The Genetic History of Northern Europe - Another Begemoth DNA study on Baltics

arvistro

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http://biorxiv.org/content/biorxiv/early/2017/03/03/113241.full.pdf

Recent ancient DNA studies have revealed that the genetic history of modernEuropeans was shaped by a series of migration and admixture events betweendeeply diverged groups. While these events are well described in Central andSouthern Europe, genetic evidence from Northern Europe surrounding theBaltic Sea is still sparse. Here we report genome-wide DNA data from 24 ancientNorth Europeans ranging from ~7,500 to 200 calBCE spanning the transitionfrom a hunter-gatherer to an agricultural lifestyle, as well as the adoption ofbronze metallurgy. We show that Scandinavia was settled after the retreat of theglacial ice sheets from a southern and a northern route, and that the firstScandinavian Neolithic farmers derive their ancestry from Anatolia 1000 yearsearlier than previously demonstrated. The range of Western EuropeanMesolithic hunter-gatherers extended to the east of the Baltic Sea, where thesepopulations persisted without gene-flow from Central European farmers untilaround 2,900 calBCE when the arrival of steppe pastoralists introduced a majornot peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.bioRxiv preprint first posted online Mar. 3, 2017; doi: http://dx.doi.org/10.1101/113241. The copyright holder for this preprint (which was2shift in economy and established wide-reaching networks of contact within theCorded Ware Complex.

Still to read, but so far no N in Baltics.
 
From the paper:

"The two samples from Karelia cluster with previously published Mesolithic EHG."

"EHG carry a genetic component (green component in Fig. 2b) that is maximized in hunter-gatherers from the Caucasus (CHG) and shared with Neolithic farmers from Iran and Steppe populations from the Bronze Age, suggesting some common ancestry for these populations, consistent with previous results21."

"Despite its geographically vicinity to EHG, the eastern Baltic individual associated with the Mesolithic Kunda culture shows a very close affinity to WHG in all our analyses, with a small but significant contribution from EHG or SHG, as revealed by significant D-statistics."

"Neither the Kunda individual nor SHG exhibit the major ADMIXTURE component shared between EHG and CHG (green in Figure 2b), bringing into question a direct contribution of EHG into the Mesolithic individuals from Scandinavia and the eastern Baltic. However, using qpWave we cannot reject the previously published result of SHG being formed by admixture of WHG and EHG 6."

"Both EHG and SHG share a non-negligible component in ADMIXTURE analysis that is maximized in some modern Native American populations which points towards ancient North Eurasian ancestry, as represented by the MA1 and AG3 samples from Palaeolithic Siberia13 (crimson component in Fig. 2a). Indeed, D-statistics show that EHG and SHG share significantly more alleles with MA1 and AG3 than both Baltic and Western HG (Supplementary Information Table S9). Additionally, mtDNA haplogroups found among EHG point toward an eastern influence: R1b in UzOO77 was previously found in the Palaeolithic Siberian AG35 and a haplogroup related to branches within the C1 clade, which appears today in highest frequencies in northeast Asia and the Americas, was described in several samples from Yuzhnyy Oleni Ostrov24,25. Furthermore, in SHG the derived variant of the EDAR allele was discovered, which is found today in high frequency in East Asians and Native Americans4 ."

"In contrast to EHG and SHG, Kunda can be modelled as directly derived from WHG (p=0.18) (Supplementary Information Table S6). The almost complete absence of the additional ancestry shared by SHG and EHG to the south of the Baltic Sea suggests that it was brought into Scandinavia via a northern route through Finland and admixed in Scandinavia with a WHG-like population that derived from a migration northward over the land-bridge that connected Denmark and southern Sweden at the time, a scenario that is in concordance with the archeological record."

"
The results for the Kunda individual are mirrored in the four later eastern Baltic Neolithic hunter-gatherers of the Narva culture...That Narva individuals derive directly from Kunda without additional admixture cannot be rejected (p=0.12), however it can also be accounted for by admixture of Kunda with either EHG, SHG or WHG (Supplementary Information Table S4). Specifically we see a greater proportion of possible admixture into the two samples excavated at the more eastern site Kretuonas (13±3% EHG or 33±7% SHG) than into the two Narva individuals from the more western sites."

"all our Baltic foragers carry the derived HERC2 allele which codes for light iris color, and like SHG and EHG they already possess an increased frequency of the derived alleles for SLC45A2 and SLC24A5, coding for lighter skin color (Extended Data Table 2)."

