This week’s paper, Collins et al (2019), gave an interesting overview and comparison between various CO1, cytochrome b, 12S, and 16S primers. I may be slightly biased, knowing a bit more about 12S primers than CO1 primers, but I was relieved to see the performance of the MiFish primers. The paper brings up the important point of having an adequate reference database to compare sequence data to, and I was glad to hear that work is being done on that front. I will likely end up using the MiFish primers, so that is a good tidbit to keep in mind.
Erin brought up an interesting point about using a multiplex qPCR in place of metabarcoding when the community of interest is really only 10 or 12 species. Multiplexing is a fairly new concept to me, but this is really intriguing as I plan to do some metabarcoding. When I define my community of interest beyond just “GoM fish + seals,” it may end up being that this is a better route for some of my work. I’m curious what prep would need to go in for primer design, and other steps in order to multiplex, but it does seem like that could be more efficient than the library prep and analysis component of metabarcoding. Depending on how the index sites and alewife coastal sites are analyzed, I’d also be curious as to how the two methods compare.