Yukon River Chinook Genetic Baseline Improvements

A baseline is a tool used in genetic mixed stock analysis (MSA) to reference the genetic composition of many populations. In MSA, stock of origin is estimated by comparing the genetics of a sample to the known genetic compositions of a baseline to determine which population the sample is most likely to have originated from. The current baseline used for Yukon River Chinook salmon MSA was last updated in 2014 and contains the genetic composition of 36 populations at 41 genetic positions (single nucleotide polymorphisms, SNPs). While this baseline has proven successful at determining stock-compositions at the country of origin (U.S. vs Canada) level of resolution, it has proven difficult to report to more specific regions while still meeting required guidelines for reporting (JTC, 1997). Here, we propose methods to increase the number of populations in the Yukon River Chinook salmon baseline from 36 to 48 and the number of markers from 41 to 299 in order to provide more specific reporting groups to all Yukon River Chinook salmon projects utilizing MSA.