Mal'ta boy had autosomal genes present in populations with Y-haplogroups M, P, Q & R

[Maciamo]

Mal'ta boy had autosomal genes present in populations with Y-haplogroups M, P, Q & R

Two weeks ago, Raghavan et al. published a paper on the genome of an Upper Palaeolithic Siberian individual, known as the Mal'ta boy. It is by far the oldest human genome tested to date.

The authors reported that the autosomal admixture of that 24,000-year-old individual was a blend of European, South Asian, Amerindian with a little bit of Papuan. I don't know if anybody mentioned this before, but it strikes me that this particular admixture could in fact be the original source DNA representing descendants of haplogroup MP. What links Europeans and South Asian is essentially haplogroup R. Amerindians are Q and Papuans belong too M.

It has recently been found that haplogroup M fits in between NO and P in the Y-chromosomal phylogeny. In other words, there was once a haplogroup MP, which split into M and P, then P split into Q and R.

Since the Mal'ta boy belongs to R*, it makes sense that his autosomal genes should be closest to the populations with the highest percentages of haplogroup R today, namely (North) Europeans and South Asians. And indeed his genome resembles at 71% that of Europeans and South Asians. The second closest group is Q, which is mostly Amerindians. 26% of his genome matches that of Amerindian. Surely this is something inherited from the common roots of Q and R, which had split from each others only a few millennia before the Mal'ta boy's lifetime.

The Mal'ta boy also shared 4% of similarity with modern Papuans, which may come as a surprise at first, until one realises the close phylogenetic relationship between the dominant Papuan paternal lineage (M) with Q and R. However since the split happened longer ago, the genetic similarity is more limited than with Q. Besides, there is a good chance that modern Papuans only have a small percentage of Eurasian genes themselves, and that the original carriers of Y-haplogroup M intermingled with a lot of other populations on their long journey from Central/North Asia to Papua. It is possible that only a small group of men belonging to haplogroup M came to replace the older native paternal lineages of New Guinea (C-RPS4Y711 and C-P55), just as O replaced them in East Asia and R in South Asia and Europe. Even Q might represent the post-Clovis migration that replaced older lineages (C3 ?) among Amerindians.

So we shouldn't see the Mal'ta boy as a multi-hybrid of European, South Asian and Siberian/Amerindian ethnicities, but rather as an example of the source population which invaded those geographic regions and hybridised with the natives there. It would be interesting to use the Mal'ta boy's genome as a reference population and see how much of modern populations inherited from the original PQR people, instead of looking at it the other way round. There might be a correlation between the percentage of similarity with his autosomal genes and the frequency of haplogroups Q and R in modern populations. Nonetheless I would expect that autosomal DNA got progressively diluted along the way as R people moved into Europe and South Asia, so the maximum percentage of similarity would probably lie between Bactria and Northwest India and in Eastern Europe.

 

[Maciamo]

This topic prompted me to wonder whether agriculture developed thanks to the original carriers of macro Y-haplogroup K ?

 

[Alan]

Two weeks ago, Raghavan et al. published a paper on the genome of an Upper Palaeolithic Siberian individual, known as the Mal'ta boy. It is by far the oldest human genome tested to date.

The authors reported that the autosomal admixture of that 24,000-year-old individual was a blend of European, South Asian, Amerindian with a little bit of Papuan.

This component which they are labeling as "South Asian" here is actually Gedrosia. Better labeled would be West_South_Central Asian.

As we can see here

The populations they took as reference for South Asia are mostly borderline population which are high in Gedrosia too. Also the fact that this "South Asian"(Green) component is also quite frequent in the Near East and Europe seems to confirm that this component is mostly Gedrosia with likely some ASI. Otherwise I can't explain the high green portion in European Near Eastern populations.

this Mal'ta boy seems to be pred. "Gedrosia+North European with significant Amerindian admixture. So I was right with my assumption that Gedrosia, North European (Caucasus too which is basically Gedrosia with additional Med component) had a common origin Somewhere in Central Asia/Iran. Just that it seems we can add Amerindian and ASI to this common origin too.

 

[Angela]

This component which they are labeling as "South Asian" here is actually Gedrosia. Better labeled would be West_South_Central Asian.

