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Monday, March 13, 2017

Ancient Egyptians less Sub-Saharan than modern-day Egyptians


SAA 2017 abstracts are now online (see here). Thanks to Sarkoboros for the remainder. I reckon dead cat bounce man Johannes Krause is gonna steal the show this year, unless Afrocentrics get him beforehand. Stay alert Johannes.

Ancient Egyptian Mummy Genomes Suggest an Increase of Sub-Saharan African Ancestry in Post-Roman Periods

Krause et al.

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 mtDNA and nuclear DNA from mummified humans recovered from Middle Egypt that span around 1,300 years of ancient Egyptian history from the Third Intermediate to the Roman Period. Our analyses reveal that ancient Egyptians shared more Near Eastern ancestry 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.

53 comments:

nee4speed111 said...

Based on that summary of the Ancient Egyptian genomes, it looks like modern copts will be the population they cluster closest to, as expected.

Rob said...

This'll be interesting (abstract + added comments from linked blogger)

Ancient Genomics of Neolithic to Bronze Age Baikal Hunter-Gatherers
Damgaard, Peter de Barros (Center for GeoGenetics, University of Copenhagen), Jeremy Choin (Center for GeoGenetics, University of Copenhagen), Andrzej Weber (Department of Anthropology, University of Alberta), Martin Sikora (Center for GeoGenetics, University of Copenhagen) and Eske Willerslev (Center for GeoGenetics, University of Copenhagen)

Genome-wide data from hunter-gatherer populations of the Upper Paleolithic to Neolithic has provided unprecedented insight into the human evolutionary and demographic trajectory. However such datasets have hitherto been largely confined to Western Eurasia. The sole representative of Inner Asian past populations post-dating the split between paleolithic Europeans and Asians, as well as paleolithic Siberians and East Asians, are the Mal’ta and Afontova Gora individuals, the Ancient North East Asian (ANE) branch, clouding the dating of the population split, and subsequent admixture events, between ANE and East Asian hunter-gatherers. Our genome data (~1X) reveal that Baikal Hunter-Gatherers (BHG) are an uncharacterized genetically homogeneous branch of Inner Asian hunter-gatherers, displaying highest shared genetic drift with present-day East Asians. Targeted sampling strategies coupled to excellent biomolecule preservation has permitted the generation of an advantageous sample size dataset (n = 31), rendering possible to estimate allele frequencies within these groups, thereby optimizing population tests. BHG model as an excellent proxy for an Inner Asian source population admixing into the late Bronze Age Andronovo groups, becoming Iron Age steppe nomads. With genomes allowing for kinship analyses, pathogen detection and strontium ratios, coupled to archaeological interpretative approaches we extend possible means to elucidate behavioral processes and cultural transformation.

Good to see the Baikal-Hokkaido Archaeological Project collaborating with a top-rate palaeogenomics lab. The Middle Holocene Cis-Baikal region has preserved well-stratified habitation sites and formal hunter-gatherer cemeteries of continental importance, which continue to lend remarkable insights into Neolithic South Siberian social configurations and ecological strategies.

The archaeology and earlier ancient uniparental marker work (mtDNA and Y-DNA from Early Neolithic Kitoi and Late Neolithic–Bronze Age Isakovo/Glazkovo samples) suggested an interesting discontinuity across the Middle Neolithic — maybe involving shifts in relatedness to ancestral Yeniseians. However, if Kitoi and succeeding Late Neolithic groups were both members of a homogeneous “BHG”, these cultural transformations and uniparental lineage turnovers must belie a bigger picture of substantial genome-wide continuity, potentially going as far back as the Mesolithic

Gioiello said...

@ Rob

"uniparental lineage turnovers"

Kjontendor001 said...

We waz kaangs n shieeeet

nee4speed111 said...

So who wants to best that modern copts will be the population that most closely clusters with the Ancient Egyptian samples?

Davidski said...

