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Thread: First Genomes from Ancient Egypt

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    2 out of 2 members found this post helpful.

    First Genomes from Ancient Egypt

    https://www.nature.com/articles/ncomms15694

    Check it out.

    Very little SSA compared to modern Egyptians, and very similar to Bronze Age Levant

    The three males' Y HG calls from Genetiker are below:

    JK2134 Pre-Ptolemaic 776–569BC J1a2a2-Z2329 calls
    JK2911 Pre-Ptolemaic 769–560BC J2b1-PF7314 calls
    JK2888 Ptolemaic 97–2BC E1b1b1a1b2-V22 calls
    Last edited by holderlin; 02-06-17 at 18:04.

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    No surprise that they would be Levantine in nature.

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    They did have SSA. Less than modern Egyptians though.

    On the PCA modern Egyptians are close but shifted towards Arabs ISTM.

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    Quote Originally Posted by Megalophias View Post
    They did have SSA. Less than modern Egyptians though.

    On the PCA modern Egyptians are close but shifted towards Arabs ISTM.
    I guess they do say this, but compared to modern day populations it's very small. I can't even see it on the plots.

    I edited the OP.

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    I'm a little bummed there's no Old Kingdom, but if simple spatial logic is applied they should look closer to Natufian with less Anatolian Neo, and Iranian Neo.

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    Thanks, Holderlin.

    We started a preliminary discussion based on the abstract here:
    http://www.eupedia.com/forum/threads...ient+Egyptians

    "Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level."

    I think some pertinent questions were raised, but they'll have to be examined in light of the data we now have from the actual paper.

    "So the samples are from 1070 BC forward, and after the Hyksos and Sea Peoples, but also after the time of Rameses III and his SSA yDna, yes? Interesting."

    I also wondered how the Copts would compare.


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    @Angela didn't see that, thanks.

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    Actually, this is the time period and what they were examining:
    "all sampled remains derive from this community in Middle Egypt and have been radiocarbon dated to the late New Kingdom to the Roman Period (cal. 1388BCE–426CE, Supplementary Data 1). In particular, we seek to determine if the inhabitants of this settlement were affected at the genetic level by foreign conquest and domination, especially during the Ptolemaic (332–30BCE) and Roman (30BCE–395CE) Periods."

    The site is
    Abusir el-Meleq, which is sortNile of mid . I probably shouldn't comment as I'm just starting to read, but doesn't it seem an odd place to look for Greek and Roman introgression? It was in the delta, in Alexandria, where Greeks were perhaps half of the population.

    Ah, it's near Fayum.

    Ed. Honestly, is it my allergies or early senility. I made a stupid word substitution and a typo!

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    2 out of 2 members found this post helpful.
    Quote Originally Posted by Megalophias View Post
    They did have SSA. Less than modern Egyptians though.

    On the PCA modern Egyptians are close but shifted towards Arabs ISTM.
    No because on this graphic the ancient egyptian samples did not have yoruban-like admixture.

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    Quote Originally Posted by Angela View Post
    Actually, this is the time period and what they were examining:
    "all sampled remains derive from this community in Middle Egypt and have been radiocarbon dated to the late New Kingdom to the Roman Period (cal. 1388BCE–426CE, Supplementary Data 1). In particular, we seek to determine if the inhabitants of this settlement were affected at the genetic level by foreign conquest and domination, especially during the Ptolemaic (332–30BCE) and Roman (30BCE–395CE) Periods."

    The site is
    Abusir el-Meleq, which is sort of mid isle. I probably shouldn't comment as I'm just starting to read, but doesn't it seem an odd place to look for Greek and Roman introgressio? It was in the delta, in Alexandria, where Greeks were perhaps half of the population.

    Ah, it's near Fayum.

    That makes me also wonder,
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    Nice admixture graph. Slightly off-topic, but this visual is a nice illustration of why PCA is only one way of looking at the data. Unless I'm reading it wrong, on the PCA the ancient Egyptians look like they're sitting right on top of Bedouin A, and yet the admixture run shows they're quite different.

