Evolutionary Breakpoints in Gibbon Figure 4. Visualization of gibbon rearrangements relative to the human genome. This visualization was generated using Circos software (http://mkweb.bcgsc.ca/circos/). The lines in the inner circle represent inter-chromosomal (red) and intra-chromosomal (blue) rearrangements in gibbon relative to human. The outer circles provide genomic context. The outermost circle displays human chromosomes along with genomic coordinates and G-banding stains (NCBI Build 36.1). Purple lines represent human segmental duplications from the UCSC Segmental Dups Track. (http://genome.ucsc.edu/cgi-bin/hgTrackUi?g = genomicSuperDups). Orange lines represent gibbon segmental duplications we predicted based on read coverage. Green lines represent human genes from the UCSC RefSeq Genes Track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=refGene. doi:10.1371/journal.pgen.1000538.g004 duplications may be explained by independent reuse of a breakpoint in regions susceptible to rearrangements [24]. Nevertheless, we do not believe that SDs can be considered an underlying cause of the breakpoints, as we have only few examples of erroneous recombination events in these regions (Table 2). Very similar observations have very recently been reported [5]. When studying evolutionary chromosomal rearrangement, it is tempting to search for sign of selection on genes that have been disrupted by the breakages. Recent work by Girirajan et al. [5] found evidence that 3 of their 11 genes disrupted by breakpoints exhibited signatures of relaxed evolutionary constraint (average dN/dS = 1.09). Our approach was different, as we looked at all the genes within the sequenced BACs, and compared them with randomly selected regions of the gibbon genome. We did, however, identify 5 genes in our sample that are disrupted by breakpoints and for which we had adequate coverage. Although PLoS Genetics | www.plosgenetics.org 6 June 2009 | Volume 5 | Issue 6 | e1000538