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Thread: Ancestral contributions to contemporary European complex traits

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    Ancestral contributions to contemporary European complex traits

    https://www.biorxiv.org/content/10.1...08.03.454888v1

    The contemporary European genetic makeup formed in the last 8000 years as the combination of three main genetic components: the local Western Hunter-Gatherers, the incoming Neolithic Farmers from Anatolia and the Bronze Age component from the Pontic Steppes. When meeting into the post-Neolithic European environment, the genetic variants accumulated during their three distinct evolutionary histories mixed and came into contact with new environmental challenges.

    Here we investigate how this genetic legacy reflects on the complex trait landscape of contemporary European populations, using the Estonian Biobank as a case study.

    For the first time we directly connect the phenotypic information available from biobank samples with the genetic similarity to these ancestral groups, both at a genome-wide level and focusing on genomic regions associated with each of the 27 complex traits we investigated. We also found SNPs connected to pigmentation, cholesterol, sleep, diastolic blood pressure, and body mass index (BMI) to show signals of selection following the post Neolithic admixture events. We recapitulate existing knowledge about pigmentation traits, corroborate the connection between Steppe ancestry and height and highlight novel associations. Among others, we report the contribution of Hunter Gatherer ancestry towards high BMI and low blood cholesterol levels.

    Our results show that the ancient components that form the contemporary European genome were differentiated enough to contribute ancestry-specific signatures to the phenotypic variability displayed by contemporary individuals in at least 11 out of 27 of the complex traits investigated here



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    So, if I understood well the graphic: high stature is correlated with Yamnaya, blond hair with Anatolia N, green eyes with Siberia (?), blue eyes with WHG and Anatolia N, Body Mass Index with WHG etc.



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    Quote Originally Posted by Cato View Post
    So, if I understood well the graphic: high stature is correlated with Yamnaya, blond hair with Anatolia N, green eyes with Siberia (?), blue eyes with WHG and Anatolia N, Body Mass Index with WHG etc.



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    Cato: I think, based on what I have read in the past, Blond Hair was relate to Ancient North Eurasians and Eastern European/Scandanavian Hunter Gatherers. This is from the Supplement (Figure S2.2) from the paper by Mathieson et al 2018 "The genomic history of southeastern Europe" published in Nature (March 2018).

    "The derived allele of the KITLG SNP rs12821256 that is associated with – and likely causal for – blond hair in Europeans7,8 is present in one hunter-gatherer from each of Samara, Motala
    and Ukraine (I0124, I0014 and I1763), as well as several later individuals with Steppe ancestry. Since the allele is found in populations with EHG but not WHG ancestry, it suggests
    that its origin is in the Ancient North Eurasian (ANE) population. Consistent with this, we observe that the earliest known individual with the derived allele (supported by two reads) is
    the ANE individual Afontova Gora 3,6 which is directly dated to 16130-15749 cal BCE (14710±60 BP, MAMS-27186: a previously unpublished date that we newly report here). We
    cannot determine the status of rs12821256 in Afontova Gora 2 and MA-1 due to lack of sequence coverage at this SNP.9"



    So if that paper is stating what you wrote, it is not in line with that this paper found.

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    I'm not sure about blond hair (BTW If I remember correctly in one study an Anatolian farmer individual had blond hair and blue eyes) but in the paper they clearly state that Yamnaya is connected with high statures, dark hair and eyes and WHG with BMI and light (blue) eyes

    Also about green eyes "Lastly, the Siberia ancestry is connected with dark eye and hair pigmentation, but also green eye color and lower age at menarche."

    I have green eyes but I don't think I have Siberian ancestry

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    Cato: I think you are correct, the Yamnaya are related to the Ancient North Eurasians but I think they are a mix between Eastern European Hunter Gathers and the Caucus Hunter Gathers. I think the Blonde hair specifically though is related to the Eastern European Hunter Gathers per the Mathieson et al 2018 Nature Paper I linked above

    Wang et al 2019 (Nature) document the Yamnaya having mostly EHG+CHG with some, not insignificant Early European Farmer (See Figure 5)

    https://www.nature.com/articles/s41467-018-08220-8

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    Thanks to Cato for bringing this to our attention. As to the paper, any paper written by or under the supervision of Mait Metspalu deserves our respect and consideration.

    In terms of the graphic, the results are based on the chromosomes where the codes for the traits appear. This area is the most heritable, so imo, those results may be closest to ¨accurate¨. For anyone who might have difficulty interpreting it, the area on the right means high correlation. So, just look for high correlation by color.

