Genetics of Mesolithic Scandinavia

Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adapt

http://www.biorxiv.org/content/biorxiv/early/2017/07/17/164400.full.pdf

This article is a preprint and has not been peer-reviewed

Scandinavia was one of the last geographic areas in Europe to become habitable for humans afterthe last glaciation. However, the origin(s) of the first colonizers and their migration routes remainunclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavatedacross Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among theScandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient thatopposes the pattern seen in other parts of Mesolithic Europe. This result suggests thatScandinavia was initially colonized following two different routes: one from the south, the otherfrom the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along whichnovel and advanced pressure-blade stone-tool techniques may have spread. These two groups metand mixed in Scandinavia, creating a genetically diverse population, which shows patterns ofgenetic adaptation to high latitude environments. These adaptations include high frequencies oflow pigmentation variants and a gene-region associated with physical performance, which showsstrong continuity into modern-day northern Europeans. Finally, we were able to compute a 3Dfacial reconstruction of a Mesolithic woman from her high-coverage genome, giving a glimpseinto an individual’s physical appearance in the Mesolithic.

What surprises me that no R1a or b was found in Scandinavian individuals so far, though they are almost half and half WHG/EHG, sometimes even more than half EHG.

Let's see her face too. They say they used her genome for reconstruction, not bones. I knew the time will come soon when we could do that. Just a start, but here it comes...

LeBrok said:

Let's see her face too. They say they used her genome for reconstruction, not bones. I knew the time will come soon when we could do that. Just a start, but here it comes...

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What do you mean exactly?

LeBrok said:

What surprises me that no R1a or b was found in Scandinavian individuals so far, though they are almost half and half WHG/EHG, sometimes even more than half EHG.

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But it suggests that R1 was somewhere around or was in low frequency.
They did not test thousands of samples but few - so it means nothing.
It can be of course, that admix was from female side, but I doubt if it
was exclusivly that way. Motala and other had how many %? 12%?
It would mean, that eventual R1 was 3 out of 50 IF it was admixed
proportionaly and men and women were in equal parts. I doubt if they
were, but even in such scenario, finding R1 among 5-10 samples is
really very unlikly... It would be the same even if it would be 1 of 10.

bicicleur said:

http://www.biorxiv.org/content/biorxiv/early/2017/07/17/164400.full.pdf

This article is a preprint and has not been peer-reviewed

Scandinavia was one of the last geographic areas in Europe to become habitable for humans afterthe last glaciation. However, the origin(s) of the first colonizers and their migration routes remainunclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavatedacross Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among theScandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient thatopposes the pattern seen in other parts of Mesolithic Europe. This result suggests thatScandinavia was initially colonized following two different routes: one from the south, the otherfrom the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along whichnovel and advanced pressure-blade stone-tool techniques may have spread. These two groups metand mixed in Scandinavia, creating a genetically diverse population, which shows patterns ofgenetic adaptation to high latitude environments. These adaptations include high frequencies oflow pigmentation variants and a gene-region associated with physical performance, which showsstrong continuity into modern-day northern Europeans. Finally, we were able to compute a 3Dfacial reconstruction of a Mesolithic woman from her high-coverage genome, giving a glimpseinto an individual’s physical appearance in the Mesolithic.

Click to expand...

LeBrok said:

What surprises me that no R1a or b was found in Scandinavian individuals so far, though they are almost half and half WHG/EHG, sometimes even more than half EHG.

Let's see her face too. They say they used her genome for reconstruction, not bones. I knew the time will come soon when we could do that. Just a start, but here it comes...

Click to expand...

What they say above.

See:Torsten Gunther et al
"Genomics of Mesolithic Scandinavia reveal colonization routes and high latitude adaptation
http://www.biorxiv.org/content/biorxiv/early/2017/07/17/164400.full.pdf

"Scandinavia was one of the last geographic areas in Europe to become habitable for humans afterthe last glaciation. However, the origin(s) of the first colonizers and their migration routes remainunclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavatedacross Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among theScandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient thatopposes the pattern seen in other parts of Mesolithic Europe. This result suggests thatScandinavia was initially colonized following two different routes: one from the south, the otherfrom the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along whichnovel and advanced pressure-blade stone-tool techniques may have spread. These two groups metand mixed in Scandinavia, creating a genetically diverse population, which shows patterns ofgenetic adaptation to high latitude environments. These adaptations include high frequencies oflow pigmentation variants and a gene-region associated with physical performance, which showsstrong continuity into modern-day northern Europeans. Finally, we were able to compute a 3Dfacial reconstruction of a Mesolithic woman from her high-coverage genome, giving a glimpseinto an individual’s physical appearance in the Mesolithic."