    Strange that the Saudi group they tested has no SSA. Going by this it looks like the ancient Egyptians are closest to Bronze Age Levant and these strangely non SSA Saudis. Other things are about as expected. North African Jews picked up some Berber, but it was before the North Africans got all that SSA it looks like. Tunisians and Algerians are very similar. Bedouin A has SSA, Bedouin B doesn't. Anybody know if the Bedouin tribes that went to Palestine and Jordan were predominantly Bedouin A?

    Well, here's one thing I was very wrong about, along with a lot of other people. The Druse were not a good proxy for the Neolithic migrations to Europe. They have a lot of Iran Chl, even a lot more than in the Levant Bronze Age. Maybe what they represent is the population in the Levant around the beginning of the modern era? Or, do they have more Iran Chl for one reason or another

    Why on earth no Copts?

    Do they do an analysis elsewhere using East Africans? Or would that just pick up all that shared ancestry? Is most of Saudi "African" ancestry actually East African? From what I remember even regular Saudis, not peripheral groups, have a ton of African mtDna.

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    @Hauteville,

    They may not show it in Admixture, but it's there. I have to read the Supplement, but they probably are using Mbuti for some of these tests.

    " Finally, we used two methods to estimate the fractions of sub-Saharan African ancestry in ancient and modern Egyptians. Both qpAdm35 and the f4-ratio test39reveal that modern Egyptians inherit 8% more ancestry from African ancestors than the three ancient Egyptians do, which is also consistent with the ADMIXTURE results discussed above. Absolute estimates of African ancestry using these two methods in the three ancient individuals range from 6 to 15%, and in the modern samples from 14 to 21% depending on method and choice of reference populations (see Supplementary Note 1, Supplementary Fig. 6, Supplementary Tables 5–8). We then used ALDER40 to estimate the time of a putative pulse-like admixture event, which was estimated to have occurred 24 generations ago (700 years ago), consistent with previous results from Henn and colleagues16. While this result by itself does not exclude the possibility of much older and continuous gene flow from African sources, the substantially lower African component in our 2,000-year-old ancient samples suggests that African gene flow in modern Egyptians occurred indeed predominantly within the last 2,000 years."

    Well, that may be overstating it a tad, yes? It's not a huge jump from 6 to 14%, or from 15 to 22%, and this is just one site. Sites further south might have been quite different.

    Well, I guess we know now that Ramses' African "Y" was not a fluke. The Egyptians of this era did have some SSA, even if it wasn't very substantial. It remains to be seen what it was like further back in time.

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    Honestly, not the correct site, as they themselves implicitly acknowledge.

    " Abusir el-Meleq’s proximity to, and close ties with, the Fayum are significant in the context of this study as the Fayum in particular saw a substantial growth in its population during the first hundred years of Ptolemaic rule, presumably as a result of Greek immigration33,43. Later, in the Roman Period, many veterans of the Roman army—who, initially at least, were not Egyptian but people from disparate cultural backgrounds—settled in the Fayum area after the completion of their service, and formed social relations and intermarried with local populations44. Importantly, there is evidence for foreign influence at Abusir el-Meleq. Individuals with Greek, Latin and Hebrew names are known to have lived at the site and several coffins found at the cemetery used Greek portrait image and adapted Greek statue types to suit ‘Egyptian’ burial practices2,45. The site’s first excavator, Otto Rubensohn, also found a Greek grave inscription in stone as well as a writing board inscribed in Greek46. Taken together with the multitude of Greek papyri that were written at the site, this evidence strongly suggests that at least some inhabitants of Abusir el-Meleq were literate in, and able to speak, Greek45. However, a general issue concerning the site is that several details of the context of the individuals analysed in this study were lost over time."

    This verges on the silly. You need the context of the samples to make a determination that they are likely to show any introgression that occurred. It doesn't exist for these three samples.

    How disappointing. If the Egyptian government allowed access to samples from more promising sites, we might get some answers as to the amount, if any, of Greek and Roman introgression, or if it was sort of like the German communities in the Balkans, where they lived alongside the natives for hundred of years, but didn't intermingle.

