Age of mtDNA haplogroup L3: about 70 thousand years

There are two aspects to this paper: first, it appears to be a solid attempt at inferring the age of mtDNA haplogroup L3. This haplogroup contains several subclades, including M and N, the two macrohaplogroups of the vast majority of Eurasians.

I am usually skeptical of very tight age estimates, but there appear to be no obvious flaws in the paper, and alternative mutation rates are used to derive the 70ka bound. Moreover, the 70ka age is consistent with what appears to be no longer in doubt, namely the arrival of fully anatomically and behaviorally modern humans all over the Old World, starting from the 50-40ka period.

The second aspect of this paper is its claim that pre-70ka dispersals are irrelevant to modern human origins. Indeed, if the early anatomically modern humans from the Levant (Qafzeh/Skhul) or the pre-Toba layers in Asia were ascribed to Out-of-Africa humans, then we would expect their genetic differentiation with East African mtDNA to trace back to Marine Isotope Stage 5 (~130-75ka), and indeed to its early stages, to account for the Mount Carmel hominins.

So, have we solved the Out-of-Africa riddle? Did the Out-of-Africa expansion take place after 70ka? I don't think so, not because there is anything wrong with the mtDNA age, but because the competing hypothesis, that is rarely, if ever discussed, is that there was an Into-Africa event post-70ka.

mtDNA furnishes the best evidence that humans trace their ultimate origins to Africa, since L3, of which M and N are subclades, is a young twig of the mtDNA phylogeny. As the authors of the current paper note:

Although the tree is highly starlike at shallower time depths, suggesting numerous episodes of rapid growth in the human population in the more recent past, it is only at a third of the time depth of the entire tree with the emergence of the L3 haplogroup that the first multifurcating them all the ancient diversity observed outside Africa) (Behar et al. 2008; Torroni et al. 2006; Watson et al. 1997).

Whatever humans were doing between ~200ka (when the first anatomically modern specimen is found in Ethiopia, and when the mtDNA phylogeny coalesces) and ~70ka (when the L3 node does), they were certainly not yet in the overdrive mode we find them c. 50ka when they begin making their grand entrance all over the surface of the planet.

So, while the ultimate roots of modern mankind are in Africa, there is no clear picture -yet- whether the post-70ka major expansion of humans originated in Africa. Certainly, it cannot have originated too far from it, because non M and N mtDNA is virtually absent throughout most of the world. But, it is not possible, yet, to exclude a Near Eastern post-70ka expansion that would make the ~100ka Levantine hominins ancestral to most modern humans, rather than irrelevant sidebranches.

There are several reasons why this may be the case:

1. East African L3 subclades are found in Arabia, where one finds a rich assortment of basal N subclades, as well as a not insignificant amount of M. These are often dismissed as the result of recent introgression, but they could in fact, and in part, be remnants of an older population, perhaps associated with the Persian Gulf Oasis hypothesis, and certainly absorbed by J1-bearing Arabian ancestors from further north.
2. The Y-chromosome phylogeny has no clear signal of Out-of-Africa ~70ka. On the contrary, Eurasia possesses DE*, D and E haplogroups, as well as CF, the major human lineage, with C being totally Asian. While Africa possesses the oldest Y-chromosome lineages (basal to CT), the evidence tilts towards Asia being the homeland of CT, which has the closest parallels to a post-70ka event.
3. Finally, Africa, including East Africa, shows, at present no sign for the presence of fully modern humans at the crucial time period. We do have, of course, Omo ~195ka, crucial anatomically modern humans in Ethiopia, but no clear sign of a bubbling volcano of a population c.70ka ready to errupt onto the Eurasian landmass.

At present, I consider the possibility that the recent post-70ka expansion of modern humans was initiated in the Near East as a possibility that cannot be dismissed. The evidence seems ambiguous, at present, since Eurasia may have a better case for such an expansion in Y-chromosomes, while Africa may have a better case in mtDNA (since it has more basal L3 clades than Eurasia).

A better characterization of Near Eastern mtDNA, especially from Arabia, as well as increased archaeological/palaeoanthropological investigations in East Africa/the Near East/South Asia is needed to finally uncover the material counterpart of the major human expansion that is written in our genes.

