Data from: Indirect genetic control of migration in a salmonid fish
Kelson, Suzanne; Carlson, Stephanie; Miller, Michael (2020), Data from: Indirect genetic control of migration in a salmonid fish, Dryad, Dataset, https://doi.org/10.6078/D1TM5T
The paper titled "Indirect genetic control of migration in a salmonid fish" examines the genetic architecture of migration in a partially migratory salmonid fish, Oncorhynchus mykiss. We assess the shared genetic basis between early life growth and migration, and find a shared allelic basis on the Omy05 region of the genome. We then test if early life growth differs among resident/migratory genotype juvenile fish in streams in the South Fork Eel River watershed, in Northern California, USA. In summary, we find that the shared genetic basis for migration and physiological traits suggest that the genetic basis of migration is likely indirect, where migration is status-dependent strategy.
This Dryad deposit contains two datasets. The first is the set of 128 SNPs that we used to compare alleles between migratory/resident genotype groups and fast vs. slow developing clonal lines. This dataset includes the position of each SNP on Omy05, the major allele for the resident/migraotry genotype groups, the minor allele frequency for each group, and the allele for each clonal line. The second is a dataframe with sex and life history genotype for wild, juvenile fish in the study streams.
Additional data that are used in this paper have been previously published.
Sequence data for wild O. mykiss from the South Fork Eel River are available at NCBI, SRA accession: PRJNA599015
Data on fish (capture date and location, and body size) are available on Dryad:
Kelson S, Miller M, Thompson T, O’Rourke S, Carlson S. 2020. Dataset from: Temporal dynamics of migration-linked genetic variation are driven by streamflows and riverscape permeability. https://doi.org/10.6078/D1DM6G.
Sequence data for clonal lines are available in the following publications:
Miller MR, Brunelli JP, Wheeler PA, Liu S, Rexroad CE, Palti Y, Doe CQ, Thorgaard GH. 2012 A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Mol. Ecol. 21, 237–249. (doi:10.1111/j.1365-294X.2011.05305.x)
Gao G, Nome T, Pearse DE, Moen T, Naish KA, Thorgaard GH, Lien S, Palti Y. 2018 A new single nucleotide polymorphism database for rainbow trout generated through whole genome resequencing. Front. Genet. 9, 1–11. (doi:10.3389/fgene.2018.00147)
See methods in paper and references within.
Read me files are included.
National Science Foundation, Award: NSF GRF-2015179641
National Science Foundation, Award: NSF CZO-EAR-1331940
University of California Berkeley, Award: Wildlife Fund
Natural Reserve System, University of California, Award: Mildred E. Mathias Award