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Thread: Quantitative Human Paleogenetics: Ancient DNA and Complex Trait Evolution

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    Quantitative Human Paleogenetics: Ancient DNA and Complex Trait Evolution

    Quantitative Human Paleogenetics: Ancient DNA and Complex Trait Evolution

    Inspired by the recent paper below, please feel free to use this thread for further discussion. While there is an extensive review of the literature in this paper, additional citations are especially welcome.

    Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?

    Evan K. Irving-Pease, Rasa Muktupavela, Michael Dannemann and Fernando Racimo

    Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations.

    ...

    Ancient DNA and Complex Trait Genomics
    Skin, hair and eye pigmentation are among the least polygenic complex traits; though more than a hundred pigmentation-associated loci have been found, their heritability is largely dominated by large-effect common SNPs (Sulem et al., 2007; Eiberg et al., 2008; Han et al., 2008; Sturm et al., 2008; Hider et al., 2013; Liu et al., 2015; O’Connor et al., 2019). Additionally, several of these variants have signatures of past selective sweeps detectable in present-day genomes (Lao et al., 2007; Sabeti et al., 2007; Pickrell et al., 2009; Rocha, 2020). Nevertheless, genomic analyses in previously understudied populations—like sub-Saharan African groups—suggest that perhaps hundreds of skin pigmentation alleles of small effect remain to be found (Martin et al., 2017b). Similarly, recent studies have shown that eye pigmentation is far more polygenic than previous thought (Simcoe et al., 2021). Recent quantitative and molecular genomic studies are painting an increasingly complex picture of the architecture of these traits, featuring more considerable roles for epistasis, pleiotropy and small-effect variants than were previously assumed (for an extensive review of skin pigmentation, see Quillen et al., 2019).
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    “Ancient DNA and Complex Trait Genomics
    Skin, hair and eye pigmentation are among the least polygenic complex traits; though more than a hundred pigmentation-associated loci have been found, their heritability is largely dominated by large-effect common SNPs (Sulem et al., 2007; Eiberg et al., 2008; Han et al., 2008; Sturm et al., 2008; Hider et al., 2013; Liu et al., 2015; O’Connor et al., 2019). Additionally, several of these variants have signatures of past selective sweeps detectable in present-day genomes (Lao et al., 2007; Sabeti et al., 2007; Pickrell et al., 2009; Rocha, 2020). Nevertheless, genomic analyses in previously understudied populations—like sub-Saharan African groups—suggest that perhaps hundreds of skin pigmentation alleles of small effect remain to be found (Martin et al., 2017b). Similarly, recent studies have shown that eye pigmentation is far more polygenic than previous thought (Simcoe et al., 2021). Recent quantitative and molecular genomic studies are painting an increasingly complex picture of the architecture of these traits, featuring more considerable roles for epistasis, pleiotropy and small-effect variants than were previously assumed (for an extensive review of skin pigmentation, see Quillen et al., 2019).”



    Maybe out of context but do you think that Gingers have a similar gene to Pongo Orangutans? Like does the red hair come from the same source? Or rather convergent evolution?

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    Quote Originally Posted by KHAN View Post
    Maybe out of context but do you think that Gingers have a similar gene to Pongo Orangutans? Like does the red hair come from the same source? Or rather convergent evolution?
    Good question, definitely in the scope of this thread.

    "The presence of a functional, MSH-responsive MC1R in orangutan demonstrates that the mechanism of red hair generation in this ape is different from the prevalent mechanism in European human populations."
    High Diversity in Functional Properties of Melanocortin 1 Receptor (MC1R) in Divergent Primate Species Is More Strongly Associated with Phylogeny than Coat Color


    I have brown hair but I am a carrier for a rare allele (~0.004) for red hair: rs11547464.
    Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability

    Cheddar Man was also a carrier (https://www.nhm.ac.uk/content/dam/nh...tion-data.xlsx).

    I'm also a carrier for two other, less common, variants in the same gene, rs188004548 and rs140481921. They are in LD with rs11547464. I got those two from a WGS, they do not seem to be covered by 23andMe or AncestryDNA.

    Coincidentally, I once spent two weeks wrangling orangutans with a film crew in Malaysia (see my profile photo on the side). Some were more reddish than others.
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    Ancestral contributions to contemporary European complex traits

    In particular WHG ancestry is linked to lower cholesterol levels, higher BMI and putatively con-
    2 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 associated
    4 with these features also appear to have undergone selection in Estonians. Secondly, although
    5 WHG seems to have an association with hip circumference, caffeine consumption and brown
    6 hair pigmentation, these evidences are ambiguous.
    7 An enriched Yamnaya ancestry in the pigmentation candidate regions, in contrast with the
    8 genome wide analysis, is linked to dark eye and hair colors, consistently with what inferred
    9 from aDNA data from the Baltic region. This ancestry is also linked to a strong build, with
    10 high stature (in agreement with previous literature) and large hip and waist circumferences,
    11 both at genome-wide and region-specific levels, but also high cholesterol concentrations when
    12 focusing on candidate regions. The associations of Yamnaya and WHG ancestries to respec-
    13 tively higher and lower cholesterol levels, together with the clues of selection at loci connected
    14 to cholesterol and BMI, add a critical element to the knowledge of post-neolithic dietary adap-
    15 tation and might have important health-related implications.
    16 Caffeine consumption, although having significant associations, is difficult to connect to a spe-
    17 cific ancestry: Yamnaya ancestry seems to be linked with lower consumption, whereas the
    18 direction of Siberia and WHG associations depends on the genomic regions included in the
    19 analysis.
    20 An enriched Anatolia N ancestry in the pigmentation candidate regions has implications op-
    21 posite to Yamnaya, again in contrast with the genome-wide signal. This recurring localized
    22 peculiarity of pigmentation loci possibly reflects selection specific to strong GWAS hits as al-
    23 ready seen for skin pigmentation. Notably, Anatolia N enrichment in trait-related genomic
    24 regions is connected with a reduced BMI-corrected waist/hip ratio and heart rate. After con-
    25 sidering covA ICs, this connection between Anatolia N and heart rate seems to be the one
    26 driving the apparent associations of all other ancestries.
    27 Lastly, the Siberia ancestry is connected with dark eye and hair pigmentation, but also green
    28 eye color and lower age at menarche. Again, even if this last trait has ambiguous associations
    29 with Anatolia N and WHG ancestries, covA ICs provide a clue to disentangle their interactions
    30 in favour of a more robust connection with the Siberia ancestry.
    31
    Last edited by pmokeefe; 08-05-2021 at 01:36 AM.
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    Wasn’t Cheddar man a WHG with dark hair and his haplogroup was I2? He had MC1R gene him or? the Also thank you very much for answering my question!

