Tag Archives: Egypt

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.

Spotted on Dienekes, I’ll dig up the full text to add to my Egyptian DNA page later. I’d debate that the J1 was all historic though, bearing in mind the Capsian J1 input into the area, but it is pretty far North. It’s a pretty small sample size (35) for the Y chr info.

Egyptian Y DNA and mt DNA reference

All the info I could find, collected in one place from assorted studies, mainly for my own ease of reference. I’ve kept putting this off, but finally here I am.

Egyptian  Y chromosomes

From Luis et al 2004.


 Which places the African Y chromosomes (this is a lower Egyptian sample group) at about 42%. I was most interested by the expansion time for the Eurasian hg’s. Luis et al estimated an expansion time of 13.7–17.5 ky for the K2 lineages in Egypt, although it also states the K2 could have accompanied R1*-M173 back into Africa in the paleolithic along with the U and M1.

Like the R1*-M173 males, the M70 individuals could represent the relics of an early back migration to Africa from Asia, since these chromosomes are not associated with the G-M201, J-12f2, and R1-M173 derivatives, lineages that represent more-recent Eurasian genetic contributions.

It also describes J-12f2 as a marker of the Neolithic expansion. Although looking through the Sudanese Y chromosome study it Hassan puts it down as a recent Arab marker, although no expansion dates are mentioned in his paper, so I’m not sure on what basis that conclusion was drawn. The J is complicated to unravel. After a read of Cruciani 2004 it would seem about 90% of the  J-12f2 is Arabic in origin, but the M172 (J2) is rather older and probably Neolithic, although this doesn’t seem to agree with the age estimates for J-12f2 in this paper. It would seem that J has made several entrances to North Africa.

From Lucotte 2003, which needs this Keita paper to understand it. Haplotypes V, XI and IV are all Pn2 derived (E). VII and VIII are considered Arabic, so I’m assuming J1 is VIII and VII is J2.


The other study that deals with numbered and not named groups is by Franz et al. This puts Hg 1 (E) at 44% in Egypt (Cairo) and J  (Hg 9) at 35%, but unfortunately the rest of the information is a bit vague.

From Arredi 2004 which had a small study of upper and lower Egyptians as part of a North Africa overview.

Lower Egypt (0f 44 samples)

  • 1 A3b2*
  • 4 E3b3a
  • 12 E3b1
  • 2 E3b
  • 5 E3b2
  • 1 J2f1
  • 3 J2
  • 3 F
  • 4 J
  • 1 O
  • 1 K2
  • 4 R1
  • 1 R1a*
  • 2 P

Upper Egypt (of 29 samples)

  • 2 E3b3a
  • 5 E3b1
  • 2 E3b2
  • 1 I
  • 1 J2
  • 5 F
  • 6 J
  • 3 K2
  • 4 R1

Which places AfricanY DNA at 59%, and J at 18% in Lower Egypt, which is close to the Lucotte study. Upper Egypt has a much more diverse profile (oddly) with J at 20% and African Y chromsomes at a much lower 31% with the ‘old in Africa’ R1 and K making up 24% of this (pretty small) sample. Having seen this study I’ve been obliged to dig into the origin of F, and it does look like an ‘ancient in Africa’ Y chromosome (Karafet 2008) as it turns up in the Bantu in South Africa.

From Wood et al 2005,which is in here provisionally until I can check the paper personally as I’ve borrowed it from Maju’s comments.

3/92 = 3.3% A3b2-M13
2/92 = 2.2% B2a1a-M152
1/92 = 1.1% E-SRY4064(xE1a-M33, E2-M75, E1b1-P2)
1/92 = 1.1% E1a-M33
2/92 = 2.2% E1b1a-P1(xE1b1a7-M191)
1/92 = 1.1% E1b1a7-M191
8/92 = 8.7% E1b1b1-M35(xE1b1b1a-M78, E1b1b1b-M81)
28/92 = 30.4% E1b1b1a-M78
4/92 = 4.3% E1b1b1b-M81

2/92 = 2.2% F-P14(xG-M201, H1-M52, I-P19, J-12f2, K-M9)
2/92 = 2.2% G-M201
1/92 = 1.1% I-P19
21/92 = 22.8% J-12f2
1/92 = 1.1% K-M9(xL-M20, M1-M4, N1-LLY22g, O-M175, P-P27, T-M70)
7/92 = 7.6% T-M70
1/92 = 1.1% R-M207(xR1-M173)
2/92 = 2.2% R1-M173(xR1a1-SRY10831b, R1b1-P25)
4/92 = 4.3% R1b1-P25(xR1b1b2-M269)
1/92 = 1.1% R1b1b2-M269

T formerlyK2, I believe. Finally I find a source for the R1b in the Sudan and Cameroon.

