Fig. 3

Result plots for chromosome 1 in offspring ID-256 and chromosome 21 in offspring ID-258. (A, E) The grandparental-of-origin of informative alleles at all SNPs along chromosome 1 in offspring ID-256 (A) and chromosome 21 in offspring ID-258 (E). Each dot represents an allele at a specific SNP for the paternal or maternal chromosomes. Dots are plotted with noise on the y-axis to alleviate the degree of overlap. Colouration indicates different scaffolds on the chromosomes in the great reed warbler genome assembly [15]. (B, F) Visualization of the result from the proportional difference (PD) algorithm shows the absolute difference of the proportion of the grandpaternal alleles compared to that of grandmaternal alleles along chromosome 1 in offspring ID-256 (B) and chromosome 21 in offspring ID-258 (F). Five recombination positions were indicated by the local maxima for offspring ID-256, and one recombination position were indicated by the local maximum for offspring ID-258. (C, G) Visualization of the result from the cumulative continuity score (CCS) algorithm shows the CCS for the paternal and maternal chromosomes along chromosome 1 in offspring ID-256 (C) and chromosome 21 in offspring ID-258 (G). Five recombination positions in offspring ID-256 and one recombination position in offspring ID-258 were indicated (see maternal chromosome; border between orange and light blue at position ca. 3 Mb). (D, H) The local density of informative SNPs along chromosome 1 in offspring ID-256 (D) and chromosome 21 in offspring ID-258 (H)