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Dryad

SNP genotype dataset from brown and anadromous trout

Cite this dataset

King, Andrew (2024). SNP genotype dataset from brown and anadromous trout [Dataset]. Dryad. https://doi.org/10.5061/dryad.1ns1rn92w

Abstract

Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species’ marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed the high-confidence assignment of known-origin individuals to the region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.

README: SNP genotype dataset from brown and anadromous trout

https://doi.org/10.5061/dryad.1ns1rn92w

Data for trout (Salmo trutta) samples genotyped at 95 single nucleotide polymorphism (SNP) markers (Osmond et al. 2023). Data consists of 3067 baseline trout samples, 435 known-origin individuals, and 371 anadromous trout caught in marine and estuarine areas.

Description of the data and file structure

The data file is a Microsoft Excel file, in GenAlEx format (Peakall & Smouse 2006, 2012), containing six tabs: Baseline_sample_info, Baseline, Known_origin_sample_info, Known_origin_samples, Marine&Estuarine_sample_info, and Marine&Extuarine.

SNP data is coded as 1 - A, 2 - C, 3 - G, and 4 - T. Missing data is coded as zero.

Tab: Baseline_sample_info

A table presenting details of the rivers and hatchery populations from which brown trout were sampled to construct the genetic baseline, including river code name, country, reporting group to which each river belongs, grid reference (latitude, longitude) of each river mouth, and baseline sample size.

Tab: Baseline

Data for 3067 baseline brown trout individuals were sampled from 107 English, Irish, French, and Danish rivers and two French hatchery stocks. Samples were genotyped at 95 single nucleotide polymorphism markers (Osmond et al. 2023) on the Fluidigm EP1 Genotyping System using 96.96 Dynamic Genotyping Arrays and scored using the Fluidigm SNP Genotyping analysis software. Details of sampled rivers are given in the Baseline_sample_info tab.

Essential parameters are given in Row 1. These are cell A1 – number of loci; cell B1 – number of individual genotypes in the datasheet; cell C1 – number of populations; cells D1 to DH1 – the number of individual genotypes in each river or hatchery population.

Tab: Known_origin_sample_info

A table presenting details of the rivers from which ‘known-origin brown trout were sampled to test the genetic baseline, including river code name, country, reporting group to which each river belongs, and sample size.

Tab: Known_origin_samples

Data for 435 known-origin brown trout individuals, sampled from 23 English, Irish, and French rivers. Samples were genotyped at 95 single nucleotide polymorphism markers (Osmond et al. 2023) on the Fluidigm EP1 Genotyping System using 96.96 Dynamic Genotyping Arrays and scored using the Fluidigm SNP Genotyping analysis software. Samples were used to test the accuracy of assignments to the genetic baseline. Details of sampled rivers are given in the Known_origin_sample_info tab.

Essential parameters are given in Row 1. These are cell A1 – number of loci; cell B1 – number of individual genotypes in the datasheet; cell C1 – number of populations; cells D1 to AB1 – the number of individual genotypes in each known-origin sample.

Tab: Marine&Estuarine_sample_info

A table presenting details of the location of marine and estuarine samples of anadromous trout including code name, country, sample types (estuarine or marine), and sample size.

Tab: Marine&Estuarine

Data for 371 anadromous trout individuals, sampled from 12 English, French, and Dutch marine and estuarine areas. Samples were genotyped at 95 single nucleotide polymorphism markers (Osmond et al. 2023) on the Fluidigm EP1 Genotyping System using 96.96 Dynamic Genotyping Arrays and scored using the Fluidigm SNP Genotyping analysis software. Details of sampled regions are given in the Marine&Estuarine_sample_info tab.

Essential parameters are given in Row 1. These are cell A1 – number of loci; cell B1 – number of individual genotypes in the datasheet; cell C1 – number of populations; cells D1 to O1 – the number of individual genotypes in each marine or estuarine sample.

References

Osmond, D. R., King, R. A., Stockley, B., Launey, S., & Stevens, J. R. (2023). A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) is suitable for exploring genetic diversity at a range of spatial scales. Journal of Fish Biology, 102 (1), 258-270. doi:10.1111/jfb.15258

Peakall, R., & Smouse, P. E. (2006). GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Resources, (1), 288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x

Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics28 (19), 2537–2539. https://doi.org/10.1093/ bioinformatics/bts460

Methods

All individuals were genotyped at 95 biallelic single nucleotide polymorphism (SNP) loci (Osmond, King, Stockley, Launey, & Stevens, 2023) on the Fluidigm EP1 Genotyping System using 96.96 Dynamic Genotyping Arrays and scored using the Fluidigm SNP Genotyping analysis software.

Funding

European Union, Interreg France (Channel) England (FCE) programme