Taxonomic resolution and treatment effects – alone and combined – can mask significant biodiversity reductions

Taxonomic resolution or uncertainty poses an important problem in biodiversity research. Assessment of biodiversity at the species level is most informative and preferred, but requires effort and expertise. Alternatively, researchers often bin species into higher taxa because they are unable to recognize them, or to save money and time. Here we analyse, by simulation and analytical modelling, the combined effects of dose-dependent mortality and taxonomic binning on biodiversity indices for a fictitious community of organisms. We asked (1) how binning species in a sample into higher taxa significantly affects biodiversity measures, and (2) whether dose-dependent mortality effects, alone or in combination with taxonomic uncertainty, are duly captured by classic biodiversity indices. Our study shows that haphazard binning into various taxonomic levels is legitimate and preferable to orderly binning (all taxa binned at the same level), because it provides the best resolution. We further show that binning will regularly obscure statistical detection of biodiversity differences, if only due to scaling of mean and variance. Also, treatment effects in combination with taxonomic uncertainty can introduce estimation biases of at times complex nonlinear and non-intuitive nature under any taxonomic resolution scenario, potentially including relative increases in the biodiversity index when intuitively decreases would be expected. We recommend being specific about the expected qualitative and quantitative effects of any treatment or natural comparison before formulating a hypothesis regarding biodiversity reductions. Our theoretical study should aid in this endeavour