Mixed-stock analysis reveals long-distance movements and few populations with large harvest contributions in lake-migratory brook trout

Effective fishery management relies on knowing the relative contributions of distinct populations to mixed-stock harvests. Mixed-stock analyses increasingly adopt single-nucleotide polymorphism (SNP) panels but could make better use of precise spatial information to improve understanding of population distributions, movements, and structure. Together with local partners, we collected and georeferenced 1051 samples of lake-migratory brook trout between 2020-2022 from three large lakes in Quebec (Mistassini, Mistasiniishish, Waconichi). We then used a GT-seq (Genotyping-in-Thousands by sequencing) SNP panel to infer population genetic structure and determine spatial harvest contributions of genetically distinct populations. Our results revealed population structure in two of three study lakes, with few populations (n = 1-2) contributing the majority (> 80%) of mixed-stock harvest in each lake. We also detected extensive movements of brook trout within and between lakes, spatial segrega..., , , # Mixed-stock analysis reveals long-distance movements and few populations with large harvest contributions in lake-migratory brook trout

[https://doi.org/10.5061/dryad.wdbrv15z2](https://doi.org/10.5061/dryad.wdbrv15z2)

## Description of the data and file structure

This compressed folder contains all input data as well as scripts/code required to generate outputs from that data. The data is organized in folders, and each folder is named after its related analysis (e.g., the folder \"CPUE\" contains all data and code associated with catch-per-unit-effort analyses discussed in our research article \"Mixed-stock analysis reveals long-distance movements and few populations with large harvest contributions in lake-migratory brook trout\").

### Files and variables

#### Folder: CPUE

**Description:** Contains two sub-folders: mistassini_rivers_cpue & mixed-stock_fishery_cpue. Each folder contains an R file to run the respective analyses (e.g., R file \"annual_mixed_stock_fishery_cpue_analysis...,