Ancient MtDna from Europe-Single Dispersal from Africa and Population Turnover

Angela

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These are complete mito-genomes. Some very interesting stuff.

See:
http://www.cell.com/current-biology...m/retrieve/pii/S0960982216000877?showall=true

[h=1]Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe[/h]

  • Newly generated pre-Neolithic European mtDNA genomes triple the number available
  • •Clade M found for the first time in Europe, prior to the Last Glacial Maximum bottleneck
  • •Rapid single dispersal of all non-Africans less than 55,000 years ago
  • •Previously unknown major population shift in Europe at the end of the Pleistocene
[h=2]"Summary[/h]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."

I've only skimmed it so far. I'll have more to post later. It seems great grandmama's U2 was once all over northwestern Europe but was replaced in good measure, only to re-emerge later further east. Of course, M was also replaced.

I had always suspected that U5a came from another refugium.

I'm not sure, as always, about the dating.
 
Loads of New mtDNA from Paleo-Europe

Paleo-Euro mtDNA results weren't totally unexpected. Pre-LGM mtDNA is all extinct: U5*, U2*, U8*, U2'3'4'7'8'9*, U*, M*, R*, N*. Post-LGM mtDNA is under deep subclades of U5b and U5a that are found today. The results from Italy are consistent with Central Europe, probably because it was not isolated by ocean back then. The same type of extinct U8(U8c) was found in Italy and Czech Republic dating over 30,000 years.

27,000 year old U2 from Belgium is pre-U2e


EDIT: Paleo-U2(27,000 years old) from Belgium shared 16092C with U2s from Neolithic Europe, but that might be a coincidence. I was wrong to assume this means they're related. The Paleo-U2s also share mutations with U2e(16129c, 16189C!) that the EEF U2s lack. It's possible the EEF U2s are also related to U2e, and therefore related to the Paleo-U2s.


The Paleo-U2 from Belgium is pre-U2e. It shares T5426C, G16129c, T16189C!, and 217C with U2e. 217C according to phylotree markes U2e1'2'3, but these new samples prove this is false. 217C is apart of U2e and the U2e1'2'3 branch doesn't exist, it is just plain U2e.
 
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I'm looking forward to your update. So we have a great expansion 55 thousand years ago and expansion of new people into Europe 14,500 years ago. I bet they are WHGs. :) Great, now we have to look for their source. Was it Spain or Anatolia?
 
and expansion of new people into Europe 14,500 years ago
Or just within Europe (from one part to other regions).
 
it suggests the same as has been suggested Y-DNA in certain areas : sometimes a small tribe expands and occupies large territories at the expense of other tribes

I find
(B) Post-LGM re-expansion in Europe while ice sheets retracted
and
(C) Late Glacial shift in mtDNA hg frequency.
most intriguing.
 
Motala 2 is Y-I2c2 and mt-U2e1, probably descending from post-LGM northward expanding reindeer hunters
the other Motala with known Y-DNA, Loschbour and Bichon are all Y-I2a1 and, with only 1 exception mt-U5, probably descending from tribes expanding with forest growth in Europe

so forest HG-Fishers (Azilian, Tardenoisian, Sauveterrian, Maglemosian, ...) are replacing (Magdalenean) reindeer hunters
 
In case everyone hasn't seen this:

https://www.newscientist.com/articl...campaign=hoot&cmpid=SOC|NSNS|2016-GLOBAL-hoot

From the article:

"About 14,500 years ago, when Europe was emerging from the last ice age, the hunter-gatherers who had endured the chilly conditions were largely replaced by a different population of hunter-gatherers.


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.

Lazaridis also chimed in:

"“The population turnover after 14,500 years ago was completely unexpected,” says Iosif Lazaridis at the Harvard Medical School in Boston. “It seems that the hunter-gatherers of Europe braved the worst of the ice age during the last glacial maximum but were then replaced when the ice age had begun to subside.”"