I reckon they'll cluster with Sardinians. But I won't be anything on that. I'd rather spend it on a case of double India Pale Ale. Oh yeah.

nee4speed111 said...

Hmm, Sardinians is an interesting one, while I suppose its possible, the study does use more Near Eastern and Less SSA than modern Egyptians, which fits copts to a T in terms of genetic profile.

Nirjhar007 said...

I don't know, but since Egyptians were less SSA, it means northern India would have been less ASI.

Salden said...

Where were the remains found?

I ask since even while accounting for the Arab invasion and West West African slave trade today, Egyptians phenotypically look more Tropical African (if still largely Near Eastern) the more south you go.

Karl_K said...

Well. This isn't what I think of when I think 'Ancient Egyptians' in any case. All of this is after the Bronze Age Collapse. People are REALLY interested in much older Egyptians.

Karl_K said...

Show me the genome of Tutankhamun at the least!

nee4speed111 said...

Remains were found in Middle Egypt, and are dated from the 3rd intermediate period, which begins in 1070 BC, all the way up to the Roman period.

Karl_K said...

@Nirjhar007

"I don't know, but since Egyptians were less SSA, it means northern India would have been less ASI."

Finally, you are making sense! A+B=C

Rami said...

All North Africans have some archaic SSA ancestry , even Atlas Berbers do varying from 10-30% depending on which North African population. It makes sense SSA admixture would increase over time as a result of urbanization and religion.
They are not like Sardinians more related to a Natufian like population.
I would think Copt would be close to Dynastic Egyptians but a good portion of them especially ones from Alexandria do claim Greek ancestry, which does makes sense if you consider Alexandria did once have a large Greek population and was run by the Ptolemys and Byzantines till the 7th century. The Fayum portraits reflect that.

Chris Davies said...

"I reckon they'll cluster with Sardinians."

Good prediction, I agree with this.
Sardinian populations share HLA haplotypes with Egypt, Libya, Tunisia, Algeria, Sudan, and Chad far more than they do with Anatolia or Levant from data that I've seen.


Of course the mummy genomes only represent the Ancient Egyptian elite.

Rami said...

If those samples are from post 1300 BC , then obviously thats not really classical Dynastic Egypt as Karl mentioned, as Egypt was overun by Near Eastern invaders like Hyksos, Sea Peoples , as well people probably streaming from the Levant with the Bronze Age collapse by then so there would be a new influx of Near Eastern ancestry. Old Dynasty Egypt was much more culturally involved with peoples to the South (Sudan and the Horn).


Samuel Andrews said...

@Rami,

Any genetic/racial association to Black/Sub Sahara Africans given to ancient Egyptians was created by African Americans or any other Africans who have been oppressed by white people and told their ancestors were dirt.

That's it. Besides that there's nothing suggesting a recent influx of Near Easterners into Egypt. Let's focus on what the data suggests, which is Egypt was more or less apart of a large Near Eastern gene pool.

andrew said...

The problem with drawing broad conclusions here is that the mummies tested were almost surely parts of the Egyptian elite and not representative of the ancient Egyptian population at large at the time. The elites, for example, probably received more of a genetic contribution from the Hyskos 15th Dynasty and from diplomatic and trading partners in the Eastern Mediterranean than non-elite ancient Egyptians.

These are interesting data points that aren't irrelevant, but I would suspect that you would see a differential in sub-Saharan African ancestry by social class, even in modern Egypt, just as you see differential in gene pools related to social class in India. The conclusion the abstract reaches is too broad.

Also, I think the abstract's explanation of where Egypt is in its first parenthetical clause is overkill. I'm pretty sure that anyone attending SAA 2017 knows where Egypt is.

capra internetensis said...

Covering the periods of Assyrian, Kushite, Persian, Greek, and Roman domination hopefully. If they have enough samples they may be able to quantify the impact of the various invaders and the Arabs. But yeah, can't really project it back to the Old Kingdom.

andrew said...

