Experimental design and protocols for conducting pilot studies to assess the implementation of genomic methods into fisheries research surveys

A report to describe the protocols used by the FishGenome Consortium to: i) collect biological and environmental samples – Sampling Protocols ii) isolate DNA from biological and environmental samples – DNA isolation Protocols iii) perform the laboratory work required for the application of each technique iv) analyse bioinformatically the sequences derived from the laboratory procedures for the purpose of assessing fish and fish communities using Close Kin Mark Recapture (CKMR), environmental DNA (eDNA) and epigenetic age determination (DNAm). Sampling protocols detailed in this document have been designed tailoring the specific needs of the MEDITS and IBTS research surveys to allow implementation without disturbing the standard procedures carried out on board during the regular Fisheries research surveys. Application to other surveys may require small adjustments of the sampling protocols.