Finally a study of J (Giacomo 2004) found the Egyptian sample to be 23.4% J and with more clarity this was..

  • 6 J1
  • 1 J2*
  • 2 J2
  • 1 J2f
  • 1 J2fl

I can’t help noticing there’s a fair amount of variance between these studies. But still the overall picture you get from Lower Egypt is about half native African, with most of the other Eurasian Hg’s dating back into prehistory.

Lower Egypt is about 55% African, mainly E3b, E and then A.

The next largest group is J, which is unfortunately a bit hard to separate out from Neolithic expansion, Capsian expansion, earlier historic population movements and the Arab expansion, but it averages out at 25% from all five studies, with possibly a third of it attributable to non historic expansions (J2, a little  Capsian J1).

After this comes the ‘old in Africa’ haplotypes, which make up the bulk of the remaining Y chromosomes about 19% (again averaging the studies, the HG vary in proportion but they came up near 19% overall).

Which takes Lower Egypt into the low 80% area for paternal ancestry traceable to the dynastic era and earlier. One would assume the Arab expansion didn’t bring anywhere near as much maternal DNA with it, although some tribes did settle in Egypt.

Egyptian mitochondrial DNA

From Berbers at Siwa Oasis (north west Egypt) and from Egyptians at Gurna (upper Egypt area) Detail here.

Siwa; Of 78 samples.

  • Eurasian  45
  • Asian (M) 1
  • North African (U6 and M1) 13
  • Sub Saharan 19

24% SSA, 75% Eurasian/N African.


  • H 5 14.7
  • I 2 5.9
  • J 2 5.9
  • L1a 4 11.7
  • L1e 2 5.9
  • L2a 1 2.9
  • M1 6 17.6
  • N1b 3 8.8
  • T 2 5.9
  • U 3 8.8
  • U3 1 2.9
  • U4 2 5.9
  • L3*(a) 2 5.9
  • L3*(b) 1 2.9

29% SSA, 71% Eurasian/N African.

Surprisingly little difference between them. Lower Nubia came in at about 60% Eurasian an ancient mummy test– and while it’s correct that L3 also comes into the category marked out as Eurasian, it’s actually pretty close to the DNA study of modern Nubians. Unless the invading armies of history were all women there’s no plausible scenario to explain such a huge influx of Eurasian ancestry in such a relatively short space of time, as the Y chromosome presence of Arabs in the area just isn’t that massive in the modern lower Nubia area.

From Krings 1999. Which also shows that Egyptian maternal DNA is roughly 25% sub Saharan and 75% Eurasian. 



Ancient Egyptian DNA

To obtain the frequencies of these mtDNA types, amplification of the HVRI region and three RFLP markers was conducted. The authors succeeded in analysing RFLP markers in 34 samples and HVRI sequences in 18 of the samples. Both populations, ancient and contemporary, fit the north-south clinal distribution of “southern” and “northern” mtDNA types (Graver et al. 2001). However, significant differences were found between these populations. Based on an increased frequency of HpaI 3592 (+) haplotypes in the contemporary Dakhlehian population, the authors suggested that, since Roman times, gene flow from the Sub-Saharan region has affected gene frequencies of individuals from the oasis.

Which suggests the proportion of sub Saharan lineages is higher now than it once was at Dahkleh (SW Egypt). Bearing in mind that the Arab slave trade in African women seems to have accounted for about 10-15% of the maternal DNA in Arabia, this would seem the most likely cause in the increase of sub Saharan lineages. It would seem that post dynastic inflow maternal from sub Saharan African is passably close match to the paternal immigration from Arabs, and that these are probably the two most influential factors in immigration in post dynastic Egypt.

Not strictly speaking Egyptian but still relevant.

Copts from the Sudan, from Hassan 2008.

  • 13/33 J1
  • 5/33 B
  • 2/33 E3b
  • 5/33 E3b1
  • 2/33 J2
  • 1/33 K
  • 5/33 R1b

Nubians from the Sudan

  • 3/39 B
  • 3/39 E3b
  • 6/39 E3b1
  • 4/39 F
  • 2/49 I
  • 16/39 J1
  • 1/39 J2
  • 4/39 R1b

The high level of J1 is quite a surprise in both of these. Particlarly since Copts aren’t supposed to marry out. A y chr study of Cairo Copts could be informative as to just how much mixing there has been between the two groups there.

One thing that became apparent after reading through these DNA studies was that there was a somewhat higher level of African male ancestry in Egyptians than in a lot of the East African groups, and that the Horn Africans and Egyptians are really made up of very similar ancestries (West Asian, North East African and East African with a little Bantu here and there) but in varying ratios.

Reference list.

