Abstract
The western North American Arctic char (AC, Salvelinus alpinus), Dolly Varden (DV, Salvelinus malma), and bull trout (BT, Salvelinus confluentus) are described as a “species complex” due to their close inter-relationships, variable morphology, and tendency to hybridize. Consequently, there has been considerable historical debate about the taxonomic status of the three species, and their physical identification is often problematic. A genotyping-by-sequencing (GBS) library of AC, DV, and BT samples from across the North Pacific and Arctic Canada was exploited to find species-specific single nucleotide polymorphisms (SNPs) to design and test TaqMan™ assays for efficient species identification. A total of 10 AC/DV and 10 DV/BT TaqMan™ assays were developed and tested for efficient, cost-effective, and accurate genotyping of sympatric char species and their hybrids in samples from diverse subspecies, and phylogeographic lineages, and geographic groups. Both in silico and lab genotyping tests using these diagnostic SNPs resulted in highly concordant and accurate identification when compared to previous identifications using microsatellite, single copy nuclear DNA, GBS SNP data and information on geographic distributions. The TaqMan™ assays confirmed the utility of a relatively small number of diagnostic markers to identify these species and F1 hybrids, and samples that were moderately admixed between species. This work represents the first SNP-based diagnostic markers for these three species that can be used for a wide variety of applications in research and monitoring in the char species complex.
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Acknowledgements
We thank J. Shen for technical assistance in preparing the Salvelinus GBS library. Contributions from many collaborators and former students in providing samples, and the support of the Zoology Computing Unit at UBC, is greatly appreciated. We thank members of the Ben Koop lab (University of Victoria) for providing access to the Nauyuk Lake and Tree River sequence data. Comments provided by two reviewers also improved the manuscript.
Funding
This research was supported by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) Equipment and Discovery grants awarded to EBT. This project also benefited from GBS data generated under a contract awarded to EBT by British Columbia Hydro.
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Research questions and study design were created by EBT, AG, and AL. The Salvelinus genotyping-by-sequencing library was prepared by AG. Genotyping and statistical analyses were conducted by AL. Manuscript was written and edited by AL with feedback and comments from EBT and AG.
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Liu, A., Geraldes, A. & Taylor, E.B. Development and testing of diagnostic molecular markers to differentiate among three species of Salvelinus: Arctic char, Dolly Varden, and Bull trout. Conservation Genet Resour 15, 83–96 (2023). https://doi.org/10.1007/s12686-023-01305-7
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DOI: https://doi.org/10.1007/s12686-023-01305-7