Genetic ancestry changes in Stone to Bronze Age transition in the East European plain

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Transition from the Stone to the Bronze Age in Central and Western Europe was a period of major
population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide
sequence data from 28 individuals from the territory north of this source area – from the under-studied
Western part of present-day Russia, including Stone Age hunter-gatherers (10,800–4,250 cal BC) and
Bronze Age farmers from the Corded Ware complex called Fatyanovo Culture (2,900–2,050 cal BC).
We show that Eastern hunter-gatherer ancestry was present in Northwestern Russia already from around
10,000 BC. Furthermore, we see a clear change in ancestry with the arrival of farming – the Fatyanovo
Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe
and European early farmer ancestry and thus likely originating from a fast migration towards the
northeast from somewhere in the vicinity of modern-day Ukraine, which is the closest area where these
ancestries coexisted from around 3,000 BC.

https://www.biorxiv.org/content/10.1101/2020.07.02.184507v1
 
All the samples are from Northwest Russia, between Moscow and Vologda, except the two Mesolithic samples which are north of Vologda.

The only male Mesolithic sample is R1a5-YP1301 (under YP1272).

The Neolithic male sample is Q1a2-L54 (the Proto-Ameridian and Mongolian branch, also found in Scandinavia today as L804).

All the Bronze Age Fatyanovo samples are R1a, with 4x R1a-M417, 4x R1a-Z645 and 6x R1a-Z93.

A quick reminder of where they fit on the tree.

R1a-tree.png


Here is a summary of the samples.

IndividualCulturemt-haplogroupY-haplogroup
BER001Volosovo/LyalovoK1+16362Q1-L54
KAR001VeretyeT2a1b1-
PES001VeretyeU4a1R1a5-YP1301 (under YP1272)
BOL001FatyanovoH1bR1a-M417
BOL002FatyanovoJ1c1b1a1-
BOL003FatyanovoH41aR1a2-Z93
GOL001FatyanovoT2bR1a-M417
HAL001FatyanovoN1a1a1a2R1a2-Z93
HAN001FatyanovoNA-
HAN002FatyanovoU5a1a1R1a2-Z93
HAN003FatyanovoNA-
HAN004FatyanovoH6a1aR1a2-Z93
IVA001FatyanovoU4a1b-
MIL001FatyanovoU5b2c-
MIL002FatyanovoH-
MOT001FatyanovoU2e1b-
NAU001FatyanovoT2a1b1aR1a2-Z93
NAU002FatyanovoU5b2a1a2R1a2-Z93
NIK001FatyanovoU-
NIK002FatyanovoU5a1a1R1a-Z645
NIK003FatyanovoH15a1R1a-M417
NIK004FatyanovoT2a1a-
NIK005FatyanovoJ1c1b1a1-
NIK006FatyanovoW1c-
NIK007FatyanovoU5a1b-
NIK008AFatyanovoH5bR1a-Z645 (xZ283)
NIK008BFatyanovo
RDT001FatyanovoNA-
RDT002FatyanovoT2b-
RDT003FatyanovoNA-
RDT004FatyanovoNA-
SKO001FatyanovoU2e1b-
TIM001FatyanovoK1b1a1+199NA
TIM002FatyanovoN1a1a1a2-
TIM003FatyanovoNA-
TIM004FatyanovoNANA
TIM005FatyanovoT1a1+@152-
TIM006FatyanovoW6-
TIM008FatyanovoK1c1R1a-Z645
TIM009FatyanovoW6-
TIM010FatyanovoT2a1b1NA
TIM011FatyanovoU5b2a1a+16311-
VOD001FatyanovoJ1c1b1a-
VOR001FatyanovoI1a1-
VOR002FatyanovoH2a1-
VOR003FatyanovoH6a1aR1a-Z645
VOR004FatyanovoW6-
VOR005FatyanovoK2a5bR1a-M417
 
Autosomally, the Fatyanovo individuals are very similar to the other Corded Ware people as well as (presumably northern) Bell Beaker samples.