  1.  Luis 2004
  2.  Cruciani 2004
  3. Lucotte 2003
  4. Wood 2005
  5. Franz 2002
  6. Hassan 2008
  7. Krings 1999
  8. Arredi 2004
  9. Karafet 2008
  10. Giacomo 2004

mtDNA Analysis of Nile River Valley Populations: A Genetic Corridor or a

mtDNA Analysis of Nile River Valley Populations: A Genetic Corridor or a Barrier to Migration?

To assess the extent to which the Nile River Valley has been a corridor for human migrations between Egypt and sub-Saharan Africa, we analyzed mtDNA variation in 224 individuals from various locations along the river. Sequences of the first hypervariable segment (HV1) of the mtDNA control region and a polymorphic HpaI site at position 3592 allowed us to designate each mtDNA as being of “northern” or “southern” affiliation. Proportions of northern and southern mtDNA differed significantly between Egypt, Nubia, and the southern Sudan. At slowly evolving sites within HV1, northern-mtDNA diversity was highest in Egypt and lowest in the southern Sudan, and southern-mtDNA diversity was highest in the southern Sudan and lowest in Egypt, indicating that migrations had occurred bidirectionally along the Nile River Valley. Egypt and Nubia have low and similar amounts of divergence for both mtDNA types, which is consistent with historical evidence for long-term interactions between Egypt and Nubia. Spatial autocorrelation analysis demonstrates a smooth gradient of decreasing genetic similarity of mtDNA types as geographic distance between sampling localities increases, strongly suggesting gene flow along the Nile, with no evident barriers.We conclude that these migrations probably occurred within the past few hundred to few thousand years and that the migration from north to south was either earlier or lesser in the extent of gene flow than the migration from south to north.

I know I’ve posted the abstract, but I couldn’t find the full text before. Finally…


I see the maternal Eurasian DNA in modern Nubia is about the same as the Nubian mummy study-60% vs 54% L3 being included as Eurasian in the other study not withstanding.

Domestication of the donkey: Timing, processes, and indicator


Abydos donkeys in brick tombs.

Domestication of the donkey: Timing, processes, and indicator

Domestication of the donkey from the African wild ass transformed ancient transport systems in Africa and Asia and the organization of early cities and pastoral societies. Genetic research suggests an African origin for the donkey, but pinpointing the timing and location of domestication has been challenging because donkeys are uncommon in the archaeological record and markers for early phases of animal domestication are hard to determine.We present previously undescribed evidence for the earliest transport use of the donkey and new paleopathological indicators for early phases of donkey domestication. Findings are based on skeletal data from 10 ~5,000-year-old ass skeletons recently discovered entombed in an early pharaonic mortuary complex at Abydos, Middle Egypt, and a concurrent study of 53 modern donkey and African wild ass skeletons. Morphometric studies showed that Abydos metacarpals were similar in overall proportions to those of wild ass, but individual measurements varied. Midshaft breadths resembled wild ass, but midshaft depths and distal breadths were ntermediate between wild ass and domestic donkey. Despite this, all of the Abydos skeletons exhibited a range of osteopathologies consistent with load carrying. Morphological similarities to wild ass show that, despite their use as beasts of burden, donkeys were still undergoing considerable phenotypic change during the early Dynastic period in Egypt. This pattern is consistent with recent studies of other domestic animals that suggest that the process of domestication is slower and less linear than previously thought.

As the paper says at one point:

In the 1980s zooarchaeologists working in southwestern Asia found bones attributable to donkey from sites in Syria, Iran, and Iraq dating to ca. 2800–2500 B.C.

the oldest date at 4,800 BP is from the Iranian highlands. So logically the domestiction of the ass in Africa would date to a substantial amount before 2,800 BC, and given the rate of expansion of camels and other livestock I’d say 6,000 years would be more realistic.

The case for and against cattle domestication and sorghum cultivation at Nabta Playa

First of all a link to a Fred Wendorf paper on Nabta PLaya.

Nabta Playa and Its Role in Northeastern African Prehistory

Nabta Playabasin offers an unprecedented longitudinal view on the emergence, consolidation and complexification on human–livestock relationships, from the early stage of the Early Holocene (c. 11,000 cal. B.P.) to 6000 B.P. The problem of cattle domestication in Northeastern Africa is considered and hopefully ‘‘solved’’ in the light of new mtDNA evidence which suggest an early late Pleistocene split between African, Asian, and Eurasian wild Bospopulations. The paper presents a contextualized analysis of almost all the components of archaeological investigation, including climatic change, culture history of Early to Mid-Holocene Nabta-Playans, the development of social differentiation, and probably ranking with ‘‘labor-consuming’’ megalithic features with the emergence of characteristic features of pastoralideology and religions. As far as the emergence and adoption of new food ways are concerned, the cultural development outlined with the Nabta Playa  archaeological record is important for the understanding of the Holocene prehistory of Africa as a whole.


