Insights into Modern Human Prehistory Using Ancient Genomes

[Jovialis]

Highlights

-Eurasia ∼45–35 ka shows the presence of at least four distinct populations: early Asians and Europeans, as well as populations with ancestry found hardly or not at all in present-day populations.

-Europeans from around 34–15 ka show high internal population structure.

-Approximately 14–7.5 ka, populations across Eurasia shared genetic similarities, suggesting greater interactions between geographically distant populations.

-Ancient modern human genomes support at least two Neanderthal admixture events, one ∼60–50 ka in early ancestors of non-African populations and a second >37 ka related to the Oase 1 individual.

-A gradual decline in archaic ancestry in Europeans dating from ∼37 to 14 ka suggests that purifying selection lowered the amount of Neanderthal ancestry first introduced into ancient modern humans.


The genetic relationship of past modern humans to today’s populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45 000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa.


https://www.sciencedirect.com/science/article/pii/S016895251730210X

https://phys.org/news/2018-01-ancient-eurasian-dna-sequencing-revealing.html

Here's a review of past genetic studies of predominately pre-agricultural groups that was published today. Too bad it's behind a paywall though. Nevertheless, here's the highlights, as well as a map from the paper provided by phys.org.

 

[bicicleur 2]

the second Neanderthal admixture only affected Oase I, an extinct branch, none of this 2nd admixture affected the rest of the European population

Goyet Q116 is Aurignacian (C1a-V20), which originated 43.5 ka in Austria, along the Danube and soon after spread upstream into southern Germany
ca 39 ka Aurignacian also spread eastward into the Kostenki area

first people arrived in Kostenki area ca 42 ka
Kostenki 14 is haplo C1b1*
Kostenki 12 is probably C1a2xV20 - that is the later Sunghir population

IMO the Gravettian originated in the Kostenki-Caucasus area through admixture between incoming haplogorup I and IJ* and the local Kostenki population
the Vestonice cluster is a mixture of these populations

the El Miron cluster is an admixture of incoming haplogorup I from the Caucasus area with local west-European Aurignacian - like Goyet 116

the Villabruna cluster are I2 originating somewhere around the Aegean where they were replaced ca 15 ka by incoming mesolithic EEF from southern Anatolia

I believe Basal Eurasian came from Indusdelta and Gujarat area, they - haplo G and H2 - arrived in SW Asia during early LGM when the Thar desert expanded. They brought with them geometric microliths and the bow and arrow.

BTW - what is EAS and NE ?

 

[IronSide]

@bicicleur

I think NE is Near East and EAS is East Asia.

Any explanation on how Basal Eurasian turned into Natufians ? they should be about 50% Basal and the other 50% a population that is related to WHG but not actual WHG, who were they ?

 

[bicicleur 2]

this is the full text

http://www.cell.com/trends/genetics/fulltext/S0168-9525(17)30210-X

 

[Jovialis]

this is the full text

http://www.cell.com/trends/genetics/fulltext/S0168-9525(17)30210-X

Table 1 seems very helpful in describing the samples.

http://www.cell.com/action/showFullTableImage?isHtml=true&tableId=tbl0005&pii=S016895251730210X

 

[holderlin]

This is a great broad strokes review. It's difficult to reconcile Basal Eurasian vs Crown Eurasian with Y Hg's except for C. All of the Crown Eurasian lines besides C are descended from presumed Basal Eurasian line M578.

I'm sure that I'm thinking too simplistically about this, but perhaps BE is just a group that stayed put while the crown Eurasian group HIJK moved on to acquire more Neanderthal DNA, which is the only real difference between the two. The additional Neanderthal DNA may have come from C groups and not necessarily neanderthals themselves. Am I missing something?

I haven't thought about this stuff in depth in a while go easy on me.