Basically, it seems to me to be a confirmation of the fact that the SHG were a combination of WHG and EHG.

More interesting, the results could be interpreted to mean that EDAR might have been prevalent among the EHG, signifying genetic ties with East Asian populations, and that did we have more EHG samples we might see EDAR in the EHG as well as the SHG.

The authors maintain that there is indeed a connection between high latitude environments and de-pigmentation, although they also confirm that these snps probably first appeared in West Asia, and long before 6000 years ago. In support of that, the data from Anatolia and other parts of the Near East has been re-examined and the levels of derived SLC45A2, the pre-eminent "European" de-pigmentation snp, among the people there are much higher than first reported. So, did the levels in West Asia decrease after the departure of the first farmers for Europe, perhaps because of migrations, or did the more favorable conditions in more northern parts of Europe just increase the frequency there, and then migrations spread them elsewhere. The latter is a little more tenuous, in my opinion, if, as the authors claim, there wasn't much genetic impact from the SHG on the modern European gene pool.

In this context, the authors speculate that the first farmers may already have had pigmentation similar to that of Sardinians, and much fairer than that of the WHG, who did, again, have blue eyes. The EHG again, it is maintained, had fairer skin and dark hair and eyes.

So, still questions to be answered.

Angela, this study was already posted before :
http://www.eupedia.com/forum/thread...l-colonization-routes-and-high-latitude-adapt
can you merge them?

Somehow, I must not have read it. Thanks for the heads up, Bicicleur. I'll merge with your thread.

Angela said:

See:Torsten Gunther et al
"Genomics of Mesolithic Scandinavia reveal colonization routes and high latitude adaptation
http://www.biorxiv.org/content/biorxiv/early/2017/07/17/164400.full.pdf



In this context, the authors speculate that the first farmers may already have had pigmentation similar to that of Sardinians, and much fairer than that of the WHG, who did, again, have blue eyes. The EHG again, it is maintained, had fairer skin and dark hair and eyes.

So, still questions to be answered.

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Somebody read suplementary pdf? It's much more info there. http://www.biorxiv.org/content/biorxiv/suppl/2017/07/17/164400.DC1/164400-2.pdf

Eastern hunter-gatherers (EHGs)
The Karelian and Samaran Russian Mesolithic hunter gatherers (82) are currently the best representatives of a group of EHGs that migrated and admixed with WHGs to form SHGs.
Mathieson et al (122) recently reported data from another Karelian Mesolithic hunter gatherer (sample I0211), with low coverage (0.136X across all captured SNPs), preventing pigmentation characterization. Hirisplex skin and hair color predictions suggest some opposing pigmentation patterns for the EHG individuals. The Karelian individual presents high probabilities of being brown-eyed (0.99), and having a dark hair (0.96). Without speculating about the genetic
architecture of skin pigmentation, we suggest an intermediate skin-pigmentation phenotype for the Karelia individual, as it carried the ancestral allele at rs16891982 and the derived allele at rs1426654 (Supplementary Table 1). The presence of the rs1426654 light-skin allele, in addition to five additional C11 -associated alleles at haplotype defining SNPs (Supplementary Table 1) suggests that the Karelian individual carried the C11 light-skin haplotype. The Samaran
individual exhibits high probabilities of being blue-eyed (0.88), light hair shade (0.99); most likely being blond (0.75). The two skin pigmentation SNPs suggest that the Samaran individual was light-skinned. In summary, the EHGs had high frequencies of the light-skin variants and intermediate frequencies of the blue-eye variants.

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Interestingly, the eye and light skin pigmentation phenotypes observed in all SHGs could potentially be explained by admixture between WHG and EHG groups. The high relative-frequency of the blue-eye color allele in SHGs, resembles WHG, while the intermediate frequencies of the skin color determining SNPs in SHGs seem more likely to have come from EHG, since both light-pigmented alleles are virtually absent from WHG. However, for all three well-characterized skin and eye-color associated SNPs, the SHGs display a frequency that is greater for the light-skin variants and the blue-eye variant than can be expected from a mixture of WHGs and EHGs. This observation indicates that the frequencies may have increased due to continued adaptation to a low light conditions.

