Adapting genetic technology for marine conservation

Methods

Summary

We will be using methods described by Miya et al. 2015 to amplify fish eDNA using MiFish primers in PCR. MiFish primers have been used to characterize fish communities around the world, but have some limitations for groups that have experienced a recent evolutionary radiation like rockfish. Rockfish (species in the genus Sebastes) are a diverse and long-lived group of fish common in coastal California, and a popular target for recreational angling. MiFish will only be able to tell us if any rockfish are present, and does not generally have the power to identify individual species. In order to identify rockfish, we will use new methods described by Min et al. 2021 to target rockfish species. 

We conduct data analysis using Python and R programming languages. We use cutadapt and DADA2 to identify fish species from genetic sequence data obtained from eDNA. We use phyloseq and other R packages for data analysis and visualization. We will use the R package Shiny to build an interactive web portal that will allow anyone in the world to see our results overlaid on a map of our study sites.