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Thursday, March 22, 2018

Siberian ancestry and Y-haplogroup N1c spread across Northern Europe rather late in prehistory (Lamnidis et al. 2018 preprint)


A claim often made in popular culture is that the Saami people of Fennoscandia and Northern Russia are the last indigenous Europeans. I saw some guy blurt this out on a random cooking show the other day. But it's been obvious for a while now, thanks to analyses of modern-day DNA, that the Saami, and indeed almost all other Uralic-speaking groups in Europe, have a somewhat more complex population history than the majority of non-Uralic-speaking Europeans.

Now, ancient DNA is helping to cement these findings. The quotes and figure below are from a new preprint at bioRxiv by Lamnidis et al. [LINK] focusing on the spread of Siberian ancestry across Northeastern Europe from the late stone age onwards. It's a phenomenon that had the biggest impact on the Uralic-speaking populations of Fennoscandia, and is, in all likelihood, related in a profound, albeit complex, way to the ethnogenesis and expansion of the proto-Uralic people. Emphasis is mine:

The six ancient individuals from Bolshoy show substantially higher proportions of the Siberian component, which comprises about half of their ancestry (49.4-65.3 %), whereas the older Mesolithic individuals from Motala do not share this Siberian ancestry. The Siberian ancestry seen in EHG probably corresponds to a previously reported affinity towards Ancient North Eurasians (ANE)​ [2,24]​ , which also comprises part of the ancestry of Nganasans. Interestingly, results from uniparentally-inherited markers (mtDNA and Y chromosome) as well as certain phenotypic SNPs also show Siberian signals in Bolshoy: mtDNA haplogroups Z1, C4 and D4, common in modern Siberia​ 18,25,26​ , in individuals BOO002, BOO004 and BOO006, respectively (confirming previous findings​ [18​] ), as well as Y-chromosomal haplotype N1c1a1a (N-L392) in individuals BOO002 and BOO004. Haplogroup N1c, to which this haplotype belongs, is the major Y chromosomal lineage in modern North-East Europe and European Russia, especially in Uralic speakers, for example comprising as much as 54% of Eastern Finnish male lineages today​ [27​]. Notably, this is the earliest known occurrence of Y-haplogroup N1c in Fennoscandia.

...

We formally tested for admixture in north-eastern Europe by calculating ​ f3(​Test;Siberian source, European source) using Uralic-speaking populations - Estonians, Saami, Finnish, Mordovians and Hungarians - and Russians as ​ Test populations. Significantly negative ​ f ​ 3 values correspond to the ​ Test population being admixed between populations related to the two source populations​ [34]​. Additionally, the magnitude of the statistic is directly related to the ancestry composition of the tested source populations and how closely those ancestries are related to the actual source populations. We used multiple European and Siberian sources, to capture differences in ancestral composition among proxy populations. As proxies for the Siberian source we used Bolshoy, Mansi and Nganasan, and for the European source modern Icelandic, Norwegian, Lithuanian and French. Our results show that all of the test populations are indeed admixed, with the most negative values arising when Nganasan are used as the Siberian source (Supplementary Table 3).

...

Consistent with f3​-statistics above, all the ancient individuals and modern Finns, Saami, Mordovians and Russians show excess allele sharing with Nganasan when used as Test populations. Of all Uralic speakers in Europe, Hungarians are the only population that shows no evidence of excess allele sharing with Nganasan, consistent with their distinct population history as evidenced​ by​ historical​ sources​ (see​ ref​ 35 and​ references​ therein).

...

While the Siberian genetic component described here was previously described in modern-day populations from the region​ [1,3,9,10​], we gain further insights into its temporal depth. Our data suggest that this fourth genetic component found in modern-day north-eastern Europeans arrived in the area around 4,000 years ago at the latest, as illustrated by ALDER dating using the ancient genome-wide data from Bolshoy Oleni Ostrov. The upper bound for the introduction of this component is harder to estimate. The component is absent in the Karelian hunter-gatherers (EHG)​ [3] dated to 8,300-7,200 yBP as well as Mesolithic and Neolithic populations from the Baltics from 8,300 yBP and 7,100-5,000 yBP respectively [8]​. While this suggests an upper bound of 5,000 yBP for the arrival of Siberian ancestry, we cannot exclude the possibility of its presence even earlier, yet restricted to more northern regions, as suggested by its absence in populations in the Baltic during the Bronze Age.

