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Thread: Principal component and qpAdm analyses confirm European admixture in Chinchorro DNA

  1. #11
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    About the hair -
    "Ancient humans found with red hair weren't necessarily redheads in life, but may have acquired their carrot tops after death, a new study finds. A team of researchers examined the processes that degrade locks, ranging from exposure to the sun's powerful rays or being eaten away by microbes. These processes, many of which begin while a person or animal is still alive, can leave hair with an unnatural, reddish hue. The findings are not only important for archaeology, but also for conservation efforts and forensic investigations, according to the study published Oct. 21 in the journal Proceedings of the Royal Society B."
    http://www.livescience.com/48384-anc...head-myth.html
    Interpreting biological degradative processes acting on mammalian hair in the living and the dead: which ones are taphonomic? Silvana R. Tridico, Sandra Koch, Amy Michaud, Gordon Thomson, K. Paul Kirkbride, Michael Bunce - Published 22 October 2014. DOI: 10.1098/rspb.2014.1755
    http://rspb.royalsocietypublishing.o.../1796/20141755

    How would European admixture arrive in South America only in that remote places thousands of years ago ? Absolutely not scientifically credible without a scientific revolution with new evidences and facts.
    J1 FGC5987 to FGC6175 (188 new SNPs)
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    Y-DNA - Milhazes, Barcelos, Minho, Portugal.
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    North_Swedish + PT + PT + PT @ 3.96 EUtest 4

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  3. #12
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    Quote Originally Posted by genetiker View Post
    None of that has any bearing on what the results for the Chinchorro sample are.

    There aren't any Australoid uniparental markers in South American Indians, and yet no one has any problem with the idea that Australoids were in South America thousands of years ago. It's only the idea that Europeans were in South America thousands of years ago that everyone for some reason regards as heresy.
    There is no problem with "Australoids" being in South Asia and South Pacific cause it can easily be explained by coastal migration and island hopping.
    Now you're proposing that utterly primitive folks (and Aurignacian UP Europeans certainly don't strike me as technologically advanced) could have magically sailed up to South America by crossing the Atlantic?

    Carthageneans or Vikings arriving there is at least in the realm of possible

  4. #13
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    Quote Originally Posted by genetiker View Post
    qpAdm isn't going to be able to discern exactly which Caucasoid population the additional Caucasoid admixture in the Chinchorro sample is from, at least not with the amount of data currently available.

    Exactly which population? Maybe not...
    A lot more specific than without West Eurasian outgroups added? Hell yes.

    If your theory is early Aurignacian or Gravettian...than Kostenki14 should serve as a decent outgroup, as it appears to be an outgroup to the actual Aurignacian and Gravettian samples we have. Iran_Neolithic should also have no special relation to either. Probably more could be considered.
    Last edited by Kale; 03-16-2017 at 06:19 PM.

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  6. #14
    Quote Originally Posted by RCO View Post
    About the hair -
    http://www.livescience.com/48384-anc...head-myth.html
    Interpreting biological degradative processes acting on mammalian hair in the living and the dead: which ones are taphonomic? Silvana R. Tridico, Sandra Koch, Amy Michaud, Gordon Thomson, K. Paul Kirkbride, Michael Bunce - Published 22 October 2014. DOI: 10.1098/rspb.2014.1755
    http://rspb.royalsocietypublishing.o.../1796/20141755
    The Live Science article you cite states the following:

    Hair contains two kinds of pigments, one that produces dark hair and one for red hair. The sun degrades these pigments in a process known as photo-oxidation, but the hair pigment for darker hair isn't as stable as the one for red hair, so hair turns a reddish color when exposed to sunlight for long periods of time. This is why the hair of ancient aboriginal people in Australia has a reddish tint, Tridico said.
    The dark hair and red hair pigments they're referring to are eumelanin and pheomelanin, respectively. But the paper that the article is based on cites this 2010 paper, the abstract of which states just the opposite:

    Dark hair is more resistant to photodegradation than light hair, because of the higher photostability of eumelanin when compared with pheomelanin. But, hair damages caused by ultraviolet (UV) exposure are related not only to the melanin type of each hair but also to the total amount of melanin. Pheomelanin is far more sensitive to UV light than eumelanin, though these two types of melanin are similarly sensitive to VIS light.
    There is also this 2014 paper, which states:

    Both eumelanin and pheomelanin are affected by sunlight, and they form semiquinoid-type free radical species and then typical free radical species from water, but eumelanin is quite stable and large enough to scavenge the originated species. In contrast, pheomelanin has been shown to be rather photolabile under sunlight at physiological conditions, and it is easily involved in the high production of superoxide [160]. It cannot scavenge all the derived reactive species, and thus, pheomelanin may easily become a photosensitized agent rather than a photoprotector [161].
    The paper that the Live Science article is based on gives a sample of Australian aborigine hair as its only example of lightening in humans. It states the following about this sample:

    Pigment granules in the oldest part of the hair (tip end or distal shaft) were significantly lighter in colour in comparison to the younger part of the hair (electronic supplementary material, figure S7a). In an ante-mortem context, other factors can impact on bleaching of pigment granules (e.g. chemicals), but in the case of the Aboriginal youth [13] it is reasonable to assume that the older parts of the hair have had more exposure to sunlight.
    The hair of many ancient Peruvian mummies does not show this pattern of changing color along the length of the hair, which would be expected if the lighter color was due to the effects of sunlight. Instead it is uniformly the same brown, chestnut, red, or blond color along the entire length of the hair, from root to tip, implying that the hair was naturally that color during life.

