Comparing morphological and DNA-based bioassessment methodologies for macroinvertebrates in Neotropical streams: a case study from Ecuador

As unimpacted freshwater environments decline worldwide, developing effective and accurate biomonitoring approaches is critical for detecting ecosystem deterioration and facilitating conservation efforts. Freshwater macroinvertebrate communities comprise several phyla and thus a broad taxonomic expertise is required to identify these precisely. Molecular approaches for characterizing invertebrate communities have the potential to be more accurate, time-effective, and thus less costly than traditional morphological methods. However, evaluations comparing the two methods for macroinvertebrates are lacking in the Neotropics, where rapid deployment and increased accuracy are critical due to the escalating deterioration of freshwater environments. In this study, we compared the performance of DNA bulk tissue metabarcoding using an eDNA primer pair (fwhF2 & EPTDr2n) and morphological methodologies for identifying macroinvertebrate communities. Our aim was to evaluate the suitability of metabarcoding for assessing the biological quality of Ecuadorian streams along an altitudinal gradient. We found low taxonomic overlap between methods at family and genus ranks, though many molecular OTUs were unclassified at family and genus levels. Morphological identification resulted in higher Andean-Amazonian Biotic Index (AAMBI) scores for each site, with only three sites classified into the same biological category for both methodologies. One reason is that only family-level information is used for AAMBI. Existing DNA barcode reference libraries contained incomplete coverage of Ecuadorian taxa for specimens determined with the morphological approach, indicating a need to improve the representation of Ecuadorian taxa in these libraries to generate more accurate and complete metabarcoding determinations. Our study suggests that metabarcoding requires more development for freshwater biomonitoring in the Neotropics and should, at the moment, be used complementary to traditional identification approaches.