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Thread: First Genomes from Ancient Egypt

  1. #151
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    Quote Originally Posted by Jovialis View Post
    https://www.nature.com/articles/ncomms15694/figures/5

    The article has this graphic that demonstrates which population is closest.

    According to the map in figure A. Sardinians and the Basque have the highest frequency of similarity with Ancient Egyptians in modern populations.

    In ancient times, the Linearbandkeramik and Neolithic Anatolians also shared a strong similarity. Thus, they were a lot like the EEF too.
    You have to be careful with terminology. This is a shared drift diagram. The shared drift is largest, obviously, with EEF, Anatolia Neolithic, and Levant Neolithic. After that, with Bronze Age Levant. Then and only then with Sardinia and Basques as far as modern populations, because they are the modern populations with the largest amount of what we could call ancient "western" Neolithic ancestry ancestry, i.e. Anatolia/Levant.

    First, as to genetic drift in general, it's the evolutionary mechanism which produces random changes in a population over time. It's different from natural selection, whereby only beneficial changes become fixed. In genetic drift the changes occur by chance, and so both beneficial and disadvantageous mutations can become fixed. It occurs more often in small populations. Bottlenecks and founder effects are examples of when it's most operative. (Sorry if I'm telling you what you already know.)

    When geneticists are talking about shared genetic drift or shared drift patterns, they're saying that the populations in question share a long genetic history. Shared drift means shared evolutionary history. In terms of Sardinians/Basques and Egyptians, they both have lots of that ancient Neolithic ancestry.

    What happened with the Egyptians is that they got a bigger dose of "eastern" Neolithic ancestry, plus the SSA.

    I hope I explained that properly. If someone else wants to have a go, be my guest.


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    Quote Originally Posted by Angela View Post
    You have to be careful with terminology. This is a shared drift diagram. The shared drift is largest, obviously, with EEF, Anatolia Neolithic, and Levant Neolithic. After that, with Bronze Age Levant. Then and only then with Sardinia and Basques as far as modern populations, because they are the modern populations with the largest amount of what we could call ancient "western" Neolithic ancestry ancestry, i.e. Anatolia/Levant.

    First, as to genetic drift in general, it's the evolutionary mechanism which produces random changes in a population over time. It's different from natural selection, whereby only beneficial changes become fixed. In genetic drift the changes occur by chance, and so both beneficial and disadvantageous mutations can become fixed. It occurs more often in small populations. Bottlenecks and founder effects are examples of when it's most operative. (Sorry if I'm telling you what you already know.)

    When geneticists are talking about shared genetic drift or shared drift patterns, they're saying that the populations in question share a long genetic history. Shared drift means shared evolutionary history. In terms of Sardinians/Basques and Egyptians, they both have lots of that ancient Neolithic ancestry.

    What happened with the Egyptians is that they got a bigger dose of "eastern" Neolithic ancestry, plus the SSA.

    I hope I explained that properly. If someone else wants to have a go, be my guest.
    Thank you for the explanation! I'm not familiar with the terms. I was a history and poli-sci major; the little I know about genetics is self-taught from reading articles online.

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    Quote Originally Posted by Angela View Post
    You have to be careful with terminology. This is a shared drift diagram. The shared drift is largest, obviously, with EEF, Anatolia Neolithic, and Levant Neolithic. After that, with Bronze Age Levant. Then and only then with Sardinia and Basques as far as modern populations, because they are the modern populations with the largest amount of what we could call ancient "western" Neolithic ancestry ancestry, i.e. Anatolia/Levant.

    First, as to genetic drift in general, it's the evolutionary mechanism which produces random changes in a population over time. It's different from natural selection, whereby only beneficial changes become fixed. In genetic drift the changes occur by chance, and so both beneficial and disadvantageous mutations can become fixed. It occurs more often in small populations. Bottlenecks and founder effects are examples of when it's most operative. (Sorry if I'm telling you what you already know.)

    When geneticists are talking about shared genetic drift or shared drift patterns, they're saying that the populations in question share a long genetic history. Shared drift means shared evolutionary history. In terms of Sardinians/Basques and Egyptians, they both have lots of that ancient Neolithic ancestry.

    What happened with the Egyptians is that they got a bigger dose of "eastern" Neolithic ancestry, plus the SSA.