    This yields results showing, for example, that Yamnaya was black haired, dark eyed, tall, etc. WHG was blue eyed, had high BMI. Blonde hair is definitely tied to Anatolia Neolithic, regardless of where it might first have been found, and green eyes are tied to Siberia.

    The genome wide associations in Figure 2 show different results. They also used PCA.

    I think I would go with their own conclusions looking at all the results.

    ¨As a whole, the most affected traits include pigmentation and34 anthropometric traits together with blood cholesterol levels, caffeine consumption, heart rate35 and age at menarche.¨

    ¨In particular WHG ancestry is linked to lower cholesterol levels, higher BMI and putatively con2 tributed light (but not green) eye color to the contemporary Estonian population. Importantly,3 these associations stand when carefully considering covA ICs and, in addition, loci associated4 with these features also appear to have undergone selection in Estonians.

    Secondly, although5 WHG seems to have an association with hip circumference, caffeine consumption and brown6 hair pigmentation, these evidences are ambiguous.7

    An enriched Yamnaya ancestry in the pigmentation candidate regions, in contrast with the8 genome wide analysis, is linked to dark eye and hair colors, consistently with what inferredfrom aDNA data from the Baltic region69 . This ancestry is also linked to a strong build, withhigh stature (in agreement with previous literature5,710 ) and large hip and waist circumferences,11 both at genome-wide and region-specific levels, but also high cholesterol concentrations when12 focusing on candidate regions.

    The associations of Yamnaya and WHG ancestries to respec13 tively higher and lower cholesterol levels, together with the clues of selection at loci connected14 to cholesterol and BMI, add a critical element to the knowledge of post-neolithic dietary adaptation6,32,3315 and might have important health-related implications.16

    Caffeine consumption, although having significant associations, is difficult to connect to a spe17 cific ancestry: Yamnaya ancestry seems to be linked with lower consumption, whereas the18 direction of Siberia and WHG associations depends on the genomic regions included in the19 analysis.20

    An enriched Anatolia N ancestry in the pigmentation candidate regions has implications op21 posite to Yamnaya, again in contrast with the genome-wide signal. This recurring localized22 peculiarity of pigmentation loci possibly reflects selection specific to strong GWAS hits as already seen for skin pigmentation823 . Notably, Anatolia N enrichment in trait-related genomic24 regions is connected with a reduced BMI-corrected waist/hip ratio and heart rate. After con25 sidering covA ICs, this connection between Anatolia N and heart rate seems to be the one26 driving the apparent associations of all other ancestries.27

    Lastly, the Siberia ancestry is connected with dark eye and hair pigmentation, but also green28 eye color and lower age at menarche. Again, even if this last trait has ambiguous associations29 with Anatolia N and WHG ancestries, covA ICs provide a clue to disentangle their interactions30 in favour of a more robust connection with the Siberia ancestry.31

    Some ancestry/trait associations that were not considered significant at a genome-wide level,32 are instead discovered when comparing candidate regions to the rest of the genome, possibly due33 to the higher sensitivity of this approach. On the other hand, the opposite happens for alcohol34 consumption, depression, sleep duration, social jetlag, diopters, pulse pressure, creatinine levels.35 This might be due to a misleading or incomplete tagging of the actual functional regions by36 the GWAS catalog hits, or to an incomplete correction of socioeconomic and other non-genetic37 factors. In case of sleep-connected traits and DBP, the reported signal of recent or ongoing38 selection for loci associated to these phenotypes suggests a yet more complex picture.39 ¨


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    Quote Originally Posted by Cato View Post
    So, if I understood well the graphic: high stature is correlated with Yamnaya, blond hair with Anatolia N, green eyes with Siberia (?), blue eyes with WHG and Anatolia N, Body Mass Index with WHG etc.