"The Narva individual Spiginas1 (dated to ca. 4440–4240 cal BCE) belongs to a mitochondrial haplogroup of the H branch providing the first direct evidence that this branch was present among European foragers without gene-flow from farmers (Extended Data Table 1). Notably, in addition to haplogroup H, the maternal lineages seen in eastern Baltic samples (n=31; Extended Data Figure 5) encompass all of the major haplogroups identified in complete mtDNA genomes from Holocene Scandinavian and western European hunter-gatherers (n=21:U2, U5a, U5b) 12, as well as haplogroup U4 which has been found in high frequency in Mesolithic foragers from Russia24 and K1, a derivate of the U8 branch found in Scandinavian foragers."

"We see in Baltic foragers no genomic evidence of gene-flow from Central European farmers or any Y-chromosomal or mitochondrial haplogroups that are typical for them, suggesting that any traces of agriculture and animal husbandry in the Baltic Early and Middle Neolithic were due to local development or cultural diffusion."

Anyone have a link to what kind of agriculture, if any, that would be?

"The individuals associated with the Early Neolithic TRB culture (EN TRB) cluster with Middle and Early Neolithic farmers from Europe on the PCA (Fig. 2A) and in the ADMIXTURE analysis exhibit the component maximized in Levantine early farmers (orange component in Figure 2b). The statistic D(EN_TRB, Middle Neolithic Central Europe; X, Mbuti) does not yield significantly positive results and EN TRB can be modeled as derived from a single source identical with Middle Neolithic (MN) Central Europe."

"All Baltic Late Neolithic (LN) individuals (ca. 3,200 to 1,750 calBCE) fall in PCA space in the diffuse European LNBA cluster formed by individuals admixed between Early and Middle Bronze Age (EMBA) pastoralists from the Yamnaya culture of the eastern Pontic Steppe and Middle Neolithic European farmers (Fig. 2A) and carry the genetic component that was introduced into Europe with this pastoralist migration (green in Fig. 2B)."

"we see novel mitochondrial haplogroups (I, J, T2, W), not found in the preceding foragers, in half of our samples (Extended Data Figure 5), and I2a Y-chomosomal haplogroups replaced by R1a types (Supplementary Information Section 3, Extended Data Table 1). qpWave estimates that the Baltic LN samples, when analysed as a population, are consistent with being derived from the same source as Central European CWC samples."

"Analysed individually, however, this model is rejected for three LN samples: Gyvakarai1 and Plinkaigalis242, which is dated to the very beginning of the LN, are instead consistent with being derived from the same source as EMBA Steppe pastoralists...which corresponds with their ADMIXTURE profiles that lack the early farmer component also missing in EMBA Steppe samples (orange component in Fig. 2b). Coinciding with this steppelike genetic influx is the first evidence of animal husbandry in the eastern Baltic15, suggesting import of this technology by an incoming steppe-like pastoralist population independent of the agricultural societies that were already established to the south and west."

This might be what the other paper was getting at in talking about other avenues for CHG in northeastern Europe than just CWC? So, CWC as a farming group with some animal husbandry, and an earlier pastoral group?

"Furthermore, the individual Spiginas2, which is dated to the very end of the Late Neolithic, has a higher proportion of the hunter-gatherer ancestry, as seen in ADMIXTURE (darker blue component in Fig. 2b), and is estimated to be admixed between 78±4% Central European CWC and 22±4% Narva."

That's part of the reason that modern north east Baltic populations are more WHG than the CWC people. I've been saying that for I don't know how long. There was also gene flow from more "southern" groups.

"Direct evidence of this exists in the Baltic BA sample that appears as an outlier on the PCA, falling within the larger European LNBA cluster instead of the tight Baltic BA cluster (Fig. 2a) and archaeological evidence supports that the site Kivutkalns, which is represented by eight of our individuals, was a large bronze-working center located on a trade route that opened to the Baltic Sea on the west and led inland following the Daugava river31. The Baltic BA was furthermore the first eastern Baltic population to show an increased frequency of the derived LCT allele, which is responsible for lactase persistence, i.e. the ability to digest unprocessed dairy (Extended Data Table 2). This rise in frequency could be due to either gene-flow carrying the allele into the region or a strong positive selection for this phenotype."

