Fig. 3.

Evolution of sequences homologous to human and chimpanzee palindromes. (A) Heatmaps showing coverage for each palindrome in each species in the multispecies alignment (the last column includes all palindromes) and box plots representing copy number (natural log) of 1-kb windows which have homology with human or chimpanzee palindromes (the last box plot is for X-degenerate genes; the data for human and chimpanzee can be found in SI Appendix, Table S7). (B) The great ape phylogenetic tree (not drawn to scale) with evolution of human (shown in blue) and chimpanzee (red) palindromic sequences overlayed on it. Palindrome names in boldface indicate that their sequences were present in two or more copies. Negative (-) and positive (+) signs indicate loss and gain of palindrome sequence (possibly only partial), respectively. Arrows represent gain (↑) or loss (↓) of palindrome copy number. If several equally parsimonious scenarios were possible, we conservatively assumed a later date of acquisition of the multicopy state for a palindrome (SI Appendix, Supplemental Note S5, for additional details; the data are shown in SI Appendix, Table S7).