I'm not sure the data prove that, although Razib Khan also seems to be convinced.
http://www.unz.com/gnxp/human-popul...ion&utm_source=twitterfeed&utm_medium=twitter

"The ubiquity of population replacement is the reason I recent predicted that the first Aurignacian genome would show no relation to modern Europeans. (I was correct for what it’s worth) That is, modern humans in Europe have no special relationship to the first modern humans that settled Europe 45,000 years ago. The work on ancient DNA does suggest that modern Europeans have hunter-gatherer ancestry…but how deep does this go? I hazarded that perhaps the Gravettians are the earliest candidates for being the direct ancestors of the “Western Hunter-Gatherers” (WHG), who contribute a substantial portion of their genes to modern Europeans through Mesolithic hunter-gatherer populations. But, I wouldn’t be surprised if the genomic character of European Mesolithic hunter-gatherers was determined after the Last Glacial Maximum, ~20,000 years ago.

I think the first part may well be correct. As to the second part I'm really not sure. They seem to be saying that U5b is a signal of this replacement, and since they mention a possible Balkan refugia, that would mean very little role for the repopulation of Europe from Franco Cantabria, wouldn't it, other than perhaps the U2 that showed up in Motala, and the U8 clade that they seem to think is extinct?

Yet this conclusion seems to me to be largely drawn from the changes in central Europe. There are whole swathes of Iberia unaccounted for, and parts of Italy, and, of course, the Balkans. These Central European scientists like Haak and Brandt and Krause have this tendency to see "Europe", and changes that effect "Europe" as being equal to what has happened in "Central Europe". I'm surprised that Lazaridis follows suit. Of course, the Reich Lab has a whole mess of ancient Dna from southeastern Europe upon which they're sitting, so perhaps they all know something we don't know?

Also, there was some U5 in Europe before the LGM, eastern Europe to be precise, so, taking both things together, I don't see why this couldn't just mean a population bottleneck, even in more central Europe, although I suppose it could be both. Khan does address that possibility but seems to believe it's not enough of an explanation.

"The lineage that to a great extent has been canonical as that of European hunter-gatherers, U5, seems to have increased in frequency only late in the Pleistocene, during the above warm period. Because of the nature of random genetic drift we do expect lineage to go extinct over time. These are mtDNA, direct maternal lineages, so only one locus in the genome (though mtDNA is copious, so tends to be low hanging fruit for any new extraction technique). The combination of low long term effective population sizes and meta-population dynamics on the Eurasian fringe might mean that these are not unexpected results. But as suggested in the paper there is also a great possibility that the disruption of the interstadial resulted in some advantage to a particular subset of Pleistocene Europeans, who expanded rapidly, replacing their competitors. Many of the hunter-gatherers of the Mesolithic have relatively low genetic diversity in comparison to modern populations, suggestive of the small population sizes on the European frontier. The expansion of U5 at the expense of other lineages though around ~14,500 years ago does seem to not be attributable purely to chance according to the models tested within the paper. "

So, if it's not pure chance, and it's some advantage, was it in the tool kit? This would be the Gravettian tool kit we're talking about, yes? Where did that start?

Oh, only one mtDna "H" showing up. That brings up all those old questions about the reliability of those results for "H" in ancient Iberia.
 
there seems to have been replacement upon replacement upon replacement in Europe
even before the arrival of farmers and of Indo-Europeans the European population has been replaced several times
 
@Angela,

I agree with you. I've noticed the press will look for one big idea and act as if it is fact/proven. When in reality it's not proven and more complex. And you're right Central Europe=Europe in lots of ancient DNA studies. For the most part other regions went through the same stages, but we have nothing SouthEast of Hungary after or before Neolithic which is a huge hole in data.

IMO, we'll get lots this year and we'll see differnt things were going on there. I remember after Laz 2014 and it seemed everything was figured out, some argued all data is from West Europe and we need data East of Germany to get a fuller picture(esp. ANE) of what changed after Neolithic. And this turned out to be very prophetic. I think the same will be true for data from SE Europe.
 