    Many of the Peruvian mummies with European hair color were never exposed to sunlight, being wrapped in textiles or mummy bundles and then buried underground, as the blond-haired Paracas mummies were.

    There are many cases where Peruvian mummies found in the exact same location have completely different hair colors, which would be impossible if all the hair started out as black and was then changed by the local environment. This photo and this photo from my White Gods post give two examples from the Nazca culture's Chauchilla Cemetery of brown-haired mummies sitting side-by-side with red-haired mummies. This photo from my post More proof of Whites in ancient Peru and Chile shows a pile of skulls from the Wari culture's cemetery of Huaca Malena, where one skull has brown hair, another skull has red or reddish-brown hair, and a third has dark blond hair. And this photo from the same post shows two side-by-side heads found at the Ychsma culture city of Pachacamac, where the head on the left has brown hair and the head on the right has blond hair. Both of those heads have European skin color and cranial morphology.

    The More proof of Whites post also includes material demonstrating that the hair of many ancient Peruvian and Chilean mummies is European rather than Amerindian not only in its color, but also in its structure. Microscopic examination of the hair's cross section has shown it to have the smaller width characteristic of European hair, and not the larger width characteristic of hair in populations with high frequencies of the 370A EDAR mutation, which is fixed or close to being fixed in all pure Amerindian populations.

    I could keep going on and on, refuting the notion that the European hair color seen in ancient Peruvian mummies is due to post-mortem changes, but I would just end up reproducing much of the material on my blog in this comment, and I find that tedious. Anyone with intelligence and objectivity should be able to look at what I've posted on my blog and be able to connect the dots.

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  8. #15
    I've posted the first of a series of high-resolution admixture analyses of the European admixture in the Chinchorro sample on my blog:

    High-resolution K = 4 analysis of the European admixture in Chinchorro DNA

    If my belief about the source of the European admixture is correct, then the pattern of non-Amerindian components in the Chinchorro sample should continue to be similar to the pattern of components seen in the pre-LGM European samples.

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  10. #16
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    So...no go on details? What fun is a mystery if it's solved I guess...
    .
    Last edited by Kale; 03-18-2017 at 07:36 AM.

  11. #17
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    I'll just echo Kale here, we need qpAdm confirmation that the donor population could be from UP Europe.

  12. #18
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    Quote Originally Posted by Padre Organtino View Post
    There is no problem with "Australoids" being in South Asia and South Pacific cause it can easily be explained by coastal migration and island hopping.
    Now you're proposing that utterly primitive folks (and Aurignacian UP Europeans certainly don't strike me as technologically advanced) could have magically sailed up to South America by crossing the Atlantic?

    Carthageneans or Vikings arriving there is at least in the realm of possible
    genetiker is talking about absence of Australoid uniparental markers in Amazon area Indians.
    Similarly non-Africans have no Neanderthal uniparental markers but admixture is now considered proven.

    Also in the Karitiana and the Surui we see:
    "In addition to the Karitiana, the Surui, and the Maya, the G allele is also present in the Muscogee, the Quechua, and the Cheyenne."
    "The G allele is present in the Karitiana at a frequency of 0.346, and 7.7% of them are homozygous for it."
    https://genetiker.wordpress.com/2013...e-frequencies/
    https://genetiker.wordpress.com/2013...p-populations/

    Anzick1 had blue eyes markers too.

    Not only do they have G at rs12913832, the Karitiana are 25% A at rs1129038* too. https://alfred.med.yale.edu/alfred/m...euid=SI018623U

    To me this looks like common ancestry or some later but still very old admixture which ADMIXTURE sees but can't discern:

    "K=5 breaks the ENA component down into one maximized in the Karitiana from the Americas ... This analysis further suggests that the ENA affinity of
    Hunter-Gatherers is related to the Karitiana component
    .

    K=6 reveals a south Eurasian component maximized in Papuans, which is also represented in South
    Asians. MA1 shows some affinity to this component, in contrast to more recent Eurasian hunter-gatherers who continue to mainly show ties to Native Americans"
    http://biorxiv.org/content/biorxiv/s...1/001552-3.pdf
    Last edited by parasar; 03-18-2017 at 03:09 PM.

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  14. #19
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    K=4 coupled with a low number of markers is likely not adequate, as differences between populations will be minimized. The lower the K, and markers, the more the covergence towards ancestral human. For ex, at K=2 or 3 most Eurasians look similar.

    How do things look at higher K, and how many overlapping markers are being used?

    Another consideration is the problem of agreement at loci due to ancestral alleles.

    Edit: An extreme example of the above is ADMIXTURE showing archaics as mostly African (Ascertainment bias in the markers used in the microarrays which seem optimized for derived alleles in Europeans)
    Last edited by Kurd; 03-18-2017 at 04:35 PM.

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  16. #20
    I've written a paper on my discovery of European admixture in a Chinchorro mummy DNA sample, and it's now published on bioRxiv:

    European admixture in Chinchorro DNA

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