February 08, 2016

mtDNA from 55 hunter-gatherers across 35,000 years in Europe

The fact that UP Europeans had mtDNA haplogroup M really destroys any lingering justification for a coastal migration that first brought (M, N) to Asia and then a subset (N) into Europe.

Another justification for the "Asia-first" model was the presence of Y-haplogroup C in Australians and Asians. But, that too was found in UP Europeans (K14).

So, I think things are looking good for my theory that Eurasians came out of Arabia northwards, interbred with Neandertals, headed both west and east, populating both Europe and Asia. The inferred date for both M and N (55kya) is on the cusp of the 50kya technological transition.

The authors also propose a major turnover in Europe at 14.5kya that replaced (not necessarily completely) the previous occupants. The authors write:
In European hunter-gatherers, our model best explains this period of upheaval as a replacement of the post-LGM maternal population by one from another source. Although the exact origin for this later population is unknown, the inferred demographic history (Figure 3 and 2b in Figure S2) suggests that it descended from another, separate LGM refugium.
Where was this LGM refugium?
Exactly where this new population came from is still unclear, but it seems likely that they came from warmer areas further south. “The main hypothesis would be glacial refugia in south-eastern Europe,” says Johannes Krause at the Max Planck Institute for the Science of Human History in Jena, Germany, who led the analysis.

Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2016.01.037

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe

Cosimo Posth et al.

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [ 1, 2 ]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [ 3–5 ]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [ 6–9 ]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [ 3–5, 8, 9 ]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

Link

13 comments:

terryt said...

"The fact that UP Europeans had mtDNA haplogroup M really destroys any lingering justification for a coastal migration"

I have never, for a moment, felt that theory was at all likely. For a start any coastal migration would have been confined to such a narrow ecological region that inbreeding depression would have rapidly become a huge problem. However I admit I have long thought that mt-DNA M probably entered East Asia from South Asia. But I have thought it increasingly likely that even M1'20'51 had originated in the Burma/China/northeast India region. Therefore, unlike N, M has left no trace of its movement east from Africa (or Arabia). But this paper provides an answer. M moved east north of the Tibetan Plateau but the branches it left as it passed have all become extinct.

Nathan Paul said...

Sounds Logical. If you incorporate LGM and Y haplo radiation of F,G,H, JKL the refuge most probably the corner of Middle East + South Asian border.

Kurti said...

I have been saying this for some time. When recently in ancient data from Caucasus mtDNA M appeared people were arguing about an "eastern migration into the region during the Neolitic."

But this doesn't make sense. We have pockets of local mtDNA M in North Africa as well mtDNA M in South Asia. Now we have mtDNA M in UP Europe as well ancient West Asia.

If we have mtDNA M in North Africa and South Asia`does it make sense to assume an eastern origin of mtDNA M? Doesn't it appear much more logical that both mtDNA M in North Africa as well in South ASIA are the result of migration from a third region which preferably is located inbetween? Something like West Asia maybe?

Obviously mtDNA M and N diverged in Western Asia and spred around the globe.

eurologist said...

The paper has a few high points and also some weird low points.

If I understand correctly (including the supplement), the authors conclude that L3 is no longer ancestral to M and N, but all three are subgroups of something older, closely related to L2.

Now, for me, that should be a strong hint that a subgroup of L2 migrated ooA, forming a chain of descendants of which only M and N survived ooA after Toba, while one subgroup (L3) was able to back-migrate to safety (mostly found in NE Africa, today). And L2 has been dated to upwards of 110,000 ya - fitting with the best archaeological and climatic ooA dates of ~ 120,000 to 105,000 ya.

Also, finding HG M in early AMH in Europe should not come as a surprise, since all major European male and female haplogroups appear to either originate from or are similar to those in SE or S Asia (and to a lesser extend, likely W Asia: ~Pakistan and a Red Sea refugium).

Again, this new evidence is in accordance with a spread of modern humans from S/SE/SW Asia ~ 55,000 - 50,000 ya (as evidenced by archaeological finds in the Levant and in Europe) - not at contradiction with it. However, trying to equate this expansion with ooA is borderline ludicrous.

Martin Lewitt said...

Since the Solutreans predate the 14,500 year turnover, have we been looking for the wrong genetic signature in modern and ancient Native Americans for evidence confirming the Solutrean hypothesis?

NeilB said...

Hi Dienekes, is it just me or has anyone else noticed that this paper states that Native Americans have mtdna haplogroups M and N? I thought thier mtdna haplogroups were confined to A,B,C,D and X. So where did the M and M come from. I apologise in advance if this is a totally idiotic question but can you point at a paper that details this? If nothing else my lack of knowledge may give you a good laugh. Any help would be most appreciated. NeilB

Slumbery said...

NeilB

The naming of the haplogroups (both mtDNA and yDNA) is a tad arbitrary. Just because two haplogroups both have a single letter as code that does not mean that they are on the same level of the "tree". M and N are upstream branches. C and D are subgroups of M, while A, B, and X are subgoups of N.

capra internetensis said...