@Samuel Andrews

"Besides that there's nothing suggesting a recent influx of Near Easterners into Egypt."

Sure there is.

* The Hyskos Dynasty (ca. 1650 BCE to 1545 BCE) was from the Levant and preceded by mass Levantine migration to Egypt starting ca. 1800 BCE.
* Egypt's political boundaries extended into modern Lebanon ca. 1450 BCE in the Hittite era.
* Bronze Age Collapse sent migrants from the North to Egypt (although the ethnically Mycenean Greek Philistines were diverted to what is now the Gaza strip).
* Egypt has vigorous trade and diplomatic relations in the Eastern Mediterranean region during the Phoenician era and the Roman era.
* Then, the rise of the Islamic empire starting in the 7th century CE led to a further influx of Near Easterners.

Sub-Saharan admixture was probably greater pre-1800 BCE, probably declined over the period study, and probably grew afterwards (particularly after ca. 1500 CE when trade and exchange with Sub-Saharan Africa increased).

Karl_K said...

I think that the strictly more recent dates on these results tells us that there will very soon be a paper with results from many more and older mummies.

This is a teaser. Soon we will be able to determine actual genetic relationships between pharoahs.

Each of those publications will be a singular cover story, and they will be very drawn out, with hundreds of authors.

Anthro Survey said...

I highly doubt they will cluster with Sardinians. They were definitely more BE, owing the near certainty that their non-SSA portion consisted of Levant_Neo/Natufian-like DNA, not Neolithic Anatolian as is the case with Sardinians.

Anthro Survey said...

http://anthromadness.blogspot.com/2016/01/african-ancestry-in-west-asian-north.html?m=1

Highly relevant blog entry from AA from some time ago. In a nutshell, the SSA in MENA populations does not stem from one single source. Muslims there tend to have both EastAfrican-like SSA and West/Central-like SSA. Christians and Jews(copts, yemenites, etc) mainly just have the (archaic?) east african ssa. The of the slaves coming to the Arab world would have been more west/central african-like.

Matt said...

Re: ancient Egyptians "additional Sub-Saharan admixture" sounds as if they will still have *some* African ancestry. Modern day Egyptians have a good 20% (judging by Eurogenes K15 or Dienekes Globe13 admittedly not based on adna), so there's a fair amount of room for a substantial 10% of some such even.

Will certainly frustrate those ahistorical Afrocentrics (to the amusement of rational people of all ethnic backgrounds), but might also give some of the same to the "Ancient Egypt was 100% Levantine Neolithic and West Eurasian, before Roman and Islamic slavery!" crowd.

@ Rob: Re: "Ancient Genomics of Neolithic to Bronze Age Baikal Hunter-Gatherers - uncharacterized genetically homogeneous branch of Inner Asian hunter-gatherers, displaying highest shared genetic drift with present-day East Asians"

I had a tentative prediction around ancient East Eurasians as follows:
Although they may or may not have the same complicated clades structure as in West Eurasian (with all ancient populations forming a clade to varying degrees with Ust Ishim and ENA), the ancestral East Asians we find will be akin to WHG, EHG, CHG and the Boncuklu Epipaleolithic in West Eurasia (as well as the Lapita ancients in Polynesia) in terms of having extremely high f3 sharing with others in the same population.

Much higher sharing of f3 and homogenity within population than recent people, then broken down by heavy later admixture, like what we find with WHG, EHG, CHG, Boncuklu.

I see a hint this may bear out in the comment on the homogenity of the BHG, but we'll see if this means my tentative prediction regarding East Asian ancients bears out...

Olympus Mons said...

@Karl_K. The lead author is the same man that used 4900 BC and not 5000bc for migration from south caucasus into steppe. You all know why it was!

Now having this same author in a paper regarding the land of"my Merimda and El Omari"...oh boy,oh boy. This is going to be gigantic in those upcoming papers.!!

Olympus Mons said...

