Skip to main content
. Author manuscript; available in PMC: 2012 Nov 11.
Published in final edited form as: Cell. 2012 May 3;149(4):912–922. doi: 10.1016/j.cell.2012.03.033

Figure 2. Evolutionary characterization of SRGAP2 duplications.

Figure 2

(A) A depiction of the gene structure of SRGAP2 with respect to the three assembled contigs. Homologous segments are shown using Miropeats (Parsons, 1995) where green lines indicate nearly identical segments (s = 1,000) shared between SRGAP2A and the duplicate SRGAP2 paralogs; blue lines delineate the larger (>515 kbp) extent of homology between SRGAP2B and SRGAP2C. The 244.2 kbp genomic region shared among all three contigs is highlighted (red box) with clusters of Alu repeats at the breakpoints (arrows). Also see Figure S2 for detailed representation of Alu elements and segmental duplications across duplicated regions. (B) An unrooted neighbor-joining tree was constructed based on a 244.2 kbp multiple sequence alignment of the three loci. Both 1p12 and 1q21.1 branches show accelerated rates of substitution (p = 0.00001 and p = 0.0249; Tajima’s relative rate test). The actual (no parentheses) and adjusted (parentheses) number of substitutions for locus-specific acceleration is indicated above each branch along with the bootstrap support at each node. We estimate the timing assuming chimpanzee and human diverged 6 mya. Also see Table S2 for molecular evolution of the shared SRGAP2 coding regions. (C) FISH experiments on metaphase human chromosome 1, as well as the orthologous chimpanzee and orangutan chromosomes, were performed to discern the order of duplication events. Locations of probes with respect to the contigs are shown in part (A). A probe (yellow) targeting sequence adjacent to the original SRGAP2 duplicate region hybridizes to 1q21.1 in chimpanzee and orangutan, suggesting the original SRGAP2 duplicate paralog maps to the region homologous with nonhuman primate 1q21.1. A probe (green) targeting unique sequence on the p-arm of chromosome 1 proximal to SRGAP2C hybridizes to the chromosome 1p-arm in orangutan, refuting the possibility that SRGAP2C moved to the p-arm via a simple pericentromeric inversion (Szamalek et al., 2006) and distinguishing the p-arm from the genomic region at 1q21.1 where the original SRGAP2 duplicate paralog maps. A probe (blue) was used to distinguish the chromosome 1q-arm.