Data files for the manuscript: 'Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod' by Therkildsen et al. Six data files are available: SNP_identity.txt SNP_genotypes_1047.txt Genepop_1047.gen SNP_genotypes_160.txt Genepop_160.gen Env_and_demographic_data.txt The content and format of each file is described below: SNP_identity.txt ------------------------------------------------------------------------------- This tab-separated file contains a complete list of the SNPs analyzed in the study. For each SNP we provide the linkage group and specific linkage map position (where available), the accession reference ID (dbSNP), the original publication for the SNP discovery (source), whether the locus was included in the quality-filtered 1047 and 160 SNP data sets (see below), and any miscellaneous notes. Where possible, linkage map positions were inferred from the published linkage map (Hubert et al. 2010, Borza et al. 2010). Additional SNPs were anchored to linkage groups by mapping the flanking sequences to the genome scaffolds (see Supporting information, Note 1). These SNPs could be assigned to linkage groups, but the position within the linkage groups remains unknown (hence they can be identified as the SNPs with data in the column for Linkage_group, but no data in the column for Position). Missing data are indicated with blanks. References: Borza, T, Higgins B, Simpson G, Bowman S (2010) Integrating the markers Pan I and haemoglobin with the genetic linkage map of Atlantic cod (Gadus morhua). BMC Research Notes, 3, 261. Hemmer-Hansen J, Nielsen EE, Meldrup D, Mittelholzer C (2011) Identification of single nucleotide polymorphisms in candidate genes for growth and reproduction in a nonmodel organism; the Atlantic cod, Gadus morhua. Molecular Ecology Resources, 11, 71–80. Hubert S, Higgins B, Borza T, Bowman S (2010) Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC genomics, 11, 191. Moen T, Hayes B, Nilsen F et al. (2008) Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection. BMC Genetics, 9, 18. Nielsen EE, Hemmer-Hansen J, Poulsen NA et al. (2009) Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evolutionary Biology, 9, 276. Pogson GH (2001) Nucleotide polymorphism and natural selection at the pantophysin (Pan I) locus in the Atlantic cod, Gadus morhua (L.). Genetics, 157, 317–330. SNP_genotypes_1047.txt ------------------------------------------------------------------------------- This tab-separated file contains the genotype data for the initial analysis of the 4T 1928 and the 4T 2008 samples with the full 1047 SNP panel. Each line shows data for one individual, indicating the management area and the year of collection as well as the observed genotype at each SNP. The file shows the data retained after quality filtering that removed genotypes with a GenCall score <0.4, SNPs yielding <0.7 reproducibility rate between genotypes in replicate samples, and SNPs and samples with call rates <0.5. Missing data are indicated by NA. Genepop_1047.gen ------------------------------------------------------------------------------- The data from file "SNP_genotypes_1047.txt" presented in Genepop format. SNP_genotypes_160.txt ------------------------------------------------------------------------------- This tab-separated file contains the genotype data for samples from 4T, 3Ps, 3NO and 4VsW analyzed with the 160 SNP panel. Each line shows data for one individual, indicating the management area and the year of collection as well as the observed genotype at each SNP. The file shows the data retained after quality filtering that removed genotypes with a GenCall score <0.4, SNPs yielding <0.7 reproducibility rate between genotypes in replicate samples, and SNPs and samples with call rates <0.5. Missing data are indicated by NA. A number of SNPs in the 160 panel are not included in the final 1047-SNP data file because data for these loci did not fulfill the quality criteria in the 1928 sample (and they were therefore excluded from the analysis). Genepop_160.gen ------------------------------------------------------------------------------- The data from file "SNP_genotypes_160.txt" presented in Genepop format. Env_and_demographic_data.txt ------------------------------------------------------------------------------- This tab-delimited file contains the environmental and demographic data used in the correlation analysis of temporal trends within the 4T management area. Description of the variables and the data sources can be found in Table S1. PMRNmean is fish length in cm, the mean individual weight at ages 5-7 is in kg, the biomass at ages 3+ is in tons, the mortality indices (M, F and Z) are estimated instantaneous rates, and the temperature variables are in degrees Celcius. Missing (not available) data are indicated by blanks.