Motala 2 is Y-I2c2 and mt-U2e1, probably descending from post-LGM northward expanding reindeer hunters
the other Motala with known Y-DNA, Loschbour and Bichon are all Y-I2a1 and, with only 1 exception mt-U5, probably descending from tribes expanding with forest growth in Europe

so forest HG-Fishers (Azilian, Tardenoisian, Sauveterrian, Maglemosian, ...) are replacing (Magdalenean) reindeer hunters

I think this is a sensible theory, that HG's who lived in a southern refuge expanded back north after the glaciers retreated and were possibly better adopted to handle the new climate in europe because their southern refuge resembled it while the native inhabitants struggled as their primary food source began to disappear.
 
@Angela,

I agree with you. I've noticed the press will look for one big idea and act as if it is fact/proven. When in reality it's not proven and more complex. And you're right Central Europe=Europe in lots of ancient DNA studies. For the most part other regions went through the same stages, but we have nothing SouthEast of Hungary after or before Neolithic which is a huge hole in data.

IMO, we'll get lots this year and we'll see differnt things were going on there. I remember after Laz 2014 and it seemed everything was figured out, some argued all data is from West Europe and we need data East of Germany to get a fuller picture(esp. ANE) of what changed after Neolithic. And this turned out to be very prophetic. I think the same will be true for data from SE Europe.

I just don't get how they can make statements like "It seems that the hunter-gatherers of Europe braved the worst of the ice age during the last glacial maximum but were then replaced when the ice age had begun to subside." This assumption that only Central Europe is Europe just rubs me the wrong way. If the early pre-U2e and U8 of western and central Europe did get overwhelmed by new U5b2, and they came from the Balkans, it's just one regional European group overwhelming another one. Both groups are European hunter-gatherers, although maybe WHG wouldn't fit anymore as a name.

Of course, I don't know that there's a consensus as to where the Gravettian formed. Perhaps in the east somewhere beyond whatever mystical line is chosen as the division between Europe and Asia, but also perhaps in the Near East somewhere, in which case they are "newer" to Europe, but do even serious scientists think in terms of which group was more "European"? It's ridiculous. If we go by chronology, the first and original Europeans might have been yDna "C" and mtDna M and U2e. If native equals first arrivals, then the number of modern Europeans who are descended from the natives is vanishingly small.
 
"The ubiquity of population replacement is the reason I recent predicted that the first Aurignacian genome would show no relation to modern Europeans.

This has already been pretty much known before, that Gravettians largely replaced Aurignacians.

Peștera cu Oase1 (mtDNA N, Y-DNA F) and Kostenki14 (Y-DNA C1, mtDNA U2) were Aurignacians, AFAIK. However, Y-DNA F (basal paragroup) and C1 as well as mtDNA U2 appear in Europe as minority lineages also in Upper Paleolithic, Mesolithic and Neolithic times. So the extinction of Aurignacians was not complete but instead their descendants were partially assimilated by Gravettians (possibly also by First Farmers outside of Europe).

That Aurignacian Y-DNA probably still exists in Europe also today, but at extremely low frequencies:

http://www.ancestraljourneys.org/palaeolithicdna.shtml

The new genome with R* mtDNA is actually described as Proto-Aurignacian, not Aurignacian proper:

http://www.ancestraljourneys.org/palaeolithicdna.shtml

About 14,500 years ago, when Europe was emerging from the last ice age, the hunter-gatherers who had endured the chilly conditions were largely replaced by a different population of hunter-gatherers.

I'm not sure - we have U5 before LGM, and more U5 after LGM - so why do they think that someone came from outside of Europe?

And why do they think that those M*, R*, N* etc. lineages had endured the LGM before getting replaced ???

Maybe they simply did not endure the LGM. Did I miss something in the article which says that they survived the LGM ???

Without autosomal and Y-DNA analyses of pre-LGM and post-LGM samples, they shouldn't be drawing such sweeping conclusions.
 
If we go by chronology, the first and original Europeans might have been yDna "C" and mtDna M and U2e. If native equals first arrivals, then the number of modern Europeans who are descended from the natives is vanishingly small.

U2e is still present in Europe today.

