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Thread: Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe (Lamnidis et al. 2018)513 days old

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    Default Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe (Lamnidis et al. 2018)


    European history has been shaped by migrations of people, and their subsequent admixture. Recently, evidence from ancient DNA has brought new insights into migration events that could be linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known so far about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and Northwest Russia. We show that the specific genetic makeup of northern Europe traces back to migrations from Siberia that began at least 3,500 years ago. This ancestry was subsequently admixed into many modern populations in the region, in particular populations speaking Uralic languages today. In addition, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age than today, which adds to historical and linguistic evidence for the population history of Finland.

    [...]

    The genetic structure of Europeans today is the result of several layers of migration and subsequent admixture. The incoming source populations no longer exist in unadmixed form, but have been identified using ancient DNA in several studies over the last few years1–8. Broadly, present-day Europeans have ancestors in three deeply diverged source populations: European hunter-gatherers who settled the continent in the Upper Paleolithic, Europe’s first farmers who expanded from Anatolia across Europe in the early Neolithic starting around 8,000 years ago, and groups from the Pontic Steppe that arrived in Europe during the final Neolithic and early Bronze Age ~4,500 years ago. As a consequence, most Europeans can be modelled as a mixture of these three ancestral populations3.

    The model of three ancestral populations, however, does not fit well for the present-day populations from north-eastern Europe such as Saami, Russians, Mordovians, Chuvash and Finns: they carry an additional ancestry component seen as increased allele sharing with modern East Asian populations1,3,9,10. The origin and timing of this East Asian-related contribution is unknown. Modern Finns are known to possess a distinct genetic structure among today’s European populations9,11–14, and the country’s geographical location at the crossroads of eastern and western influences introduces a unique opportunity to investigate the migratory past of North-East Europe. Furthermore, the early migrations and the genetic origins of the Saami people in relation to the Finnish population call for a closer inspection, with the linguistic evidence suggesting that Saami languages have dominated the whole of the Finnish region before 1,000 CE15–17. Here, the early Metal Age, Iron Age, and historical burials analysed provide a suitable time-transect to ascertain the timing of the arrival of the deeply rooted Siberian genetic ancestry, and a frame of reference for investigating linguistic diversity in the region today.

    In this study we present new genome-wide data from 11 individuals from Finland and the Russian Kola Peninsula who lived between 3,500 to 200 years ago. In addition, we present a new high-coverage genome from a modern Saami individual for whom low coverage data was published previously1. Our results suggest that a new genetic component with strong Siberian affinity first arrived in Europe around 4,000 years ago, as observed in our oldest analysed individuals from northern Russia, and that the gene pool of modern north-eastern Europeans in general, and speakers of Uralic languages in particular, is the result of multiple admixture events between Eastern and Western sources since that first appearance. Additionally, we gain further insights into the genetic history of the Saami in Finland, by showing that during the Iron Age, close genetic relatives of modern Saami lived in an area much further south than their current geographic range.


    [...]

    To investigate the genetic affinities of the individuals sampled, we projected them onto principal components computed from 1,320 modern European and Asian individuals (Figure 2a, Supplementary Figures 3a&b for a version focusing on West Eurasia). As expected, PC1 separates East Asian from West Eurasian populations. Within each continental group, genetic variability is spread across PC2: The East Asian genetic cline spans populations between the Siberian Nganasan (Uralic speakers) and Yukagirs at one end, and the Ami and Atayal from Taiwan at the other end. The West Eurasian cline along PC2 spans from the Bedouins on the Arabian Peninsula to north-eastern Europeans including Lithuanians, Norwegians and Finns. Between these two main Eurasian clines exist multiple clines, spanning between West and East Eurasians. These clines are likely the result of admixture events and population movements between East and West Eurasia. Most relevant to the populations analysed here is the admixture cline between north-eastern Europe and the North Siberian Nganasan, including mostly Uralic-speaking populations in our dataset (marked in light purple in Figure 2a).

    Ten of the eleven ancient individuals from this study fall on this Uralic cline, with the exception of one individual from Levänluhta (JK2065), who is instead projected closer to modern Lithuanian, Norwegian and Icelandic populations. Specifically, two Levänluhta individuals and the two historical Saami from Russia are projected very close to two previously published modern Saami (Saami.DG)23 and the new Saami genome generated in this study (as well as the previously published genome of the same individual, here labelled “Saami (WGA)”1), suggesting genetic continuity in the North from the Iron Age to modern-day Saami populations. In contrast, the six ancient individuals from Bolshoy are projected much further towards East Asian populations, in an intermediate position along the Uralic cline and close to modern-day Mansi.