One of the most interesting bits (my POV) from this paper was the presence of legumes at about 10,000 BC.

One of these sites yielded charred seeds of wild millet and two varieties of legumes (Wasylikowa, report to F. Wendorf 1996)

It also has a reference to possible early domesticated sorghum. Although again the case is bit weak. There’s more reference to it here. The seeds don’t appear to resemble any kind of cultivated sorghum though. They did seem to be harvesting and storing them in large amounts; some of the houses had storage pits for the grains.

Preliminary chemicalanalyses by infrared spectroscopy of the lipids in the archaeological sorghum show closer resemblance to some modern domestic sorghum than to wild varieties (Wasylikowa et al. 1993)

In a later publication (97)  Wasylikowa describes the Sorghum as more likely to be wild, after another study of the seeds showed them to be typically wild seeds. 

Smaller grain size and the lack of any spikelets containing attached branchlets of the inflorescence or rachis fragments suggest that the material harvested and eaten at the Nabta Playa site were of a wild type.

This sorghum doesn’t seem to ‘spread out’, as farmers tend to expand massively into their hunter gatherer neighbours very rapidly. The expansion of domesticated sorgum doesn’t seem to begin until the expansion  of the domesticated donkey, which parallels it’s spread into Asia quite well, and the donkey seems to have been domesticated about 6,000 BP.

It also mentions the barley from this site, once thought to be an ancient domesticate, but now known to be a neolithic contaminant.

The barley recovered from this site during the 1977 excavations (Hadidi in Wendorf and Schild 1980: 347) is regarded as intrusive.

And the first appearance of goats and sheep.

Around 8000 cal B.P. there was an important new addition to the food economy of the Middle Neolithic. Domestic caprovids, either sheep or goat, or both, were introduced from Southwest Asia, probably by way of the Nile Valley (although the oldest radiocarbon dates now available for the Neolithic along the Nile are about 500 years later)

Since the only legumes I know of come from Anatolia, I shall dig a bit deeper into this. This could possibly be a breadcrumb for my ‘proto-Neolithic’ expansion from the near east, circa 13,000 to 14,000 years ago. The paper has made me warm a bit more to pastoralism there in the Holocene, although I’m not sure that it went beyond providing water to keep the cattle around. The claims for dairying are a bit dubious IMO. There’s a link here to a Wendorf item on the Saharan cattle. I think analysing lipids on the surviving pottery from the era might be a good way forward in this case. There have done some kind of analysis along these lines already (sorghum lipids) but there was no sign of milk fats -I’m sure Wendorf would have mentioned them  if they had been found. If there were dairy fats in the pots that would be a different story, a wild cow isn’t going to let a human near her udders. One of my main objections to the very early pastoralism at Nabta PLaya is that it should have seen a population expansion from the area, and to date no sign of that is to be found.

Also, to quote another source…

Grigson’s study concluded cattle from all periods at Nabta Playa were morphologically wild (2000).

Smith’s study: morphologically wild prior to and including the El Nabta/Al Jerar Maximum (7050 – 6150 BC), but domesticated from the Ru’at El Ghanam phase (5900 – 5500 BC) onward

From the Wendorf item on cattle domestication, it states that domesticated sheep, goats etc are all included in the proto Sahelian, but (as he says above) they all arrive with the early neolithic from the near East about 8,000 years ago along with agriculture (they have been shown to be native Asian domesticates, not African, and the date is more like 7,500 years), so the 9,000 year time depth given for proto Sahelian seems unlikely, 7,500 years or younger would make more sense. These Sahelian words appear to be words of Neolithic and not older origin. You’d also expect the domesticated cattle dates in Mali and Mauritania to be a lot older than 4,200 years if the Sahara was the source of very early domesticated cattle.

Another issue is how long it takes animals to show physical signs of domestication. The domestication of Asian cattle now seeming about 11,000 years old) didn’t show any real changes until about 9,500 years ago, a similar situation is seen with domesticated donkeys-they show signs of load bearing and heavy labour for about 1000 years  before they begin to change physically. This would suggest some leeway in the morphologically studies of the cattle. However, there should still have been physically differentiated domesticated African cattle existing right across the Nile region and the Sahara/East Africa by about 7,5000 BP; domesticates spread out quickly, as does pastoralism/agriculture, and there is no sign of fully domesticated cattle at so early a date in Africa. If there were, they should be definably different to the Asian domesticates (through drift) by the time the sheep, goats, and cereals arrive from Asia. So far, domesticated cattle track the arrival of the rest of the neolithic, evidence for domestication in Nabta is still negligible.