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    I recently posted myself on Eupedia a phenotypic analysis of an Anatolian farmer individual 10, 000 years ago, who was blond. That said, according to a study Yamanya individuals carried a mutation to the KITLG gene associated with blond hair, as several individuals with Steppe ancestry are later found to carry this mutation. The Ancient North Eurasian population, who contributed significant ancestry to Western Steppe Herders, are believed to be the source of this mutation. Plus another genetic paper from 2015 found that Yamnaya had the highest ever calculated genetic selection for height of any the ancient populations tested. Furthemore, the earliest known individual that carries the derived rs12821256 allele, is a female ANE individual from Afontova Gora 3 site, from 18 k years ago. She carried the KITLG genes which are associated with lightened skin and hair color in Europeans. One of these polymorphisms is associated with blond hair. Besides, David Reich also claimed that the KITLG gene for blond hair entered continental Europe in a massive population migration from the Eurasian steppe, by a population carrying substantial Ancient North Eurasian ancestry. Hanel and Carlberg (2020) likewise concluded that populations bearing ANE ancestry were responsible for lightening European skin and hair color. So, this new paper is in contrast to all the previous studies concerning which ancestry was the source for blond hair in Europeans. The thing is, that Northern Europeans who are 50% Yamanya-like are the palest and blondest of all Europeans. In contrast, Sardinians who are the closest living relatives to ANFs are the least light-haired and light-eyed Europeans. Hence, it doesn't make sense to attribute blond hair of Europeans to ANF. What is clear though, is that the rather short height in Southern Europeans can be attributed to ANF ancestry.


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    Ok, so Mait Metspalu hasn´t read any of the ancient Dna papers, hasn´t read Reich, even though he´s worked with him, didn´t look at any of the ancient dna results for the ancestral populations heś using for comparison, and just generally doesn´t know what heś talking about.

    Good to know.

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    Quote Originally Posted by Angela View Post
    Ok, so Mait Metspalu hasn´t read any of the ancient Dna papers, hasn´t read Reich, even though he´s worked with him, didn´t look at any of the ancient dna results for the ancestral populations heś using for comparison, and just generally doesn´t know what heś talking about.

    Good to know.


    No need for getting sarcastic here. So, do you think ANF ancestry is the source for blond hair in Europeans and not ANE/WSH? Mait Metspalu worked with Reich? And? Matter of fact, David Reich (like other geneticists) doesn't associate blond hair with Anatolian Farmers but with ANE and Yamanya. Anyway, I referred to genetic studies that came to a different conclusion than Metspalu. However, it appears that you just dismiss what I wrote, as if I had pulled my arguments out of thin air without having a scientific source that backs up my claims. Besides, when I once argued that some ancient Roman emperors could be indeed naturally blond or blue-eyed, I was accused by you of being a Nordicist. Just saying. Mait Metspalu knows what he is talking about. But so do Reich, Hanel, and Carlberg who linked blondism in Europeans to ANE/ WSH. It's not as if Mespalu is the only professional and Reich, Hanel, or Carlberg are a bunch of bloody amateurs. To me, the conclusion of Reich and the others geneticists who attribute blond hair to WSH/ANE ancestry is much more plausible. Anyway, what all geneticists agree on is that the tallness of Northern Europeans can be attributed to Yamanya/WSH ancestry, while the short stature of Southern Europeans to ANF ancestry.

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    Quote Originally Posted by real expert View Post
    I recently posted myself on Eupedia a phenotypic analysis of an Anatolian farmer individual 10, 000 years ago, who was blond. That said, according to a study Yamanya individuals carried a mutation to the KITLG gene associated with blond hair, as several individuals with Steppe ancestry are later found to carry this mutation. The Ancient North Eurasian population, who contributed significant ancestry to Western Steppe Herders, are believed to be the source of this mutation. Plus another genetic paper from 2015 found that Yamnaya had the highest ever calculated genetic selection for height of any the ancient populations tested. Furthemore, the earliest known individual that carries the derived rs12821256 allele, is a female ANE individual from Afontova Gora 3 site, from 18 k years ago. She carried the KITLG genes which are associated with lightened skin and hair color in Europeans. One of these polymorphisms is associated with blond hair. Besides, David Reich also claimed that the KITLG gene for blond hair entered continental Europe in a massive population migration from the Eurasian steppe, by a population carrying substantial Ancient North Eurasian ancestry. Hanel and Carlberg (2020) likewise concluded that populations bearing ANE ancestry were responsible for lightening European skin and hair color. So, this new paper is in contrast to all the previous studies concerning which ancestry was the source for blond hair in Europeans. The thing is, that Northern Europeans who are 50% Yamanya-like are the palest and blondest of all Europeans. In contrast, Sardinians who are the closest living relatives to ANFs are the least light-haired and light-eyed Europeans. Hence, it doesn't make sense to attribute blond hair of Europeans to ANF. What is clear though, is that the rather short height in Southern Europeans can be attributed to ANF ancestry.