    I hope I explained that properly. If someone else wants to have a go, be my guest.
    Wait, if the Egyptians were like Neolithic farmers then how can we explain those charts and pca in the last page?
    mmmmmmmmm dooouuughhhnuuuutz

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    Quote Originally Posted by davef View Post
    Wait, if the Egyptians were like Neolithic farmers then how can we explain those charts and pca in the last page?
    I didn't say they're like Neolithic farmers. I said they have shared genetic drift with Neolithic farmers, as do Sardinians.

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    Quote Originally Posted by Angela View Post
    I didn't say they're like Neolithic farmers. I said they have shared genetic drift with Neolithic farmers, as do Sardinians.
    Got it. I guess I'll need to read up on what shared genetic drift is.

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    Quote Originally Posted by davef View Post
    Got it. I guess I'll need to read up on what shared genetic drift is.
    Yea, this is something I will need to look into myself.

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    Quote Originally Posted by Angela View Post
    Levant Bronze Age is very similar to the ancient Egyptian sample, which I think will turn out to be close to the Egyptian Copts. They don't at all look Cypriot to me.



    Greek Cypriots:

    Obviously, there are a few non-Cypriots in the following. :)

    Plus, didn't the paper on the Canaanites tell us that these Bronze Age Canaanite samples have no derived SLC45A2, so not only different than people in the Levant today, but also quite a bit darker than the people of the Anatolia Neolithic and the EEF of Europe, who did have reasonably high percentages of derived SLC45A2. In fact, I think a recent paper revised those estimates upwards from where they were a while ago.. This might suggest that most of the Iran Chl, like the CHG themselves, only had the derived SLC25A2 allele, and thus were rather darker than not only Anatolia Neolithic, but also Levant Neolithic, since some of them also had derived SLC45A2, although the Natufians did not.
    The admixture run isn't optimal, but going by that the Bronze Age Levant doesn't look all that different from the Saudis. So, maybe tribal Saudis or Yeminis without obvious SSA?


    Who knows, though?
    The second picture that you used was taken after a bomb killed several victims.

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    1 members found this post helpful.
    I hoped this paper would have focused more on the ethnogenesis of modern and Ancient Egyptians beyond the question of them having SSA ancestry or not?

    Like how, when, and by whom the Iran_N ancestry in Ancient Egyptians appeared? what was the structure of the population before them?

    SSA is interesting, but why focus on that alone?

    Well, given the extreme interest in SSA in Near Easterners, someone up thread wondered why Saudis wouldn't have it? the admixture run was wrong in not detecting that in Saudis, who do have East African ancestry. similar to Dinka.

    from Lazaridis et al(2016), a negative f3 statistic of the form f3(Saudi, Anatolia_N, Dinka) = -0.00326, Z_score = -5.1

    That means it must exist, the allele frequency in the Saudi population is intermediate between Dinka and Anatolia_N or any population ancestral to them. it exists from 1% to 5% in various Saudi tribal groups, the origin of that I would assume is ancient, because the British Roman outlier also had it.

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    Quote Originally Posted by IronSide View Post
    I hoped this paper would have focused more on the ethnogenesis of modern and Ancient Egyptians beyond the question of them having SSA ancestry or not?

    Like how, when, and by whom the Iran_N ancestry in Ancient Egyptians appeared? what was the structure of the population before them?

    SSA is interesting, but why focus on that alone?

    Well, given the extreme interest in SSA in Near Easterners, someone up thread wondered why Saudis wouldn't have it? the admixture run was wrong in not detecting that in Saudis, who do have East African ancestry. similar to Dinka.

    from Lazaridis et al(2016), a negative f3 statistic of the form f3(Saudi, Anatolia_N, Dinka) = -0.00326, Z_score = -5.1

    That means it must exist, the allele frequency in the Saudi population is intermediate between Dinka and Anatolia_N or any population ancestral to them. it exists from 1% to 5% in various Saudi tribal groups, the origin of that I would assume is ancient, because the British Roman outlier also had it.
    Well, it's not exactly easy to get ancient samples from Egypt. The researchers are sort of reduced to using old samples in museums. Let's hope for more in the future.

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    1 members found this post helpful.
    Quote Originally Posted by IronSide View Post
    I hoped this paper would have focused more on the ethnogenesis of modern and Ancient Egyptians beyond the question of them having SSA ancestry or not?

    Like how, when, and by whom the Iran_N ancestry in Ancient Egyptians appeared? what was the structure of the population before them?

    SSA is interesting, but why focus on that alone?