Fatyanovo-admix.jpg
 
Does it make sense to call Q1a2-L54 the photo-Amerindian and Mongolian branch? Did it originate in a population that was similar to Amerindians and Mongolians or did it admix into them from an ANE population?
 
Does it make sense to call Q1a2-L54 the photo-Amerindian and Mongolian branch? Did it originate in a population that was similar to Amerindians and Mongolians or did it admix into them from an ANE population?

If I say it, it is because it makes sense and there is evidence for it. Please refer to my history of haplogroup Q. Anyway it's not news that hg Q1a was found among ancient Northeast Europeans.
 
If I say it, it is because it makes sense and there is evidence for it. Please refer to my history of haplogroup Q.

I could be way off base there but yes I get that it is the dominant clade in Amerindians and Mongolians. However, I don't see any ancient DNA proving it originated in a predominantly East Eurasian population.

Anzick-1 is dated to 12600 ybp while Q-L54 formed 18000 ybp with a TMRCA of 15800 ybp (and yfull has been known to underestimate both figures by 10-15% so they might be even older). It would make more sense to be that it originated in a predominantly ANE population that then admixed with East Eurasians to form Native Americans.

I mean Q-F746's descendants are mostly Chinese but AG2 belonged to that clade and it makes more sense for this to be an ANE lineage like P and R than something AG2 got from an upsampled ENA population.

I also see Q1b there is also considered "Mongoloid". Given its distribution (with one clade found predominantly in Central,South and West Asia and another restricted to South Asia) wouldn't it make more sense for it to be associated with WSHG who can be modeled as 30% EHG, 50% ANE and 20% ENA?
 
Also interesting is this table of phenotypes across the ages in Northeast Europe. I have laid over colours to visualise the evolution more easily. Fatyanovo R1a-Z93 tribes had an overall pigmentation similar to that of modern upper-caste North Indians. If they weren't nearly as light as modern Northeast Europeans, it isn't surprising that Indo-Aryans also weren't lighter skinned or haired, even without blending with other populations along the way. It's really during the Iron Age that Northeast Europeans started becoming blue-eyed blonds. Mesolithic EHG were as dark overall as Sub-Saharan Africans (imagine them looking more Ethiopian or Somalian). Mesolithic Latvians had blue eyes, but they were admixed with WHG (Y-hg I2), while Mesolithic Russians were pure EHG (Y-hg R1a).

attachment.php
 
Also interesting is this table of phenotypes across the ages in Northeast Europe. I have laid over colours to visualise the evolution more easily. Fatyanovo R1a-Z93 tribes had an overall pigmentation similar to that of modern upper-caste North Indians. If they weren't nearly as light as modern Northeast Europeans, it isn't surprising that Indo-Aryans also weren't lighter skinned or haired, even without blending with other populations along the way. It's really during the Iron Age that Northeast Europeans started becoming blue-eyed blonds. Mesolithic EHG were as dark overall as Sub-Saharan Africans (imagine them looking more Ethiopian or Somalian). Mesolithic Latvians had blue eyes, but they were admixed with WHG (Y-hg I2), while Mesolithic Russians were pure EHG (Y-hg R1a).

attachment.php

How did Fataynovo have a pigmentation similar to upper-caste North Indians? Their frequency of blue eyes was 25%. Their frequency of blonde + dark blonde hair was 21% while another 21% had brown/dark brown hair. That's lighter pigmented than any population in Asia.
 
I could be way off base there but yes I get that it is the dominant clade in Amerindians and Mongolians. However, I don't see any ancient DNA proving it originated in a predominantly East Eurasian population.

Anzick-1 is dated to 12600 ybp while Q-L54 formed 18000 ybp with a TMRCA of 15800 ybp (and yfull has been known to underestimate both figures by 10-15% so they might be even older). It would make more sense to be that it originated in a predominantly ANE population that then admixed with East Eurasians to form Native Americans.

