Thursday, June 14, 2012

Autosomal Genetic Mutation Rates

Maju takes the occasion of the sequencing of the bonobo genome to succinctly take advantage of a very solid long term calibration point for establishing the mutation rate of the genome in Great Apes as about half as great as indicated in the paper describing the result. This is possible because a reasonable well dated geological event, the formation of the Congo River, is closely associated with the Bonobo-Pan divergence date. One of the authors provides an encouraging comment noting limitations of the date in the paper and the reasons that it is likely wrong in the direction that Maju suggests based on other data sets. Maju concludes:

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 [i.e. human-chimpanzee], as I have discussed again and again. Assuming that the 4.5:1 ratio 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.

This matters directly, because it strongly influences how we fit archaeologically dated bones into the chain of evolutionary events that gave rise to modern humans. For example, Homo Erectus is about three-quarter of the way from the Homo-Pan divergence to modern humans with an 8 million years ago estimate, but only about half way with a 4.5 million year estimate. Similarly, Ardi is about half way on the timeline from the Homo-Pan divergence to modern humans with the 8 million years ago estimate, but appears almost at the very moment of the Homo Pan divergence with the 4.5 million year estimate.

This also matters because mutation rate date calibration has broad importance for the interpretation of almost all genetically estimated dates in pre-history and ancient history, and a factor of two error rate is easily enough to throw a population divergence date from one historical era to another. The longer the calibrating time period involved, the more likely it is to reflect the long term average and avoid systemic errors in other dates.

Autosomal genomes, because they are some much more data rich and have lots of apparently selectively neutral sequences, are more attractive dating tools than uniparental Y-DNA which has been empirically shone to be incoherent in mutation rate terms, probably because it is subject to so much more selective pressure.

The lack of qualification within the paper on the estimate for the divergence date is really quite unfortunate because, while the sequencing of the bonobo genome has wide relevance in all sorts of areas, the divergence data is one of the most digestable nuggest of knowledge in the paper for an educated layman or for other genetics researchers, and hence one of the most likely to be widely disseminated.

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