Data from: Congruent population structure across paralogous and non-paralogous loci in Salish Sea chum salmon (Oncorhynchus keta)

Whole genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently paralogs are often excluded from studies. The effects of an ancient whole genome duplication (approximately 88MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing (RADseq) on ten collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and re-diploidized regions of the genome. We use a pedigree and high-density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous genetic loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid-derived species.linkage mapTab-delimited text file giving the linkage group (LG) and cM (centiMorgan) position of each SNP. The remaining columns give different identifiers for the positions. "Contig" = aligned reference contig. "resolved_locus" = genetic locus, for non-duplicated loci this is the contig. For paralogous loci, multiple loci are associated with a contig. "stacks_CatID" and "stacks_SNP" give the identifiers given by the Stacks program. "LEPname" gives the locus identifier given by the LEPmap program.Genome scan summary statisticsTab-delimited text file giving summary statistics for each locus. See the README for column descriptions.genome scan.txtStacks Haplotypes.tsv file"Haplotypes" file produced by Stacks, in text format. See Stacks documentation.complete.haplotypes.tsvnon_paralogs.mapLocus list (in PLINK .map format) of non-paralogous loci. Associated with non_paralogous.pednon_paralogs.pedGenotype data (in PLINK .ped format) for non-paralogous loci. For use with the non_paralogs.map file.complete.dom.mapLocus list for the dominance-coded data set with both non-paralogous and paralogous loci (in PLINK .map format).complete.dom.txtnon-delimited text file with Genotype data for dominance-coded genotypes at paralogous and non-paralogous loci. Each genotype takes one character: 1 = present, 0 = absent, 9 = missing. One row per locus, loci are given in complete.dom.map. One column per individual, individuals are listed in non_paralogs.ped