"The individual from Olsund in north-eastern Sweden was dated to the Late Neolithic (ca. 2,600 to 2,100 calBCE) when agriculture had been introduced to the coastal areas of Northern Sweden with the Battle Axe Culture, the regional variant of the CWC, while foraging persisted as an important form of subsistence...Baltic BA as a single source for either modern Lithuanians or Estonians is rejected (Supplementary Information Table S4). The statistic D(Lithuanian, Baltic_BA; X, Mbuti) reveals significant positive results for many modern Near Eastern and Southern European populations which can be caused by Lithuanians having received more genetic input from populations with higher farmer ancestry after the Bronze Age (Supplementary Information Table S8). As this applies to nearly all modern populations besides Estonians, especially for Central and Western Europe, limited gene-flow from more south-western neighbouring regions is sufficient to explain this pattern."

"In contrast, the statistic D(Estonian, BA_Baltic; X, Mbuti) gives the most significant positive hits for East Asian and Siberian populations (Supplementary Information Table S8) as previously suggested2 . This might be connected to the introduction of the Y-chromosomal haplogroup N that in Europe is found in highest frequencies in Finland and the eastern Baltic states, and in similar high frequencies in the Uralic speaking populations of the Volga-Ural region36. The spread of N into north-eastern Europe was proposed to have happened with speakers of Uralic languages from the east who contributed to the male gene pool of eastern Baltic populations and left linguistic descendants in the Finno-Ugric languages Finnish and Estonian37,38. As we do not see Y-haplogroup N in any of the male samples from Lithuania and Latvia dated as late as 230 calBCE we propose that this element was brought into the gene pool of the more southern region of the Baltic coast after the Late Bronze Age."

Ed. Wow, I got carried away. :) Well, for those not interested in any more detail, now you don't have to read the whole paper and supplement, which is much longer!
 
I am in desperate need for visualization of all those new data and samples with dates and Y-dna and autosomal components :)
 
Looks like Baltic WHG may have been more depigmented than EHG, on average. This might explain why the Steppe didn't show widespread depigmentation until after admixture with North and Central Europe.
 
I am in desperate need for visualization of all those new data and samples with dates and Y-dna and autosomal components :)

The Admixture Chart on page 19 helps. (It makes more sense to me than the one in the Estonian paper, but I'm still not sure about the amount of CHG that they find at early periods, before, of course, it would have been brought by large numbers of "Caucasus" wives.)

I can't seem to get it to post here. All someone would have to do is add the date, place, yDna and mtDna if they're interested.
 
Both Narva guys had I2a1. Interestingly one had NorthEast European-specific "Saami" mHG U5b1b1a. Also one Narva sample surprisingly had mHG H11a, today it's European-specific.
 
Notes how suddenly in the Bronze age mHG H, lactose persistence, and light skin come to dominate. Is that a coincidence? I don't think so, I think natural selection caused all that to happen and I think it happened most of Europe during the same time period.
 
Some other hints on developments after BA in Baltics:

"Gene-flow into the eastern Baltic after the Bronze AgeDespite the close clustering of modern eastern Baltic populations with Baltic BA onthe PCA plot and Lithuanians and Estonians exhibiting the highest allele sharing forancient Baltic populations with any modern population (Extended Data Figure 2),Baltic BA as a single source for either modern Lithuanians or Estonians is rejected(Supplementary Information Table S4). The statistic D(Lithuanian, Baltic_BA; X,Mbuti) reveals significant positive results for many modern Near Eastern andSouthern European populations which can be caused by Lithuanians having receivedmore genetic input from populations with higher farmer ancestry after the Bronze Age(Supplementary Information Table S8). As this applies to nearly all modernpopulations besides Estonians, especially for Central and Western Europe, limitedgene-flow from more south-western neighbouring regions is sufficient to explain thispattern. In contrast, the statistic D(Estonian, BA_Baltic; X, Mbuti) gives the most significantpositive hits for East Asian and Siberian populations (Supplementary InformationTable S8) as previously suggested2. This might be connected to the introduction of theY-chromosomal haplogroup N that in Europe is found in highest frequencies inFinland and the eastern Baltic states, and in similar high frequencies in the Uralicspeaking populations of the Volga-Ural region36. The spread of N into north-easternEurope was proposed to have happened with speakers of Uralic languages from theeast who contributed to the male gene pool of eastern Baltic populations and leftlinguistic descendants in the Finno-Ugric languages Finnish and Estonian37,38. As wedo not see Y-haplogroup N in any of the male samples from Lithuania and Latviadated as late as 230 calBCE we propose that this element was brought into the genepool of the more southern region of the Baltic coast after the Late Bronze Age."
 
