Evolutionary Breakpoints in Gibbon Figure 2. Examples of Alu–Alu mediated recombination events. (A) Two examples of Alu–Alu mediated recombination events in the gibbon discovered by comparing the gibbon and great apes orthologous locations. In the example 1 (clone CH271-389E1) the AluY and the AluS on human chromosome 17 (HSA17) share high homology in two locations. In gibbon the AluS was broken as result of the inversion and the AluY was lost. A simple scenario is illustrated in example 2: two identical Alus located at the breakpoint boundaries on human chromosomes 2 and 17 (HSA2 and HSA17) recombined and most likely caused the translocation whose breakpoints was identified in clone CH271-262E11; (B) distance from breakpoints to Alus showing a decline in Alu content when moving from the breakpoint. (C) the proportion of CpGs per 100 bp is higher for Alus or Alu fragments closer to the breakpoints. doi:10.1371/journal.pgen.1000538.g002 Figure 3. Results of bisulfite allelic sequencing of orthologous Alus in gibbon and human. Alus at orthologous locations in human and gibbon would have been inserted into the genome of the common ancestor and would therefore be the same age in the two lineages. Even though the Alus are the same age, there is a difference in the methylation levels at the CpG sites skewing towards lower methylation in the gibbon. One exception is the Alu D (CH271-263C9) which shows lower methylation in human. doi:10.1371/journal.pgen.1000538.g003 PLoS Genetics | www.plosgenetics.org 5 June 2009 | Volume 5 | Issue 6 | e1000538