As we can see here

The populations they took as reference for South Asia are mostly borderline population which are high in Gedrosia too. Also the fact that this "South Asian"(Green) component is also quite frequent in the Near East and Europe seems to confirm that this component is mostly Gedrosia with likely some ASI. Otherwise I can't explain the high green portion in European Near Eastern populations.

this Mal'ta boy seems to be pred. "Gedrosia+North European with significant Amerindian admixture. So I was right with my assumption that Gedrosia, North European (Caucasus too which is basically Gedrosia with additional Med component) had a common origin Somewhere in Central Asia/Iran. Just that it seems we can add Amerindian and ASI to this common origin too.

I apologize if it seems as if I'm nitpicking, but If I'm reading the graphic correctly, it seems that the dark green component peaks in the Sakili of South Asia, and in the Malays of southeast Asia. It's only with the next highest area that the Balochi and the Pathans come into play. Then comes West Asia (the Caucasus) and South West Asia, except for some of the Bedouin, and only then Europe and Central Asia.

I think Central Asia has been emptied and crossed and repopulated so many times that it's extraordinarily difficult to use modern distributions there to draw any conclusions at all about paleolithic and mesolithic gene flow. I still think, regardless, that from this component we can trace a population movement north from south east Asia, then perhaps to south central Siberia, then perhaps back down into Central Asia and then on from there; it didn't drop out of the sky into Central Asia, after all...I just think you have to reel it back a little further.

I do agree with your basic conclusion...it looks like a population that moved out from Central Asia in a number of directions, including south into the Levant and west into Europe, and that we have perhaps been calling "West Asian". It seems as if the more "Eastern" component is absorbed by the Nganassan cluster.

 

[Alan]

I apologize if it seems as if I'm nitpicking, but If I'm reading the graphic correctly, it seems that the dark green component peaks in the Sakili of South Asia, and in the Malays of southeast Asia. It's only with the next highest area that the Balochi and the Pathans come into play. Then comes West Asia (the Caucasus) and South West Asia, except for some of the Bedouin, and only then Europe and Central Asia.

I think Central Asia has been emptied and crossed and repopulated so many times that it's extraordinarily difficult to use modern distributions there to draw any conclusions at all about paleolithic and mesolithic gene flow. I still think, regardless, that from this component we can trace a population movement north from south east Asia, then perhaps to south central Siberia, then perhaps back down into Central Asia and then on from there; it didn't drop out of the sky into Central Asia, after all...I just think you have to reel it back a little further.

I do agree with your basic conclusion...it looks like a population that moved out from Central Asia in a number of directions, including south into the Levant and west into Europe, and that we have perhaps been calling "West Asian". It seems as if the more "Eastern" component is absorbed by the Nganassan cluster.

you might be true here, that this component is not exclusively Gedrosia but it seems to mw that this component which they labeled as "South Asian" is a modern "zombie" (doesn't need to mean that it wasn't one source component in the past) component. This is because I can't remember any component which peaks in Southeast Asia and is so frequent in Europe and the Near East.

This is why I start to believe this component might be some sort of ancient West-South-Southeast Asian connection. So some Gedrosia must be in it.

 

[Angela]

you might be true here, that this component is not exclusively Gedrosia but it seems to mw that this component which they labeled as "South Asian" is a modern "zombie" (doesn't need to mean that it wasn't one source component in the past) component. This is because I can't remember any component which peaks in Southeast Asia and is so frequent in Europe and the Near East.

This is why I start to believe this component might be some sort of ancient West-South-Southeast Asian connection. So some Gedrosia must be in it.

I agree that there is definitely some connection.

Just generally, I think the paper is rather confusing...I'm waiting to see what will come out of the Reich lab.

 

[Alan]

I agree that there is definitely some connection.

Just generally, I think the paper is rather confusing...I'm waiting to see what will come out of the Reich lab.

Now I am definitely sure this aDNA test was made in the "lower Ks". Means they just differ in "World Regions" but didn't specify the exact genes they labeled under "Europe", "South Asian" and "America".

I am confident that this "South Asian" is actually Gedrosia+ASI+Southeast Asian in modern components. But they might have been genetically closer in ancient times. Who knows?

