To this end, we generated Illumina shotgun sequences from two western, seven eastern, and seven central chimpanzees ( Fig. To investigate whether bonobos and chimpanzees exchanged genes subsequent to their separation, we used a test (the D statistic 10) to investigate the extent to which the bonobo genomes might be closer to some chimpanzees than to others ( Supplementary Information, section 10). The tendency of new L1 integrants to accumulate near neuronal genes on evolutionary timescales may mimic the somatic variation found in the brain. In humans, L1 retrotransposition has been shown to occur preferentially in neuronal precursor cells and has been speculated to contribute to functional diversity in the brain 9. We found that, as in mice 8, African-ape-specific L1 insertions are enriched near genes involved in neuronal activities or cell adhesion and are depleted near genes encoding transcription factors or involved in nucleic-acid metabolism ( Supplementary Information, section 6). We identified two previously unreported Alu subfamilies in bonobos and chimpanzees, designated AluYp1, which is present in 5 copies in the human genome and in 54 and 114 copies in the bonobo and chimpanzee genomes, respectively, and AluYp2, which is absent from humans and present in 24 and 37 copies, respectively, in the two apes. In agreement with previous results 6, we find that Alu insertions accumulated about twice as fast on the human lineage as on the bonobo and chimpanzee lineages ( Fig. The bonobo genome can therefore serve as a high-quality sequence for comparative genome analyses.Īs in other mammals, transposons, that is, mobile genetic elements, make up approximately half of the bonobo genome ( Supplementary Information, section 6). We used the finished chimpanzee sequence of chromosome 21 together with the human genome sequence to estimate an error rate of approximately two errors per 10 kb in the bonobo genome, with comparable qualities for the X chromosome and autosomes. Owing to over-collapsing of duplications, only 14.6 Mb are present in the final assembly ( Supplementary Information, section 4), a common error seen in assemblies from shorter-read technologies 7. Segmental duplications affect at least 80 Mb of the bonobo genome, according to excess sequence read-depth predictions. Compared with the 6× Sanger-sequenced chimpanzee genome 6 (panTro2), the bonobo genome assembly has a similar number of bases in alignment with the human genome, a similar number of lineage-specific substitutions and similar indel error rates ( Table 1 and Supplementary Information, sections 2 and 3), suggesting that the two ape genomes are of similar quality. To understand the evolutionary relationships of bonobos, chimpanzees and humans better, we sequenced and assembled the genome of a female bonobo individual (Ulindi) and compared it to those of chimpanzees and humans. That ancestor may in fact have possessed a mosaic of features, including those now seen in bonobo, chimpanzee and human. No parsimonious reconstruction of the social structure and behavioural patterns of the common ancestor of humans, chimpanzees and bonobos is therefore possible. Thus, chimpanzees and bonobos each possess certain characteristics that are more similar to human traits than they are to one another’s. Compared with chimpanzees, bonobos are playful throughout their lives and show intense sexual behaviour 3 that serves non-conceptive functions and often involves same-sex partners 4. They do not form alliances with one another and there is no evidence of lethal aggression between groups 3. By contrast, bonobo males are commonly subordinate to females and do not compete intensely for dominance rank 1. For example, male chimpanzees use aggression to compete for dominance rank and obtain sex, and they cooperate to defend their home range and attack other groups 3. However, the behaviour of the two species differs in important ways 1. Nature volume 486, pages 527–531 ( 2012) Cite this articleīonobos and chimpanzees are highly similar to each other in many respects. The bonobo genome compared with the chimpanzee and human genomes
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