Dating of the human ape splitting by a molecular clock
These unique variants create nodes in the mt DNA tree at the base of regional mt DNA lineages (haplogroups).
These nodes must be taken into account when calculating genetic distances.
However, uncertainty in the alignment is ignored, resulting, possibly, in overstated certainty in phylogeny estimates.
We develop a joint model for co-estimating phylogeny and sequence alignment which improves estimates from the traditional approach by accounting for uncertainty in the…
Between the nodes are periods of the accumulation of seemingly "neutral" mutations which can be considered as acting in a clock-like fashion.
Having determined this, we concluded we could use the accumulation of mt DNA variation between nodes to calculate relative ages of regional populations.
Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creature, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting.
I have learned a lot more from your response than reading many papers.
I hope that I will be able to receive your insights on many important issues in our field.
I would love to hear your comments on some of them so that we can carry out additional research.
The most striking thing to me upon reading your letter was that you have seemingly unknowingly admitted a fatal flaw in the field of molecular phylogeny that would qualify this field as it is presently practiced as, I am afraid to say, pseudoscience.