Linguistic evidence

The Proto-Northern Sudanic language contains root words such as “to drive,” “cow, “grain,””ear of grain,” and “grindstone.” Any of these might apply to food production, but another root word meaning “to milk” is cetainly the most convincing evidence of incipient pastoralism. There are also root words for “temporary shelter” and “to make a pot.” In the succeeding Proto-Saharo-Sahelian language, there are root words for “to cultivate”, “to prepare field”, to “clear” (of weeds), and “cultivated field.” this is the first unambiguous linguistic evidence of cultivation. There are also words for “thornbush cattle pen,” “fence,” “yard,” “grannary,” as well as “to herd” and “cattle.” In the following Proto-Sahelian period, there are root words for “goat,” “sheep,” “ram,” and “lamb,” indicating the presence of small livestock. There are root words for “cow,” “bull,” “ox,” and “young cow” or “heifer” and, indeed, a variety of terms relating to cultivation and permanent houses

The word for grindstone could date back to about 25k ago, so it’s not likely to be associated with agriculture, and wild grains were being eaten in the area for a very long time, as were cattle. As for the word ‘to milk’, it’s suggestive but again not exactly solid. Pottery in the Sahara does go back that far though, and the main word for pot seems to have derived from water pot, which is interesting. There are cached book links here and here that go into this in more depth, but as they’ve already make a miscalculation for the age of proto Sahelian judging by the inclusion of sheep and goats which dates it securely to the arrivval of the neolithic-as sheep and goats are not native to Africa and only appear when the domesticates are being herded in from Asia. Non- pastoral people in the Sahara were penning and keeping wild animals (Barbary sheep at Uan Afada); so assuming terms that describe fencing in animals must be from domestication is a fallacy. In essence the presence of the words goat and sheep in proto Sahelian, that can only date to the Neolithic, torpedoes a lot of the linguistics argument, and means proto Sahelian probably has a date of 7,500 BP or slightly younger. This would bring proto Sahara Sahelian within the range of the Neolithic as well, as it’s only slightly older (estimated). A link to the Nilo Saharan Language family family tree. In fact, I’d suggest the presence of agricultural terms dates the arrival of the Neolithic, rather than showing agriculture there at an earlier date. This also casts some major doubt on Ehrets dates for proto Sudanic if it’s estimated by the same method.

This linguistic information would really depend on the dating of the age of proto Sudanic. One inaccuracy I’ve spotted in these links is that Proto Indo European is down as 6,000 years old; it’s now estimated at more like 9,000 years, seems to come from Turkey and is a very good match for the start date and location of the Neolithic expansion. There’s another link that discusses the claimed domestication.

So,  predating the Asian domestication seems unlikely (since it now dates pretty reliable back to 11,000 Bp, the same as sheep and goats), and in a lot of African sites domesticated cattle bones don’t show up until sheep, goats and grain do. It’s not convincing for a very early domestication in the Sahara, although there does seem to have been a specific domestication of African cattle at some point, similar to the domestication of the Zebu In Pakistan. My theory is that the Asian cattle just weren’t up to the local climate and parasites and tended to die in droves, making a local domestications necessary. I’d suggest African cattle domestication probably dates to the Neolithic, sometime between 8,000 and 6,000 BP, and so does sorghum.

Egyptians are not Arabs, they are Egyptians.

Modern Upper Egyptians


A strange title for a blog entry I know. But this is a result of a little nosing through the DNA studies available of modern Egypt, and some irritation at modern Egyptians being incessantly called ‘thieving Arabs’ by on-line Afrocentrists.

This is more focussed on the Egyptians around Luxor, where old upper Egypt was located. A recent DNA study by Cruciani that focused on the Y chromosome E-M78 revealed that it was ‘born’ in North East Africa , not East Africa as previously thought. This means, that an Egyptian with an m78 Y chromosome has had a male line ancestry reaching back to the Pleistocene inhabitants of Egypt; as far back as the Halfan culture about 24,000 years ago.

Southern Egyptians Y Chromomses are mainly native to Africa, both sub and supra Saharan. This makes a grand total of 80.3% definitively African non-Arab ancestry in the upper Egypt region. Y chromosomes possibly attributable to Arab males are very much in the minority in this area. A rough estimate (since no women invaded Egypt) is that about 5% or less of this population are from non dynastic Egyptian peoples, and not all of these would be Arabs.

Northern Egyptians are a bit more cosmopolitan in their ancestry  64.8% indigenous African. About 20% of the Y chrom0somes are near Eastern in origin, and 10.5 % are R Y chromosomes. However, some of these near eastern and European Y chromosomes show an ancient entry to Africa (G, K2, R1, R1b are 8,000 BP and older) and any historical contribution from foreign men is more likely to be in the 15% area. Divided by two (no recent female contribution to speak of). This makes non-dynastic Egyptian population around the 7% mark in Lower Egypt; and only some of this is Arab.