    Unsupervised genetic clustering analysis as implemented in the ADMIXTURE20 program suggests a similar profile: north-eastern European populations harbour a Siberian genetic component (light purple) maximized in the Nganasan (Figure 2b). The hunter-gatherer genetic ancestry in Europeans (blue) is maximized in European Upper Palaeolithic hunter-gatherers, including the 8,000-year-old Western European hunter-gatherers from Hungary and Spain (WHG), the 8,000-year-old Scandinavian hunter-gatherers from Motala (SHG) and the 7,000-year-old individuals from Karelia in north-eastern Europe (EHG). An ancestry component associated with Europe’s first farmers (orange) is maximized in ancient individuals from Neolithic Anatolia. Within modern Europeans, the Siberian genetic component is maximized in the Saami, and can also be seen in similar proportions in the historical Saami from Chalmny Varre and in two of the Levänluhta individuals. The third Levänluhta individual, JK2065, falling also in an outlier position on the PCA, lacks the Siberian component. 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 Siberia18,25,26, in individuals BOO002, BOO004 and BOO006, respectively (confirming previous findings18), 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 today27. Notably, this is the earliest known occurrence of Y-haplogroup N1c in Fennoscandia. Additionally, within the Bolshoy population we observe the derived allele of rs3827760 in the EDAR gene, which is found in near-fixation in East Asian and Native American populations but is extremely rare elsewhere28, and has been linked to phenotypes related to tooth shape29 and hair morphology30,31 (Supplementary Table 7). Scandinavian hunter-gatherers from Motala in Sweden have also been found to carry haplotypes associated with this allele4. Finally, we see high frequencies of haplotypes associated with diets rich in high poly-unsaturated fatty acids, on the FADS genes4,32,33. The FADS haplotype observed here has previously been linked with Greenlanders32, and is found in lower frequencies within Europe33.

    The​ ​arrival​ ​of​ ​Siberian​ ​ancestry​ ​in​ ​Europe
    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 f3 values correspond to the Test population being admixed between populations related to the two source populations34. 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). Among the European sources, Lithuanians gave the most negative results for Estonians, Russians and Mordovians. For modern Hungarians, the European source giving most negative results was French, while both Bolshoy and Nganasan gave equally negative results when used as the Siberian source. With Finns as test, modern Icelanders were the European source giving most negative statistics. Finally, the present-day Saami as a Test produced the most negative, though non-significant, result when Icelanders and Nganasan were used as the European and Siberian sources respectively. This non-significance is likely a result of the low number of modern Saami individuals in our dataset (n=3). To further test differential relatedness with Nganasan in European populations as well as the ancient individuals in this study, we calculated f4(Mbuti, Nganasan; Lithuanian, Test) (Figure 3a). 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).

    We further estimated the amount of Siberian ancestry in these populations using qpAdm3. All ancient and modern individuals from the Baltics, Finland and Russia were successfully modelled as a mixture of five lines of ancestry, represented by Karelian EHG, Yamnaya from Samara, LBK from the early European Neolithic, western Mesolithic hunter-gatherers (from Spain, Luxembourg and Hungary), and Nganasan, or subsets of those five (Supplementary Table 4). Our motivation in including Karelian EHG as well as Yamnaya as sources in our model, although Yamnaya has been shown to contain large amounts of EHG ancestry3, is that the six Bolshoy individuals share significantly more alleles with Karelian EHG than with Yamnaya (Figure 3b). The 3,500-year-old ancient individuals from Bolshoy evidence the earliest presence, as well as the highest proportion of Siberian ancestry in this region (Figure 4). The geographically proximate ancient hunter-gatherers from the Baltics (8,000 and 8,300 BP) and Motala (~8,000 BP), who predate Bolshoy, lack this component. In our models, Karelian EHG lack this component by construction, since they are one of the source populations. All later ancient individuals in this study have lower amounts of Siberian ancestry than Bolshoy, probably as a result of admixture with other populations from further south and dilution, as suggested by the increased proportion of early European farmer ancestry related to Neolithic Europeans (Figure 2b, Figure 3a).

    [...]

    In terms of ancient human DNA, north-eastern Europe has been relatively understudied. In this study we extend the available information from this area considerably, and present the first ancient genome-wide data from Finland. While the Siberian genetic component described here was previously described in modern-day populations from the region1,3,9,10, 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. Our study also presents the earliest occurrence of the Y-chromosomal haplogroup N1c in Fennoscandia. N1c is common among modern Uralic speakers, and has also been detected in Hungarian individuals dating to the 10th century35, yet it is absent in all published Mesolithic genomes from Karelia and the Baltics3,8,45,46.