    Also you seem to know your genome quite in detail. What DNA test have you done to know that much?

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    Quote Originally Posted by KHAN View Post
    Wasn’t Cheddar man a WHG with dark hair and his haplogroup was I2? He had MC1R gene him or? the Also thank you very much for answering my question!

    Also you seem to know your genome quite in detail. What DNA test have you done to know that much?
    Iirc Cheddar Man did have a variant of M1cr but it was one of the ones with a weaker association with red hair. You generally need two copies of the same mutation to actually have red hair, and Cheddar man only had a single variant.

    M1cr mutations are also present in some other mesolithic samples as well as early steppe samples but all the cases were single copy carriers. Some early Neolithic farmers have too so I guess you had an early distribution amongst European and Anatolian hunter-gatherer populations but at very low rates making the likeihood of double carriers incredibly small.

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    Quote Originally Posted by CopperAxe View Post
    Iirc Cheddar Man did have a variant of M1cr but it was one of the ones with a weaker association with red hair. You generally need two copies of the same mutation to actually have red hair, and Cheddar man only had a single variant.

    M1cr mutations are also present in some other mesolithic samples as well as early steppe samples but all the cases were single copy carriers. Some early Neolithic farmers have too so I guess you had an early distribution amongst European and Anatolian hunter-gatherer populations but at very low rates making the likeihood of double carriers incredibly small.
    I always thought (ignorantly) that the spread of red hair was due to Indo-European expansion, I see that apparently not.

    What can be said about other pigmentations like blonde? How did it spread in Europe and Asia?

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    Quote Originally Posted by alejandromb92 View Post
    I always thought (ignorantly) that the spread of red hair was due to Indo-European expansion, I see that apparently not.

    What can be said about other pigmentations like blonde? How did it spread in Europe and Asia?
    Well in some way it was linked with the IE expansions as there are some M1cr copies in early steppe populations and it is with the Bell Beakers and Sintashta peoples where you see the first noteworthy amounts of redheads pop up in the ancient dna record.

    But for example cases of red hair in the Levant or North Africa or something are probably not all that linked to them no. Anatolian ancestry seems to have brought blue eyes with it in the Levant so maybe red hair too?

    Blondism can be tricky as you have several snps that can cause it or add to the likelihood of blondism (from a west eurasian perspective, not talking about the blondism variants in southeast Asia and Oceania). Its also a bit more subjective than red in my opinion. "Strong" blondism is mostly associated with KITLG mutations but it isn't the only one that plays a role. Oldest evidence of that mutation is with one of the Afontova Gora samples still, unless I missed something. Fast forward a bit and its present amongst Eastern European hunter-gatherers and Scandinavian hunter-gatherers.

    I think it mostly positive selection which drived an increase, and if there was a slow but exponential increase you eventually had a "tipping point" which seems in Europe seems to be somewhere in the third millenium b.c because from there on there is a significant sweep phenotype wise.


    Lets say you have a hypothetical population of 500. If 5% carries one derived copy of KITLG , then the chance of someone getting two copies is roughly 0.25%. So basically 1 person out of he 500 would have 2 derived copies. If it is the double at 10% the percentage would be roughly 1%, thus 5 people out if the 500.

    Lower population sizes in the northern parts in Europe probably aided the selection processes. Because you see a similar pattern with lactase persistence and height too.

    I don't really buy into the popular take that Funnelbeakers or Globular Amphora had high amounts of fair features either, they were pretty dark too from what I can tell and looked similar to the other I2 WHG rich farmers.

    I'd say for Central Asia and such you can blame most of it directly on the Indo-Iranians although given the ANE and EHG related ancestries in the region prior to the Indo-Iranian migrations you might have had a minor presence of those features already there.
    Last edited by CopperAxe; 08-05-2021 at 11:51 AM.

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    Quote Originally Posted by KHAN View Post
    Wasn’t Cheddar man a WHG with dark hair and his haplogroup was I2? He had MC1R gene him or? the Also thank you very much for answering my question!

    Also you seem to know your genome quite in detail. What DNA test have you done to know that much?
    I have done WGS from both Dante Labs and Nebula Genomics. I eventually received good results from both, but unfortunately they both seem to have chronic service issues lately, so I can't wholeheartedly recommend either one at the moment.
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    Quote Originally Posted by CopperAxe View Post
    I don't really buy into the popular take that Funnelbeakers or Globular Amphora had high amounts of fair features either, they were pretty dark too from what I can tell and looked similar to the other I2 WHG rich farmers.
    What about those?






    Also, blonde hair already found in Peloponnese Neolithic:



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