As for the maternal inheritance; this is more varied. From a study at Gurna (of modern upper Egyptians):

H 14.7%, I  5.9%, J   5.9%, L1a   11.7%, L1e   5.9%, L2a   2.9%, M1   17.6%, N1b   8.8%, T   5.9%, U   8.8%  U3   2.9%, U4   5.9% ,L3*(a)  5.9%, L3*(b)  2.9%, Other   2.9%.

Of these, the L haplotypes are typically sub Saharan (23.7%), M1 and U are ancient Eurasian, present at least 30,000 years and many of the other Eurasian haplotypes have been found in 12,000 year old bones in Morocco. The N an I  are possibly attributable to Arab ancestry, about 15% non-Arab in upper Egypt. But still, most of that would easily be attributable to the Neolithic input from Asia- and very little of this would be attributable to Arabs

To sum up, there doesn’t seem to be majority ‘Arab’ genetic component to the Egyptian DNA pool,  20% absolute maximum. And a lot of the non African DNA is traceable to the Neolithic farming expansion that swept across North Africa, so it would be a lot lower in reality.

In upper Egypt a maximum of 20% of the Y chromosomes are non African (the Mt DNA has been shown to be the same since dynastic times from Nubian mummy studies).. so how these people are supposed to have magically changed appearance in the past few thousand years with so little foreign input I’d like to know.

Egyptians are Egyptian, not Arab.


Very simplified Y chromosome information from Lucotte 2003.

The ancient North Africans.

I was looking about for classical descriptions of Egyptians and Libyans. Where the term Libyan is used, it refers to Caucasian North Africans, Ethiopian is the classical term for black Africans, at one point Herodotus writes about the the Ethiopians that live in parts of Libya. Herodotus considered Egyptians to be the third race of people in Egypt in north Africa.


Libya to the Egyptians and Greeks meant all of North Africa.

This is a map drawn by Herodotus himself. He names the Libyan people as the Nasamones, and interestingly, the Nile was believed to originated in the Atlas mountains instead of it’s real origin , a straight line southwards.

Foreign prisoners of Ramesses III: Libyan, Nubian, Syrian, Shasu Bedouin, and Hittite (The Hittites were an Indo-European people from Turkey).

A Libyan and a Nubian on king Tutankhamun’s staff.

And the mural of the races from the tomb of Ramses, from Belzoni’s illustration and the rather damaged original. Showing Libyans, a Nubian, a Syrian and an Egyptian.

And another freize showing various people, Syrians, Nubians and Libyans.

The Tassili Ladies, dated about 3,000 BC from  Southern Algeria.

The Greek historian Herodotus, who lived from c.480 – c.425 B.C wrote of the Nasamones..

They are a numerous race, who in the summer leave their flocks behind by the sea and go up to the region of Augila to gather the fruit of the date-palms, which grow in great numbers and very large and are all fruit-bearing: they hunt the wingless locusts, and they dry them in the sun and then pound them up, and after that they sprinkle them upon milk and drink them.
Their custom is for each man to have many wives, and they make their intercourse with them common in nearly the same manner as the Massagetes, that is they set up a staff in front of the door and so have intercourse. When a Nasamonian man marries his first wife, the custom is for the bride on the first night to go through the whole number of the guests having intercourse with them, and each man when he has lain with her gives a gift, whatsoever he has brought with him from his house.

The forms of oath and of divination which they use are as follows: they swear by the men among themselves who are reported to have been the most righteous and brave, by these, I say, laying hands upon their tombs; and they divine by visiting the sepulchral mounds of their ancestors and lying down to sleep upon them after having prayed; and whatsoever thing the man sees in his dream, this he accepts. They practice also the exchange of pledges in the following manner, that is to say, one gives the other to drink from his hand, and drinks himself from the hand of the other; and if they have no liquid, they take of the dust from the ground and lick it.

 The Nasamones bury bodies in a sitting posture, taking care at the moment when the man expires to place him sitting and not to let him die lying down on his back.

They have dwellings composed of the stems of asphodel entwined with rushes, and so made that they can be carried about.

Herodotus, Histories, 4.172-173, 190

Herodotus also describes the Garamantes, the Lotophagi (lotus eaters) and Macae.

Further inland to the southward, in the part of Libya where wild beasts are found, live the Garamantes, who avoid all intercourse with men, possess no weapons of war, and do not know how to defend themselves. Along the coast to the westward the neighbours of the Nasamones are the Macae. These people wear their hair in the form of a crest, shaving it close on either side of the head and letting it grow long in the middle; in war they carry ostrich skins for shields. The river Cinyps, which rises on a hill called the Hill of the Graces, runs through their territory to the sea. The Hill of the Graces is about twenty-five miles inland, and is densely wooded, unlike the rest of Libya so far described, which is bare of trees.