I mean Q-F746's descendants are mostly Chinese but AG2 belonged to that clade and it makes more sense for this to be an ANE lineage like P and R than something AG2 got from an upsampled ENA population.

I also see Q1b there is also considered "Mongoloid". Given its distribution (with one clade found predominantly in Central,South and West Asia and another restricted to South Asia) wouldn't it make more sense for it to be associated with WSHG who can be modeled as 30% EHG, 50% ANE and 20% ENA?

Q1a is North Asian rather than East Asian. I think that the fact that the first Amerindians (Clovis culture) were all Q1a-L54 is proof enough of a Siberian origin over 14,000 years ago. According to Yfull, Q-L54 has a TMRCA of 15,800 years.
 
How did Fataynovo have a pigmentation similar to upper-caste North Indians? Their frequency of blue eyes was 25%. Their frequency of blonde + dark blonde hair was 21% while another 21% had brown/dark brown hair. That's lighter pigmented than any population in Asia.

You are making me doubt. I thought that the table showed the allele frequency, since no population has 100% of blue eyes or blond hair and the table would suggest that Iron Age Ingrians did. That's why I only coloured over the most likely phenotype based on these allele frequencies.

But the table does say phenotype and not genotype. I wonder if that's a mistake. If it's not, then Fatyanovo had people with black, brown and blond hair, but almost all with intermediate to dark skin. Blond hair with dark skin is an extremely unlikely phenotype (unless the hair is discoloured by malnutrition).

Nevertheless blue/grey eyes are relatively common among upper-caste Indians.

images


main-qimg-7734c06fb54518a7f63fb226603f4e52.webp
 
Q1a is North Asian rather than East Asian. I think that the fact that the first Amerindians (Clovis culture) were all Q1a-L54 is proof enough of a Siberian origin over 14,000 years ago. According to Yfull, Q-L54 has a TMRCA of 15,800 years.

I agree with a geographical origin in Siberia. North Asia is just a region though. There were everything from ANE to Tianyuan like people there and probably everything in between. I just think it arose in a more ANE like than Tianyuan like population. Amerindians have a lot of ANE so there's nothing that precludes this from being true. Just my opinion.
 
You are making me doubt. I thought that the table showed the allele frequency, since no population has 100% of blue eyes or blond hair and the table would suggest that Iron Age Ingrians did. That's why I only coloured over the most likely phenotype based on these allele frequencies.

But the table does say phenotype and not genotype. I wonder if that's a mistake. If it's not, then Fatyanovo had people with black, brown and blond hair, but almost all with intermediate to dark skin. Blond hair with dark skin is an extremely unlikely phenotype (unless the hair is discoloured by malnutrition).

Nevertheless blue/grey eyes are relatively common among upper-caste Indians.

images


main-qimg-7734c06fb54518a7f63fb226603f4e52.webp

I believe Iron Age Ingrians were a small sample size no?

And the table says phenotype prediction which leads me to believe its not an error.

Also I doubt colored eyes are common among upper caste Indians (maybe compared to lower caste Indians sure). I used to work with a lot of Indians and I didn't see one with light eyes. According to Razib Khan only 10% of the alleles in Punjabis,Gujaratis and Bengalis(all northern I believe?) are of the derived allele which would give a frequency of light eyes of about ~1% according to him. He says the other genes would make this even lower. Even if we separated out upper castes from lower castes no population in India (or even Central Asia , Levant, Iran, Turkey) nobody's approaching any significant frequency of light eyes much less the 25% of Fataynovo. He also says this 25% is in line with the Sintashta data.

He also says its unlikely they had dark skin (especially in the sense of black skin).



Also dark skin here I believe is based on a few alleles for pigmentation.
 
Actually here's exactly what he said.

This group has been assembling a lot of data on phenotypic SNPs over time transects in Northeast Europe. One has to take these results with a grain of salt because the predictions are trained on modern samples. I do not think, for example, that European hunter-gatherers had “black skin.” I suspect that the Mesolithic populations were genetically different enough that their “light alleles” may not be in our panels, though my suspicion is that they’d be of darker hue as Inuit people are. That being said, selection work aligns with these results that Europeans, in particular, seem to have been getting lighter in many areas down to the present.

