My own opinions on this matter have been repeated ad nauseam in this blog, so I will only briefly touch on a couple of points in this new article.
Contrary to the authors' claim that: "The size of the mtDNA database is very substantial: currently there are almost 13,000 complete non-African mtDNA genomes available, not one of which is pre-L3." there are plenty of pre-L3 mtDNA in Eurasia. Some (or indeed most?) of these might represent more recent African admixture, and one could argue why they believe that to be the case, but no one has ever studied pre-L3 Eurasian mtDNA to conclude that none of it had an ancient presence in Eurasia. The native non-existence of pre-L3 in Eurasia is a viewpoint, not a fact.
Second, the authors present the following table:
Note, however, that they have chosen to date the common ancestor of all African sublineages (to ~70.2ky using ML method), but they have not done the same for the common ancestor of all non-African sublineages (i.e., M+N). A recent study estimates M+N to be 77KBP and L3 to be 78.3KBP, with other possibilities depending on method and portion of the molecule examined.
At present, I see no good reason to think that haplogroup L3 originated either in Africa or Eurasia; one could argue for an African origin, but temporal priority for African L3 is not established. The only thing that seems to be established is that there are "more" L3 subclades in Africa, which is phylogenetically meaningless until the bifurcating structure of the L3 subtree is resolved. And, we should also not forget that the Toba eruption did not cause a volcanic winter in Africa, nor was Africa affected by the drying up of the Sahara-Arabia belt c. 70kya, both of which may have suppressed Eurasian mtDNA variation within L3, irrespective of its ultimate origins. And, as I've argued before, both Toba and the post-70kya ecological crisis are excellent candidates for a Eurasian bottleneck caused by pre-existing populations surviving in refugia such as this.
Finally, the authors dismiss the possibility of an overestimated autosomal mutation rate and its implications for human history: "Recent reestimates of the autosomal mutation rate from whole-genome pedigree data suggest a European–Asian split time of 40–80 ka, although they do not, as has been suggested, lend any support to a dispersal fromAfrica before 80 ka (36) (Genetics)."
Actually, the most recent estimate might be consistent with a ~96ky split of Africans from non-Africans, and the mutation rate issue is material to the timing of the African/non-African split. It's not clear where the needle will settle when the issue is resolved, but there's plenty of room for both pre- and post-Toba Out-of-Africa as things stand.
PNAS doi: 10.1073/pnas.1306043110
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia
Paul Mellars et al.
It has been argued recently that the initial dispersal of anatomically modern humans from Africa to southern Asia occurred before the volcanic “supereruption” of the Mount Toba volcano (Sumatra) at ∼74,000 y before present (B.P.)—possibly as early as 120,000 y B.P. We show here that this “pre-Toba” dispersal model is in serious conflict with both the most recent genetic evidence from both Africa and Asia and the archaeological evidence from South Asian sites. We present an alternative model based on a combination of genetic analyses and recent archaeological evidence from South Asia and Africa. These data support a coastally oriented dispersal of modern humans from eastern Africa to southern Asia ∼60–50 thousand years ago (ka). This was associated with distinctively African microlithic and “backed-segment” technologies analogous to the African “Howiesons Poort” and related technologies, together with a range of distinctively “modern” cultural and symbolic features (highly shaped bone tools, personal ornaments, abstract artistic motifs, microblade technology, etc.), similar to those that accompanied the replacement of “archaic” Neanderthal by anatomically modern human populations in other regions of western Eurasia at a broadly similar date.