Fig 3. Analysing the dynamics of palindrome arms.

a) An ideogram of the Y chromosome with the different regions colored accordingly to their type. The positions of the palindromes are marked and the protein-coding genes are shown below. b) Due to the high similarity of the palindromes many reads will map to both arms and only when there are differences between the arms will the reads map uniquely. However, if only one arm of the palindrome is used the palindrome can be treated as a pseudo-diploid chromosome with differences between arms corresponding to SNVs. Comparing different individuals for which a single phylogenetic tree exists can be used to identify mutations (position 2 in individual 1) and gene conversions (positions 2 and 3 in individual 2 and position 1 in individual 1, 2 and 3). c) The gene conversions are grouped based on if the ancestral or derived base is used as a donor sequence. Ancestral->derived means that an ancestral base is converted to the derived base and Derived->ancestral means that the derived based is converted to the ancestral base. The number of gene conversion events for each base transition is shown and the bars are colored according to transitions or transversions classification. d) Number of base changes grouped by event type (being gene conversion or mutation). The bars are colored based on if they are transitions or transversions and whether they are found in one individual or father/son pair (private) or in more individuals (common). e) Part of the phylogeny and genotypes for palindrome 5 and the y1/y2 segments of palindrome 1 (see part a) are shown. The individuals’ IDs are made up of family ID and a number plus a 01 for fathers and 03 and above for sons. In palindrome 5 the coverage of the segment has increased from around 60X to 90X, suggesting that three copies of this segment now exist. In palindrome 1, the coverage has decreased from 60X to around 30X, suggesting that only one copy of the segment exist.