The eye color prediction I somewhat trust since it’s quasi-Mendelian (~75% of the variance is due to one genetic location in Europeans). For the pigmentation, I would focus on the trend, not the absolute value. Anyone who has been to the Northeast Baltic (I have) knows that these are amongst the fairest people in the world. It is very unsurprising that these people have been getting paler over time.

There have been various arguments on this blog and elsewhere as to what the Sintashta people would look like. I’ve posted the Narasimhan et al. data before. The results are broadly similar to the ones above for the Fataynovo.

The Fataynovo do not have the pigmentation genetic architecture that is similar to Nordic people. But, neither are they out of keeping with some European peoples. The Sintashta would be ~25% blue-eyed according to Narasimhan et al.’s data. In the 1000 Genomes about 10% of the alleles in Punjabis, Gujaratis, and Bengalis is the derived variant so common in Northern Europe, giving a recessive frequency ~1% of so blue-eyed, which is too high since other genes have an influence in these cases (though this allele is found in West Asia at appreciable frequencies, including in very old ancient DNA).


https://www.brownpundits.com/2020/07/04/the-arctic-home-of-the-aryans/
 
I believe Iron Age Ingrians were a small sample size no?

And the table says phenotype prediction which leads me to believe its not an error.

Also I doubt colored eyes are common among upper caste Indians (maybe compared to lower caste Indians sure). I used to work with a lot of Indians and I didn't see one with light eyes. According to Razib Khan only 10% of the alleles in Punjabis,Gujaratis and Bengalis(all northern I believe?) are of the derived allele which would give a frequency of light eyes of about ~1% according to him. He says the other genes would make this even lower. Even if we separated out upper castes from lower castes no population in India (or even Central Asia , Levant, Iran, Turkey) nobody's approaching any significant frequency of light eyes much less the 25% of Fataynovo. He also says this 25% is in line with the Sintashta data.

He also says its unlikely they had dark skin (especially in the sense of black skin).



Also dark skin here I believe is based on a few alleles for pigmentation.

About 30% of Iranians have light eyes but most of them are light brown: https://www.sciencedirect.com/science/article/pii/S2452232518300210

911_iraneyes.jpg
 
I believe Iron Age Ingrians were a small sample size no?

Exactly. In fact all these ancient populations have small sample size (anything under 100 is tiny, and under 1000 is still small when it comes to determining the evolution of phenotypes in a population). That's why it would have been much more useful to mention genotypes than phenotypes. A phenotype is only applicable to one specific individual with a specific set of genes. But genes, or rather alleles, get mixed at every generation. If you take two hypothetical populations mixing, with always one parent from each group. Let's say that one group is pure blue eyed (2 blue eye alleles) and the other group is pure brown eyed (2 brown eye alleles). In terms of phenotypes and genotypes, we get 50% blue eyes and 50% brown eyes. However, after these couples have children, the first generation will almost all have brown eyes (or yellow or hazel). So we get the exact same genotype in the population (50% blue, 50% brown), but a completely different phenotypic population (0% blue, 100% brown/hazel/yellow). Population geneticists should look at genotypes within a population, because phenotypes change at every generation, and knowing the alleles does not predict with 100% certainty the phenotype anyway. That's why I assumed that a scientific paper by professional population geneticists would list genotypes. But it would seem that they did choose phenotypes instead.

Also I doubt colored eyes are common among upper caste Indians (maybe compared to lower caste Indians sure). I used to work with a lot of Indians and I didn't see one with light eyes. According to Razib Khan only 10% of the alleles in Punjabis,Gujaratis and Bengalis(all northern I believe?) are of the derived allele which would give a frequency of light eyes of about ~1% according to him. He says the other genes would make this even lower. Even if we separated out upper castes from lower castes no population in India (or even Central Asia , Levant, Iran, Turkey) nobody's approaching any significant frequency of light eyes much less the 25% of Fataynovo. He also says this 25% is in line with the Sintashta data.

