DOI: 10.5061/dryad.w9ghx3ftq
title: Sources of coaster brook trout (Salvelinus fontinalis) revealed by genomic analysis of brook trout populations along Minnesota’s shoreline with Lake Superior

description: 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 NE 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.
description: We used a restriction site-associated DNA (RAD) capture panel to
 survey genome-wide SNPs in wild-caught brook trout
 (<em>Salvelinus</em> <em>fontinalis</em>) 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. 
description: 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: sample_metadata.wild.csv -
 metadata for wild-caught brook trout listed in Table 1 of the accompanying
 publication. sample_metadata.hatchery.csv - metadata
 for hatchery-sourced brook trout listed in Table 2 of the accompanying
 publication. id_highest_maf_snp.R - R script for
 identifying the SNP with the highest minor allele frequency on each
 RADtag. README.txt - a README file containing the
 information listed here.