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    Estimating phenotypes

    Finally, we analysed several functionally relevant SNPs in sample JK2911, which had low contamination and relatively high coverage. This individual had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia41, consistent with the ancestral affinity shown above. Other relevant SNPs carry the ancestral allele, including HERC2 and LCT, which suggest dark-coloured eyes and lactose intolerance (Supplementary Table 9).
    Seems expected. I wonder if their procedures to rule out contamination were only for modern contamination or also apply to the mummy prep. These mummies would have been extensively handled and processed by possibly those of slave status. Or maybe not? Still makes me wonder.

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    This is after the Hyksos, and its a Hyksos site, so perhaps explaining the Iran Chl. Like I said, wrong site.

    Plus, depends what you mean by ancient, right? Maybe more introgression from the Near East lowered the amount of the SSA.

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    Quote Originally Posted by Angela View Post
    Nice admixture graph. Slightly off-topic, but this visual is a nice illustration of why PCA is only one way of looking at the data. Unless I'm reading it wrong, on the PCA the ancient Egyptians look like they're sitting right on top of Bedouin A, and yet the admixture run shows they're quite different.

    Strange that the Saudi group they tested has no SSA. Going by this it looks like the ancient Egyptians are closest to Bronze Age Levant and these strangely non SSA Saudis. Other things are about as expected. North African Jews picked up some Berber, but it was before the North Africans got all that SSA it looks like. Tunisians and Algerians are very similar. Bedouin A has SSA, Bedouin B doesn't. Anybody know if the Bedouin tribes that went to Palestine and Jordan were predominantly Bedouin A?

    Well, here's one thing I was very wrong about, along with a lot of other people. The Druse were not a good proxy for the Neolithic migrations to Europe. They have a lot of Iran Chl, even a lot more than in the Levant Bronze Age. Maybe what they represent is the population in the Levant around the beginning of the modern era? Or, do they have more Iran Chl for one reason or another

    Why on earth no Copts?

    Do they do an analysis elsewhere using East Africans? Or would that just pick up all that shared ancestry? Is most of Saudi "African" ancestry actually East African? From what I remember even regular Saudis, not peripheral groups, have a ton of African mtDna.
    Is today's Cyprus population the closest possible to Levant, at the time of ancient Egypt?
    I am trying to picture how did the Levant people looked back then

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    Quote Originally Posted by DuPidh View Post
    Is today's Cyprus population the closest possible to Levant, at the time of ancient Egypt?
    I am trying to picture how did the Levant people looked back then
    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?

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    1 out of 1 members found this post helpful.
    Interestingly, modern Near Easterners are the construct of BA mixing, a similar process as in Europe in BA. Well, there are some changes since, but not that dramatic.

    Looks like modern Palestinians and Bedouin A are the closest to Levant BA and BA Egypt. Was Levant BA the Semitic birthplace?
    Last edited by LeBrok; 31-05-17 at 06:17.
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    Hmmm....by the graph, it seems that the ancient Egyptians were closest to modern north (east) Africans. Makes sense. I always figured that far northeast africans (by far I mean way up north near the Mediterranean and east as in near the Levant) were Levantines with a dash of Sub Saharan.

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    3 out of 3 members found this post helpful.
    Quote Originally Posted by davef View Post
    Hmmm....by the graph, it seems that the ancient Egyptians were closest to modern north (east) Africans. Makes sense. I always figured that far northeast africans (by far I mean way up north near the Mediterranean and east as in near the Levant) were Levantines with a dash of Sub Saharan.
    From the graphic posted I don't see that at all, unless you're coining your own definitions for population groups. Northeast Africans are Horners.

    The only "Africans" the ancient Egyptians from this period plot close to are North Africans, who are mostly Levantines with SSA, more than half of it coming in the last 2000 years, presumably through the Arab slave trade, plus whatever traces of the prior population(s) are left. None of that is a surprise.

    Anyone who has been paying attention to the papers knows that two major population flows moved out of the Near East, the western farmers, and then a few thousand years later a population related to the Iranian farmers. Both spread over vast distances and mixed with earlier populations where ever they went. The first group spread all along the southern coast of the Mediterranean, among many other places, and even deep into Africa. We can see the traces of the second major Near East group in northern Africa too, but in much smaller percentages.

