Data from: Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations

R code for single-locus and multivariate regression analyses used for "Admixture mapping in Populus"R code to obtain candidate QTL and parameter estimates. Runs with example input files 'linkage_Ita_f.edited', 'linkage_Ita_ss.edited', 'Marker.csv', and 'phenotypes_Ita.txt'.AdmixtureMapping.RMicrosatellite genotype data for all individuals from four Populus hybrid zonesGenotypic data are in 2 rows for each individual, in a slightly modified Structure input format. Columns: individual number; source population (Italy, Austria, Hungary, Spain); individual ID; species assignment (0, hybrid; 1, P. alba; 2, P. tremula); use population flag in Structure (0, no; 1, yes); followed by microsatellite fragment sizes for 77 loci (-9, missing data; 222, band absent for dominant markers).Genotypes.csvPhenotype measurements for all 22 traits and all individuals from four Populus hybrid zonesColumns: individual number; source population (Italy, Austria, Hungary, Spain); individual ID; species assignment (H, hybrid; A, P. alba; T, P. tremula); followed by phenotypes for all 22 phenotypic traits measured/calculated. Phenotype measurements represent averages over 5 leaves measured per tree.Phenotypes.csvResult of Structure run for Italy, using linkage model (Input file for R code; text file)Columns: individual number; individual ID; percent missing data; proportion of ancestry from cluster 1 (P. tremula); proportion of ancestry from cluster 2 (P. alba); followed by their 90% probability intervals.linkage_Ita_f.editedResult of Structure run for Italy, using linkage model, site-by-site output (Input file for R code; text file)Columns: individual number; locus number; followed by 4 columns for LSA estimates (probability that both alleles are from P. alba; probability that first allele is from P. alba, second from P. tremula; probability that first allele is from P. tremula, second from P. alba; probability that both alleles are from P. tremula).linkage_Ita_ss.editedInformation on microsatellite markers used (Input file for R code)Columns: locus number; abbreviated locus name used in this study; locus name published; chromosome; position on chromosome in bp; position in bp/200,000 as proxy for cM; marker type (dominant or co-dominant).Marker.csvPhenotype measurements for Italy, admixed individuals only, 8 mapping traits (Input file for R code)Rows give measurements for individuals in the same order as in Structure files; columns give 8 main phenotypic traits used for admixture mapping. Phenotype measurements represent averages over 5 leaves measured per tree.phenotypes_Ita.txt