A third aspect of the paper is that the human expansion was linked to climate and not on the emergence of symbolic behavior. I have my own reservations on the whole concept of "symbolic behavior". We do see early evidence of such behavior in Africa, such as Blombos Cave in South Africa and North Africa. The authors of the current paper write:

There is an intriguing possible rider to this conclusion. North Africa has been entirely depopulated and repopulated, at least with respect to mtDNA variation (Pereira et al. 2010), since the time of the Aterian industry, where modern symbolic behavior is attested very early, similar to Southern Africa, and in contrast to Eastern Africa (Barton et al. 2009). We might therefore contemplate a possible North Africa ancestry for L3, with its rapid radiation corresponding to an early range expansion into Eastern Africa. However, any potential dispersal between the Mediterranean and the Horn of Africa around the time of the MIS4/3 transition would face severe environmental difficulties, unlike the “green Sahara” conditions of MIS5 and the early Holocene (Drake et al. 2010). We therefore conclude that an indigenous origin for L3 in Eastern Africa remains by far the most likely scenario.

As Mellars (2006) has argued, the early evidence for symbolically mediated behavior in both North and Southern Africa rules out any simple direct link for the expansion of L3 to (Ambrose 1998; Watson et al. 1997). Evidence of engraved ochre now extends back to at least 100 ka (Henshilwood et al. 2009), Nassarius marine shell beads were evidently present across the range of early modern humans from Southern Africa to North Africa and the Levant before 80 ka – possibly tens of thousands of years earlier (Barton et al. 2009; Bouzouggar et al. 2007; d'Errico et al. 2009; Mellars 2006; Vanhaeren et al. 2006) – and evidence for burial ritual is found in early modern humans in the Levant dating to 90–110 ka (Mellars 2006; Shea 2008). Thus, as suggested by Basell (2008) the demographic expansionsthat led to the first successful dispersal out of Africa seem better explained by the play of palaeoenvironmental forces than by recourse to the advantages of “modernity”.

The absence of markers of behavioral modernity in East Africa at the crucial time seems puzzling. Climate may have caused Out-of-East-Africa, but why would Out-of-East-Africans without clear signs of behavioral modernity be able to outcompete the "behaviorally modern" people of North/South Africa and the Levant? This observation, coupled with the absence of any clear identifiable palaeoanthropological population in East Africa at the time in question raises my unease about this scenario.

Moreover, while we can definitely ascribe symbolic thinking to the cases mentioned in the quoted text, but these may represent precursors, and not the full "package" of behaviors that allowed (or even prompted) our ancestors to spread around the planet around the middle of the last 100,000 years.

Mol Biol Evol (2011) doi: 10.1093/molbev/msr245

The expansion of mtDNA haplogroup L3 within and out of Africa

Pedro Soares et al.

Although fossil remains show that anatomically modern humans dispersed out of Africa into the Near East ∼100–130 ka, genetic evidence from extant populations has suggested that non-Africans descend primarily from a single successful later migration. Within the human mtDNA tree, haplogroup L3 encompasses not only many sub-Saharan Africans but also all ancient non-African lineages, and its age therefore provides an upper bound for the dispersal out of Africa. An analysis of 369 complete African L3 sequences places this maximum at ∼70 ka, virtually ruling out a successful exit before 74 ka, the date of the Toba volcanic super-eruption in Sumatra. The similarity of the age of L3 to its two non-African daughter haplogroups, M and N, suggests that the same process was likely responsible for both the L3 expansion in Eastern Africa and the dispersal of a small group of modern humans out of Africa to settle the rest of the world. The timing of the expansion of L3 suggests a link to improved climatic conditions after ∼70 ka in Eastern and Central Africa, rather than to symbolically mediated behavior, which evidently arose considerably earlier. The L3 mtDNA pool within Africa suggests a migration from Eastern Africa to Central Africa ∼60–35 ka, and major migrations in the immediate postglacial, again linked to climate. The largest population size increase seen in the L3 data is 3–4 ka in Central Africa, corresponding to Bantu expansions, leading diverse L3 lineages to spread into Eastern and Southern Africa in the last 3–2 ka.

Link