    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 BCE48,49. Additionally, the nearest counterparts of Vardøy ceramics, appearing in the area around 1,600-1,300 BCE, can be found on the Taymyr peninsula, much further to the east48,49. Finally, the Imiyakhtakhskaya culture from Yakutia spread to the Kola Peninsula during the same period18,50. 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 area51. 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.

    The novel genome-wide data here presented from ancient individuals from Finland opens new insights into Finnish population history. Two of the three higher coverage individuals and all six low coverage individuals from Levänluhta showed low genetic affinity to modern-day Finnish speakers of the area. Instead, an increased affinity was observed to modern-day Saami speakers, now mostly residing in the north of the Scandinavian Peninsula. These results suggest that the geographic range of the Saami extended further south in the past, and hints at a genetic shift at least in the western Finnish region during the Iron Age. The findings are in concordance with the noted linguistic shift from Saami languages to early Finnish. Further ancient DNA from Finland is needed to conclude to what extent these signals of migration and admixture are representative of Finland as a whole.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    So, the two most relevant million dollar questions:

    1) Are the Saami the true indigenous people of Finland and Scandinavia?

    2) Were the Nordic countries completely inhabited by Uralic speakers before Indo-Europeans came along and ruined the party?
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    Quoted for truth:
    Quote Originally Posted by Alaron View Post
    Anatolian Urhemait supporters are mostly butthurt Meds.
    For the lulz:
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    Poland is a misunderstanding. It is a country which lies on the frontier between western and slavic world, and which combines elements of both.
    In fact, they are not even the Europeans in strict sense, meaning European as in bearing the responsibility and understanding of European interests. Poland has always been an subordinate country, on one side sucking German dick, on the other side -- Russian one, some kind of "novice" europeans, who are full of inferiority complexes, hysteria and obsessity neuroses. This is also true for all Baltic countries

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    Quote Originally Posted by EliasAlucard View Post
    So, the two most relevant million dollar questions:

    1) Are the Saami the true indigenous people of Finland and Scandinavia?
    Geneticly, probably not. The Saami has been a marginal phenomenon in our history. Interesting results although.

    2) Were the Nordic countries completely inhabited by Uralic speakers before Indo-Europeans came along and ruined the party?
    Actually some nordic scientists believed that during the 1700s already. Why would uralic be so incredibly archaic? Could be any language.
    Last edited by Blue3001; 2018-03-22 at 18:09.

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    Here is a facial reconstruction of one of the Levänluhta (Leväluhta) skulls:

    https://kalmistopiiri.wordpress.com/...selle-tytolle/

    Most of the sampled Levänluhta remains show affinity with the modern Sami. This particular girl hasn't been sampled, though, so I don't know if she is genetically similar to the Sami-like individuals or if she is more like the one non-Sami-like Levänluhta individual. Also, because she hasn't been sampled, her real eye and hair colours aren't known.

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    Quote Originally Posted by Aino View Post
    Here is a facial reconstruction of one of the Levänluhta (Leväluhta) skulls:

    https://kalmistopiiri.wordpress.com/...selle-tytolle/

    Most of the sampled Levänluhta remains show affinity with the modern Sami. This particular girl hasn't been sampled, though, so I don't know if she is genetically similar to the Sami-like individuals or if she is more like the one non-Sami-like Levänluhta individual. Also, because she hasn't been sampled, her real eye and hair colours aren't known.
    Interesting reconstruction...





    Reminds me of a Finnish girl I know
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    Quoted for truth:
    Quote Originally Posted by Alaron View Post
    Anatolian Urhemait supporters are mostly butthurt Meds.
    For the lulz:
    Quote Originally Posted by drgs View Post
    Poland is a misunderstanding. It is a country which lies on the frontier between western and slavic world, and which combines elements of both.
    In fact, they are not even the Europeans in strict sense, meaning European as in bearing the responsibility and understanding of European interests. Poland has always been an subordinate country, on one side sucking German dick, on the other side -- Russian one, some kind of "novice" europeans, who are full of inferiority complexes, hysteria and obsessity neuroses. This is also true for all Baltic countries

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    Quote Originally Posted by EliasAlucard View Post
    Interesting reconstruction...





    Reminds me of a Finnish girl I know
    She looks standard Nordic, nothing Saami about her.
    The Future was better before

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    Quote Originally Posted by Litvin View Post
    Hands off of R1a, Finno-Ugrics! It is an Indo-European marker.
    Lol, I try to be realistic. The steppe admixture is much too big in Finland to be connected to any forest zone hunter population.

