89% of diversity and less than 10% bias while reducing costs by about one-third. Only for phylogenetic α-diversity, the best solution was not clear and required surveying with both mist nets and acoustic recorders. Widespread use and regular repetition of optimized and standardized sampling protocols would dramatically improve global inventory and monitoring of biodiversity. We strongly encourage global adoption of sampling protocols for both inventory and monitoring of taxonomic, phylogenetic and functional diversity.