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Thread: Population genomics of the Viking world (Margaryan et al 2020)

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    Satyavrata Maciamo's Avatar
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    Post Population genomics of the Viking world (Margaryan et al 2020)

    A new paper just came out: Population genomics of the Viking world (Margaryan et al 2020)

    Abstract

    The maritime expansion of Scandinavian populations during the Viking Age (about AD 750–1050) was a far-flung transformation in world history. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci—including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response—in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

    Here is the supplementary information (178 pages). There are also Excel tables in supplements. I haven't read anything yet.

    "The 442 ancient individuals were divided into five broad categories (Figure 1 in the main text) and the majority (n=376) were sequenced to between 0.1 and 11X average depth of coverage. The data set includes Bronze Age (n=2) and Iron Age (n=10) individuals from Scandinavia; early VA (n=43)individuals from Estonia (n=34), Denmark (n=6), and Sweden (n=3); ancient individuals associated with Norse culture from Greenland (n=23), VA individuals from Denmark (n=78), the Faroe Islands(n=1), Iceland (n=17), Ireland (n=4), Norway (n=29), Poland (n=8), Russia (n=33), Sweden (n=118),the Isle of Man (n=1), Scotland (n=8), England (n=32), Wales (n=1), and Ukraine (n=3), as well as individuals from the medieval and early modern periods from the Faroe Islands (n=16), Italy (n=5),Norway (n=7), Poland (n=2), and Ukraine (n=1). The VA individuals were supplemented with published genomes from Sigtuna, Sweden (n=21, samples VK557-VK578)35, and Iceland."
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    2 members found this post helpful.
    Here is the summary of the Y-DNA of all samples in the study.



    The paper says:

    "The ancient samples in the present study are mainly distributed in two clades, I1a1b1-L22, which accounts for 71% of the I1 haplotypes in a Y chromosome survey of Finland, and I1a2a-S246. Of particular interest, the clade I1a2a1a1d1a-S247 is especially well represented inEstonian samples, and is found mostly in present-day Finnish and northern Scandinavian groups."

    I checked the Excel tables, but unfortunately the Y-DNA list does not give the SNPs. I wanted to know what percentage of R1b-L21 was present in Scandinavia, and especially in Norway, before the Vikings settled Britain and Ireland.

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    1 members found this post helpful.
    Here is what the study says regarding the skin, hair and eye pigmentation of the Vikings. It's almost identical to modern Danes.

    "The SNPs with strongest association with lighter hair and eye pigmentation phenotypes such as theones in HERC2, OCA2, and TYR genes in humans are elevated in the Viking population, and theprofile of allele frequency distribution is close to the present-day northern European populationrepresented here by the 'CEU' (1000 Genomes Project) and the modern Danish population ('DK')from IPSYCH case-cohort study. The frequencies of informative SNPs associated with pigmentationare presented in Figure S13.1. This suggests that the genetic profile of pigmentation SNPs we observein northern Europeans today had been largely formed at the onset of the Viking period."



    According to these charts, the main difference between the Vikings tested and modern Danes is that the Vikings had twice the frequency of derived OCA2 (rs1800407), one of the mutation associated with blue eyes. That doesn't mean much as modern Tuscans have an even higher frequency of derived OCA2.

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    Quote Originally Posted by Maciamo View Post
    Here is what the study says regarding the skin, hair and eye pigmentation of the Vikings. It's almost identical to modern Danes.

    "The SNPs with strongest association with lighter hair and eye pigmentation phenotypes such as theones in HERC2, OCA2, and TYR genes in humans are elevated in the Viking population, and theprofile of allele frequency distribution is close to the present-day northern European populationrepresented here by the 'CEU' (1000 Genomes Project) and the modern Danish population ('DK')from IPSYCH case-cohort study. The frequencies of informative SNPs associated with pigmentationare presented in Figure S13.1. This suggests that the genetic profile of pigmentation SNPs we observein northern Europeans today had been largely formed at the onset of the Viking period."



    According to these charts, the main difference between the Vikings tested and modern Danes is that the Vikings had twice the frequency of derived OCA2 (rs1800407), one of the mutation associated with blue eyes. That doesn't mean much as modern Tuscans have an even higher frequency of derived OCA2.
    The scientists who wrote the study stated on daily mail and National geographic the contrary. They concluded that Vikings back then were much darker than the average modern Dane. Plus according to the authors modern Scandinavians have only 15-30% Viking DNA. What is your take on this paper? I personally think this genetic study is misleading.

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    Quote Originally Posted by real expert View Post
    The scientists who wrote the study stated on daily mail and National geographic the contrary. They concluded that Vikings back then were much darker than the average modern Dane. Plus according to the authors modern Scandinavians have only 15-30% Viking DNA. What is your take on this paper? I personally think this genetic study is misleading.
    The study itself is fine, but their communication to the press regarding the results has been borderline dishonest in my opinion, and misleading at best.

