eDITH: an R-package to spatially project eDNA-based biodiversity across river networks with minimal prior information

Abstract

Ecological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups and the assessment of ecological indices. Yet, most current approaches are not exploiting the full potential of eDNA data, largely interpreting results in a localized perspective. In riverine networks, by explicitly modelling hydrological transport and associated DNA decay, hydrology-based models enable upscaling eDNA-based diversity information, providing spatially integrated inference. To capitalize from these unprecedented biodiversity data and translate into space-filling biodiversity projections, a streamlined implementation is needed.Here, we introduce theeDITHR-package, implementing the eDITH model to project biodiversity across riverine networks with minimal prior information. eDITH couples a species distribution model relating a local taxon’s eDNA shedding rate in streamwater to environmental covariates, a mass balance expressing the eDNA concentration at a river’s cross-section as a weighted sum of upstream contributions, and an observational model accounting for uncertainties in eDNA measurements. By leveraging on spatially replicated eDNA measurements and minimal hydromorphological data, eDITH enables disentangling the various upstream eDNA sources, and produces space-filling maps of a taxon’s spatial distribution at any chosen resolution. eDITH is applicable to both eDNA concentration and metabarcoding data, and to any taxon whose DNA can be retrieved in streamwater.TheeDITHpackage provides user-friendly functions for single-run execution and fitting of eDITH to eDNA data with both Bayesian methods (via theBayesianToolspackage) and non-linear optimization. An interface to theDHARMapackage allows model validation via posterior predictive checks. Necessary preliminary steps such as watershed delineation and hydrological characterization are implemented via therivnetpackage. We illustrateeDITH’s workflow and functionalities with two case studies from published fish eDNA data.TheeDITHpackage provides a user-friendly implementation of eDITH, specifically intended for ecologists and conservation biologists. It can be used without previous modelling knowledge but also allows customization for experienced users. Ultimately, eDITH allows upscaling eDNA biodiversity data for any river globally, transforming how state and change of biodiversity in riverine systems can be tracked at high resolution in a highly versatile manner.