The Genetic History of North-Eastern Europe

[Peterski]

A new paper, just published yesterday:

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

http://biorxiv.org/content/biorxiv/e...13241.full.pdf

http://biorxiv.org/content/biorxiv/s...1/113241-1.pdf

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.

[Peterski]

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%)

Apparently N1c "chinks" came to the region later.

[Peterski]

MtDNA haplogroup H present among Baltic hunter-gatherers:

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.

Baltic Corded Ware derived from the Steppe:

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).

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.

Yamnaya-derived Corded Ware pastoralists mixed with Narva hunter-gatherers:

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.

Spread of N1c haplogroup linked with Siberian and East Asian admixtures:

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.

Compared to BA_Baltic, modern Estonians are more Siberian / East Asian admixed.

[Peterski]

And here a related study with ancient DNA from Latvia:

http://www.theapricity.com/forum/sho...=1#post4222076

[Harkonnen]

But no any N1c haplogroup was found:



No N1c in Baltic Corded Ware culture:



Apparently N1c "chinks" came to the region later.

Kivutkalns and the rest of the posse are a bit too southern for the Proto-Finnic area, so it was not really expected to find N1c1 from these samples.

Anyway you little Balto-Slavic piece of shit - why do you find this all so funny?

[Lucas]

So proto-Finnic N1 carriers are later newcomers to this area than Balto-Slavs. Interesting

[XenophobicPrussian]

Kretuonas4 and Kretuonas2 were 100% derived for SLC45A2, even Karelia HG was only half derived for that and 3 Motala and Samara were fully. I wish they had that specific sample on the first PCA plot, but they probably will be around the other HGs otherwise the paper probably would've said so. It's weird as the other 2 Narva samples had none and none of the Latvian HGs from the other paper also had any SLC45A2.

Also, the Baltic Bronze Age samples are the most lactose tolerant ancient population we have so far.

[Harkonnen]

So proto-Finnic N1 carriers are later newcomers to this area than Balto-Slavs. Interesting

This fits with the fact that Finnics are not descendent from the Corded Ware culture.

This was really the most informative part of the paper:

Also, modern populations speaking Uralic (including Finnic) languages
of Europe and Siberia along with all other Siberians were more similar to Estonian CCC than
to CWC (Fig 5). These results were confirmed by D statistic in the form D(Yoruba, CCC/CWC;
Estonian, Y) (S7 Figure; S7 Table). This points to extant Siberians and European Uralic
speakers having less Steppe ancestry than Estonian CWC did."

This means that Proto-Finnics were living somewhere Northeast from Corded Ware with minimal contact to them. Exactly as I've been saying for long time.

Interestingly, modern Estonians showed a bigger proportion of the blue
component (EHG?) than CWC individuals. Comparing to CCC individuals, modern Estonians lack the
red component (LBA?). This, together with the absence of Y chromosome hg N in CCC and CWC,
points to further influx and change of genetic material after the arrival of CWC.

[Pahli]

This fits with the fact that Finnics are not descendent from the Corded Ware culture.

This was really the most informative part of the paper:



This means that Proto-Finnics were living somewhere Northeast from Corded Ware with minimal contact to them. Exactly as I've been saying for long time.

You forgot that the Northern parts of Latvia was inhabited by Livonians prior to the arrival of Baltic speaking tribes, an ethnic group related to Estonians.

[Harkonnen]

You forgot that the Northern parts of Latvia was inhabited by Livonians prior to the arrival of Baltic speaking tribes, an ethnic group related to Estonians.

Livonians were rather recent arrivals from Karelia to their current extinct whereabouts.