fundamentals of eDNA

I was initially surprised by the low degree of overlap between fish species found by eDNA metabarcoding and species found by traditional fish sampling in the Collins et al. (2019) study. This really emphasizes that even primers specifically designed for one taxon will not necessarily work as envisioned. It also highlights the need for more extensive reference sequence libraries, as many of these mismatches were due to a lack of reference sequences. In my searches for terrestrial vertebrate (mammal and bird) reference sequences, I did notice that several birds had no available sequence data for the MiFish primer my group is using. I’m now realizing that some of these species do have sequence data available, but only for the COI locus and not the 12S locus. This also highlights the importance of choosing metabarcoding vs. PCR early on in a study: depending on the reference data available, metabarcoding may amplify too many anonymous operational taxonomic units (OTUs).