It looks like that the farmer gene input in Bronze Age Lithuania is due to "considerable mobility and a network of contacts throughout the range of the CWC" that allowed farmer genes to spread eastwards "possible through exogamous marriage practices" rather than influx of another farmer mixed CWC from the steppe.
At least that is how I read the study (p.10)

 
It looks like that the farmer gene input in Bronze Age Lithuania is due to "considerable mobility and a network of contacts throughout the range of the CWC" that allowed farmer genes to spread eastwards "possible through exogamous marriage practices" rather than influx of another farmer mixed CWC from the steppe.
At least that is how I read the study (p.10)


exogamy was the rule in mesolithic times, and probably already long before
in CWC increased mobility was added to that
and I think chiefs got many women as a 'gift' which would have enhanched mtDNA diversity in the upper classes
 
Both Narva guys had I2a1. Interestingly one had NorthEast European-specific "Saami" mHG U5b1b1a. Also one Narva sample surprisingly had mHG H11a, today it's European-specific.

archeology said Kunda and Narva were Swiderian-derived
untill all that R1a and R1b was found
 
Looks like Baltic WHG may have been more depigmented than EHG, on average. This might explain why the Steppe didn't show widespread depigmentation until after admixture with North and Central Europe.

what remains is to find out is why depigmentation was favoured by nature
 
Looks like Baltic WHG may have been more depigmented than EHG, on average. This might explain why the Steppe didn't show widespread depigmentation until after admixture with North and Central Europe.

I kind of agree. Some hunter gatherers and EEF farmers could have been pretty pale. Natural selection definitely played a part though.
 
Links:

http://biorxiv.org/content/early/2017/03/03/113241

http://biorxiv.org/content/biorxiv/early/2017/03/03/113241.full.pdf

http://biorxiv.org/content/biorxiv/suppl/2017/03/03/113241.DC1/113241-1.pdf

IBCr24x.png


Y-DNA haplogroups:

Supplementary Information Section 3

Y chromosomal haplogroup analysis

We were able to determine the Y chromosomal haplogroup by examining a set of
diagnostic positions on chromosome Y using the ISOGG database (http://isogg.org/,
accessed in 2016 March). In order to perform this analysis, we restricted our analysis
to only include reads with a mapping quality higher than 30. Afterwards, we
determined the haplogroups by identifying the most derived Y chromosomal SNP in
our individual.

Spiginas1 could be assigned as I2a1a2a1a based on L233:G→A (2x). This individual
also has one upstream mutations for haplogroup I2a1a2a (L1286: G→A at 1x) and
one mutation for I2a1 (PF4004: T→C at 1x) and I2a (L460: A→C at 1x).

Kretuonas2 has a derived allele at I2a1b1:C→T, however only with coverage of 1x.
Due to missing significance at that position we are not confident in this assignment.
We were however able to find multiple upstream mutations assigning this individual
to I2a1b (CTS176, CTS1293, CTS1802, CTS5375, CTS7218, and S2702). We are
confident that the placement of this sample in Y chromosomal haplogroup I2a1b is
correct.

Gyvakarai1 could be assigned as R1a1a1b based on S441:G→A (6x) and
S224:C→T (3x). This individual also has two upstream mutations for haplogroup
R1a1a1 (M417 and Page7) and multiple mutations for R1a1a (M515, M198, L168,
M512, and L449) and R1a1 (PF6234, M459, and M448). We are confident that the
placement of this sample in Y chromosomal haplogroup R1a1a1b is correct.

Kunila2 has a derived allele at R1a1a1b:C→T, however only with coverage of 1x.
Due to missing significance at that position we are not confident in this assignment.
We were able to find one upstream mutation assigning this individual to R1a1a1
(Page7: C→T at 1x), two mutations assigning this individual to R1a1a (M198:C→T
at 2x and M512:C→T at 1x) and one mutation to R1a1 (PF6234: C→T at 1x).

Spiginas2 could be assigned as R1a1a1b based on S441:G→A (3x). This individual
also has multiple upstream mutations for haplogroup R1a1a (M515, L168, M512,
M514, L449), R1a1 (PF6234 and L120) and R1a (L63 and L146).
Olsund could be assigned as R1a1a1b based on S441:G→A (3x). This individual
also has multiple upstream mutations for haplogroup R1a1a (M515, L168 and L449),
R1a1 (M459) and R1a (L63 and PF6175).

Turlojiske3 could be assigned as R1a1a1b based on S441:G→A (1x). This individual
also has one upstream mutation for haplogroup R1a1a (L168:A→G at 1x), R1a1
(PF6234:C→T at 2x) and R1a (L62 and L63).