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    Quote Originally Posted by Bygdedweller View Post
    The study itself is fine, but their communication to the press regarding the results has been borderline dishonest in my opinion, and misleading at best.
    There is a pattern. This is not the first study that was presented in the media in a very misleading way where the gullible public was misinformed.

    To me it's frustrating that genetic studies are often not used in a strictly scientific, neutral and educational way.

    The data as such isn't the issue, a problem, but the fact that the data is being presented in a sophisticated way to say what certain people want it to say. In my opinion this Viking study is being and will be used to shake the Scandinavian's national identity. The media and certain scientific magazines already played the same game with the Cheddar man in order to challenge, question the native British identity. And I also remember the headlines about the Roman paper that stated: Ancient Romans had more in common with Greeks, modern Syrians and Lebanese than Europeans. Plenty people after reading the article falsely believed that modern Italians had nothing to with the ancient ones.
    Last edited by real expert; 17-09-20 at 22:05.

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    Quote Originally Posted by real expert View Post
    The scientists who wrote the study stated on daily mail and National geographic the contrary. They concluded that Vikings back then were much darker than the average modern Dane. Plus according to the authors modern Scandinavians have only 15-30% Viking DNA. What is your take on this paper? I personally think this genetic study is misleading.
    Why would they say the opposite of what they write in their paper to the Daily Mail? Or is it the journalists from the Daily Mail who distorted what he said?

    It's completely ridiculous to say that modern Scandinavians have only 15-30% of Viking DNA! What would be the remaining 70-85% then?

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    Quote Originally Posted by Maciamo View Post
    Here is what the study says regarding the skin, hair and eye pigmentation of the Vikings. It's almost identical to modern Danes.

    "The SNPs with strongest association with lighter hair and eye pigmentation phenotypes such as theones in HERC2, OCA2, and TYR genes in humans are elevated in the Viking population, and theprofile of allele frequency distribution is close to the present-day northern European populationrepresented here by the 'CEU' (1000 Genomes Project) and the modern Danish population ('DK')from IPSYCH case-cohort study. The frequencies of informative SNPs associated with pigmentationare presented in Figure S13.1. This suggests that the genetic profile of pigmentation SNPs we observein northern Europeans today had been largely formed at the onset of the Viking period."



    According to these charts, the main difference between the Vikings tested and modern Danes is that the Vikings had twice the frequency of derived OCA2 (rs1800407), one of the mutation associated with blue eyes. That doesn't mean much as modern Tuscans have an even higher frequency of derived OCA2.
    They also concluded this:
    A binomial test of the number of black hair color risk alleles found in higher frequency in the VA sample and the present-day sample, also returned a significant difference.

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    It is a shame that WGExtract is unable to process these BAM files. If there is another means to do so, I would like to utilize it.
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    Quote Originally Posted by Maciamo View Post
    Why would they say the opposite of what they write in their paper to the Daily Mail? Or is it the journalists from the Daily Mail who distorted what he said?

    It's completely ridiculous to say that modern Scandinavians have only 15-30% of Viking DNA! What would be the remaining 70-85% then?

    I'm only informing people here about what's going on outside the archeogenetic community, and how this Viking study was presented to the public by the media. I read articles about the Vikings in daily mail, National Geographic, the Guardian to see how they differ in their report. But daily mail, NG, the Guardian basically reported the same, that Vikings were dark and modern Scandinavians are only a bit Viking. However, when I tried to set the record straight a smartass told me to deal with the fact that Vikings were all dark haired, swarthy and that modern Scandinavians have not much Viking blood. In my opinion the researchers are part of the problem because they play by the rules and games of the media. My assumption is that the authors picked up Vikings who were of mixed heritage or Vikings that were Picts or Celts and compared their genes with those of the modern Scandinavians. Therefore, I suspect that they used flawed, questionable methods to make modern Scandinavians appear less related to the Vikings. This is my guess. Anyway, anyone who learnt how to read genetic papers knows that you can make populations look closer related to their ancestors or less related depending on the methods you use. The thing is that not only the media but also the authors of genetic studies find sensationalism more exciting that confirming what was already known. Therefore, sometimes they exaggerate the results of their paper. Scientists want to make headlines too or break stereotype, old beliefs, etc.

    Again, when going by the interviews of the researchers from the mainstream media you think that the Vikings weren't that Scandinavian and modern ones didn't have much of them in their ancestry. We live in crazy times.

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    What Y DNA is the red at
    the top?

