I wrote my previous post (The mtDNA clock ticks out of time) on the reliability of the mitochondrial DNA "clock" after doing my research on the D4h3 haplogroup (hg) in America for my post on it [mtDNA D4h3a (Continued)].
At the time, the variability in the amount of mutations along each lineage drew my attention. How could all these living people who came from a common root have differing amounts of mutations? After all, if there was a clock ticking of mutations at a steady rate, then all these people would have the same quantity of mutations. Well they don't. So, I suspected the clock was not reliable.
The smoking gun
The following image shows part of the tree that drew my attention:
I will just take a part of the whole tree to make my point:
- Between the root at D4 and D1 there are 2 mutations (marked in red on the image as 2 m), and the time that has passed is 23.5 - 17.8 ky. That is: one mutation every 11.72 - 8.9 ky.
- Between root D4 and D4h3 there are 7 mutations (7 m), so you would expect them to be 77 to 63 ky apart, but no, surprisinglythis branch is between 500 and 2,500 years YOUNGER than its root. What sort of a tree is this? branches are born before the root?
- Between D4h3 and some extant humans which I have chosen and marked with violet, we have:
- 10 mutations to individual #01
- 9 mutations to individual #26
- 18 mutations to individual #17
- Between D4h3a (in blue) and the extant humans on the bottom row, the amount of mutations varies between 3 and 12. A Four fold difference. The average is 6.95 mutations. I made a graph with these mutations and, surprise, it has a roughly bimodal distribution (the type I mentioned in my previous post). See below:
- Finally, the D4h3a haplogroup is dated at 18 - 14.3 kya, so based on the maximum and minimum mutations mentioned above (12 and 3) the clock can tick anywhere between: 1,191 and 6,000 years per mutation! (compare that to the 11,720 to 8,900 years calculated further up and you can see why the clock is pointless).
Implications of mtDNA clock violations
Despite these blatant violations of a mtDNA clock I thought that somehow I had misinterpreted the data or not understood how the mechanism works, so I did some research into the "clock" issue. The outcome was yesterday's post which substantiates (based on scholarly papers) that the clock ticks with variable rates.
The sad part is that time and time again, paper after paper I see dates defined for our Most Recent Common Ancestors (MRCA) and entry dates into America based on this non-existent clock.
Take the following example (Behar et al, 2014): “As the clock violation was observed only in a restricted number of specified cases, we applied the best available tools for estimating the ages of ancestral nodes.” .
The "best available tools" may surely be the orthodox point of view: A very long (>100 ky) incubation period in Africa, a small failed entry into the Middle East where modern humans briefly occupied the region some 90 kya. A sudden migration "out of Africa" some 50 kya followed by a quick expansion across southern Asia, Europe and Australia. A slower march north across East Asia and Siberia and a very late (<25 ky) entry into America.
I now believe that the mtDNA clock is irrelevant, it is guesswork and adjusted "by hand" to fit the dates defined by the orthodox point of view.
With this in mind, I believe that it is very likely that a group of humans could have left Africa with L3 haplogroup (hg). anytime between the 200 - 80 kya (yes the "failed" migration that took place 90 kya, could have been earlier), and then mutated along the M hg and D hg branches in say, 20 ky, allowing an entry into America of Modern Humans anytimg between 180 and 60 kya.
And I specifically give a very ancient date of 200 kya for the appearance of modern humans based on a Y chromosome haplogroup (Mendez et al, 2013) named A00 which was dated to: "338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. "
This early date is resisted by orthodoxy arguing that mtDNA and skeletal remains give more recent dates and therefore argue that the mutation rate used to estimate the TMRCA for the Y chromosome was simply too low . (I don't trus the mtDNA clock, and regarding bones... maybe the oldest human fossils have not yet been found.)
An early and rapid dispersion across Central and Eastern Asia could account for ancient Humans such as those found at Zhirendong, China with a minimum age of 100 - 113 kya (Wu et al, 2010). Fossils which prove that the "90 kya" migration into Asia was not a failure, the migrating humans settled in China.
These fossils have a mosaic of modern and archaic features (like a chin) that:
" any “dispersal” involved substantial admixture between dispersing early modern human populations
It therefore indicates a prolonged (>50,000 y) coexistence of late archaic and early modern humans across portions of Eurasia, and not just between Africa and Eurasia. Those late archaic humans include the Neandertals in western Eurasia until mid-MIS 3. They also encompass MIS 3 archaic humans in central Asia and Siberia and into at least MIS 5 in northern China..." 
Here we have a good explanation for the high proportion of Neanderthal genome in modern East Asians (Vernot and Akay, 2014) who have +20% more Neanderthal genes than Europeans.
It is a pity that Amerindians were not included in the study, it is likely that they have even more Neander genome than East Asians (based on other traits that they have inherited in a higher proportion than East Asians).
Have you noticed that Native Americans are rarely included in these studies?
Apparently 30% of Neanderthal's genome ended up in humans, of course no individual has more than 1 to 3%, but combine all those bits and pieces and it is one third of H. sapiens genome.
But getting to the point. Vernot and Akay suggest that Asians have more Neanderthal genes because there were two admixture events. One just after modern Humans left Africa and before they split into the Asian and European populations. And another, between Asians and Neanderthals after they split from the forebearers of modern Europeans. This double admixture gave them a higher dosage of Neanderthal DNA.
 Fig. S1. From Ugo Perego et al, Current Biology, Volume 19 1. Supplemental Data Distinctive Paleo-Indian Migration Routes from Beringia Marked by Two Rare mtDNA Haplogroups
 Wu Liua et al., (2010). Human remains from Zhirendong, South China, and modern human emergence in East Asia www.pnas.org/cgi/doi/10.1073/pnas.1014386107
 Vernot, B. and Akay, J., (2014). Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science, DOI: 10.1126/science.1245938
 Behar, D., et al., (2014). A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root. American Journal of Human Genetics, Volume 90, Issue 4, 675-684, 6 April 2012 doi:10.1016/j.ajhg.2012.03.002
 Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.
 Wilson Sayres, Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al. http://arxiv.org/ftp/arxiv/papers/1304/1304.6098.pdf
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