The authors write:
One of numerous critics of «effective» mutation rate is D. Pontikos, who published in 2008 the results of his own calculations in his popular blog (Pontikos, 2008 ). Fig. 11 shows the results of Pontikos for a fixed interval of genealogical tree with the final size of 750000 – 1250000 individuals ... Those data match well with approximation (6), and the difference between them is only 0.3% and 1.4%, correspondingly.I have not checked all the details of this paper, but it should be a good read for anyone interested in the subject. Hopefully as more people look at the evidence, age estimation in mainstream journals will catch up with the state of the art.
I will not repeat the long and involved arguments and observations of my Y-STR series, but to summarize the argument for new readers:
- Most recent population genetics papers use an "effective" mutation rate that is about 3 times slower than the observed "germline" rate (of father-son pairs) and leads to age estimates that are about 3 times older than is justified.
- This mutation rate is applicable to the constant population case in which a man has 1 son on average. Population size may vary stochastically under this model, but it generally does not grow to large numbers within the time frame of Homo sapiens. For example, in the 2,000 or so generations since Y-chromosome Adam, a lineage evolving under this model would have 1,000 descendants on average, and the probability that it would have millions of descendants (like most real-world haplogroups in non-tribal populations) is practically zero.
- If the constant population case does not hold, due to selection, or demographic growth, or social dominance, then the effective rate is not applicable, and age estimates using the germline rate are much closer to the truth.
- The population sizes of real-world haplogroups are huge and could not have been generated by stochastic variation in a model where each man has 1 son on average. Most Y-chromosome age estimates in the mainstream literature are overestimates, and ascribe Paleolithic origins to Neolithic and Bronze Age founders.
About the influence of population size on the accuracy of TMRCA estimation, done by standard methods using STR locus complex
Dmitry Adamov, Sergey Karzhavin
Model calculations of influence of a population growth from the common male ancestor towards the final (present-day) population on the TMRCA estimation have been done. The estimation was made by linear and quadratic methods using STR locus of Y-chromosome. The modeling was done using computer simulation of a tribal population during fixed number of generations.
Universal approximations, allowing estimate the average correction for population effects as a function of the final population size, have been obtained. Authors calculated the variance of age estimations for an initial ancestor, which appears due to different types of population effects. Precision of the ancestral allele determining in a STR from the final population haplotypes set have been studied. An algorithm has been proposed for TMRCA calculation for a paternal (tribal) population, taking into account its total population size.