    Well I am not looking to get into any tit for tat with you. However, the KITLG gene is associated with Hair color, that is pretty much established in all the papers going back 10 or so years. As you note, the SNP rs12821256 is associated with blonde hair (per SNPedia and several research papers). However, I am not sure it has as much impact on skin as you are suggesting. Do you have a cite that documents the impact on skin tone that KITLG has. I think I read some years ago that the KITLG working together with OCA2 (i.e and Interaction term in a OLS Regression framework) might have some impact on skin. But still, the SLC24A5 gene which accounts for 25% to 38% of the skin tone variation between Europeans and equatorial populations, which seems to be one of the genes that is most significantly related to skin variation across populations. I for example on SLC24A5-rs1426654 am AA and on SLC45A2-rs16891982 am GG, but I don't have blonde hair since on rs12821256 am TT and OCA2- rs1800401 I am heterozygous AG (so obviously Brown eyes).

    However, the skin tone and SLC24A5 (rs1426654) as I noted based on what I have read is the one that provides the largest impact on skin tone variation of Europeans vs. Populations near the Equator, etc. Mathieson et al (2015) in "Genome-wide patterns of selection in 230 ancient Eurasians" documents that the SLC45A2-rs16891982 was not anywhere near fixed in ancient Europeans but they did document that among the Neolithic Anatolian Farmers the rs1426654 allele was fixed.

    Skoglund and Mathieson (2018) in a review paper (3 years old but still a good Literature review) document again regarding SLC24A5:

    https://www.annualreviews.org/doi/10...-083117-021749


    "A main conclusion from ancient DNA studies is that Upper Paleolithic Eurasians and Mesolithic western Europeans carried ancestral (i.e., relatively dark skin) alleles at the two loci that are most important for light skin pigmentation in present-day Europe, SLC24A5 and SLC45A2 (28, 57, 72, 73, 84, 101, 130). In the Mesolithic, both of these alleles were present in eastern Europe and Anatolia (73). The derived SLC24A5 allele was introduced to Europe at high frequency by the Anatolian Neolithic migration, while the derived SLC45A2 allele was introduced at lower frequency and subsequently
    selected. Both of these alleles are now virtually fixed in Europe."

    Now as for blond hair and the Anatolian Farmers, the new paper is interesting in that an early Farmer had blond hair. I would still want to see all the Early Farmer phenotypes from all the samples published. Obviously they seem to be the first Ancient European population to be fixed on SLC24A5 and I would still think the majority would have brown eyes and darker hair. In other words, a common phenotype found in Southern Europeans. That does not rule out of course that there were Blond Anatolian Farmers which this new paper finds.
    Last edited by Palermo Trapani; 18-08-21 at 05:49.

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    Quote Originally Posted by real expert View Post
    No need for getting sarcastic here. So, do you think ANF ancestry is the source for blond hair in Europeans and not ANE/WSH? Mait Metspalu worked with Reich? And? Matter of fact, David Reich (like other geneticists) doesn't associate blond hair with Anatolian Farmers but with ANE and Yamanya. Anyway, I referred to genetic studies that came to a different conclusion than Metspalu. However, it appears that you just dismiss what I wrote, as if I had pulled my arguments out of thin air without having a scientific source that backs up my claims. Besides, when I once argued that some ancient Roman emperors could be indeed naturally blond or blue-eyed, I was accused by you of being a Nordicist. Just saying. Mait Metspalu knows what he is talking about. But so do Reich, Hanel, and Carlberg who linked blondism in Europeans to ANE/ WSH. It's not as if Mespalu is the only professional and Reich, Hanel, or Carlberg are a bunch of bloody amateurs. To me, the conclusion of Reich and the others geneticists who attribute blond hair to WSH/ANE ancestry is much more plausible. Anyway, what all geneticists agree on is that the tallness of Northern Europeans can be attributed to Yamanya/WSH ancestry, while the short stature of Southern Europeans to ANF ancestry.
    Yamnaya had mostly dark hair and eye. The process that made northern Europe mostly blonde hair blu was likely due to exogamy with the northern europeans farmers ( TRB and GAC) that probably harbored among the female population a high proportions of these traits likely because they had a lot of WHG/SHG ancestry. So steppe is involved but in an indirect way. Gentlemens ( from the steppe) prefer the blondes was evidently a popular movie even back then!
    Besides the forefathers of the Yamnaya, Dneper Don foragers ( archaic IE ) were overpacked with WHG ancestry and Sredni Stog ( full formed PIE) had a strong EEF input. So even if Yamnaya had some nordic traits it would be from these western sources anyway
    Keep in mind as a side note that ANE is upper palolithic europeans ( 75% mostly of aurignacian dna) and 25% east asian. So basically an older version of the WHG.