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    Quote Originally Posted by Joanne View Post
    What Y DNA is the red at
    the top?
    you mean in second post of maciamo .....
    i think the red is -
    Q1B -0.35%
    known ancestery:
    Sefhardi/ aschenazi/ mizrahi/ bulgarian
    Eurogenes k13 updated closest:
    4.70345618 Greek_Andros_Island

    eurogenes k13 ancient closeset:
    4.86806943 R136_Lazio_Rome_italy_Late_Antiquity
    http://www.ianlogan.co.uk/sequences_by_group/h3aa-av_genbank_sequences.htm

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    I'm only informing people here about what's going on outside the archeogenetic community, and how this Viking study was presented to the public by the media. I read articles about the Vikings in daily mail, National Geographic, the Guardian to see how they differ in their report. But daily mail, NG, the Guardian basically reported the same, that Vikings were dark and modern Scandinavians are only a bit Viking.
    The paper actually finds that pigmentation phenotype in VA Scandinavians may not have differed much from the present-day occupants of the region. Margaryan et al. (2020) also find that present-day populations are still structured according to the ancient Viking population groups within Scandinavia. The component that associated as Norwegian-like is present at 45-65% in present-day Norway. Moreover, the ancient Swedish-like ancestry is present at 15-30% within Sweden. Of the four Swedish clusters, one cluster is more related to the ancient Finnish, and a second cluster is more related to Danes and Norwegians. Danish-like ancestry is high across the whole region today. Margaryan et al. (2020) further detect an influx of low levels of “eastern” ancestry starting in the early VA, mostly constrained among groups from eastern and central Sweden with contributions of either East Asian- or Caucasus-related ancestry (Supplementary Note 10).

    Pigmentation-associated SNPs

    Exploring twenty-two SNPs with large effect associated with eye color and hair pigmentation, we observe that their frequencies are very similar to those of present-day Scandinavians (Supplementary Note 13). This suggests that pigmentation phenotype in VA Scandinavians may not have differed much from the present-day occupants of the region (although see section on complex traits below for an analysis including alleles of small effect). Nevertheless, it is important to stress that there is quite a lot of variation in the genotypes of these SNPs across the sequenced samples, and that there is therefore not a single ‘Viking phenotype’. For example, two of the ancient samples with the highest coverage have different pigmentation phenotypes: VA individual VK42 from Skara, Sweden has alleles associated with brown eyes and darker hair coloration while VK1 from Greenland was likely to have had blue eyes and lighter hair.
    Last edited by ThirdTerm; 19-09-20 at 01:06.
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    summary of yDNA Viking paper

    Maciamo, please label red section at top of circular diagram.

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    It is a bit sad we do not have SNPs. The rough breakdown is still useful, but rather not informative and relevant to the time period.
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    2 members found this post helpful.
    What do they think by "Viking": all Scandinavians of a time, or rather a lifestyle and specific brotherhood involving non-Scandinavians too?
    As others, I think the MOST of the media, papers an Co are found of sensationalism, what a pity in a world subject to changes and doubts about history.

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    Viking skin, hair, and eye pigmentation

    Maciamo, what is the population labelled TSI in the 6th diagram - lower far right

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    Quote Originally Posted by Joanne View Post
    Maciamo, what is the population labelled TSI in the 6th diagram - lower far right
    Pretty sure that’s Italians from Tuscany.

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    Quote Originally Posted by Bygdedweller View Post
    Pretty sure that’s Italians from Tuscany.
    Weren't the Italians samples from medieval Foggia? Southern Italy is where the Normans had territory. TSI could just be a proxy for that. TSI is usually used as a generic Italian population in DNA studies.

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    4 members found this post helpful.
    We see an increase of CHG and Anatolian_N across the board in Northern Europe from the Iron Age to the present. Perhaps that has to do with intermingling with Southern Europe in general within that timeframe:



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    @Jovialis
    Thanks for some docs I had not seen.
    I have some doubt sometimes concerning admixture charts. That said, some increase in "foreign" DNA in far North is sensible by time; Now, a nb 11 sample for a country is too low, if it is supposed to represent all regions of a vaste country, spite it's sufficient for an homogenous region.

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    Quote Originally Posted by Joanne View Post
    Maciamo, what is the population labelled TSI in the 6th diagram - lower far right
    Tuscans from Italy.


    Quote Originally Posted by Jovialis View Post
    Weren't the Italians samples from medieval Foggia? Southern Italy is where the Normans had territory. TSI could just be a proxy for that. TSI is usually used as a generic Italian population in DNA studies.

    TSI is Tuscans from Italy. It's used also in Raveane, and all individuals from TSI join one of northern-central clusters of Italy.

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    Quote Originally Posted by Pax Augusta View Post
    Tuscans from Italy.
    TSI is Tuscans from Italy. It's used also in Raveane, and all individuals from TSI join one of northern-central clusters of Italy.
    Indeed, South Italian or Sicilian samples would probably be better samples to use. Those are the populations the Normans interacted with.

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    Quote Originally Posted by Jovialis View Post
    Indeed, South Italian or Sicilian samples would probably be better samples to use. Those are the populations the Normans interacted with.

    I have given up expecting completely accurate genetic studies.

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    @Jovialis

    Do you have any info , more than this for .......

    Varnhem ( 950 yBP - Viking Age )

    VK398 ( 950 ± 100 yBP )

    Y-DNA: T1a2
    mtDNA: H1b1+16362
    Fathers mtdna ... T2b17
    Grandfather mtdna ... T1a1e
    Sons mtdna ... K1a4o
    Mum paternal line ... R1b-S8172
    Grandmum paternal side ... I1d1-P109
    Wife paternal line ... R1a-Z282

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