    I recognize that now after writing all this my life is cheap and I'll spend dangerous time
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    2. Finnish I1 (around 30% of all Finns) has Germanic roots from the late Bronze Age or the early Iron Age.
    3. As to the Finnish prehistory we have no evidences about any Iron Age (or later) east-to-west migration, but many unquestionable evidences about west-to-east migrations.

    Väinämöinen - R1a
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    Quote Originally Posted by Janos View Post
    She looks standard Nordic, nothing Saami about her.
    That reconstruction definitely looks like a young Finnish woman. Sure, Nordic, but if I had to guess her ancestry, my first first guess would be Finnish, not Swedish or Norwegian.

    Anyway, Duwa, it seems like this study cements the connection between N1c, Uralic speakers and Siberian admixture, once and for all?

    2 posts about blog advertisement, deleted. Discuss the topic here, don't promote your blogs with empty click bait links. Thanks.

    //mod
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    Quoted for truth:
    Quote Originally Posted by Alaron View Post
    Anatolian Urhemait supporters are mostly butthurt Meds.
    For the lulz:
    Quote Originally Posted by drgs View Post
    Poland is a misunderstanding. It is a country which lies on the frontier between western and slavic world, and which combines elements of both.
    In fact, they are not even the Europeans in strict sense, meaning European as in bearing the responsibility and understanding of European interests. Poland has always been an subordinate country, on one side sucking German dick, on the other side -- Russian one, some kind of "novice" europeans, who are full of inferiority complexes, hysteria and obsessity neuroses. This is also true for all Baltic countries

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    Quote Originally Posted by EliasAlucard View Post
    Anyway, Duwa, it seems like this study cements the connection between N1c, Uralic speakers and Siberian admixture, once and for all?
    It certainly does, the correlation is unmistakable.

    Edit: One thing I'll add is that Bolshoy's allele-sharing with Mesolithic Karelians could have very important linguistic implications, especially in the framework of the Indo-Uralic hypothesis. If we are enclined to accept it as valid (it is the most convincing high-level relationship for PIE) then this could even mean that Pre-Proto-Indo-European speech arose in an R1a-rich group as R1a-M459 was found in the Karelian EHGs. This might also be a stretch however since J1 was also found in two Karelian EHGs (one from Yuzhnyy Oleni Ostrov and another more recent sample from Popovo).
    Last edited by Semitic Duwa; 2018-03-22 at 20:56.


    Quote Originally Posted by MnM View Post
    Morocco is a western lapdog.
    Quote Originally Posted by NonFingo View Post
    Those Bronze Age samples are just red herrings to distract you from the actual arrivals of populations with Semitic ancestry. Don’t take the bait by focusing on the wrong samples, lol. He is passing off Bronze Age Levantines with no evidence of strong predynastic input, as “Semites“. This way, he can flip it around and say Proto-Semitic speakers and predynastics were more or less identical to the Bronze Age Levantines sampled so far.
    Quote Originally Posted by NonFingo View Post
    @Semitic Duwa

    Wonder what the resident Proto-Semite has to say about this. I thought unmixed Egyptians were supposed to be Abusir with less/zero Chl?

    In your view, does this prove you wrong, or is it just a coincidence () that M1 is absent in one of the three subsamples from Abusir, and rare overall?

    And don’t change your signature now, please. I’m looking forward to you looking more and more incompetent as more aDNA is published. Wish there was a way to speed this up. But the extra wait and seeing you with your pants down every day, kinda has its own appeal, too.

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    Quote Originally Posted by Semitic Duwa View Post
    It certainly does, the correlation is unmistakable.
    Yes, it does, but it doesn't explain why downstream mutations of ancient Kola people are common in Baltic countries, neither the route of Baltic-Finnic languages to Fennoscandinavia. I am quite sure that the Kola N1c1 explains the Siberian admixture, actually have written it about in my blog for years
    Blog: http://terheninenmaa.blogspot.fi/, with essence "Believe me, or I'll nuke you".

    H39 - Thracia 1650 BC, Hungary 5000 BC
    I1 - Transdanubia 5000 BC

    Three simple facts about Finns:
    1. Baltic Finnic languages (including Finnish) never came from the Volga basin along with ancestors of present-day Finns.
    2. Finnish I1 (around 30% of all Finns) has Germanic roots from the late Bronze Age or the early Iron Age.
    3. As to the Finnish prehistory we have no evidences about any Iron Age (or later) east-to-west migration, but many unquestionable evidences about west-to-east migrations.

    Väinämöinen - R1a
    Lemminkäinen - I1
    Joukahainen - N

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