Human impacts on Great Lakes walleye Sander vitreus structure, diversity, and local adaptation

Artificial propagation and wild release may influence the genetic integrity of wild populations. This practice has been prevalent in fisheries for centuries and is often termed “stocking”. In the Laurentian Great Lakes (Great Lakes here-on), walleye populations faced declines from the 1950s to the 1970s, prompting extensive stocking efforts for restoration. By the mid-2010s, walleye populations showed signs of recovery, but the genetic legacy of stocking on population structure at the genomic level remains unclear. Using a dataset of 45,600 genome-aligned SNP loci genotyped in 1,075 walleye individuals, we investigated the genetic impacts of over 50 years of stocking across the Great Lakes. Population structure was associated with both natural geographic barriers and stocking from non-native sources. Admixture between Lake Erie walleye and walleye from the re-populated Tittabawassee River indicate that stocking may have re-distributed putatively adaptive alleles around the Great Lakes. ..., Sampling design and DNA extraction
Major walleye spawning populations throughout the Great Lakes were identified through expert knowledge and discussion with state and provincial agency biologists. Many of the selected populations had been sampled for previous studies that have shown local genetic structure (e.g., Wilson et al., 2007; Stepien et al., 2009). Hatchery stocking took place at or near almost all our identified spawning sites at least once in the past with the exception of Lake Erie spawning sites (Table S1). Walleye continue to be stocked in many locations around the Great Lakes today with hundreds-of-thousands of yearling-equivalent walleye stocked annually (USFWS/GLFC, 2023). From the list of identified spawning populations, 29 were selected as target sample locations based on the availability of DNA or tissue archives, historical importance to fisheries, and geographic distribution (Figure 1). Two populations outside of the Great Lakes Lake Gogebic, Michigan and Oneida La..., , # Human impacts on Great Lakes walleye Sander vitreus structure, diversity, and local adaptation

[https://doi.org/10.5061/dryad.zkh1893k9](https://doi.org/10.5061/dryad.zkh1893k9)

## Description of the data and file structure

These data were collected as part of a population genetic assessment of Walleye (*Sander vitreus*) in the Great Lakes. All sequence data was collected using BestRAD sequencing and PSTI restriction site enzyme digest. Sequence data was processed using STACKS2 and a reference aligned pipeline. Detailed methods can be found in the open access publication Euclide et al., 2024: [https://doi.org/10.1111/mec.17558. ](https://doi.org/10.1111/mec.17558)

### Files and variables

#### File: Filt1.mac4.R10.mm20.minDP10.ind90.mm80.ind20.maf05.ind20.HDPlot.recode.vcf.gz

**Description:** This file contains all of the genotype information used in the final analysis.

Genotyped SNP variants were filtered to retain high-quality loci using VCFTOOLs v.0.1.16 (Danecek et al., 2011...,