Yellowstone cutthroat trout allele frequencies plotted against linkage maps. Selected linkage groups show RYHyb01 in Females 1 and 2 and RYHyb09 in Males 1 and 2. A 25 centiMorgan sliding window was used to identify blocks of loci with Yellowstone cutthroat trout (YCT) allele frequencies that deviated significantly from expected frequencies. Linkage maps are in p to q orientation. * indicates P < 0.05 and ** indicates P < 0.01. See Additional file2 for YCT allele frequencies within each mapping parent for all linkage groups.