June 14, 2012

Bonobo genome sequenced

Ulundi (source)
The last great ape* to be sequenced has been the bonobo, it complements the Homo sapiens, Neanderthal, Denisovan (probably a hybrid), chimpanzee, gorilla and orangutan genomes:

The reference genome was sequenced from a female bonobo captive at Leizpig Zoo, known as Ulundi.

The genome will, hopefully, help understand better the genetic basis of our being as humans and, maybe also get some inferences on our prehistory. 

Stubbornly under-estimating divergence times by almost 100%

In this sense I want to emphasize that the paper insists in producing Pan-Homo and internal Pan divergence times that are irrationally low. The cause of this systematic error that persists through some literature seems to be rooted on the Homo-Pongo divergence estimate, which I do not know the details about but seems from context to be an extreme under-estimate. 

The matter was already debated in 2008 by Jenniffer L. Caswell, who explained that the Bonobo-Chimpanzee split cannot be more recent than 1.5 to 2.0 million years because it was then when the Congo River was formed separating the two populations radically (allopatric speciation). This is quite apparent in the distribution of bonobos and chimpanzees:

fig. 1a

So unless the geology is wrong, bonobos and chimpanzees diverged 1.5 to 2 million years ago, and not a mere million years ago, as this paper claims.

This has important implications for the Homo-Pan divergence age, as I have discussed again and again. Assuming that the 4.5:1 ration estimated in this paper is correct, then the actual Homo-Pan divergence age ranges between 6.8 to 9.0 million years ago (and not a mere 4.5 Ma), with a median of 7.9 Ma, quite similar to the 8 Ma estimate I have been defending since the Caswell paper was published in 2008.

See also


* Note: I know someone will say that Homo sp. are not "apes" but I say Homo are a subset of the great apes clade (Hominidae) phylogenetically and therefore great apes ourselves - something to be irrationally proud of, of course.


  1. I am one of the people responsible for the low divergence estimate, but I actually agree that it is probably too low. The estimate is based on a molecular clock, calibrated from an assumption of the genome divergence between humans and chimpanzees, of about 1e-9 mutations per base pair per year. We used this in the paper because it is what is typically used, but there are good reasons to think it is too high (and thus the split time is too low).

    For humans we now think that the mutation rate is almost half of this, and the substitution rate is going to be that low as well, of course, but using the lower rate leads to other problems. In the gorilla genome analysis we therefore proposed a slow-down hypothesis, and if we use this here the split between chimps and bonobos fits better with the Congo river hypothesis for the chimp/bonobo split.

    The two analyses were done in parallel, though, and the slow down hypothesis didn't catch up with the bonobo analysis, thus the low divergence time estimate.

    1. Thanks for commenting so sincerely, Mailund. I truly appreciate it.

      I am naturally seduced by the idea of the slow-down hypothesis (whichever the details), which would tend to solve the main problems I have spotted like those mentioned here or the fact that the human estimates often also fall under what the archaeology rather strongly suggests (vide Petraglia and others), for example for the migration out-of-Africa. That alone should be enough for people like myself most interested in human evolution and prehistory and with only a peripheral interest in general primatology.

      However I included in the "see also" section a reference to Michael Heads' 2010 apology of a Jurassic origin of primates and its contradiction with the usual molecular clock estimates. His argument is quite simple but solid: the ancestors of New World monkeys (which are often kept in islets in modern zoos because most just will never get in the water, no matter what) could not have crossed a growingly wide Atlantic Ocean between Africa and South America, instead they must have been in South America when it began diverging from Africa.

      This I reckon has no direct fossil support but is really hard to question in its logic and, if correct, would also support a simply much slower actual molecular clock for all the primate branch. A major problem I see is that fossils, when they exist, are only a 'terminus ante quem' and not an absolute first date (maybe not even close at all to the real divergence).

      Just food for thought. Whatever the case I am glad that researchers like you are pondering all the sides of the issue and I hope to see some open academic debate soon, because the matter really deserves a good discussion.

      Keep up the good work and thanks for sharing it. Cheers.


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