The same with the "European" I assume that some of this European is likely "Caucasus", just look how it reaches levels of ~40% in North and West Caucasus.


And this "Middle Eastern" component, is very likely the original farmer component, which is basically Southwest Asian minus the East African shift and Mediterranean without the Hunters&Gatherers admixture.

 

[Angela]

Now I am definitely sure this aDNA test was made in the "lower Ks". Means they just differ in "World Regions" but didn't specify the exact genes they labeled under "Europe", "South Asian" and "America".

I am confident that this "South Asian" is actually Gedrosia+ASI+Southeast Asian in modern components. But they might have been genetically closer in ancient times. Who knows?

The same with the "European" I assume that some of this European is likely "Caucasus", just look how it reaches levels of ~40% in North and West Caucasus.

Part of my problem with the paper is that there are internal contradictions that the authors don't address, including the fact that they seem to be saying that Amerindians are a product of admixture between a "west Eurasian" like group, presumably Mal'ta, and East Asian, and then they post admixture results which show that the Mal'ta sample is at least 1/3 Amerindian. So, was there a distinct "Amerindian" component present at that time or not?

Either the Mal'ta population is an admixed one with approximately two thirds belonging to some sort of ancestral "West Eurasian" component, and one third to an ancestral "Amerindian" component, or the population is an as yet undifferentiated, now extinct, north Eurasian population, (which arrived in the area from Southeast Asia) which then contributed to both West Eurasians and Amerindians. You can't have it both ways.

I don't think it's yet at all clear how it should be interpreted...but I'll tell you one thing...any garden variety Nordicist will not want to believe that Mal'ta and Afontova Gora, and perhaps, who knows, even hunter gatherers further west possessed any actual "Amerindian" component which they could have bequeathed to Europeans.

And this "Middle Eastern" component, is very likely the original farmer component, which is basically Southwest Asian minus the East African shift and Mediterranean without the Hunters&Gatherers admixture.

I'm afraid I don't think that's at all clear yet either. As has been pointed out by others on other sites, Neanderthals were divided along a north south cline in Europe...perhaps there was such a division in Paleolithic AMH's as well. All of them shared the Aurignacian, but perhaps the Gravettian affected them differently? There are some people on this Board who seem to be expert in this area, so perhaps they'll chime in.

For my part, I really don't know, and I don't think anyone can definitely know about any of this until we get some samples from the Paleolithic and Mesolithic of the Balkans, Greece and Italy tested. Goodness knows there's bones aplenty from Italy alone that are moldering away. I guess I've just always found it a little counter-intuitive that people from, say...Thessaly, would be so different from the people in northwest Anatolia in ancient times. But then again, this whole field is full of surprises.

Also,to be honest, the promoter of this idea is one of those people who I'm afraid to say I usually find to be WEFT, so that makes me even more skeptical.

 

[Jackson]

That would make a lot of sense. There was something that i think Dienekes picked up on fairly recently, that northern Europeans (and msot Europeans i think but to a lesser extent) show some sharing with Native Americans in the order of around 8%. Also, it is very common for Europeans (again i think more northern Europeans) to get small consistent segments of 'Oceanian' and 'South Asian'.

 

[Alan]

Just as I said, the Caucasus-Gedrosia got eaten up by the Dark blue (European) and Green (South Asian) components.

Here are Mal'ta boys K19 results.



MA1 - K19
Lithuanian (N. European) 32,85%
Mbuti (Pygmy) 0,85%
Chipewyan (Amerindian) 16,73%
Mala (ASI) 11,03%
Pima (Amerindian) 6,06%
Papuan (Ocenian) 0,97%
Kalash (Caucasus+Gedrosia) 26,91%
Karitiana (Amerindian) 2,91%
Onge (Onge) 1,70%

As I thought, the Mal'ta individual seems to be "North European, Caucasus-Gedrosia, Amerindian and ASI like.

 

[ElHorsto]

From Lazaridis et al:

...