    Well, given the extreme interest in SSA in Near Easterners, someone up thread wondered why Saudis wouldn't have it? the admixture run was wrong in not detecting that in Saudis, who do have East African ancestry. similar to Dinka.

    from Lazaridis et al(2016), a negative f3 statistic of the form f3(Saudi, Anatolia_N, Dinka) = -0.00326, Z_score = -5.1

    That means it must exist, the allele frequency in the Saudi population is intermediate between Dinka and Anatolia_N or any population ancestral to them. it exists from 1% to 5% in various Saudi tribal groups, the origin of that I would assume is ancient, because the British Roman outlier also had it.
    I'm also interested in this. If it isn't too far off-topic, have you taken a look at the Taforalt paper? The ADMIXTURE analysis suggests that the African admixture in Natufian, Iran_Hotu/Iran_Neo and so forth is related to a component that is modal in the Hadza. A very unlikely source, but it looks quite solid. It's even more pronounced in the Taforalt samples and still very significant in modern Berbers, while in the Levant/Europe it seems to be reduced relative to ancient samples. The 'Hadza Component' is also what differentiates Dinka from West Africans.


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    Quote Originally Posted by markozd View Post
    I'm also interested in this. If it isn't too far off-topic, have you taken a look at the Taforalt paper? The ADMIXTURE analysis suggests that the African admixture in Natufian, Iran_Hotu/Iran_Neo and so forth is related to a component that is modal in the Hadza. A very unlikely source, but it looks quite solid. It's even more pronounced in the Taforalt samples and still very significant in modern Berbers, while in the Levant/Europe it seems to be reduced relative to ancient samples. The 'Hadza Component' is also what differentiates Dinka from West Africans.
    Unfortunately, I haven't, many times ADMIXTURE detected African related components in Natufians and Levant Neolithic, that would definitely explain haplogroup E, but then came the Lazaridis paper.

    No evidence for admixture related to sub-Saharan Africans in
    Natufians. We computed the statistic f4(Natufian, Other Ancient; African, Chimp) varying African to be
    Mbuti, Yoruba, Ju_hoan_North, or the ancient Mota individual. Gene flow between Natufians and
    African populations would be expected to bias these statistics positive. However, we find most of
    them to be negative in sign and all of them to be non-significant (|Z|<3), providing no evidence that
    Natufians differ from other ancient samples with respect to African populations.
    The Natufians don't share more alleles with (Mbuti - Yoruba - Ju_hoan_North - Mota) than the amount the EHG or WHG shares, which is null.

    this f4 test f4(Natufian, Other Ancient; African, Chimp) tests whether the population African shares alleles with the Natufians that Other Ancient and Chimp don't, if yes it would be positive, but it wasn't. see the bolded statement above.

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    Quote Originally Posted by markozd View Post

    Interesting puzzle, why would they have Hadza like admixture ?

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    Quote Originally Posted by IronSide View Post
    Unfortunately, I haven't, many times ADMIXTURE detected African related components in Natufians and Levant Neolithic, that would definitely explain haplogroup E, but then came the Lazaridis paper.



    The Natufians don't share more alleles with (Mbuti - Yoruba - Ju_hoan_North - Mota) than the amount the EHG or WHG shares, which is null.

    this f4 test f4(Natufian, Other Ancient; African, Chimp) tests whether the population African shares alleles with the Natufians that Other Ancient and Chimp don't, if yes it would be positive, but it wasn't. see the bolded statement above.
    I had looked at this, but I think I didn't notice that Lazaridis also used Mota as an outgroup, which should according to the analysis above have the Hadza component. This is very confusing.

    I find it quite difficult to fully understand intra-African diversity to be honest. What causes the Hadza to have such an unusual position in the PCA relative to South & West Africans? Based on haplotypes I'd exclude recent Eurasian admixture.

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    Quote Originally Posted by markozd View Post
    I had looked at this, but I think I didn't notice that Lazaridis also used Mota as an outgroup, which should according to the analysis above have the Hadza component. This is very confusing.

    I find it quite difficult to fully understand intra-African diversity to be honest. What causes the Hadza to have such an unusual position in the PCA relative to South & West Africans? Based on haplotypes I'd exclude recent Eurasian admixture.
    Maybe pure Basal Eurasians admixed into them, but then the Natufians and Iran_N would share ancestry with them more than the EHG for example, but they don't. a puzzle indeed.

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