BTW - Eurasians h
ave ca. 3% Neanderthal admixture even though no Neanderthal Y-DNA and mtDNA survived to modern times.

This shows that part of our autosomal ancestry can be derived from a prehistoric group even if their uniparental markers got extinct.

And this is the case also with Aurignacians - for example - because their autosomal signatures are present in modern Europeans:

Check these two articles:

http://science.sciencemag.org/conte...true&related-urls=yes&legid=sci;346/6213/1113

https://www.genomeweb.com/sequencing/ancient-human-genome-points-ancestral-meta-european-population

Autosomal maps show that Kostenki14 was most closely related to West Eurasians,
unlike Ust'-Ishim who was closer to East Asians:

1) Kostenki14:

k14ibdext1.png


2) Ust'-Ishim:


39e84d81c245.png


This shows that the genetic split of ancestors of West Eurasians and ancestors of East Asians happened mostly before the lifetimes of those men.
 
Fire Haired 14 said:
And you're right Central Europe=Europe in lots of ancient DNA studies.

Indeed.

It seems that Western-Central Europe was frequently being repopulated by migrations from Southern-Eastern Europe in prehistory. Yet, for some reason all these articles claim that "Europe was repopulated" - not that just parts of Europe were repopulated by groups from other parts of Europe and Russia. Also Northern Europe was being repopulated by groups from both South-West and South-East of Europe, as well as from Russia.

I have a suspicion that such narratives are politically motivated to fit nicely into the "Refugee Crisis" (they seem to be saying: "you see, Europeans were replaced so many times in the past, so why do you resist getting replaced too, it is not really so bad to get extinct and replaced").

Non-European immigration is more "trendy" and more politically correct nowadays than Eastern European one, for example.

"We are all Russkies" is not what people in the European Union want to hear. But "we are all MENA peoples" - why not. :)

Of course sweeping migration waves from outside of Europe also played a huge role (especially early Neolithic farmers).

But let's not exaggerate and let's not - each time we find a change in haplogroup frequencies - claim that all of Europe was repopulated. As if migrations are only possible either into or out of Europe, and not within this huge continent (or rather just a western peninsula of Eurasia).

We also really need more aDNA from outside of Europe (as well as from undertested parts of Europe) for comparison.
 
there seems to have been replacement upon replacement upon replacement in Europe
even before the arrival of farmers and of Indo-Europeans the European population has been replaced several times

See my post above - some of those replacements could be "in situ" (groups expanding just within Europe, not from outside of Europe).

For example the Corded Ware - all R1a, but subclades found in Central European CW were different than modern R1a subclades there. However, there is no doubt that modern subclades found there also originated from Corded Ware, just from another part of it. After all the Corded Ware horizon stretched from the Volga River in the east, all the way up to the Rhine River in the west. So those were expansions "within", not from outside.
 
Non-European immigration is more "trendy" and more politically correct nowadays than Eastern European one, for example.

"We are all Russkies" is not what people in the European Union want to hear. But "we are all MENA peoples" - why not. :)

Of course sweeping migration waves from outside of Europe also played a huge role (especially early Neolithic farmers).
No reason to be afraid. Look at Europeans repopulating America and Australia. That's how it goes in this world. After few centuries, what's left after you will be few short pieces of your DNA.
 
I think the first part may well be correct. As to the second part I'm really not sure. They seem to be saying that U5b is a signal of this replacement, and since they mention a possible Balkan refugia, that would mean very little role for the repopulation of Europe from Franco Cantabria, wouldn't it, other than perhaps the U2 that showed up in Motala, and the U8 clade that they seem to think is extinct?

Yet this conclusion seems to me to be largely drawn from the changes in central Europe. There are whole swathes of Iberia unaccounted for, and parts of Italy, and, of course, the Balkans. These Central European scientists like Haak and Brandt and Krause have this tendency to see "Europe", and changes that effect "Europe" as being equal to what has happened in "Central Europe". I'm surprised that Lazaridis follows suit. Of course, the Reich Lab has a whole mess of ancient Dna from southeastern Europe upon which they're sitting, so perhaps they all know something we don't know?