Oh great and ubiquitous Joahannes...give me another signal if you are trying to comunicate with me!!

Samuel Andrews said...

@andrew,

I know nothing about Egyptian history, I'll trust there's legitimate historical/archeaological evidence for Near Eastern migration, but I highly doubt it is so good that anyone should be as confident as Rami that ancient Egyptians were more Sub Saharan than modern Egyptians.

Using modern DNA and geography as my only guide my best bet is that ancient Egyptains were overwhelmingly "Near Eastern"(Natufian, EEF, IranNEo, maybe other stuff).

This is how I see it...

Hardcore ancient DNA is the only reliable evidence for genetic shifts. Archaeological evidence for genetic shifts is speculation unless it is overwhelming like in Neolithic Europe. Historical evidence is speculation unless it documents massive ethnic migration and especially linguistic takeover like in England(Anglo Saxons) and Eastern Europe(Slavs).

Modern Egyptains are supposedly ancient Egyptians who learned to speak Arabic right? As far as I know the ancient Egyptain ethnic group was never taken over by a massive migration.

Lenny Dykstra said...

I pointed this out last year!

http://www.anthrogenica.com/showthread.php?7551-Neolithic-Near-East-ADMIXTURE-Results&p=165563&viewfull=1#post165563

West African ADMIXTURE (as distinct with the more ancient, but lower frequency East African admix) in the Near East is increasingly looking to be a relic of the Islamic slave trade.

IIRC there was some blurb about a preprint coming out a while back where they found an individual's remains dating from the late Neolithic in the western Sahel that could be best be modelled as half Berber and half Khoisan... West African expansion only occurred much later IMO than some seem to think.

Kurti said...

No suprise there. ancient Egypt was basically the result of ancient Levant_Farmers moving into North Africa. Plus the Egytpian language is most closest to Semitic even before Berber and least to Cushitic.

Alberto said...

Many interesting abstracts there, though nothing too big when it comes to ancient DNA (other than the Egyptian one).

Ancient DNA of a Nomadic Population Provides Evidence of the Genetic Structure of the Royal Ancient Mongols

The genetic diversity of the ancient Mongols, especially the Gold family of Genghis Khan remains unclear. Gangga site was a nomadic site dated to the eighth to tenth centuries AD in the HulunBuir grassland, northeast China. This site belonged to the Shiwei population, believed to be the direct ancestors of the ancient Mongols. Nine graves at the Gangga site were excavated with log coffins, which were considered the characteristic burial custom of the royal ancient Mongols, included the Gold family of Genghis Khan. This suggests the Gangga people had a close relationship with the royal ancient Mongols. In this study, mitochondrial and Y-chromosome aDNA were extracted to analyze the genetic structure of the Shiwei population at the Gangga site. Haplogroups D, F, C, B, G, N9a were typed in the mtDNA. Haplogroup C-M130 was detected in Y-chromosome aDNA. Gangga people exhibited a high frequency of Haplogroup C-F3918 (belonging to C3*), indicating it may be the main Y-haplogroup in the Shiwei population. In addition, all Gangga males buried in log coffins exhibited C-F3918 suggesting that C-F3918 might be the characteristic Y-chromosome haplogroup of the royal ancient Mongols.

capra internetensis said...

I think Late Stone Age aDNA from Malawi is pretty big!

Quite a few abstracts mention aDNA in passing as part of an ongoing project. Full genomes from Liangzhu would be very nice to see.

Anthro Survey said...

@Lenny With regards to "lower frequency"/---the Omotic component in Egypt, Arabia and Greater Syria tends to be the dominant sub-component of the SSA admixture. In the Maghreb, Omotic and West African proportions tend to be roughly 1:1, though(see the link I posted above). It is reasonable that most of this West African component is relatively recent and post-Roman in areas east of the Maghreb. As for the Maghreb----SOME of the west african could be relatively archaic given geographical proximity. Do we have any samples of Kabyle, Atlas, Shawi or Riffian berbers to test this?