...

The large Siberian component in the Bolshoy individuals from the Kola Peninsula provides the earliest direct genetic evidence for an eastern migration into this region. Such contact is well documented in archaeology, with the introduction of asbestos-mixed Lovozero ceramics during the second millenium BC [47], and the spread of even-based arrowheads in Lapland from 1,900 BCE​ [48,49]​. Additionally, the nearest counterparts of Vard√ły ceramics, appearing in the area around 1,600-1,300 BCE, can be found on the Taymyr peninsula, much further to the east​ [48,49​]. Finally, the Imiyakhtakhskaya culture from Yakutia spread to the Kola Peninsula during the same period​ [18,50​]. Contacts between Siberia and Europe are also recognised in linguistics. The fact that the Siberian genetic component is consistently shared among Uralic-speaking populations, with the exceptions of Hungarians and the non-Uralic speaking Russians, would make it tempting to equate this component with the spread of Uralic languages in the area. However, such a model may be overly simplistic. First, the presence of the Siberian component on the Kola Peninsula at ca. 4000 yBP predates most linguistic estimates of the spread of Uralic languages to the area​ [51]​. Second, as shown in our analyses, the admixture patterns found in historic and modern Uralic speakers are complex and in fact inconsistent with a single admixture event. Therefore, even if the Siberian genetic component partly spread alongside Uralic languages, it likely presented only an addition to populations carrying this component from earlier.


This generally looks like a very solid preprint, so I don't expect any major changes between now and formal publication. I have to be honest though, the qpAdm analysis looks like crap. Also, the authors are using the Russian sample set from the Human Origins dataset, which comes from the Kargopol district in Northern Russia. This was actually an Uralic-speaking region until not long ago. No wonder then, that they're inferring that Russians are very similar to Uralic-speaking populations.

But I know from my own analyses that there's quite a bit of genetic substructure within European Russia. For instance, Russians from southwest of Moscow are much less Uralic-like than the Kargopol Russians, and indeed very difficult to distinguish from other East Slavs, and even West Slavs. Hence, it might be useful to sample and run a couple more regional ethnic Russian groups for comparison. This might help to strengthen the argument that Siberian ancestry is somehow intimately intertwined with the expansion of Uralic languages in Europe.

Citation...

Lamnidis et al., Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe, bioRxiv, Posted March 22, 2018, doi: https://doi.org/10.1101/285437

209 comments:

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Davidski said...

@Chad

I'm not sure you can prove with qpAdm that all Northern Europeans have Siberian admixture.

If you're using ancient outgroups and reference samples, then the algorithm might be compensating for ancient DNA damage with a few per cent of Siberian admix.

It's useful in such cases to look carefully at the standard errors, and if they're close to the Siberian coefficient, then just call it as 0%.

Slumbery said...

Johan Grip
You are confusing the questions of Uralic origin and fairly late Hungarian-related events. These are two completely different time and process. There are no old Hungarian claims about the connection of Huns and Uralics in general. Also there are a lot of possible migration routes and processes other than the Mongolian one.
And why the hell would be anybody Corded Ware slave? As if that is the only way to adopt technology.

Chad Rohlfsen said...

Using modern and ancient. It is the same on qpGraph. Standard errors in qpAdm at 1%. I feel if this were damage, every pop preference wouldn't be for Siberian, but all over the place. Could be African, SE Asian, Native American, but it's not. We have ancients to prove ENA was pretty widespread in migration period, and we haven't even touched the Alans, Avars, and other late arrivals deep into Western Europe.

Chad Rohlfsen said...

