• Inference of human pigmentation from ancient DNA bygenotype likelihoods

    From Primum Sapienti@invalid@invalid.invalid to sci.anthropology.paleo,sci.archaeology on Thu Jul 24 22:34:15 2025
    From Newsgroup: sci.anthropology.paleo


    https://www.pnas.org/doi/epdf/10.1073/pnas.2502158122

    Abstract
    Light eyes, hair, and skins probably evolved several
    times as Homo sapiens dispersedfrom Africa. In areas
    with lower UV radiation, light pigmentation alleles
    increased in frequency because of their adaptive
    advantage and of other contingent factors such as
    migration and drift. However, the tempo and mode of
    their spread is not known. Phenotypic inference from
    ancient DNA is complicated, both because these
    traits are polygenic and because of low sequence depth.
    We evaluated the effects of the latter by randomly
    removing reads in three high-coverage ancient samples,
    the Paleolithic UstrCO- Ishim from Russia, the Mesolithic
    SF12 from Sweden, and the Neolithic I5077 from current
    Croatia. We could thus compare three approaches to
    pigmentation inference, concluding that for suboptimal
    levels of coverage (<8|u), a probabilistic method
    estimating genotype likelihoods leads to the most
    robust predictions. We then applied that protocol to
    348 ancient genomes from Eurasia, describing how skin,
    eye, and haircolor evolved over the past 45,000 y.
    The shift toward lighter pigmentations turned out to
    be all but linear in time and place, and slower than
    expected, with half of the individuals showing dark
    or intermediate skin colors well into the Bronze and
    Iron ages. We also observed a peak of light eye
    pigmentation in Mesolithic times, and an accelerated
    change during the spread of Neolithic farmers over
    Western Eurasia, although localized processes of gene
    flow and admixture, or lack thereof, also played a
    significant role.

    "By a probabilistic approach, we showed that eye,
    hair, and skin color changed substantially through
    time in Eurasia. It was reasonable to imagine that
    the first hunting-gathering settlers, who came from
    warmer climates, had mostly dark pigmentation. We
    are now showing that their phenotypes persisted up
    to the Iron age. We found the earliest instance of
    light skin color in the Swedish Mesolithic, but it
    comes from only one sample in >50. Things changed
    afterward, but very slowly, so that only in the
    Bronze Age did the frequency of light skins equal
    that of dark skins in Europe; during much of
    prehistory, most Europeans were dark-skinned. A
    similar trend, with dark pigmentation long
    coexisting with an increasing, yet relatively small
    proportion of lighter traits, is observed for hair
    and eye color, although there was a temporary peak
    of light eye frequency in the Mesolithic period,
    when we inferred light pigmentation for 11 out of
    35 samples."
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  • From JTEM@jtem01@gmail.com to sci.anthropology.paleo,sci.archaeology on Sat Jul 26 04:37:03 2025
    From Newsgroup: sci.anthropology.paleo

    Primum Sapienti wrote:


    Abstract
    Light eyes, hair, and skins probably evolved several
    times as Homo sapiens dispersedfrom Africa.

    That's a conclusion.

    Homo sapiens dispersed to Africa, and back out of Africa...

    The evidence from chromosome 11 says billions of people
    can trace their ancestry to an Eurasian ancestor
    significantly older than any Mitochondrial Eve, or even
    any Y Chromosome Adam. And the oldest known y chromosome,
    A00, was likely a RECENT infusion into modern populations.
    It's associated with west Africa, the same place as
    "Unknown Ancestor" DNA and even an archaic skull of about
    13k years in age.

    Disclaimer: Paleo anthropology is about as far away from
    a real science as you can get and still be taught in
    accredited schools. The archaic skull, though clearly NOT
    modern, has been redefined as "Anatomically Modern" by the
    politicians pretending to be academics who own paleo
    anthropology. Of course, A00 is still there, the "Unknown
    Ancestor" DNA still exists and their idiocy just makes it
    all harder -- not easier -- to explain away...

    In areas
    with lower UV radiation, light pigmentation alleles
    increased in frequency because of their adaptive
    advantage and of other contingent factors such as
    migration and drift.

    Some humans were sexually selected. Period. We know this
    because we can see it even in modern humans who are not
    uniformly monogamous, and even where we can't observe
    nature we can goddamn well see anatomy. Human testicles
    fit between Chimps and Gorillas. Oddly, Gorillas have no
    sexual competition and Chimps have oodles of it. Now we
    can't be simultaneously both monogamous and promiscuous
    so it has to be a case where humans AS A GROUP or a
    population practice both, even if individuals don't.

    Of course culture plays a big role here, whether or not
    certain reproductive strategies (intended or not) are
    permissible...

    Okay, so AT LEAST some humans are sexually selected, and
    this places evolutionary pressures on neonatal traits.
    These are traits associated with the young, children, and
    supposedly trigger a "Caring" or nurturing response. But,
    they are also considered attractive. And these traits
    would include things such as hairlessness and, now get
    this, light skin...

    https://www.wildchimps.org/fileadmin/_processed_/3/3/csm_how-they-grow-up_311d542b0e.jpg

    But...

    But there's a catch. Light skin in the wrong environment
    is sunburn, skin cancer. In another environment, light
    skin is vitamin D.

    The normal explanation -- because, again, paleo anthropology
    is far from a real science -- is INTELLIGENT DESIGN. God or
    some aliens decided that some people might benefit from
    light skin so they gave light skin to people...

    The shift toward lighter pigmentations turned out to
    be all but linear in time and place, and slower than
    expected, with half of the individuals showing dark
    or intermediate skin colors well into the Bronze and
    Iron ages.

    In Europe, we have plenty of evidence for skin lightening
    even since the Black Death. I don't mean that we had the
    likes of sub Saharan Africans running the place until the
    plague hit but, look at the Welsh. Take Tom Jones for
    example. One researcher explained it this way:

    If you look at the west coast of Europe, places like
    Ireland and Wales are pretty far away from the Mediterranean.
    But if you rotate the map 90 degrees counter clockwise,
    suddenly your mind sees them as very close together. This
    is because we are wired to see movement up & down as more
    difficult than left and right.... climbing stairs as
    opposed to walking down a hall.

    Anyway, long story short: Irish ruins seem to be far more
    related to the Basque than to, say, the Vikings...

    So, European skin tones appear to have lightened since the
    plague. Nobody knows why. One simple explanation I've heard
    is that the lighter the skin, the easier to spot a flea if
    it landed on you...
    --
    https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5
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