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arly European farmers (EEF)
The Hirisplex eye and hair color prediction of 37 Early Neolithic farmers sequenced across Europe and Anatolia (81, 82, 175, 185) revealed that four individuals presented high probabilities of being blue-eyed (p=0.55-0.91), 23 were predicted to be brown-eyed (p=0.76-0.99), and 10 individuals did not have enough data to make a prediction. In total 23 individuals exhibit a high probability for dark hair pigmentation (p=0.57-0.99), five had most likely a light hair shade; the
remaining nine farmers lacked data for meaningful hair pigmentation prediction (Supplementary Table 1). The Anatolian Barcin I1583 individual (122) exhibited blue-eye color variants at the core h-1 SNP rs12913832 and its linked rs1129038 variant. Interestingly, it also presented h-1 - haplotype-defining alleles at rs7170852, rs2240203, rs916977, suggesting that this individual might have harbored the blue-eye color founder haplotype as well. No other early farmer presented direct evidence for the h-1 haplotype’s presence.
While both pigmentation alleles were observed at rs16891982 (although the derived allele in much higher proportion, see below), virtually only the light-skin allele was observed at rs1426654. Unequivocal evidence for the presence of the C11 -haplotype was observed for the central European Stuttgart sample, while (although at low coverage) only haplotype-associated alleles were observed in the Anatolian Klei10 early farmer individual.

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After investigating the presence of light-pigmentation alleles and haplotypes in different hunter-gatherers and early farmers across Europe and Anatolia, it seems as if eye and light skin pigmentation alleles entered Europe several times during different migration events. In particular, the light skin pigmentation variant arrived to Scandinavia already in the Mesolithic with migrants from the northeast, whereas the blue-eye variants probably arrived in Scandinavia with migrants from the south.
Light eye pigmentation variants were present at high frequencies in WHG, SHG, EHG and EEF (not present in PEHG), while the blue-eye color founder haplotype h-1
was found in the LaBrana, Loschbour, Villabruna WHGs, SF12, Motala1 and Motala12 SHGs and at least one early farmer. Such results suggest that the blue eye-color allele is rather old. Using an ABC modeling approach Nakagome et al. (186), predicted that the light-pigmentation allele at rs12913832 57emerged around 42,000 years ago or earlier; a date close in time to the initial peopling of Europe.
A plausible scenario of the origin of the blue-eye mutation that reconciles our results with findings from other studies is one where this variant appeared in an ancestral population before the ancestors of the WHG migrated from Near East into West and Central Europe (118).
The large effect light-skin alleles at rs16891982 and rs1426654 were present in SHG, EHG, CHG and EEF but absent in WHG and PEHG. Similarly, the C11 haplotype is present in hunter-gatherers (SHG, EHG and CHG but not WHG and PEHG) throughout Europe, as well as in at least two early farmers. This pattern is consistent with reports that the rs1426654 derived allele arose ~22,000-28,000 years ago (186, 187), and that the light-pigmentation allele at rs16891982 arose only once in Eurasians (186, 188). A possible geographical origin for these two major light-skin alleles is West Asia or the Near East (189). Later migrations across the Caucasus (CHG) and Eastern Europe would have brought it to Scandinavia, while EEF migrations introduced both alleles into central Europe.

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For rs3827760, within the EDAR gene, the derived G allele is associated with shovel-shaped teeth and hair thickness phenotype in East Asians. In the novel SHGs in this
study, only the ancestral A allele is present (SF12 is homozygote AA). The derived variant was reported in three of the six Motala SHGs which are younger than most other SHGs in this study (122). It is clear that the variant was present among SHGs (122), and it is possible that it has a continuous (but varying) distribution from Scandinavia to East Asia during the Mesolithic, and that the very low sample size of EHGs has failed to pick up the variant. It is also possible that the derived rs3827760 variant was brought to Scandinavia by migration in the Late Mesolithic, perhaps related to the specific Motala group.

