NUMTs in Pan Y Chromosome palindromes. (A) The prevalence of NUMTs per Y Chromosome sequence classification. A detailed list of these NUMTs can be found in Supplemental Table S5. (B) Schematic of palindrome structure with NUMTs on each arm. (C,D) IGV plot of Pan genus lineage-specific expansion of NUMTs in palindromic regions of the Y Chromosome, displayed for bonobo (C) and chimpanzee (D). These are ∼7 kb NUMTs distributed as pairs along each palindromic arm. Palindromes were annotated with a Q and a number, with each palindrome arm denoted as A and B according to the method of Makova et al. (2024). Not all palindromes are labeled in these plots, as some overlap. (E) An unscaled maximum parsimony tree of palindromic NUMT sequences in bonobo and chimpanzee. We utilized bonobo and chimpanzee mtDNA as outgroups. Branches contain bootstrap values. Branches with <50% support were collapsed. The suffix (+) indicates the NUMT follows the 5′ to 3′ direction, whereas (−) indicates the NUMT follows the 3′ to 5′ direction.