Obviously, since I thought the data was genotypes, 25% of blue eyes alleles would only give a few percents of actual light eyes (more often grey than blue among Indians). That's why I said above that Fatyanovo people were similar to upper-caste North Indians. Razib Khan may be right about 10% of derived blue eyes alleles in North India, but that is an average for all castes. There is a huge difference in pigmentation between upper and lower castes. I spent 5 months travelling around India and my aim was mainly to study the people, culture and history from an anthropological point of view. The upper castes, the Brahmins and the Kshatriyas, make up approximately 20 percent of India’s population, although the frequency varies by region (the highest are in Uttarakhand and Uttar Pradesh in the top north, along the border of Nepal). I wouldn't be surprised if Brahmins from Northwest India had 25% of blue eyes alleles (thus maybe 1 to 5% of actual light eyes).
 
Q1a is North Asian rather than East Asian. I think that the fact that the first Amerindians (Clovis culture) were all Q1a-L54 is proof enough of a Siberian origin over 14,000 years ago. According to Yfull, Q-L54 has a TMRCA of 15,800 years.

What is the consensus on the TMRCA of Q1A-M930? The split between Native Americans{M3} and Scandinavians {L804}.
 
Exactly. In fact all these ancient populations have small sample size (anything under 100 is tiny, and under 1000 is still small when it comes to determining the evolution of phenotypes in a population). That's why it would have been much more useful to mention genotypes than phenotypes. A phenotype is only applicable to one specific individual with a specific set of genes. But genes, or rather alleles, get mixed at every generation. If you take two hypothetical populations mixing, with always one parent from each group. Let's say that one group is pure blue eyed (2 blue eye alleles) and the other group is pure brown eyed (2 brown eye alleles). In terms of phenotypes and genotypes, we get 50% blue eyes and 50% brown eyes. However, after these couples have children, the first generation will almost all have brown eyes (or yellow or hazel). So we get the exact same genotype in the population (50% blue, 50% brown), but a completely different phenotypic population (0% blue, 100% brown/hazel/yellow). Population geneticists should look at genotypes within a population, because phenotypes change at every generation, and knowing the alleles does not predict with 100% certainty the phenotype anyway. That's why I assumed that a scientific paper by professional population geneticists would list genotypes. But it would seem that they did choose phenotypes instead.



Obviously, since I thought the data was genotypes, 25% of blue eyes alleles would only give a few percents of actual light eyes (more often grey than blue among Indians). That's why I said above that Fatyanovo people were similar to upper-caste North Indians. Razib Khan may be right about 10% of derived blue eyes alleles in North India, but that is an average for all castes. There is a huge difference in pigmentation between upper and lower castes. I spent 5 months travelling around India and my aim was mainly to study the people, culture and history from an anthropological point of view. The upper castes, the Brahmins and the Kshatriyas, make up approximately 20 percent of India’s population, although the frequency varies by region (the highest are in Uttarakhand and Uttar Pradesh in the top north, along the border of Nepal). I wouldn't be surprised if Brahmins from Northwest India had 25% of blue eyes alleles (thus maybe 1 to 5% of actual light eyes).

Okay that makes sense. 25% of the derived alleles would give about 6.25% light eyes which is in line with what you saw. I wonder why grey predominates though. I would think the order would (in decreasing frequency) hazel >green > blue > grey.
 
What is the consensus on the TMRCA of Q1A-M930? The split between Native Americans{M3} and Scandinavians {L804}.

Almost the same as L54. It split a few centuries later, circa 15,000 years ago.
 
the biggest surprise in the study is the dating
Fatyanovo existed much earlier than what was accepted till now

also interesting is the 12,7 ka Veretye HG R1a-YP1272
the 8,4 ka Karelia HG was R1a-M459*
could R1a-M459 be born between Lake Onega & the Ural Mts?

https://www.yfull.com/tree/R-M459/
 

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