STANDARD OPERATING PROCEDURES FOR PARENTAGE-BASED TAGGING FOR LAKE ONTARIO CHINOOK SALMON USING MICROSATELLITE DATA

Sampling and analysis protocols developed during the Lake Ontario Chinook Salmon parentage-based tagging pilot study (Fitzpatrick et al. 2023, Fisheries Management and Ecology). The protocols are divided into three stages: 1) the collection of tissue samples from fish relevant to implementing and assessing a parentage-based tagging program 2) the laboratory protocols for extracting and amplifying DNA from tissue samples and preparing the samples for sequencing and 3) filtering the sequencing products, generating genotypes, and performing the parentage analyses. The appendices inlcude example collection protocols, some of the datasets generated during the analyses, and associated R code.Suggested citation: Fitzpatrick KB, Sethi SA (2023) Standard operating procedures for parentage-based tagging for Lake Ontario Chinook Salmon using microsatellite data. Technical Report submitted to the NY State Department of Environmental Conservation. Cornell University, Ithaca, NY. DOI: 10.5281/zenodo.816610