Annie Mouse said...

IMO the Nile was the equivalent of the main superhighway between SSA and the rest of the world with Egypt being the main arrival "port"". I can believe SSA could be minor in Egyptions but it should be higher there than anywhere else outside of SSA. Although maybe not so much in the inbreeding elite. Plus they were a major trading partners. This population (ancient Egypt) is highly unlikely to be a racially ""pure" isolate. My best guess is that it will be in the Mediterranean group ethnically with significant SSA for its time.

Ric Hern said...

What is SSA precisely ? Is it Khoi-San like, Nilote like, Pygmy like or Congo like ?

Davidski said...

Sub-Saharan = any pop/component from below the Sahara.

Nirjhar007 said...

Okay folks , see this :

Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia

Balanovsky et al .

Abstract
Y-chromosomal variation in West Asian populations has so far been studied in less detail than in the neighboring Europe. Here, we analyzed 598 Y-chromosomes from two West Asian subregions—Transcaucasia and the Armenian plateau—using 40 Y-SNPs and 17 Y-STRs and combined them with previously published data from the region. The West Asian populations fell into two clusters: upland populations from the Anatolian, Armenian and Iranian plateaus, and lowland populations from the Levant, Mesopotamia and the Arabian Peninsula. This geographic subdivision corresponds with the linguistic difference between Indo-European and Turkic speakers, on the one hand, and Semitic speakers, on the other. This subdivision could be traced back to the Neolithic epoch, when upland populations from the Anatolian and Iranian plateaus carried similar haplogroup spectra but did not overlap with lowland populations from the Levant. We also found that the initial gene pool of the Armenian motherland population has been well preserved in most groups of the Armenian Diaspora. In view of the contribution of West Asians to the autosomal gene pool of the steppe Yamnaya archaeological culture, we sequenced a large portion of the Y-chromosome in haplogroup R1b samples from present-day East European steppe populations. The ancient Yamnaya samples are located on the “eastern” R-GG400 branch of haplogroup R1b-L23, showing that the paternal descendants of the Yamnaya still live in the Pontic steppe and that the ancient Yamnaya population was not an important source of paternal lineages in present-day West Europeans.
https://link.springer.com/article/10.1007/s00439-017-1770-2

capra internetensis said...

@Nirjhar

GG400=Y4371, equivalent to Z2103. We already know that Z2103 was dominant in the Samara and Kalmykia Yamnaya and is rare in Western Europe today (though quite common in the Balkans). This is very old news.

Gaspar said...

It just proves what they have been saying since 2011, that the ancient Egyptians ( apart from E ) where populated via the Levant from North to South.

Again proving that all haplogroups in NE-Africa who came from Haplo K where west-asian, born north of the zargos mountains

Ric Hern said...

Thanks.

Nirjhar007 said...

From the paper :

The currently available dataset does not contradict the
hypothesis that R-GG400 marks a link between the East
European steppe dwellers and West Asians, though the
route and even direction of this migration is disputable. It
does, however, demonstrate that present-day West European
R1b chromosomes do not originate from the Yamnaya
populations analyzed in (Haak et al. 2015; Mathieson et al.
2015) and raises the question of their origin. A Bronze Age
origin is more likely than a Neolithic one (Balaresque et al.
2010), but further ancient DNA studies may be necessary
to identify this source.

Folker said...

Nirjhar007
" do not originate from the Yamnaya
populations analyzed in (Haak et al. 2015; Mathieson et al.
2015)"
Except if you poslate that all Yamnaya were identical to the ones analyzed in 2015 (which it's obviously not the case), your point doesn't stand.

Folker said...

About Ancient Egypt, if we assume that SSA was partly due to Nubian emigration, it must be pointed that transition between Group A and Group B, and from Group B to Group C are seen in archeology as partial or total replacement of the preceding populations. The main possibility is migration into Nubia from nearby populations. The Nubian population itself is often considered as having been deported in Egypt as a way to securise Egyptian border. Hence probably some admixture.