    Basically, as LeBrok pointed out, the Bronze Age may be the last really major population upheaval in western Eurasia. As I stated in another thread, the second gene flow out of the Near East, which was less consequential for most of Europe was like a pincer movement into Europe, I believe, with part of it going over the Caucasus and onto the steppe, and part of it going into southeastern and southern Europe, as well as all over the Near East, and some of it even reaching North Africa.

    It looks like a modified version of the old Dienekes theory of the Womb of Nations to me, but as you have to consider also the western farmers, it's not just the Caucasus area, but the Anatolia/Levant region as well.

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    Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details). For further genes such as SLC45A2, LCT and EDAR we were unable to find derived alleles for both JK2888 and JK2911. For JK2134, there was no sufficient coverage after quality filtering at all the specific sites, which is why the analysis revealed no further clues.
    Supplementary Data 3 shows that mtDNA haplogroups for the three ancient Egyptian samples JK2134 JK2888 and JK2911 are J1d, U6a2 and M1a1, respectively. J1d and its subclades are considered Near Eastern and U6a2 is close to the East African cluster U6a2a. M1a1 was also found in Ethiopia and the majority of the M1a lineages found in Africa had a more recent Eastern African origin. These ancient Egyptian mummies had partially light skin pigmentation without further light skin pigmentation genes and they probably resembled modern-day East Africans. Ethiopians are known to plot closer to Near Easterners in PCA, suggesting a much larger Eurasian genetic component in East Africa.

    Last edited by ThirdTerm; 31-05-17 at 22:01.
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    Quote Originally Posted by Angela View Post
    From the graphic posted I don't see that at all, unless you're coining your own definitions for population groups. Northeast Africans are Horners.

    The only "Africans" the ancient Egyptians from this period plot close to are North Africans, who are mostly Levantines with SSA, more than half of it coming in the last 2000 years, presumably through the Arab slave trade, plus whatever traces of the prior population(s) are left. None of that is a surprise.

    Anyone who has been paying attention to the papers knows that two major population flows moved out of the Near East, the western farmers, and then a few thousand years later a population related to the Iranian farmers. Both spread over vast distances and mixed with earlier populations where ever they went. The first group spread all along the southern coast of the Mediterranean, among many other places, and even deep into Africa. We can see the traces of the second major Near East group in northern Africa too, but in much smaller percentages.

    Basically, as LeBrok pointed out, the Bronze Age may be the last really major population upheaval in western Eurasia. As I stated in another thread, the second gene flow out of the Near East, which was less consequential for most of Europe was like a pincer movement into Europe, I believe, with part of it going over the Caucasus and onto the steppe, and part of it going into southeastern and southern Europe, as well as all over the Near East, and some of it even reaching North Africa.

    It looks like a modified version of the old Dienekes theory of the Womb of Nations to me, but as you have to consider also the western farmers, it's not just the Caucasus area, but the Anatolia/Levant region as well.
    Sorry for mis-wording things, by northeast Africans I was referring to modern Egyptians, Tunisians, and Algerians. These groups are the closest to the ancient Egyptian samples studied in this study.

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    Those samples have an extra Iran_Neolithic, maybe they are mixed with Hyksos more than purest ancient Egyptians.

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    Quote Originally Posted by LeBrok View Post
    Interestingly, modern Near Easterners are the construct of BA mixing, a similar process as in Europe in BA. Well, there are some changes since, but not that dramatic.
    For some parts of the Middle East it occurred before the BA. The three genetic components Caucasians are makeup of; EHG, EEF, CHG were present in the Caucasus by at least 4000 BC. The same could be true for Anatolia and Mesoptamia. IranChalolithic isn't radically different from Assyrians, Kurds, Persians, etc.

    Maybe nothing like the expansion of Steppe ancestry in Europe occurred in the Middle East. It expanded from out of a pocket in Russia to most of Europe in about 500 years.

  25. #25
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    Quote Originally Posted by LeBrok View Post
    Looks like modern Palestinians and Bedouin A are the closest to Levant BA and BA Egypt. Was Levant BA the Semitic birthplace?
    I think the southern Levant is most commonly proposed as the homeland of Semitic. Those Bedouin samples incidentally are from the Negev just south of the Levant.

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