harnessing the power of regional baselines for broad-scale genetic stock identification: a multistage, integrated, and cost-effective approach

In mixed-stock fishery analyses, genetic stock identification (GSI) estimates the contribution of each population to a mixture and is typically conducted at a regional scale using genetic baselines specific to the stocks expected in that region. Often these regional baselines cannot be combined to produce broader geographical baselines due to non-overlapping populations and genetic markers. In cases where the mixture contains stocks spanning across a wide area, a broad-scale baseline is created, but often at the cost of resolution. Here, we introduce a new GSI method to harness the resolution capabilities of baselines developed for regional applications in the analysis of mixtures containing individuals from a broad geographic range. This method employs a multistage framework that allows disparate baselines to be used in a single integrated process that produces estimates along with the propagated errors from each stage. All individuals in the mixture sample are required to be genotyped..., We used existing genetic baseline to simulate synthetic mixture for this analysis. See article for details., , # Harnessing the power of regional baselines for broad-scale genetic stock identification: A multistage, integrated, and cost-effective approach

## Description of the data and file structure

* `mix_ayk_205.rda` is the mixture containing 205 individuals in the format of the Gene Conservation Lab. Columns 1 and 2 are identifications of each individual. \"SillySource\" column is the unique individual ID. \"SILLY_CODE\" is the location of the collection. SillySource and SILLY_CODE are known as \"indiv\" and \"collection\" in R package *rubias* format, respectively. Columns 3 and on identify the loci and their alleles for each individual. Missing genotypes are represented by \"NA.\"
* `base_ayk10.rda` is the broad-scale baseline, and it is in the same format as the mixture file.
* `base_yukon380_5grps.rda` is the regional baseline in the same format as the mixture and broad-scale baseline files.
* `ayk_pops60_5grps.rda` is a table containing information for the broad-scale populations. \"co...