Conservation assessment based on large-scale monitoring of eDNA: Application to freshwater mussels

Abstract

Environmental DNA (eDNA) analysis allows efficient surveys of freshwater species and is being increasingly used. However, because different authors use different methods, eDNA data cannot easily be summarised for a global overview. One promising approach is to standardise methods for long-term monitoring. Standardised eDNA metabarcoding methods have been implemented in France for an elusive group: freshwater bivalves. All French bivalve species can be detected and identified at each sampling site. Here, we analyse this comprehensive dataset (280 sites across all France; 40 species) to investigate detection probabilities, infer species distributions and reassess conservation status, and finally examine community patterns (richness) and their determinants.Our method gave over 95 % probability of detection for most species. Species distributions inferred from eDNA sampling were compared with currently known distributions. Four invasive species and one species of conservation concern were found outside their known range. Others were found in a surprisingly small number of localities, although they are currently thought to be widespread and not of conservation concern. Indeed, the databases currently used to determine conservation status are biased by the inclusion of old data, mainly based on shell records only, and may include misidentified species. The main drivers of species richness were latitude and distance from the spring. Co-occurrence of species was investigated for the first time. The results highlight the valuable data that eDNA analysis can provide when used on a large scale, for monitoring and ecological studies, as well as providing improved species distributions, which are essential for conservation policymaking.