 

[Angela]

This is a great broad strokes review. It's difficult to reconcile Basal Eurasian vs Crown Eurasian with Y Hg's except for C. All of the Crown Eurasian lines besides C are descended from presumed Basal Eurasian line M578.

I'm sure that I'm thinking too simplistically about this, but perhaps BE is just a group that stayed put while the crown Eurasian group HIJK moved on to acquire more Neanderthal DNA, which is the only real difference between the two. The additional Neanderthal DNA may have come from C groups and not necessarily neanderthals themselves. Am I missing something?

I haven't thought about this stuff in depth in a while go easy on me.

I've wondered about that too. After all, the researchers consistently say it isn't additional "African", so what is the difference?

Unless, it has some genes that stem from prior homo sapiens dispersals that survived from the coastal trek into places like India.

Maybe someone can enlighten us. I've never really gotten down into the weeds on this one.

 

[IronSide]

It has been proposed that early European farmers had Basal Eurasian ancestry based on the observation that the Stuttgart early farmer and Eurasian hunter-gatherers such as Loschbour, LaBrana, MA1, and Motala12 had significantly positive f4-statistics of the form f4(Eurasian hunter-gatherer, Stuttgart; eastern non-African, Chimp), for diverse eastern nonAfrican groups from East Asia, the Andaman Islands, Papua New Guinea, North Asia and the Americas. A parsimonious explanation for these statistics that does not involve gene flow that affected all eastern non-African groups from west Eurasia or vice versa, is that the early farmers of Europe possessed ancestry from a deeply diverged lineage that split off from other Eurasians before the split of eastern non-Africans from west Eurasian hunter-gatherers.

Subsequent research on the Ust_Ishim and Oase1 individuals has revealed that these two individuals from Upper Paleolithic Siberia and Europe respectively share more alleles with present-day eastern non-Africans than with Europeans, but are symmetrically related to eastern non-Africans and ancient European hunter-gatherers. This finding has been interpreted as supporting the idea that recent Europeans have ancestry that was not present in ancient hunter-gatherers from Eurasia and which—because of its earlier split—is diluting the affinity of these Upper Paleolithic Eurasians to present-day Europeans. The genome of Kostenki14 was interpreted as having the same kind of Basal Eurasian ancestry as early European farmers, based on the observation that east Asians do not share more alleles with it than they do with early farmers. However, this observation is also consistent with Kostenki14 having a different type of ancestry than the early farmers, or alternatively later gene flow between ancestors of present-day eastern non-Africans and Eurasian hunter gatherers.

The prediction that the Basal Eurasian ancestry in present-day Europeans came from the Near East via early farmers was not based on ancient genomes from the Near East (which were not available at the time), but rather on the observation that diverse Eurasian hunter-gatherers from Europe and Siberia do not differ significantly in their shared genetic drift with eastern non-Africans but systematically shared more than the early farmers did. As the ancient farmers could be modeled as a mixture of European hunter-gatherers and a Near Eastern source population, it followed that their Basal Eurasian ancestry was derived from the Near Eastern portion of their ancestry.

 

[IronSide]

There were a couple of haplogroup CT in Natufians, Iran Neolithic, and European farmers, maybe they represent the lineage of Basal Eurasians.

But if we accept that, then why did they disappear ? almost like H2, considering how relatively common that haplogroup was in Neolithic times compared to now, maybe the same happened with Basal CT.

Haplogroup CT has been found in various fossils that were analysed for ancient DNA, including specimens associated with the Pre-Pottery Neolithic C (1/1; 100%), Ganj Dareh Iran Neolithic (1/2 50%), Natufian (2/5; 40%), Pre-Pottery Neolithic B (2/7; ~29%), Alföld Linear Pottery (1/1 at two ALP archaeological sites; 100%), and Linearbandkeramik (1/2 at Karsdorf LBK archaeological site; 50%) cultures.

 

[Angela]

Is there a typo in this paper about the level of BE in Natufians versus Hotu?