…Ten days’ journey west of the Ammonians, along the belt of sand, there is another similar salt-hill and spring. This place, called Augila, is also inhabited and it is here that the Nasamonians come for their date harvest. Again at the same distance to the west is a salt-hill and spring, just as before, with date palms of the fruit-bearing kind, as in the other oases; and here live the Garamantes, a very numerous tribe of people, who spread soil over the salt to sow their seed in. From these people is the shortest route—thirty days’ journey—to the Lotophagi; and it is amongst them that the cattle are found which walk backwards as they graze. The reason for this curious habit is provided by the formation of their horns, which bend forwards and downwards; this prevents them from moving forwards in the ordinary way, for, if they tried to do so, their horns would stick in the ground. In other respects they are just like ordinary cattle—except for the thickness and toughness of their hide. The Garamantes hunt the Ethiopian hole-men, or troglodytes, in four-horse chariots, for these troglodytes are exceedingly swift of foot—more so than any people of whom we have any information. They eat snakes and lizards and other reptiles and speak a language like no other, but squeak like bats.

The faces of the Carthaginians

A selection of coins from Carthage showing: the goddess Tanit and the Greek Pegasus (top) then Hannibal Barca’s own coinage, and then an electrum coin from 250 BC. A cathaginian coin minted in SIcily, and a coin from Massinissa. A coin of  Hadsrubal Barca (Hannibals brother), a tetradrachm from the Carthaginians in Sicily from circa 320 BC, and finally another coin of Hannibal complete with an elephant, 230 BC.

Hannibals coins were minted by order of Hannibal himself, not on the orders of some third party. So they are probably close to what he looked like in life.

I’ve been unable to find any statues, it seems the Romans did a very thorough job of destroying them

Egyptian Y chromosome study shows a complicated ancestry.

Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa.

Laboratoire d’Anthropologie Biologique (CNRS FRE 2292); Musée de l’Homme MNHN, Paris, France.

The geographic location of Egypt, at the interface between North Africa, the Middle East, and southern Europe, prompted us to investigate the genetic diversity of this population and its relationship with neighboring populations. To assess the extent to which the modern Egyptian population reflects this intermediate geographic position, ten Unique Event Polymorphisms (UEPs), mapping to the nonrecombining portion of the Y chromosome, have been typed in 164 Y chromosomes from three North African populations. The analysis of these binary markers, which define 11 Y-chromosome lineages, were used to determine the haplogroup frequencies in Egyptians, Moroccan Arabs, and Moroccan Berbers and thereby define the Y-chromosome background in these regions. Pairwise comparisons with a set of 15 different populations from neighboring European, North African, and Middle Eastern populations and geographic analysis showed the absence of any significant genetic barrier in the eastern part of the Mediterranean area, suggesting that genetic variation and gene flow in this area follow the “isolation-by-distance” model. These results are in sharp contrast with the observation of a strong north-south genetic barrier in the western Mediterranean basin, defined by the Gibraltar Strait. Thus, the Y-chromosome gene pool in the modern Egyptian population reflects a mixture of European, Middle Eastern, and African characteristics, highlighting the importance of ancient and recent migration waves, followed by gene flow, in the region.


Y-Chromosome Biallelic Profiles. Allelic profiles of the 11 Y-chromosome lineages in the total sample of 164 North African samples are shown in Table 1. Of a total of 8 Y-chromosome Hgs observed, only two reached a frequency of > 10% (Hgs 21 and 9). Hg 21* is present at high frequency in Egypt (44%) and at higher frequencies in Moroccan Arabs (69%) and Moroccan Berbers (76%). This lineage shows the highest frequencies in North Africa with a decreasing frequency gradient towards the south, and it is also present at moderate frequencies in the northern Mediterranean basin. Hg 9** is the second most common lineage in the Egyptian population (35%) and is also present, although at lower frequencies, in the two NW African populations examined (Moroccan Arabs 14%; Moroccan Berbers 4%). This haplogroup shows the highest frequencies in the Fertile Crescent, and it has been suggested to be a genetic signature of migrations from the Middle East associated with Neolithic farmer expansions (Semino et al. 1996; Rosser et at. 2000; Quintana-Murci et al. 2001).

