Biomonitoring 2.0 Refined: observing local change through metaphylogeography using a community-based eDNA metabarcoding monitoring network.

Background: Biological data at different levels of organization is essential to support actions to mitigate the current biodiversity crisis. DNA metabarcoding is an established method to detect species/genus level taxa from bulk samples leading the way for a Biomonitoring 2.0 framework. Biomonitoring 2.0 Refined adds another dimension to Biomonitoring 2.0-high-throughput, scalable DNA metabarcoding with a higher resolution at the intraspecific level. Intraspecific diversity is key to understanding the distribution and movement of local populations for conservation efforts. Gaining reliable intraspecific information from metabarcoding data, however, is challenging due to qualitative/quantitative issues that can impact validity of the inference.

Results: Samples collected for the STREAM community-based monitoring project were used to perform an intraspecific genetic variation analysis on benthic arthropods. We targeted two non-overlapping cytochrome c oxidase subunit 1 mitochondrial DNA amplicons to assess the reproducibility of our results. Samples from the Rocky Mountains were grouped into four regions separated by mountain ranges. Significant separation (PERMANOVA, p value < 0.05) of Sørensen dissimilarity between regions was observed for community and intraspecific levels, fitting the expectation that mountains are barriers to dispersal. Two of the regions showed significant spatial structuring (Mantel test, p value < 0.05) at the intraspecific level, while all regions showed significant structuring at the community level. Results were consistent across both amplicons.

Conclusions: We show that DNA metabarcoding is applicable to intraspecific diversity analysis and it is robust to different amplicons. This paves the way for Biomonitoring 2.0 Refined, which can provide much needed fine-scale biodiversity data for ecological assessments and conservation.