They say the following:
"Regarding the BE estimates in the paper:"Basal Eurasian ancestry is highest in the Near East, with estimates ashigh as 66% in Epipaleolithic Natufian individuals from the Levant [FONT=&quot]∼[/FONT]12–9.8 ka, and 44% in a Mesolithic individual from Iran from [FONT=&quot]∼[/FONT]9.1 to 8.6 ka (i.e., Hotu)."

However, they cite Lazaridis, who gives the same figures, but reversed if I remember clearly. I'm sure people like Eurogenes would jump at this: less BE in the group that admixed with EHG and then moved into Europe. However, I don't think it's correct.

Does anyone have a handle on it?

Fu et al also says this about Mal'ta:
"First, sampling of Siberian individuals from ∼24–17 ka from the Lake Baikal region (i.e., Mal’ta 1 and Afontova Gora 3) showed that they share a stronger connection to Europeans than to Asians, but that they share the strongest connection to Native Americans"

Anyone else remember how some people, including the usual suspects, said Reich and company were crazy to see admixture in Europeans with a population similar to Native Americans? I do, vividly. All done without ancient dna.

 

[Jovialis]

Is there a typo in this paper about the level of BE in Natufians versus Hotu?

They say the following:
"Regarding the BE estimates in the paper:"Basal Eurasian ancestry is highest in the Near East, with estimates ashigh as 66% in Epipaleolithic Natufian individuals from the Levant ∼12–9.8 ka, and 44% in a Mesolithic individual from Iran from ∼9.1 to 8.6 ka (i.e., Hotu)."

However, they cite Lazaridis, who gives the same figures, but reversed if I remember clearly. I'm sure people like Eurogenes would jump at this: less BE in the group that admixed with EHG and then moved into Europe. However, I don't think it's correct.

Does anyone have a handle on it?

Fu et al also says this about Mal'ta:
"First, sampling of Siberian individuals from ∼24–17 ka from the Lake Baikal region (i.e., Mal’ta 1 and Afontova Gora 3) showed that they share a stronger connection to Europeans than to Asians, but that they share the strongest connection to Native Americans"

Anyone else remember how some people, including the usual suspects, said Reich and company were crazy to see admixture in Europeans with a population similar to Native Americans? I do, vividly. All done without ancient dna.

Angela, you're correct about the typo. They have the percents backwards.

Here's an excerpt from the original source:

https://www.nature.com/articles/nature19310

 

[holderlin]

There were a couple of haplogroup CT in Natufians, Iran Neolithic, and European farmers, maybe they represent the lineage of Basal Eurasians.

But if we accept that, then why did they disappear ? almost like H2, considering how relatively common that haplogroup was in Neolithic times compared to now, maybe the same happened with Basal CT.

Haplogroup CT has been found in various fossils that were analysed for ancient DNA, including specimens associated with the Pre-Pottery Neolithic C (1/1; 100%), Ganj Dareh Iran Neolithic (1/2 50%), Natufian (2/5; 40%), Pre-Pottery Neolithic B (2/7; ~29%), Alföld Linear Pottery (1/1 at two ALP archaeological sites; 100%), and Linearbandkeramik (1/2 at Karsdorf LBK archaeological site; 50%) cultures.

I could see that. CT hung back and CF moved on splitting to C and F->GHIJK

 

[holderlin]

Is there a typo in this paper about the level of BE in Natufians versus Hotu?

They say the following:
"Regarding the BE estimates in the paper:"Basal Eurasian ancestry is highest in the Near East, with estimates ashigh as 66% in Epipaleolithic Natufian individuals from the Levant ∼12–9.8 ka, and 44% in a Mesolithic individual from Iran from ∼9.1 to 8.6 ka (i.e., Hotu)."

However, they cite Lazaridis, who gives the same figures, but reversed if I remember clearly. I'm sure people like Eurogenes would jump at this: less BE in the group that admixed with EHG and then moved into Europe. However, I don't think it's correct.