There's these too.

result: Latvia_BA Saami Latvian -0.002164 0.000597 -3.626 780022
result: Latvia_BA Pazyryk Latvian 0.001220 0.000787 1.550 700594
result: Latvia_BA Nganasan Latvian -0.001545 0.000790 -1.955 761450
result: Latvia_BA Tundra_Nenet Latvian -0.001982 0.000707 -2.806 771610
result: Latvia_BA Mezhovskaya Latvian 0.000344 0.001003 0.343 339743
result: Latvia_BA Wichi Latvian -0.001657 0.000777 -2.133 764577
result: Latvia_BA Mota Latvian 0.000208 0.000796 0.261 769128
result: Latvia_BA CHG Latvian -0.000968 0.000794 -1.219 752242
result: Latvia_BA Steppe_EMBA Latvian 0.003385 0.000585 5.787 773870
result: Latvia_BA Kalmyk Latvian -0.002009 0.000624 -3.219 600140
result: Latvia_BA EHG Latvian 0.004577 0.000793 5.771 708254

Matt said...

I guess on this topic (post-Iron Age Siberian ancestry in Europeans) using nMonte, the most extreme samples of the Artificial Cranial Deformation Germans / Gepid are about 30-34% Scythian_Pazyryk, who are probably about 60% East Eurasian (50% per the paper), therefore about 20% East Eurasian overall.

So, you could get above 1% ancestry, in modern Germans, if the people like that were representative of about 1 in 20 of modern German ancestors.

But likely individuals like this were a bit less of the population as a whole than 5% (possibly more like 1% or 2%?), even assuming subsequent panmixia (random mating) and dynamics were probably a bit more clan like than purely panmictic.

It would also be easier to believe that significant Siberian related ancestry entered Europe during the late Iron Age-Classical era, if there was some correlation with spatial dynamics, such that you have clear offsets where populations closer to the steppe, like Romania and Hungary and Poland, have clear patterns relative to similar latitude further west. But instead the patterns among modern people largely just seem to correlate with steppe / WHG related ancestry... Even if you believe there are disruptively long range migrations at play, there should be *some* isolation-by-distance signal...

Chad Rohlfsen said...

They need not be 1 in 20 at any point in time. Even a 1% migration rate over five generations would do the same. So even 1 in 100 would be sufficient over that time. Remember, you have Scythians, Sarmatians, Huns, Alans, Avars, and more. This was a long period of movements. However, I really think it is over 1% in Germany. We'll see how this goes over time.

Anthony Haken said...

More anciant N1c has been found in IA Estonia's Tarand graves!

https://opetajateseminar.files.wordpress.com/2018/03/eestlaste-kujunemine-2018-tekst.pdf

Jace Landry said...

My theory is that the Uralic language group is purely Mongoloid/East Asian in origin; as most of it's carriers are N1c which is evidently high in East Asian/Siberian populations.

My hypothesis is, were three waves of populations that spawned the Fennoscandian and Baltic peoples:

1. The first wave were very ancient indigenous (non-IE speaking) Mesolithic Caucasoids / Europids.

2.The second population wave was an admixture with Mongoloid / East Asians; and an assimilation to Finnic and Saami languages. (this is supported by the now extinct Livonian Finnic language of Latvia.)

3. The third wave were Indo-Europeans who assimilated into and admixed the Finnic speakers; and these people later became the Balts.


Notes:


Somehow the Finnish people and the Estonians retained their Finnic language rather than the Indo-European one.

The Saami were the only Uralic group that did not manage to become admixed by the no. 3 third Indo-European population. Which explains why they have very ancient mitochondrial European DNA, and almost no Indo-European DNA markers. And only Mongoloid / East Asian Y-DNA and mtdna is found among them.

Davidski said...

@Jace Landry

3. The third wave were Indo-Europeans who assimilated into and admixed the Finnic speakers; and these people later became the Balts.

This is contradicted by ancient DNA, which shows that when Corded Ware people arrived in the East Baltic the region was populated by foragers most similar to Western European Hunter-Gatherers (WHG), albeit somewhat more easterly due to low level Eastern European Hunter-Gatherer (EHG) admixture. It's unlikely that these foragers were Finnic. See here...

https://www.nature.com/articles/s41467-018-02825-9

If you're thinking of N1c as a marker of East Asian-admixed pre-Indo-European Finnic people in the Baltic, then nope, there was no N1c in region before the Indo-European Corded Ware people got there, and there wasn't much, if any, East Asian admixture.

N1c probably arrived in the East Baltic during the Iron Age, long after Corded Ware, and it was probably spread by people who didn't inherit any East Asian ancestry, because modern-day Balts don't show it, only Estonians do.

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