The Kalash people are the only ones which get an own unique admixture component: dark green in K=20 and violet in K=17,18. In these cases, the only one else who shows this component is the the Mal'ta sample. This suggests that the Pakistan/Afghanistan area (approx. Gedrosia btw.) harbours more ancestral parts of Mal'ta, yet not completely being Mal'ta of course. The 'North-euro' part of Mal'ta is absent in the Kalash, hence it could be that Admixture just failed to reconstruct the complete Mal'ta ancestry in present-day Tiwari, Pathan, Burusho and similar peoples, showing the present-day admixtures instead. But it could be that these populations are the most similar ones to Mal'ta.

In K=19 and all others it flips into a completely different decomposition (beige + light green) which closely resembles other populations like Balochi and Brahui, who have almost no 'North-euro'-like ancestry.

 

[Alan]

From Lazaridis et al:

...

The Kalash people are the only ones which get an own unique admixture component: dark green in K=20 and violet in K=17,18. In these cases, the only one else who shows this component is the the Mal'ta sample. This suggests that the Pakistan/Afghanistan area (approx. Gedrosia btw.) harbours more ancestral parts of Mal'ta, yet not completely being Mal'ta of course. The 'North-euro' part of Mal'ta is absent in the Kalash, hence it could be that Admixture just failed to reconstruct the complete Mal'ta ancestry in present-day Tiwari, Pathan, Burusho and similar peoples, showing the present-day admixtures instead. But it could be that these populations are the most similar ones to Mal'ta.

In K=19 and all others it flips into a completely different decomposition (beige + light green) which closely resembles other populations like Balochi and Brahui, who have almost no 'North-euro'-like ancestry.

This is what Davidski says about the chart

Forget those old tests. Have a look at this ADMIXTURE analysis from the study.

http://biorxiv.org/highwire/filestream/383/field_highwire_adjunct_files/1/001552-2.pdf

It shows a cream colored component that peaks in the Caucasus and is found at decent levels in almost all Europeans, except Basques and Sardinians. MA-1 shows about a third of it in many of the higher K runs, but for him it switches to the Kalash-specific component in some of the runs.

Obviously, what we're seeing there is ANE admixture in Europe, West Asia and South Central Asia. But it's being expressed in a weird way as North Caucasian and Kalash components, similar to the old West Asian and Gedrosia components, and I'd say that's due to the isolation and drift in some of those isolated mountain communities.

That's why ADMIXTURE results are so difficult to use as signals of ancient population movements. You don't really know what you're looking at much of the time. It could be admixture from population A to population B, or in fact gene flow the opposite way, or maybe third party gene flow from population C.

But anyway, when we look at all of these results together, the thing that really sticks out is the high ANE in the North Caucasus. This is interesting, because Motala12 also had high ANE, and obviously MA-1 was purely ANE. So ANE obviously expanded into the Near East and South Central Asia from somewhere in the north, probably during the Bronze Age. What we don't know is whether this expansion was from Eastern Europe or Siberia, and only more ancient genomes can answer that question. Here's what the authors from this study say...

"A geographically parsimonious hypothesis would be that a major component of present-day European ancestry was formed in eastern Europe or western Siberia where western and eastern hunter-gatherer groups could plausibly have intermixed. Motala12 has an estimated WHG/(WHG+ANE) ratio of 81% (S12.7), higher than that estimated for the population contributing to modern Europeans (Fig. S12.14). Motala and Mal’ta are separated by 5,000km in space and about 17 thousand years in time, leaving ample room for a genetically intermediate population. The lack of WHG ancestry in the Near East (Extended Data Fig. 6, Fig. 1B) together with the presence of ANE ancestry there (Table S12.12) suggests that the population who contributed ANE ancestry there may have lacked substantial amounts of WHG ancestry, and thus have a much lower (or even zero) WHG/(WHG+ANE) ratio."

In "Davidski" and "MfA" ANE WHG EEF calculators. West Asians usually score ~17-19% (Kurds, Iranians, Turks), or ~10-12% (Assyrians, Armenians and Levant Arabs). And according to Davidski North Caucasians score even higher than the former both.

Europeans show up with 15-20% ANE and 30 to 40% WHG

weirdly in Davidskis calculator Kurds, Iranians and sometimes Turks show some % of WHG while Assyrians score even negative for it.