Does anyone have a handle on it?

Fu et al also says this about Mal'ta:
"First, sampling of Siberian individuals from ∼24–17 ka from the Lake Baikal region (i.e., Mal’ta 1 and Afontova Gora 3) showed that they share a stronger connection to Europeans than to Asians, but that they share the strongest connection to Native Americans"

Anyone else remember how some people, including the usual suspects, said Reich and company were crazy to see admixture in Europeans with a population similar to Native Americans? I do, vividly. All done without ancient dna.

I don't recall any usual suspects having a problem with "ANE" in Europeans. Mal'ta boy is R* afterall.

I do recall a bit of a controversy about CHG/Iran Neolithic's relation to EHG and how each of their Basal Eurasian content fit into all that. I believe Villabruna was also in the mix in these debates.

It actually looks like Goyet was the only Paleo-European that you could say was significantly distinct from BE.

 

[holderlin]

I have to continually remind myself how long ago all of this was. It's crazy to think how different say for example Goyet looked from an Anatolian farmer, or MA-1 from modern East Europeans. When you play it through and realize how distinct these populations were on the way to modern populations you begin to realize how different they all must have looked, and yet in the populations ancestral to modern people you could surely see exaggerated features that exist today among modern populations more diluted down through admixture. I want to see these people.

 

[halfalp]

It's just a random thought without any genetic datas, but i dont really believe to the Aurignacian C y-dna haplogroup, Gravettian I y-dna haplogroup. For me both Aurignacian and Gravettian must have been C1a / C1a2, with a slightly difference that Aurignacian must carry mtdna haplogroups M and U5 while Gravettians were mostly subgroups of U234789. The middle-eastern Aurignacian must have been mtdna U6 and also M. For y-dna haplogroup I, his first real appearance ( apart of some random guys in Vestonice and Italy [ linking with the Balkans ] ) are in German Magdalenian in the Epipaleolithic, and the first I2 is with the first R1b in the Villabruna Cluster. Pretty sure in the futur, there's gonna be theory about I haplogroup coming from Anatolia with some HV / H / V sublcades haplogroup roughly between -25'000 and -15'000 ( maybe the Solutrean ) and reexpand in the Magdalenian with some Aurignacian mtdna haplogroups. I know that what i just said is against current datas but i dont think datas are lying but mostly interpretations. I dont think for exemple that Aurignacian was coming in Europe with haplogroup C mostly with some kind of F or CT, C coming from Central Asia / Eastern Europe. I also think that the Alpine Belt road, meaning, Balkans <-> Anatolia <-> Middle-East ( in a broad term ) was very active along the years, but as we know women traveled way more in ancient times than men and i'm pretty sure mtdna haplogroup U is the core of that relation.

 

[bicicleur 2]

There were a couple of haplogroup CT in Natufians, Iran Neolithic, and European farmers, maybe they represent the lineage of Basal Eurasians.

But if we accept that, then why did they disappear ? almost like H2, considering how relatively common that haplogroup was in Neolithic times compared to now, maybe the same happened with Basal CT.

Haplogroup CT has been found in various fossils that were analysed for ancient DNA, including specimens associated with the Pre-Pottery Neolithic C (1/1; 100%), Ganj Dareh Iran Neolithic (1/2 50%), Natufian (2/5; 40%), Pre-Pottery Neolithic B (2/7; ~29%), Alföld Linear Pottery (1/1 at two ALP archaeological sites; 100%), and Linearbandkeramik (1/2 at Karsdorf LBK archaeological site; 50%) cultures.

I don't think they are CT, but they are low coverage, and downstream SNPs couldn't be identified.

 

[IronSide]

Any explanation on how Basal Eurasian turned into Natufians ? they should be about 50% Basal and the other 50% a population that is related to WHG but not actual WHG, who were they ?