Also, there was some U5 in Europe before the LGM, eastern Europe to be precise, so, taking both things together, I don't see why this couldn't just mean a population bottleneck, even in more central Europe, although I suppose it could be both. Khan does address that possibility but seems to believe it's not enough of an explanation.
I think you are right. The severe bottlenecking effect on peripheries of Europe could look like population replacement with somewhat different type of HGs. Even more if these HGs received some extra admixture from Africa or Asia while in refugium.

Many of the hunter-gatherers of the Mesolithic have relatively low genetic diversity in comparison to modern populations, suggestive of the small population sizes on the European frontier. The expansion of U5 at the expense of other lineages though around ~14,500 years ago does seem to not be attributable purely to chance according to the models tested within the paper. "
In this case I can expect the refugium to be in South Balkans and Anatolia, for WHGs. In this case West should become East.

So, if it's not pure chance, and it's some advantage, was it in the tool kit? This would be the Gravettian tool kit we're talking about, yes? Where did that start?
Were they Magdalenians at this time? Sort of cousins of Gravettians?

Thanks for the summary Angela. I can't find time to read anything these days.
 
No reason to be afraid. Look at Europeans repopulating America and Australia. That's how it goes in this world. After few centuries, what's left after you will be few short pieces of your DNA.

Tomenable isn't afraid of anything. Why would you think he's afraid? He's revealing the possible agenda of some in the media who writes about ancient European DNA. I agree because after DNA from ancient Ireland, I saw BS articles saying Irish are Middle Eastern and "Black Sea" as opposed to other Europeans. Other articles have called Yamnaya "Asian nomads"(images of Genghis Khan will wrongly come to mind).

He brings up a good point, that it is difficult for us living today to understand that the world genetically/racially was differnt 1,000s of years ago. So, 8,000 years ago the Middle East wasn't an exotic place to Europeans. And it is hard for us to understand Europe and Asia are man made locations and we need to see them as continuous pieces of land when discussing genetics.
 
My prediction is: Y DNA I2, mtDNA U5b bearing WHGs came out of a SouthWest European refugium and migrated to West Asia giving modern West Asians.

BTW, I've read leaks about upcoming paleo-European DNA. They don't tell much and have nothing to do with WHG AFAIK. But they suggest there's lots of Paleo-European ancestry in "Asia".
 
This has already been pretty much known before, that Gravettians largely replaced Aurignacians.

Peștera cu Oase1 (mtDNA N, Y-DNA F) and Kostenki14 (Y-DNA C1, mtDNA U2) were Aurignacians, AFAIK. However, Y-DNA F (basal paragroup) and C1 as well as mtDNA U2 appear in Europe as minority lineages also in Upper Paleolithic, Mesolithic and Neolithic times. So the extinction of Aurignacians was not complete but instead their descendants were partially assimilated by Gravettians (possibly also by First Farmers outside of Europe).

I'm not sure about that.

Proto-Aurigancian was in Italy and Catalunia 45 ka, not in the Balkans.
43.5 ka Aurignacian emerged along the Danube in Austria. From there it spread into Schw¨bische Alp, south-Germany.
Only around 39.5 ka it spread further along the steppe-tundra areas till Kostenki. Before that there where allready people in Kostenki. We don't know from which Kostenki 14 descends, Aurignacian or those who were there before.

As for Oase1, it was in the Balkans and afaik no culture was identified. It appeares to be a line that got extinct without any traces. Both in Y- and mt-DNA it is an isolated branch. Also autosomal DNA doesn't fit.
Oase1 is the only proof of Neanderthal admixture that happened in Europe or just before entering Europe.
Neanderthal admixture happened in the Levant or the Zagors Mountains. I don't think Aurignacians or Gravettians admixed inside Europe. Aurignacians body type was more Neanderthal-like than Gravettians, but I think not much Aurignacian DNA is left alive today.

My theory is still that Aurignacians were C1a2-V20xV86 like La Brana.
 

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