September 13, 2009

On the mtDNA molecular clock (Endicott et al. 2009)

Further research is needed to improve our confidence in
molecular estimates of human evolutionary timescales.
First, the most reliable calibrations within the human tree
need to be identified. For mitochondrial DNA, this depends
on finding well-defined haplogroups that can be precisely
associated with dated palaeoanthropological evidence [17].
Second, the variation in observed rates across different
timescales needs to be accurately quantified [16–18].
Third, these patterns of rate variation need to be investigated
for nuclear data, including the Y-chromosome and
short tandem repeats.
The chief recommendation arising from the current
state of knowledge in the field is for a movement away
from reliance on the human-chimpanzee calibration;
instead, calibrations within the human tree are preferred
made using archaeological calibrations [15–17,35],
extending the efforts of earlier authors [3,60]. Considering
recent advances in phylogenetic methodology, there is now
a compelling motivation to employ statistical models that
take into account rate heterogeneity among sites and
among lineages, that correct for multiple substitutions
(saturation), and that incorporate directly the uncertainty
in the ages of calibrations used. Some methods also allow
the statistical evaluation of competing demographic
models, which can have an important influence on estimates
of rates and timescales [17,23].






Some previous topics on the question:
Trends in Ecology and Evolution doi:10.1016/j.tree.2009.04.006

Evaluating the mitochondrial timescale of human evolution






Maju said...

I appreciate this meditation, both by the researchers and yourself.

One of the items (from you) that caught my eye is: ... if the population stays small for a long time after arrival, the common matrilineal ancestor may "reset" several times, and the population's antiquity (based on mtDNA diversity) will appear to be much younger than it really is. What surprised me favorably considering that you are an enthusiast of recentist timescales.

From the researchers, I'd emphasize: The chief recommendation arising from the current state of knowledge in the field is for a movement away from reliance on the human-chimpanzee calibration...

I have dealt once on this issue (comment on Caswell 2008) and the conclusions seem that the genetic divergence of Pan and Homo is at least 15% older. This considering the largest usually managed date (7 million years - you can also read 5 million!) and the minimal extension needed to make it fit with the actual Chimp/Bonobo split and the formation of the river Congo (the physical barrier separating both species). With the occasional 5 million y.a. false reference and with a less conservative assunption for the bonobo-chimp split, the estimates could be even 100% larger.

All that assuming that the MC is really worth anything.

Ponto said...

The dates must comply with other data no matter how flimsy. For Europe, dates of occupation of AMH has to be tempered by actual archeological and fossil evidence with correct date estimations.

The populations of hominins, Neanderthal or AMH was always very small and subject to many bottlenecks, and inbreeding events. Naturally using the existing mtDNA or Y chromosome STRs is subject to many assumptions and errors, some age estimation has to be used. Finding more ancient dna for testing, easier with mtDNA, will help correlate dates.