TMRCAs are becoming increasingly well calibrated by ancient DNA. This paper puts M and N in the 55-47 kya interval. That range coincides with an interstadial, one of the longest relatively mild and stable periods since early MIS 5. There was also a pluvial in Arabia beginning around the beginning of MIS 3 (60 kya) peaking around 54 kya; later one in the Sahara peaked around 45 kya, but maybe began around 50 kya. These were probably not full-on Green Sahara events but they would have been much nicer than MIS 4. And of course this is also around the beginnings of the Initial Upper Paleolithic and shortly before the first securely dated anatomically/genetically modern human fossils in Europe and Siberia.

It also agrees very well with the consensus dates for Y DNA C, D, F, and E, and their early subclades like K (though E could be slightly earlier, but still probably MIS 3).

Though the error bars are still large it is extremely difficult to justify stretching them far enough back to make the AMHs who probably dispersed across much of Eurasia in the first half of MIS 5 our uniparental ancestors. (Minor contribution to the autosome is a different story.) Either there was another, later Out-of-Africa, or there was an expansion, probably well post-Toba, out of some Asian oasis. We can quite reasonably put the TMRCAs of BCDEF and L2'3'4'6 during the nicer parts of MIS 5 - possibly even back to the Eemian if we really stretch the confidence intervals. But CDEF itself is very unlikely to be that old, it coalesced in late MIS 5 at best, or MIS 4. The same with L3 - it could even date to the beginning of MIS 3. It is easy to suppose E back-migrated to Africa, harder to justify all of L3, or L3 + L4, unless we put the origin in Arabia or somewhere else very close to Africa where plausibly most of the daughter lineages have died out in the meantime.

@eurologist

Their mtDNA tree has no L4, L6, or L5 samples. There are 2 African branches of L3 there besides M and N branching from the L3 node. It's just the normal tree with a limited number of African samples (because that wasn't the point of the study).

The sister to L2 is L3'4'6. L6 is actually most common in Yemen, so could be originally Arabian. L4 is East African. L3 is both African and Eurasian. It would not be too far-fetched to propose that L3'4'6 coalesced in Southwest Asia but most of the original branches there were lost over time, though obviously Africa would fit just as well or better. African L3 is not a clade, it is 5 independent sister branches to M and N. However, the time resolution on mtDNA is very coarse, a few thousand years at best, so there may have been (almost certainly was) a substructure to L3 that is not recoverable from modern data, e.g. African L3 could be a clade in truth for a short time after the MRCA of L3 - or equally M and N could each be separately related to different African branches - there is no way to tell.

@NeilB

A,B, and X are branches of N, while C and D are branches of M. All letters except L are part of M and N, and the whole alphabet is part of L.

terryt said...

"We have pockets of local mtDNA M in North Africa as well mtDNA M in South Asia. Now we have mtDNA M in UP Europe as well ancient West Asia".

The M in North Africa, as well as just one of the M branches in South Asia are M1, very much downstream of basal M. This recently discovered M in Europe doesn't belong to any previously recognised branch. It is probably a basal branch within M.

"If we have mtDNA M in North Africa and South Asia`does it make sense to assume an eastern origin of mtDNA M?"

Yes, it does. Virtually all surviving branches appear to have basal relations in East Asia although a minority are apparently South Asian. But even these quite probably originated in northeast India.

"Obviously mtDNA M and N diverged in Western Asia and spred around the globe".

And that is what this paper shows. But, unlike the case of N, western M's have become extinct. As, presumably, have many western or Central Asian Ns.

"the authors conclude that L3 is no longer ancestral to M and N, but all three are subgroups of something older, closely related to L2".

That is very interesting. Fits Dienekes' Persian Gulf hypothesis.

TheXanian said...

@NeilB

MT-haplogroups A and X are descended from N, while MT-haplogroups C and D are descended from M, thus it's correct to say that Native Americans have both lineages.

NeilB said...

Dear Martin, I don't want to encourage anyone to take the Solutrean hypothesis seriously as I am not a believer myself, but the simple answer is yes. If the population that was purported to have migrated from Europe of America via the Atlantic route carried mtdna haplogroup M then they could be the ones you are looking for. In fact mtdna haplogroup M HAS been ffound in America. Check this paper out:https://wsu.edu › pubs › Malhi_et_al_2007
It's a pdf download and details the discovery of two 5000 year old in British Columbia. So I suppose the Solutreans could have been America. Enjoy NeilB

Kurti said...

@Terryt

As far as I remember one of the East Anatolian(Transcaucasus) samples I have seen in a recent study showed basal M* Haplogroup.

terryt said...

"As far as I remember one of the East Anatolian(Transcaucasus) samples I have seen in a recent study showed basal M* Haplogroup".

Thanks. I'll try to find out more. Fits, though.