Robust discrimination between closely related species of salmon based on DNA short-reads

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Abstract

Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (CO1), using ensembles of short-reads aligned to genetic barcodes that serve as digital proxies for the holotypes of the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE 5.2 (Edgar, 2022), applied to multiple versions of each short-read perturbed according to the nucleobase identification error probabilities underlying the quality scores. The Damerau-Levenshtein distance was used to determine the genetic barcode of the candidate species that is closest to each aligned, perturbed short-read. The "votes" that the sampled short-reads cast for the different candidate species are then pooled and converted into identification probabilities, using weights determined by the entropy of the short-read specific identification probability distributions. This novel approach to discrimination between closely related species is used for robust value-assignment to reference materials supporting the ascertainment of the authenticity of seafood, for example NIST Reference Materials 8256 and 8257 (Coho salmon) (Ellisor et al, 2021).

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Uncertainty quantification

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