Complications of estimating hatchery introgression in the face of rapid divergence: A case study in brook trout (Salvelinus fontinalis)

Fish stocking has been utilized for over a century to offset extirpations or declines in abundance of many native species. These historical declines and hatchery contributions have led to uncertainty surrounding whether many contemporary populations are native, introgressed with hatchery sources, or entirely of hatchery origin. Such uncertainty is problematic for the conservation of native biodiversity as it hampers management agencies’ ability to prioritize the conservation of indigenous locally adapted populations. Fortunately, genetic and genomic tools have allowed researchers to investigate these questions, often through the use of clustering or assignment approaches that are predicated on identifiable and consistent divergence between native populations and hatchery sources. Here, we apply these methods to genomic data from 643 brook trout (Salvelinus fontinalis) originating from 13 wild populations and an exogenous hatchery strain to investigate the extent of historical extirpatio..., Sampling
Fin clips were collected from 13 wild brook trout populations in Wisconsin and the St. Croix Falls hatchery strain with a target sample size of 50 fish per population.  All wild samples were collected via backpack electrofishing from 2015-2019, St. Croix Falls hatchery strain samples were collected from broodstock maintained at the St. Croix Falls State Fish Hatchery in 2019, and all fin clips were preserved in 95% ethanol prior to DNA extraction.  Our primary objective for these collections was to examine putative fine scale population structure of seven populations originating from the Pine River watershed in the Driftless Area of Wisconsin.  However, given the diverse stocking sources used in the Wisconsin, we also included four additional populations (West Branch of Mill Creek, Lowery Creek, South Fork of the Hay River, and Lawrence Creek) that have historically or currently serve as wild brood or translocation sources.  In addition, we also sampled two additional populatio..., , # Complications of estimating hatchery introgression in the face of rapid divergence: A case study in brook trout (*Salvelinus fontinalis*)

[https://doi.org/10.5061/dryad.rbnzs7hk8](https://doi.org/10.5061/dryad.rbnzs7hk8)

These datasets contain sample and RAD sequence information for 672 brook trout samples from Wisconsin.

## Description of the data and file structure

### File Descriptions

*Erdman_PineRiver_Filtered_OriginalIDs.vcf* includes filtered genotypes for all loci and individuals passing filtering criteria (see methods for full parameter specifications.  This files uses original, unique sample identifiers than can be cross referenced with demographic and collection information in Erdman_PineRiver_DRYAD_SampleData.xlsx.

*Erdman_PineRiver_Filtered_RelabeledIDs.gen *includes filtered genotypes for all loci and individuals passing filtering criteria (see methods for full parameter specifications.  Note that these genotypes are the same as the VCF file listed above.  However,...