Orangutan Genome Sequenced
Nature has published a summary of the complete sequencing of the Orangutan DNA. The blog primatology.net has written a summary:
The orangutan genome has been sequenced and published in today’s Nature. The paper, “Comparative and demographic analysis of orang-utan genomes,” is open access for you to read for yourself. I’ll be highlighting some of the high points in this post. […]
One remarkable finding of the study is the estimated divergence between the Sumatran and Bornean species. The team calculated the two species diverged 400,000 years ago. We know that land bridge between Indonesia’s Sumatra and Borneo split at least 21,000 years ago but until now we’ve never known at what time the two speciated.
Compared to the two other great apes whose genomes have been sequenced, humans and chimps, the orangutan genome has changed much less. We’re still waiting on the gorilla genome to be finished. Oangutans originated some 12 million to 16 million years ago. Theoretically, orangutans have had more time to accumulate genetic variation compared to humans and chimpanzees, which split into their own lineages 5 million to 6 million years ago. One would expect at least twice as much variation in the orangutan genome. However, in the study, a comparison of the three genomes shows that humans and chimpanzees have lost or gained new genes at twice the rate of orangutans.
Why’s that?
The paper explains that orangutan genomes have much fewer active retrotransposons than human and chimp genomes. Retrotransposons, or Alu elements, are essentially jumping genes, that replicate, and amplify then insert into different parts of the genome. The initial 2001 draft of the human genome reported that around 42% of the human genome is made up of retrotransposons. The authors of the orangutan paper illustrate that the human genome has ~5,000 Alu elements, whereas the orangutan genome has 250. This is significantly different. The authors write,
“Reduced Alu retroposition potentially limited the effect of a wide variety of repeat-driven mutational mechanisms in the orang-utan lineage that played a major role in restructuring other primate genomes.”
Personally, and this is my thinking here nothing the authors say — a common source of many human retrotransposons are to prehistoric viruses that integrated into our ancestral DNA. Viruses are communicable. Orangutans are the most solitary Great apes. I suspect they would have much less exposure to viruses because of their social structure, and thus much less chance of insertion of retrotransposon. Again, this is a hypothesis of mine, and I could be very wrong to think this. […]
Many fascinating insights no doubt will come from extensive comparisons between all great ape DNA sequences. The details of Hominid evolution are slowly coming into focus as we unravel the mysteries of our genetic material.
The original paper in Nature is open for all to read, and can be found here: Comparative and demographic analysis of orang-utan genomes
As the primatology.net blog entry further writes, one of the curious things about the human DNA is that we and the orangutans have retained some of the genetic material common to the ancestor of humans/chimps/orangs that the chimps have lost.