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Anybody read suplementary pdf? http://www.biorxiv.org/content/biorxiv/suppl/2017/07/17/164400.DC1/164400-2.pdf

S11 Genetic testing of the post-glacial migration routes into Scandinavia The genomic affinities of the Mesolithic Scandinavians analyzed in this study suggest a complex migration pattern. Based on geography, genetics, the position of the ice-sheet on the Scandinavian peninsula and archaeology (see section S1, Figure S1.2), we hypothesize different migration routes into Scandinavia around 10,000 BP:
a) a migration of WHGs from the south,
b) a migration of EHGs from the east across the Baltic Sea,
c) a migration of EHGs from the east and along the north-Atlantic coast,
d) a migration of EHGs from the east and south of the Baltic Sea,
as well as combinations of these four migration routes (Figure S11.1).
These hypothetical scenarios allow us to formulate expectations of the genetic pattern seen in the different individuals. A migration of only WHGs would cause strong affinities of all SHGs to that group, whereas an exclusively EHG-like migration would make all SHGs very similar to EHGs.
If there were combinations of migrations from both sources, a pattern of geographic structure would emerge: different SHGs would be characterized by differential affinities to WHGs and EHGs. We formulate these affinities in terms of expected tendencies for f4 (Chimp, X; EHG, WHG) which are shown in Figure S11.1. We only give qualitative expectations as a lot of additional information regarding population splits, drift parameters and admixture proportions would be required to formulate quantitative expectations for f4 . The qualitative expectations still allow us to test rank correlations between expected values and observed values of f4 (Chimp, X; EHG, WHG) to evaluate how the different hypotheses fit the data.
These rank correlations are not informative for single migrations but the data suggests that SHGs are in fact a mixture of EHGs and WHGs. The only scenario that produces a positive rank correlation (rho=0.677, p=0.004) between observed and expected values is a combination of (a) and (c) – one migration of WHGs from the south and another of EHGs from the east following the Norwegian coast.
Such a scenario explains the higher affinities of Norwegian SHGs with EHGs as well as the higher affinities of Swedish SHGs with WHGs. The qpAdm admixture proportions (Figure 1A) are also significantly different between Norwegian and Swedish Mesolithic individuals (Wilcoxon test; p=0.01399). These affinities are consistently observed across all population genomic analyses in this study (PCA, ADMIXTURE, f4, qpAdm, TreeMix) and they are not correlated with the age of the samples (Figure S11.2).
Therefore, we conclude that two migrations into Scandinavia fit the genetic data: a migration from central Europe into southern Sweden and a second migration along the Norwegian coast and around the ice sheet covering the center of the Scandinavian peninsula. The populations spread across Scandinavia and mixed creating the geographic population structure seen in the genomic data.

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LeBrok said:

What surprises me that no R1a or b was found in Scandinavian individuals so far, though they are almost half and half WHG/EHG, sometimes even more than half EHG.

Let's see her face too. They say they used her genome for reconstruction, not bones. I knew the time will come soon when we could do that. Just a start, but here it comes...

Click to expand...

I suspect that I2 arrived along with Swiderian in Karelia before R1, and when ice retreated and R1 arrived, these I2 moved further north the the northern Scandinavian coast.

The study about ice age Europe gave us a nice picture of how I2 and WHG spread through Europe 15 ka.
It would be nice to find out how R1 spread and how EHG was formed.

She looks modern

Cato said:

She looks modern

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Can you post her picture?

Just wondering how does this fit with the results of the MDLP 22 and specific the North-European-Mesolithic component.



This peaks in Brana (80%) and is very low in nowadays Lituania (2% or less). So i can assume that the North-European-Mesolithic is very WHG.
And when we follow the WHG route to North and East Scandinavia then yes indeed the Saami score 76,40%, and indeed Finnish-North 37.30 % above Finnish-South 30.07%.
After the mesolithicum the figures declined obviously deeply! Gokhem 4 (TRB ) 12,1% (So the neolithization had an immense effect. Or do we in this case have a typical farmer (who lived along side the resisting SHG).
Nowadays Sweden; Swedish 7.79 % Swedish_V 10.09 % and Norwegian_V 9.80%, Orcadian 6.41%, North Dutch (mine) 7,5%.


In this respect the Eurogenes Hunter_Gatherer vs. Farmer Admixture Proportions is kind of rough or undifferentiated.
(Of course) it peaks in the Baltic. In Poland and the Ukraine obviously about 67%, around the old North Sea stronghold still about 55-60%, in more (South) West Europe beneath 50%. But it looks like if this admixture doesn't differentiate very well between SHG, EHG, WHG....

