Archived DNA reveals marine heatwave-associated shifts in fish assemblages

We conducted DNA metabarcoding on DNA isolated by filtering the ethanol in which paired port-side CalCOFI bongo net tow samples were preserved, thereby maintaining the integrity of the historical larvae and egg samples. Up to 125 mL of ethanol preservative was pipetted off archived samples and vacuum filtered onto 0.2 micron PVDF filters.DNA was extracted from filters using a modified Qiagen DNeasy Blood and Tissue kit (Curd et al., 2019) and amplified using the MiFish Universal Teleost (Miya et al., 2015) PCR primer set targeting the 12S rRNA mitochondrial gene region. eDNA from each extraction was amplified in triplicate with each technical PCR replicate sequenced separately to capture stochastic variation within the amplification process. This resulted in a final data set of 84 collection lots across four stations spanning 23 years that were morphologically identified as well as 90 unique DNA extractions and 244 unique PCR technical replicates that were sequenced. See Methods section in manuscript for full details.