Data from: The extent of hybridization between bull trout (Salvelinus confluentus) and brook trout (S. fontinalis) across Alberta’s Eastern slopes
Data files
Jul 03, 2025 version files 16.11 MB
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AB_hybridization_2025_BKT.map
1.80 MB
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AB_hybridization_2025_BKT.ped
7.23 MB
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AB_hybridization_2025_nonBLT.map
1.41 MB
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AB_hybridization_2025_nonBLT.ped
5.67 MB
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README.md
2.39 KB
Abstract
Identifying hybridization provides insight into risks associated with non-native species. Bull trout (Salvelinus confluentus), a charr native to Alberta, face population declines across their range and one risk may include hybridization with non-native brook trout (S. fontinalis). However, the extent of introgressive hybridization throughout Alberta is not well understood. Therefore, we aimed to quantify bull x brook trout hybridization in three ways: 1. the observed hybrid presence across Alberta, 2. the proportion of post-F1 hybrids (e.g., F2 and backcrossed), and 3. the hybrid proportion relative to brook trout in well-sampled watersheds. Using two panels of >1,000 diagnostic Single Nucleotide Polymorphisms, we identified 35 F1 and 7 post-F1 hybrids (n = 42 total) across 10 HUC 8 watersheds. Our findings show hybridization throughout the bull trout range, however, with few post-F1 hybrids found, little evidence of extensive hybrid introgression was observed. The misidentification rate was low (2.1%), but 20 of 25 misidentifications involved confirmed hybrids, suggesting a higher misidentification rate (47.6%). This work improves the understanding of hybridization risks on at-risk bull trout in Alberta.
https://doi.org/10.5061/dryad.gtht76hx8
Description of the data and file structure
All Salvelinus spp. fin clips were collected by Alberta Environment and Protected Areas (AEPA) staff between 1999 - 2022 using either electrofishing, angling, or trap netting as described in the manuscript. Samples spanned 24 Hydrologic Unit Code (HUC) 8 Watersheds in Alberta. The datasets contain Single Nucleotide Polymorphisms (SNPs) in ordinary PLINK format for analysis of ancestry estimates using ADMIXTURE 1.3 software (Alexander et al. 2009).
Files and variables
File: AB_hybridization_2025_nonBLT.map
Description: Ordinary PLINK format file containing genetic map information on 1174 Diagnostic nonBLT (non-bull trout) loci.
File: AB_hybridization_2025_BKT.map
Description: Ordinary PLINK format file containing genetic map information on 1499 Diagnostic BKT (brook trout) loci.
File: AB_hybridization_2025_nonBLT.ped
Description: Ordinary PLINK format file containing HUC8 watershed (column 1), sample name (column 2), Father/Mother/Sex/Species (columns 3,4,5,6), and genotypes for 1174 nonBLT (non-bull trout) diagnostic loci (columns 7+, where columns 7 and 8 code the two alleles for diploid locus 1, and so on).
File: AB_hybridization_2025_BKT.ped
Description: Ordinary PLINK format file containing HUC 8 watershed (column 1), sample name (column 2), Father/Mother/Sex/Species (columns 3,4,5,6), and genotypes for 1499 BKT (brook trout) diagnostic loci (columns 7+, where columns 7 and 8 code the two alleles for diploid locus 1, and so on).
Code/software
Recommended Software for Data Analysis:
- ADMIXURE 1.3 Software (ADMIXTURE manual: https://dalexander.github.io/admixture/admixture-manual.pdf).
- PLINK 1.9 command-line program (for the conversion of .ped/.map to .bed file format see: https://www.cog-genomics.org/plink/1.9/input).
References
- Alexander, D. H., Novembre, J., and Lange, K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9): pp. 1655–1664.
Genetic information on individual Salvelinus spp. samples (n=1200) collected across Alberta's Eastern Slopes. Files are data formatted for ADMIXTURE 1.3 software analyses.
