New mtDNA age estimation paper claims post-LGM expansion dates for most relevant lineages

In Europe as in Africa and Native America.

You know that I'm very much refractory to molecular-clock-o-logy because it implies many a priori speculations and assumptions that probably make the results to be wrong and yet these results are presented as if they were the genetic equivalent of the proverbial "rocket science", when they are nothing but educated guesses, often contradicting each other.

Still I think that this paper is worth mentioning for two reasons:

1. It gives age estimates that are clearly pre-Neolithic for most lineages, rebuking certain fanatic school that pretends to impose their clearly unfounded ideas of mass demographic replacement in the Neolithic and in a single direction, with a simple pattern. It is always good to have that kind of counter-arguments at hand.
2. The paper is freely available (open access) in spite of being published by Nature (in an open access  dedicated magazine titled Scientific Reports).

Hong-Xang Zhieng et al., MtDNA analysis of global populations support that major population expansions began before Neolithic Time. Scientific Reports (Nature) 2012. Open access ··> LINK [doi:10.1038/srep00745]

Abstract

Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.

Importantly, these age estimates must be considered as minimal ages (everything else assumed correct and equal) because the mutation rate used in at least some of the calibrations (Soares' rates) is clearly too fast, with even Dienekes (a former hardcore defender of very short chronologies and hyper-fast mutation rates) admitting to it as of late.

I quote from Dienekes:

Soares et al. were cautious, and they assumed an earlier Human-Chimp split than had been favored until then. However, a new paper by Langergraber et al. have used direct observation of the autosomal mutation rate and of ape generation lengths to argue for an even earlier Human-Chimp split: at least 7-8 million years ago, and as many as 13 million.

Which  is something I am quite glad that people has begun realizing because I was saying that more or less, in many different ways, since 2008 (refs.: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, etc.) And it was not just me because I was mostly reflecting what many scholars were finding here and there, publishing and seldom being listened to.

So these post-LGM dates are at best minimal dates, most probably requiring corrections that range between +15% and +85% (avg. +50%) per the Langergraber figures.

So for example, the authors estimate a 10-18 Ka window for the main expansions in Africa and Europe, that could well be a 15-27 Ka window in fact (max. 10-33 Ka.)

Figure 4: European expansion lineages from median-joining network
Blue, GBR; purple, FIN; yellow, CEU; cyan, TSI; green, IBS.

However mtDNA specifically has other major issues, absent in nuclear DNA (autosomes or Y chromosome): that the mutations happen so spaced in time for the whole mitochondrial DNA chain, which is very short, that the main factor is not the molecular tic-tac but population dynamics.

I should write more extensively on this matter but D. Pierron already did for me in 2011 (discussed here).

As I understand this problem of extremely unequal mtDNA lines, these irregularities are mostly caused by relatively large populations in which mutational change is effectively stopped by mere drift. As most women in the population experience no mutation in their mtDNA, the mutants have all the tickets to see their novel, derived, lineages drifted out by their relatives with a conservative one.

So in my understanding mtDNA "clock" must only be counted (if at all) from the root and not, as is usual, from the ends. This is a total game changer because counting from the root, H must be slightlty older than U, while counting from the ends that is impossible.

I never count mtDNA from the ends even if I know that most geneticists and aficionados do because I find such a procedure totally thoughtless, a mechanical imitation of a method that works for longer DNA chains which accumulate mutations in every generation, quite unlike mtDNA, which is much more stable.

En fin, the paper provides us with another opportunity to reconsider the highly speculative but incredibly popular field of molecular-clock-o-logy. It also provides some nice MJ networks of many haplogroups, which speak on their own, one of which (Europe), I used to illustrate this entry.