Knowledge of population-level relationships and how these relationships pertain to different life history forms is critical to developing effective management plans for native trout, char, and salmon. In the Lake Superior basin, identifying effective restoration strategies for coaster brook trout (Salvelinus fontinalis), a lake-inhabiting form of brook trout, is hampered by limited information on genetic connectivity and source-sink dynamics among brook trout populations. Here, we infer these relationships by surveying 8,178 single nucleotide polymorphisms in 234 brook trout from seven rivers along the Minnesota shoreline with Lake Superior, including from reaches above and below natural waterfalls that prevent upstream movement. We identified well-differentiated above-barrier populations that supply brook trout to below-barrier reaches. We also compared within-river brook trout to 26 coaster brook trout from Lake Superior. We identified at least four source populations for these coaster brook trout, three of which were located within rivers. Additionally, we estimated N_E for within-river populations and detected a decline across recent generations, with the most recent estimates approaching critical thresholds. Finally, comparisons with 94 domestic brook trout representing nine hatchery strains revealed a lack of domestic introgression into wild populations, demonstrating the importance of natural reproduction to population persistence. Our results offer novel insights into sources of coaster brook trout and highlight the role of within-river populations in supporting the coaster life history. Management efforts focused on instream restoration may be more important to rehabilitating coaster brook trout than previously thought, and are urgently needed given the population-level conservation status reported here.

We used a restriction site-associated DNA (RAD) capture panel to survey genome-wide SNPs in wild-caught brook trout (Salvelinus fontinalis) from seven rivers along the Minnesota shoreline with Lake Superior. We also analyzed a collection of brook trout from Lake Superior, and domestic brook trout representing nine hatchery strains. RADseq libraries were prepared following the methods of Ali et al. (2016 Genetics) and then used as a template in a RAD capture reaction prior to PE150 sequencing on an Illumina HiSeq X. 

Here we provide metadata for the 260 wild-caught brook trout and 94 hatchery-sourced brook trout that comprised the quality filtered dataset analyzed in this study. Raw sequence data for these brook trout are available via the NCBI Sequence Read Archive (BioProject PRJNA895104). We also provide a custom R script that can be used to create a list of SNPs to retain in a VCF file. The list of SNPs corresponds with a single SNP per RADtag, where the SNP exhibiting the largest minor allele frequency is retained.

The data files provided here are as follows:

1. sample_metadata.wild.csv - metadata for wild-caught brook trout listed in Table 1 of the accompanying publication.
2. sample_metadata.hatchery.csv - metadata for hatchery-sourced brook trout listed in Table 2 of the accompanying publication.
3. id_highest_maf_snp.R - R script for identifying the SNP with the highest minor allele frequency on each RADtag.
4. README.txt - a README file containing the information listed here.