Gioiello said...

@ Folker @ Nirjhar007
"do not originate from the Yamnaya populations analyzed in (Haak et al. 2015; Mathieson et al. 2015)"
Except if you poslate that all Yamnaya were identical to the ones analyzed in 2015 (which it's obviously not the case), your point doesn't stand.

Nirjhar007, but does it seems to me that there is someone who is saying that from ten years or am I wrong?
Folker, read all my more than 10000 letters and you'll know what was in Samara and what not of R-L23, and what survives now of that and what not.

Olympus Mons said...

@Nirjhar007
And now it will happen 2 things - or that paper is completely ignored (like those showing highest variance on R1b in eastern Anatolia ) or a flood of comments "proving" that this publishing scientist are just incompetent and idiots, in opposing to the "other" publishing scientist that are often cited and are just brilliant and do no foul.

Popcorn, Popcorn...!

Davidski said...

Why not just rely on coherent arguments? Like this one...

R1b-P297 is present in indigenous European foragers.

It's lacking in indigenous Near Eastern foragers and farmers.

Therefore it's an European lineage that expanded from Europe to West Asia.


Really, it's not very difficult. Everyone commenting here can do it if they try.

astenb said...

Yippee ! I get to learn more about R1b and the Steppes in a post dealing with Ancient DNA from Africa.

Karl_K said...

@astenb

But isn't it all so exciting!? Yes!

capra internetensis said...

astenb's law:

any discussion of archaeogenetics in the English language will eventually converge to a debate about the origin of West European R1b.

Son of Barca said...

Rami, really? atlas berber? aka the purest berber population ever xD wow you african-american afrocentrists cracks me up :)
http://s1.zetaboards.com/anthroscape/topic/8008678/1/

Anthro Survey said...

@sonofbarca: I don't have a lot of patience for afro-centrists but those Berbers claiming "0% ssa" and posting rare depigmented types left and right pretending to be Iberians crack me up. Anyway, if you go to a lower K value in admixture, you will see that Berbers do score about 15-20% SSA total on average. So even tho it will show 90% mozabite and like 10% yoruba at a higher K, the real ssa is not exactly 10% because Mozabites already have substantial ssa. Similarly, that MENA "component" in 23andMe already has ssa embedded in it. 23andMe isnt meant to assess ancestry on a basal level. As for Berber phenotypes-----if the SSA is ancient there it means a lot of time has passed to allow a "harmonization" of traits. That is ehy Berbers often don't resemble 1/4 black americans. But even so, those traits do show in more subtle ways. Take Djilali Mehri, a textbook Berber. I can totally see him as a harmonized mix of SSA, Levant/Natufian, and WHG. I say WHG because I suspect they inhabited the Maghreb prior to Levantine migrations. Maghrebis do show more of this signal than Middle Easterners. It also explains higher prevalence of "robust CM" facial traits there.

Awale Ismail said...

Seems like these are Late intermediate through Roman era genomes or something around that time. Makes sense... We already figured via Copts that the Egyptians of this time, especially in Lower Egypt, would be like this.

It would be more interesting if these were samples from as early as 3000 BCE or something.

Olympus Mons said...

@Awale Ismail
Nope. It will be really interesting the samples from 5000BC to 4000BC in the Delta Nile (Merimda and El-omari) or even in part Maadi.

Badarian , naqada, tasian and so forth will be just like Copts.

Salden said...

I figure the group that at least are the closest to the Ancient Egyptians from the Old Kingdom on are modern-day Upper Egyptians with the more fair skinned Levantine looking Egyptians up in the north, Copts and maybe North Sudanese. See this:

http://i.4cdn.org/his/1489980429103.jpg


Egyptian art shows a majority of brown/red Upper Egyptian types and a notable amount of fair skinned exampes comparable to modern-day Lower Egyptians (largely women).