Plural Lineages in the Human mtDNA Genome
At the time I wrote Age and Origin of the Human Species, published research on the mitochondrial genome could not support conclusions regarding human origins. Accordingly, I had to leave it an open question. The cited research by Awadalla, Eyre-Walker, and others, was challenged. Innan and Nordborg review the follow-on studies of recombination. http://walnut.usc. edu/~magnus/papers/InnanNordborg02-MBE.pdf
Bottom line, there may well be some recombination, but you can't prove it the way Awadalla tried to.
For the purposes of this discussion it isn't necessary to even understand what recombination in mtDNA means, let alone the details of how it is accomplished: we can simply treat it as an 'object' in this analysis.
There has been unanimous and vociferous insistence in the media, on one critical afrocentrist assumption: all modern human mtDNA is 'so similar' that it had to have come from a single woman. This is known to the public as the 'African Eve' theory, and researchers speak of the same idea as 'a single genealogy for the mtDNA genome'. Far from proving the out-of-Africa theory, that assumed 'single source of all modern mtDNA' is an absolutely necessary pre-condition for their theory of afro-replacement to be true. But, there is afundamental reason to reject the claim that all human mtDNA is 'so similar' that it must come from one woman!
Consider this sentence, [italic emphasis mine] from the first paragraph of the Innan & Nordborg paper, "The argument for recombination is based on the observation that the pattern of polymorphism in mtDNA is incompatible with a single genealogicaltree and unique mutations." Thus, there are three things that might account for the observed pattern of polymorphisms: 1) recombination, 2) more than one lineage, or 3) multiple mutations at many sites. Look at Figure 2 of the Innan paper and you will see that the possibly recombined or repetitively mutated sites are scattered throughout the genome, and do not occur only in the hypervariable region. Note that the quote from Innan & Nordborg implies that the less recombinationor repetitive, same-site mutation has affected the mitochondrial genome, then the LESS likely it is that there is a single genealogy for the human mtDNA genome. In other words, unless there has been enough repetitive mutation or recombination to account for the observed pattern of polymorphism, then not all mtDNA is from the same source, as claimed by proponents of the 'African Eve' or African radiation-and-replacement theories.
On the other hand, the more recombination, or repetitive mutation that has occurred, then the more Eve's age has been under-estimated. That is true because the effect of either repeated mutations at one site or recombination is to make the mtDNA genome appear younger than it really is. If we knew Eve's era from historical or anthropological data, we could compare that date with the one derived from the mtDNA coalescence algorithm. The difference between the calculated coalescence result and the historical date would reveal the combined effect of recombination and repetitive mutation. If that combined effect is obviously insufficient to account for the observed pattern of polymorphism then we may infer a plural genealogy for the human mtDNA genome.
There is nothing in the historical or anthropological record to independently establish the era of (a supposed) humans speciation in Africa. However, the situation in Eurasia is very different. There we can calibrate the coalescence date of Eurasian strains of mtDNA with an historical event, anthropological evidence, and research on the human y-chromosome. Thus we can infer the effect (hence extent) of recombination and repeated mutations, by comparing those other dates with the result of the mtDNA coalescence calculation. If the fit on all these dates is fairly close we can be assured that little recombination or repetitive mutation has occurred, hence the observed pattern of polymorphism must be interpreted to reveal a plural genealogy for the mtDNA genome.
Refer to the Mishmar paper at, http://www.pnas.org/cgi/reprint/100/1/171.pdf (second full paragraph, right-hand column, on the first page) for a brief description of the M and N mtDNA lineages. Technically, one can't say that these are 'Eurasian specific' lineages, only because they have found their way into the African population. Note Mishmar's admission concerning the afrocentrists' assertion that M and N evolved/diverged in North Africa. This paper's authors come about as close to admitting that is implausible as they can, while remaining politically correct and afro-orthodox. On the afro-view, M and N lineages diverged from the African Eve's lineage, while on my view they are the oldest surviving Eurasian lineages. One's view, as to the origin of the M and N lineages, doesn't affect the argument I am making in regard to determining the relative contribution of repeated mutation and/or recombination versus plural genealogy.
Mishmarcalculates the M and N lineages are both 65,000 years old, and there was a lot going on in Eurasia around -65 kyr. The last common paternal ancestor of Europeans lived at -59 kyr, as calculated from y-chromosome data. So we have a date for the male counterpart of Eurasian Eve, calculated from a different genome at a date within 10% of agreement. Then, 'modern' human artifacts are found in Eurasia by -50kyr. Allowing for the fact that it is unlikely that we have found the very first artifacts, and that people may have been genetically modern for awhile before developing human (Homo sapiens sapiens) culture, those dates are in remarkable agreement. Add to that, radiation into Australia by anatomically modern humans may have occurred before -60 kyrs, and no doubt that radiation took some millennia.