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    THis is also demonstrated by the difference between Yamnaya and CWC . The latter was sligthly more nordic and since the difference between the two is that CW have an uptick of EEF ancestry ( and a bit of more EuroHG also) that is exactly one would expect if the source is the EEF input.

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    Quote Originally Posted by real expert View Post
    I recently posted myself on Eupedia a phenotypic analysis of an Anatolian farmer individual 10, 000 years ago, who was blond. That said, according to a study Yamanya individuals carried a mutation to the KITLG gene associated with blond hair, as several individuals with Steppe ancestry are later found to carry this mutation. The Ancient North Eurasian population, who contributed significant ancestry to Western Steppe Herders, are believed to be the source of this mutation. Plus another genetic paper from 2015 found that Yamnaya had the highest ever calculated genetic selection for height of any the ancient populations tested. Furthemore, the earliest known individual that carries the derived rs12821256 allele, is a female ANE individual from Afontova Gora 3 site, from 18 k years ago. She carried the KITLG genes which are associated with lightened skin and hair color in Europeans. One of these polymorphisms is associated with blond hair. Besides, David Reich also claimed that the KITLG gene for blond hair entered continental Europe in a massive population migration from the Eurasian steppe, by a population carrying substantial Ancient North Eurasian ancestry. Hanel and Carlberg (2020) likewise concluded that populations bearing ANE ancestry were responsible for lightening European skin and hair color. So, this new paper is in contrast to all the previous studies concerning which ancestry was the source for blond hair in Europeans. The thing is, that Northern Europeans who are 50% Yamanya-like are the palest and blondest of all Europeans. In contrast, Sardinians who are the closest living relatives to ANFs are the least light-haired and light-eyed Europeans. Hence, it doesn't make sense to attribute blond hair of Europeans to ANF. What is clear though, is that the rather short height in Southern Europeans can be attributed to ANF ancestry.

    imo what this study suggests isn't that anatolian farmers were blonde haired nor that the genes for this trait are really associated with anatolian farmers. only that the specific population that probably contributed most of the alleles for blonde hair in modern baltics was particularly anatolian farmer heavy in ancestry. the alleles for those traits might have initially be introduced into this farmer heavey population by a different population for example SHG. or they were present in anatolian farmers and increased through selection or both things together. we don't know.

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    Gentlemen, you´ve left me almost nothing to say. I've given upvotes to each of your posts. Clearly, you've both read the paper carefully, which is, of course, essential.

    I would just add that the fact that mutation X can be found in ancient population Y does not mean that it then necessarily spread to people Z. A mutation which is beneficial in some way, in ways which we clearly don't yet completely understand, for example, in the LP gene, could arise in more than one population.

    When quoting certain experts, it's important to know when the statement was made, and which papers were published after that time. There have been two major papers published which maintain, based on ancient dna, the dark pigmentation of Yamnaya. Corded Ware was also not universally fair, but were more fair than Yamnaya, but they had different ancestry. People have to understand that Yamnaya, from which the Indo-European culture derived, is not identical genetically to the Corded Ware people.

    If one wanted to be really nitpicky, what the paper shows is through which ancient population source the trait "arrived", in the ESTONIAN population studied.

    Also keep in mind that the results for the genome wide association are slightly different from the ones in the graphic posted, which show the association based on the specific coding areas on the chromosome.

    HOWEVER, and this is a big however, the coding region is the HERITABLE region, and so it tells us which population is actually responsible for passing the alleles down to the particular population.
    Last edited by Angela; 17-08-21 at 20:04.

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    Quote Originally Posted by Ailchu View Post
    imo what this study suggests isn't that anatolian farmers were blonde haired nor that the genes for this trait are really associated with anatolian farmers. only that the specific population that probably contributed most of the alleles for blonde hair in modern baltics was particularly anatolian farmer heavy in ancestry. the alleles for those traits might have initially be introduced into this farmer heavey population by a different population for example SHG. or they were present in anatolian farmers and increased through selection or both things together. we don't know.
    I have to say it: thatś certainly a possibility.

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