On the order of half the ancestry of Natufians and Iran-Neo was Basal Eurasian, the other half derives from two distinct sources, which explain their different positions on the PCA plot. The Natufians have a WHG-like admixture. That is, some of their ancestors are nested within the broader clade which includes European hunter-gatherers, and far more distantly the Ancestral North Eurasians (ANE). Work on Pleistocene genomics indicates that there was a major increase in affinity between European hunter-gatherers and Near Easterners ~15,000 years before the present, suggesting that there was major gene flow uniting these two regions. The Near Eastern element of this movement probably fused with BEu.

From a speech by David Reich https://www.youtube.com/watch?v=IZjbp_LepPM&t=1s

If we look at the evidence of the proximity of these hunter-gatherer samples to present-day people in the Near East they're not particularly close to the Near East as you would show by a deviation down on the plot to the right until about fourteen thousand years ago when suddenly they seem to have a lot of genetic similarity to the Near East and what this is reflecting is a coming together of the populations of the ancestors of Near Easterners (Basal?) and the ancestors of hunter-gatherers in Europe beginning around fourteen thousand years ago. This is the period of the first strong warming after the last ice age, it's the period when the wall of glacial ice that separated Western and Eastern Europe finally broke and animals start being exchanged between Western and Eastern Europe and perhaps what we have is evidence of a southeastern refugee population from the Ice Age repeating and perhaps from Greece or perhaps from Asia Minor replaying and spreading both into Europe and also into the Near East and bringing these two populations together well before that happened again with farming.

R1b-V88 probably carried this ancestry to the Near East from European hunter-gatherers, its current distribution in Africa and the Near East is a legacy of Levantine farmers.

 

[bicicleur 2]

On the order of half the ancestry of Natufians and Iran-Neo was Basal Eurasian, the other half derives from two distinct sources, which explain their different positions on the PCA plot. The Natufians have a WHG-like admixture. That is, some of their ancestors are nested within the broader clade which includes European hunter-gatherers, and far more distantly the Ancestral North Eurasians (ANE). Work on Pleistocene genomics indicates that there was a major increase in affinity between European hunter-gatherers and Near Easterners ~15,000 years before the present, suggesting that there was major gene flow uniting these two regions. The Near Eastern element of this movement probably fused with BEu.

there is some flow between Near Easterns and WHG ca 15 ka, and it coïncides with the arrival of obsidian from Melos in the Franchthi cave in the Argolis Bay in the Peleponesos
also seeds from Anatolia would have arrived in the Franchthi cave

but it is not how Near Easterns got Basal Eurasians
the WHG themselves didn't have Basal Eurasian either prior to 15 ka

 

[IronSide]

there is some flow between Near Easterns and WHG ca 15 ka, and it coïncides with the arrival of obsidian from Melos in the Franchthi cave in the Argolis Bay in the Peleponesos
also seeds from Anatolia would have arrived in the Franchthi cave

but it is not how Near Easterns got Basal Eurasians
the WHG themselves didn't have Basal Eurasian either prior to 15 ka

My question wasn't how they have Basal Eurasian, but how Natufians have a WHG like ancestry.

 

[holderlin]

My question wasn't how they have Basal Eurasian, but how Natufians have a WHG like ancestry.

Well we have Villabruna in Italy 14k years ago and up until that time we have lower sea levels making the Italian Penninsula, the Balkan Penninsula, and Anatolia more connected. So there was surely an interaction zone between BEs and WHGs leading to Natufians and Anatolian Farmers. Like you said, pretty much.

But I also think that this is the only reason why Villabruna looks more closely related to middle easterners. Because the ancestors of middle eastern farmers already have ancestry similar to Villabruna.

On side note Goyet ancestry seems to have survived all the way to Corded Ware, at least by some measures. I saw this on a large admixture run, but I can't recall where I was looking at it. It showed that Corded Ware had some paleoeuropean ancestry that wasn't just Villabruna and Yamnaya did not.