It begins to look like that -65kyr coalescence date is right on target, and we could claim there is no influence from recombination and repeated mutation, so all the sites reflected in Figure 2 are evidence for plural genealogies: QED! However, that would be disingenuous, because I believe there has been some recurrent mutation, though it is possible they have fully accounted for it in their model, and some recombination, which they probably have not explicitly factored in. So, I would expect that coalescence date to be a little more recent than the era of a genetically significant event, which actually caused modern humans to differentiate from a relatively advanced population of archaic sapiens.
One reason we can expect the loss of lineages existing before the modern type differentiated, is that there could have been a population 'bottle-neck' associated with speciation itself. Moreover there must have been a severe population loss in temperate or higher latitudes when Mt. Toba erupted around -74kyrs and caused a nuclear winter in Eurasia. That savage selection event alone would account for the loss of archaic Eurasian mtDNA lineages. It may be significant that the two oldest Eurasian mtDNA lineages the same age. The fact that they both date from the same era makes it more plausible ancient lineages were lost in a specific selection event and/or population bottleneck rather than only through 'lineage sorting'. It is comparatively unlikely that two mtDNA lineages would simultaneously diverge from a putative African lineage, and both (but only they) migrate from Africa and survive to the present. It is far more reasonable and parsimonious to assume that no archaic Eurasian lineages survived two severe bottlenecks, and subsequent lineage sorting, in the indigenous Eurasian population.
So, even if we assume that the actual population constriction occurred prior to the coalescence date, and associate it with the obvious selection event of Toba's eruption, the -65kyr coalescence date still calibrates quite closely. If we compare the dates, we note that -65 kyrs is only about 12% less than the putative genetically significant date of -74 kyrs. So we can see that both recombination and repeated mutations can only have had a small effect on the calculation of a coalescence date, hence there are not many sites in the mtDNA genome that have experienced recombination or repeated mutation. But, look at Figure 2, where it is evident that many of the sites show evidence of either recombination or repeated mutation, or else they are evidence of more than one genealogy for the mtDNA genome! Accordingly, most of the sites graphed in Figure 2 must be considered as evidence for more than one mtDNA genealogy. Therefore, M and N lineages are not derived from the African genome, but represent the most ancient, surviving lineages of the Eurasian type. Hence M and N are Eurasian specific lineages that only entered Africa through radiation, rather than coming from Africa
In conclusion, recombination and repetitive mutations are not enough(by a wide margin) to explain the observed pattern of polymorphisms in the mtDNA genome. Therefore, there is more than one genealogy: there are two Eurasian maternal lineages, associated with the speciation of modern humans (Homo sapiens sapiens) in Eurasia, and another, African lineage. This falsifies the 'Afro-radiation and replacement' theory, and the politically correct shibboleth that 'we are all Africans'. As explained in Age and Origin of the Human Species, the evidence already pointed to a recent, Eurasian origin for modern humans. Only the assertion of a single genealogy for mtDNA could be construed as evidence of African replacement, and that assumption is revealed as unjustified.
Mishmar et al, is probably correct to attribute variation, in lineages derived from M and N, to natural selection. One supposes they theorize that mtDNA selection took place in the last 50kyrs (Wallace's date for an African radiation, quoted in NYT, "Ice Age Ancestry") in order to accommodate their theory to the constraints of assuming an African origin for modern humans. However, it is more plausible that such selection took place in very ancient times (when pre-human species were adapting to a cold climate) and was only retained at high latitudes, among people living at low culture levels, as the adaptations come at a fitness cost, and thus were lost when and where physical adaptations were superseded by elaborated clothing and shelter, in the temperate zone and the recent era.
FIG. 2 Evidence for recurrent mutation or recombination (or both) in human mtDNA (data of Ingman et al. 2000). Each point represents the comparison between a pair of polymorphic sites. The point is black if the pattern of polymorphism for the pair of loci is such that either recombination must have occurred between the loci or recurrent mutation affected at least one of the loci. The point is white otherwise.
If recombination has occurred, and (importantly) the probability of recombination increases with distance between sites, white points are expected to be clustered along the diagonal (because recombination is less likely to have effected closely linked sites). Recurrent mutations, on the other hand, might be expected to give rise to a pattern that does not depend on the distance from the diagonal, leading to black "crosses" against a white background. The D-loop is visible as a cluster of such crosses in the upper right corner (position 0 corresponds to the first position after the D-loop).