Northener said:

Just wondering how does this fit with the results of the MDLP 22 and specific the North-European-Mesolithic component.

This peaks in Brana (80%) and is very low in nowadays Lituania (2% or less). So i can assume that the North-European-Mesolithic is very WHG.
And when we follow the WHG route to North and East Scandinavia then yes indeed the Saami score 76,40%, and indeed Finnish-North 37.30 % above Finnish-South 30.07%.
After the mesolithicum the figures declined obviously deeply! Gokhem 4 (TRB ) 12,1% (So the neolithization had an immense effect. Or do we in this case have a typical farmer (who lived along side the resisting SHG).
Nowadays Sweden; Swedish 7.79 % Swedish_V 10.09 % and Norwegian_V 9.80%, Orcadian 6.41%, North Dutch (mine) 7,5%.


In this respect the Eurogenes Hunter_Gatherer vs. Farmer Admixture Proportions is kind of rough or undifferentiated.
(Of course) it peaks in the Baltic. In Poland and the Ukraine obviously about 67%, around the old North Sea stronghold still about 55-60%, in more (South) West Europe beneath 50%. But it looks like if this admixture doesn't differentiate very well between SHG, EHG, WHG....

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It was the Corded Ware Culture who reintroduced WHG genome directly to Northern Europe and indirectly to the South. Remember that EHG are in 2/3 WHG.
However, this map MDLP22 has stronger connection with EHG, I guess. NW Europe has more of it than Poland, Lithuania and Belarus. Looks more like EHG/CWC.

LeBrok said:

It was the Corded Ware Culture who reintroduced WHG genome directly to Northern Europe and indirectly to the South. Remember that EHG are in 2/3 WHG.
However, this map MDLP22 has stronger connection with EHG, I guess. NW Europe has more of it than Poland, Lithuania and Belarus. Looks more like EHG/CWC.

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I guess that the WHG in NorthWestern Europe is more due to HG culture Ertebølle like, around the North Sea, this was most probably a maritime culture (fisherman), the paper: "Stable isotope analysis of northern and western SHGs revealed an extreme marine diet, suggesting a maritime subsistence, in contrast to the more mixed terrestrial/aquatic diet of eastern and central SHGs .Combining these isotopic results with the patterns of genetic variation, we suggest an initial colonization from the south, likely by WHGs."
https://en.wikipedia.org/wiki/Ertebølle_culture
I assume that the TRB culture was the first one that absorbed the Ertebølle like cultures. But WHG lines, especially the maternal lines, survived in NW Europe the influxes.
I think that CW introduces more EHG to North en Northwestern Europe (what indeed could be partly reintroduce).

LeBrok said:

Can you post her picture?

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Sure



http://www.biorxiv.org/content/biorxiv/suppl/2017/07/17/164400.DC1/164400-2.pdf

Cato said:

Sure

View attachment 8942

http://www.biorxiv.org/content/biorxiv/suppl/2017/07/17/164400.DC1/164400-2.pdf

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No hair? Why in 3 shades?

LeBrok said:

No hair? Why in 3 shades?

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from the paper:

Figure S9.1 Facial reconstruction of SF12 based on diploid genotype calls The first row show the predicted facial shape, the second row adds European pigmentation to the shape, and the third row shows a modified pigmentation based on major pigmentation loci

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about the hair...i don't know

Here's another reconstruction of a mesolithic Scandinavian. Not all the SHG had the full complement of modern European depigmentation snps, so there must have been variation, with some darker and some a bit fairer, but I don't think any of them were totally like modern Scandinavians. As for the hair, it's much more difficult to predict hair color. You need a lot of snps for that and given these are ancient samples they may not have found enough of them. Maybe with advanced techniques they'll find more, as was the case with the Anatolian farmers, who upon re-examination turned out to have a lot more than 40% derived SLC42A5.



The low-rooted, short, wide, and also upturned nose seems to be a constant, as is the very wide face and high cheekbones. There must be some sort of environmental advantage for those kinds of noses in high latitude, cold environments.

I think I've posted this before: it's the 26,000 thousand year old head of an ancient man from present day Czechoslovakia.