 

[LeBrok]

This is what Davidski says about the chart


In Davidski and MfA ANE WHG EEF calculators. West Asians usually score ~17-19% (Kurds, Iranians, Turks), or ~10-12% (Assyrians, Armenians and Levant Arabs). And according to Davidski North Caucasians score even higher than the former both.

Europeans show up with 15% ANE and 30 to 40% WHG

weirdly in Davidskis calculator Kurds, Iranians and sometimes Turks show some % of WHG while Assyrians and Armenians score even negative for it.

The only weirdly looking for me is low WHG for Kurds. Looking at Y hgs distributions I would expect them to have a very strong european ancestry, and not very old either. Other than that most of these tribes pedigree is from East Indo Europeans, who were not rich in WHG.
Overall they all might have a bit more of WHG but calculator is not tuned well for populations of Near East, or even for peripheries of Europe either like Sicily or Finnland.

 

[Alan]

The only weirdly looking for me is low WHG for Kurds. Looking at Y hgs distributions I would expect them to have a very strong european ancestry, and not very old either. Other than that most of these tribes pedigree is from East Indo Europeans, who were not rich in WHG.
Overall they all might have a bit more of WHG but calculator is not tuned well for populations of Near East, or even for peripheries of Europe either like Sicily or Finnland.

I agree here but you must know WHG (West European Hunters and Gatherers) are similar to ANE. They are like a Western European shifted version of ANE. So in my opinion it is not really a surprise that Kurds didn't score allot more than 4% since it is likely a pre Indo European H&G component of Europeans while I would expect most of "European" like ancestry in Kurds from ANE people.

 

[LeBrok]

I agree here but you must know WHG (West European Hunters and Gatherers) are similar to ANE. They are like a Western European shifted version of ANE. So in my opinion it is not really a surprise that Kurds didn't score allot more than 4% since it is likely a pre Indo European H&G component of Europeans while I would expect most of "European" like ancestry in Kurds from ANE people.

I had a hunch that Kurds migrated from area of Ukraine. I admit it came from nothing more than eyeballing some y and mt haplogroups. Therefore I was expecting more of a western form of ANE, the WHG. I think the full picture of admixtures will show up when true/original Near Easter farmer will be identified and true European hunter gatherer, and even ture Caucasian (if such existed before mixing with ANE). Also other original centers of population Isolates of pre neolithic, especially on huge continent of Asia.

 

[Alan]

I had a hunch that Kurds migrated from area of Ukraine. I admit it came from nothing more than eyeballing some y and mt haplogroups. Therefore I was expecting more of a western form of ANE, the WHG. I think the full picture of admixtures will show up when true/original Near Easter farmer will be identified and true European hunter gatherer, and even ture Caucasian (if such existed before mixing with ANE). Also other original centers of population Isolates of pre neolithic, especially on huge continent of Asia.

Even if they did the thing is ancient Ukrainians are unlikely exactly the same as modern. Just like all around the world they did change too. Also do we actually know that modern Ukrainians have allot of WHG? WHG is autosomal not very different from ANE. And it is unlikely imo that Indo Europeans wre ANE exclusive more likely ANE+EEF. WHG I assume was pre Indo European, pre Neolithic Europe.

 

[LeBrok]

And it is unlikely imo that Indo Europeans wre ANE exclusive more likely ANE+EEF

I think they were more of ANE+ Early Near Eastern Farmers. EEF = mostly Early Near Eastern Farmers + minor WHG, proportions are unknown at the moment, that's why it is called Early European Farmers and not ENEF. Scientists also suspect that there is a bit of Early Near Eastern Farmer in WHG. WHG might not be the pure HG we wished for.

Like in Europe we can see changing admixtures proportions, in spectrum like pattern, between EEF and WHG. We can presume that similar spectrum pattern existed already in Asia during Bronze Age, between ENEF and ANE from almost 100% of ENEF in Near East to almost 100% ANE far North.

My guess would be that IE were 60-40 ANE to ENEF, although for west IE I would assume a bigger WHG and EEF, like Corded Ware, before Bronze Age migrations.
I think later steppes dried, forced IE farmers out of central Asia, this might caused ENEF to drop too. Later Scythians were more of nomadic kind much more rich in ANE then IE farmers of Bronze Age.