Fig. 2: Detecting de novo mutations in patrilines.

A An example of a patriline with a mutation event carried by multiple descendants (MD) leading to increased CN (2 - > 3) of the yellow amplicon. Each circle represents a male in the patriline, with lines representing the transmissions of Y chromosomes from father to son and the number inside each circle representing the observed (dark blue) or inferred (light blue) CN genotype. Red lines represent the transmissions where the mutation occurred. B For the five males with observed CN genotypes from the patriline shown in panel A, we show copy number across non-overlapping 1 kb windows for the yellow, green and red amplicons. The carriers of the mutation are indicated by a red frame. The position of each amplicon is indicated with coloured rectangles above the plots. C Boxplot representing the distribution of the CN across non-overlapping 1 kb windows within the green, red, teal and yellow amplicon, for each of the five males with observed CN genotypes in the patriline. Here we see that the 2- > 3 increase in CN affects the green, red and yellow amplicons, but not the teal amplicon. D A summary of CN genotypes of all males with sequencing data, based on the median of the medians across non-overlapping 1 kb windows for each of the four amplicons. Each circle represents one male, with colours indicating the CN genotype called. The five sequenced members of the patriline in panel A are represented by black circles. E Comparison of the mutation rate estimated from the Y chromosome phylogenetic tree and the de novo mutation rate estimated using patrilines. A schematic representation of the Y chromosome phylogenetic tree (top) and four patrilines (bottom). The phylogenetic tree was constructed from individuals with at least 10 mutational differences according to haploid genotypes from the X-degenerate region of the Y chromosome, in order to minimise overlap between transmissions in the patrilines and the phylogenetic tree. As in the case of the patrilines, CN genotypes for ancestral males in the phylogenetic tree were inferred using parsimony, conditioning on the males with observed CN genotypes and their position in the tree.