Kivutkalns19 could be assigned as R1a1a1b based on S441:G→A (4x) and
S224:C→T (1x). This individual also has two upstream mutations for haplogroup
R1a1a1 (M417 and Page7) and two mutations for R1a1a (M515 and L449) and R1a1
(PF6234 and M459). We are confident that the placement of this sample in Y
chromosomal haplogroup R1a1a1b is correct.

Kivutkalns25 could be assigned as R1a1a1b based on S441:G→A (3x). This
individual also has one upstream mutation for haplogroup R1a1a1 (M417) and two
mutations for R1a1a (M515 and L449) and R1a1 (M516 and M459). We are
confident that the placement of this sample in Y chromosomal haplogroup R1a1a1b is
correct.

Kivutkalns194 has a derived allele at R1a1a-L168:A→G. We were able to find one
upstream mutation assigning this individual to R1a (L62:A→G at 2x) and one
mutation assigning this individual to R1 (P286: C→T at 2x).

Kivutkalns209 has a derived allele at R1a1a1-Page7:C→T, however only with
coverage of 1x. Therefore we are not convinced that this represents the truth assigning
this individual to R1a1a1, due to missing significance at that position. We were
however able to find two upstream mutation assigning this individual to R1a1a
(M515: T→A at 1x, L168:A→G at 4x) and multiple mutations assigning this
individual to R1a1 (PF6234, L120 and M459). We are confident that the placement of
this sample in Y chromosomal haplogroup R1a1a is correct.

Kivutkalns222 has a derived allele at R1a1a1-M417:G→A, however only with
coverage of 1x. Therefore we are not convinced that this represents the truth assigning
this individual to R1a1a1, due to missing significance at that position. We were able
to find one upstream mutation assigning this individual to R1a1a (M512: C→T at 1x),
one mutation assigning this individual to R1a1 (M459:A→G at 1x) and one mutation
to R1a (L62: A→G at 4x) and are confident with an assignment to R1a1.

Due to low coverage no assignment could be made for Popovo2.

Light skin + light eyes among Baltic hunters:

Similar to the other Mesolithic hunter-gatherers, all our Baltic foragers carry the
derived HERC2 allele which codes for light iris color, and like SHG and EHG they
already possess an increased frequency of the derived alleles for SLC45A2 and
SLC24A5, coding for lighter skin color (Extended Data Table 2).

But no any N1c haplogroup was found:

The spread of N into north-eastern
Europe was proposed to have happened with speakers of Uralic languages from the
east who contributed to the male gene pool of eastern Baltic populations and left
linguistic descendants in the Finno-Ugric languages Finnish and Estonian37,38. As we
do not see Y-haplogroup N in any of the male samples from Lithuania and Latvia
dated as late as 230 calBCE we propose that this element was brought into the gene
pool of the more southern region of the Baltic coast after the Late Bronze Age.

No N1c in Baltic Corded Ware culture:

Based on the available markers (Table 2) all five individuals could be confidently assigned to hg R and none to hg N, which is a highly common haplogroup in modern Estonians (31%)
 
Both Narva guys had I2a1. Interestingly one had NorthEast European-specific "Saami" mHG U5b1b1a. Also one Narva sample surprisingly had mHG H11a, today it's European-specific.

If haplogroup IJ is known to be linked to mtDNA U and C1 is linked to mtDNA M all of them found in Pre-Neolithic populations of Europe. Then, H11a is the first evidence of genetic influx of a 3th group of European HGs (xP) comming from the South, probably HGs from the Balkans. And I will bet for LT, perhaps L2. In fact, L2 is found among modern Baltic populations.
 
"We see in Baltic foragers no genomic evidence of gene-flow from Central European farmers or any Y-chromosomal or mitochondrial haplogroups that are typical for them, suggesting that any traces of agriculture and animal husbandry in the Baltic Early and Middle Neolithic were due to local development or cultural diffusion."

However, there is a extremely differentiated lineage: H11a. who could has something to do with these traces of domestication.
 
These Baltic Bronze Age samples are the most lactose tolerant ancient population we have so far.
 
Notes how suddenly in the Bronze age mHG H, lactose persistence, and light skin come to dominate. Is that a coincidence? I don't think so, I think natural selection caused all that to happen and I think it happened most of Europe during the same time period.
It sounds like population replacement rather than natural selection "in situ" (among previous inhabitants).

In other words: a light-skinned, lactose-tolerant population invaded, replacing Neolithic/Mesolithic groups.

But some mixing with previous inhabitants also took place.
 

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