Results: 4

1.
Fig. 4

Fig. 4. Rates of segmental duplication. From: A Burst of Segmental Duplications in the African Great Ape Ancestor.

a) By basepair: We parsimoniously assigned the number of Mb to different branches, correcting for copy number in each species (shown in brackets). 89-99% of great-ape segmental duplications were validated by arrayCGH (square brackets). b) Further categorization of the segmental duplication data, based on arrayCGH from bonobo and gorilla, shows the greatest accumulation in the ancestor of humans and great apes. c) By event: We assigned 950 evolutionarily distinct human segmental duplication events20 to the human/great-ape phylogeny based on arrayCGH results. The red line estimates the duplication rate (per million years) and suggests an excess of large duplications in the common ancestor of human and chimpanzee but after the separation from gorilla.

Tomas Marques-Bonet, et al. Nature. ;457(7231):877-881.
2.
Fig. 1

Fig. 1. Experimental validation of duplication map. From: A Burst of Segmental Duplications in the African Great Ape Ancestor.

a) A computationally predicted orangutan-specific duplication (blue=excess depth of coverage of aligned WGS sequence) is confirmed by interspecific FISH and arrayCGH (oligonucleotide relative log2 ratios are depicted as red/green histograms and correspond to an increase and decrease in signal intensity when test/reference are reverse labeled) (see Supplementary Note for additional details). b) A comparison of duplication copy number as predicted by WSSD sequence analysis versus oligonucleotide arrayCGH between nonhuman and human primates showed a good correlation (r=0.77). Relative duplication copy number was computed as the log2 ratio of the number of aligned nonhuman primate reads against the human reference genome over the number of reads mapping to known single copy BACs.

Tomas Marques-Bonet, et al. Nature. ;457(7231):877-881.
3.
Fig. 3

Fig. 3. Convergent gene duplication expansion in African great apes but not humans. From: A Burst of Segmental Duplications in the African Great Ape Ancestor.

a) Two regions on chromosome 10 have expanded in chimpanzee, gorilla and bonobo when compared to human based on computational and interspecific arrayCGH experiments (see Fig. 1 legend). b) FISH confirms 23-50 copies in chimpanzee and bonobo, and >100 copies in gorilla (Methods). End-sequence pair analysis using gorilla and chimpanzee WGS sequences reveals that all but the ancestral location are nonorthologous, indicating independent expansions in both lineages. c) Detailed analysis of 8 homologues of gorilla chromosome 1 reveal interstitial locations of the block 2 duplication that show variation both in copy number and in terms of location.

Tomas Marques-Bonet, et al. Nature. ;457(7231):877-881.
4.
Fig. 2

Fig. 2. Shared vs. lineage-specific duplications and great-ape polymorphism. From: A Burst of Segmental Duplications in the African Great Ape Ancestor.

Segmental duplications (>20 kbp) were classified as lineage-specific or shared based on a four-way comparison of human, chimpanzee, orangutan and macaque genomes. a) Human SDs were compared to Old World monkey SDs (based on a separate analysis of the macaque assembly9). b). Since nonhuman great-ape duplications were detected based on alignment of WGS sequence against the human genome, we corrected for copy number based on the depth of coverage of WGS sequence (in brackets with the name of the species for which the correction was performed, see Table 1). b) Copy-number polymorphic regions were estimated from the results of arrayCGH hybridizations between 8 samples each of human, chimpanzee and orangutan (using the same reference as the computational prediction). The proportion of duplicated bases that showed evidence of copy-number polymorphism (i.e. gain or loss for ≥ two individuals within each species) is shown for each class of SD.

Tomas Marques-Bonet, et al. Nature. ;457(7231):877-881.

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