Other lineages are present at lower values in both Egyptian and NW African populations. Hg 1, which is present in Egyptians (8%) and NW Africans (Arabs 6%; Berbers 4%), indicates a limited degree of gene flow from Europe to North Africa, since it has been predominantly found in Europe, with increasing frequencies from the Middle East to northwestern Europe (Semino et al. 1996; Rosser et al. 2000). Hgs 2 and 26 are found at moderate and low frequencies, respectively, in the three populations. However, little information can be deduced from these lineages since they are present in both Europe and Asia and do not show any informative geographic variation along the Eurasian landscape. Hgs 7 and 8 are typically sub-Saharan African lineages, and they have been suggested to be genetic signatures of Khoisan and Bantu language families, respectively. They have not been recorded outside Africa (Hammer et al. 1998; Rosser et al. 2000), and their presence is unusual in North Africa (Bosch et al. 1999). In agreement with Bosch et al. (1999), Hg 7 is not observed in NW Africa and is present in two individuals from Egypt. Hg 8, which is considered to be of sub-Saharan origin, was found in one Egyptian, three Moroccan Berbers, and two Moroccan Arabs. One Egyptian individual was found with an Hg 4 Y chromosome. This lineage has not been observed in any European nor African populations, but it is present at high frequencies (-45%) in some East Asian populations, such as the Japanese and Tibetans (Karafet et al. 1999).

Classical genetic studies show a high degree of genetic heterogeneity in the modern Egyptian population, suggesting that this population is descended from a mixture of African, Asian, and Arabian stock (Mahmoud et al. 1987; Hafez et al. 1986). Genetic heterogeneity within the Egyptian gene pool is also supported by more recent studies using autosomal STR markers (Klintschar et al.

Related Results
Y-chromosome DNA haplotypes in North African populations
Population history of North Africa: Evidence from classical genetic markers

Here, we used ten Y-chromosome binary markers to define the male-specific gene pool in the Egyptian population and two NW African populations, in order to test contrasting hypotheses on the inter- and intrapopulation relationships and, in a more general context, the peopling processes of North Africa. The results of Y-chromosome haplogroup profiling in Egypt parallels previously published studies of autosomal loci, by demonstrating that Y-chromosome lineages, which are present at high frequencies in modern African (Hgs 7, 8, 21), European (Hg 1), and Middle Eastern (Hg 9) populations, are also found in the modern Egyptian population. The high incidence of Hg 21 in North African (44%-76%), and more especially among NW African, samples can be regarded as an autochthonous genetic layer of the region. This lineage may have originated somewhere in North Africa -20,000 YBP and remained in North Africa and the Middle East for 10,000 years, before it spread towards southern Europe (Hammer et al. 1998). The relatively low incidence of this lineage in Egypt, compared with the Moroccan populations, is probably due to substantial population movements from neighboring countries to Egypt, thereby effectively reducing the frequency of Hg 21 within Egypt. This is highlighted by the geographic distribution of Hg 9 in modern populations. From coalescence analysis, the polymorphism defining Hg 9 has been dated to approximately 14,800 YBP (Hammer et al. 2000). It shows its highest frequencies in the Fertile Crescent with a decreasing frequency cline towards Europe, North Africa, and India. This cline has been interpreted as the consequence of the Neolithic demic diffusion process of farmer economy from the Middle East towards Europe and South Asia (Semino et al. 1996; Rosser et al. 2000; Quintana-Murci et al. 2001). Interestingly, Hg 9 is also present at relatively high frequencies (25%) in the Ethiopian population, highlighting the extent to which Semitic peoples have left substantial traces in the Ethiopian gene pool at different times (Passarino et al. 1998). Hg 9 frequencies observed in Egypt are intermediate between those observed in the Middle East and those in NW Africa, suggesting an east-west cline of decreasing frequencies along the North African coast. It is interesting to note that within the Nile Valley, there is no evidence indicating the presence of agriculture technology before 4700 BC (Kasule 1998), a date confirmed by the oldest solid evidence of food production on the western side of the Nile delta (Hassan 1988). These agricultural food resources are considered to have been introduced from the Levant

One single individual belonging to Y-chromosome lineage Hg 4 was identified. This lineage, which has not been reported in European and African populations and shows highest frequencies in East Asia, was proposed to represent the ancestral state of the YAP lineage (Hammer et al. 1998). Lineages that are clearly derived from Hg 4 (Hgs 21 and 8) make up by far the major part of the sub-Saharan African Y-chromosome gene pool. The phylogeographic distribution of this lineage, with a high frequency in some East Asian populations (~45%), has been used to support a “back-to-Africa” migration of individuals carrying Asian Y chromosomes into the sub-Saharan African gene pool (Hammer et al. 1998). However, with the characterization of new diagnostic markers that refine further the Y-chromosome phylogeny, the exact geographic origin of Hg 4 is not clear (Underhill et al. 2001). One Egyptian individual with an Hg 4 Y chromosome is insufficient to determine the geographical origin of the Alu insertion defining this lineage and may well be due to recent gene flow. Hg 8, which is the most characteristic lineage among sub-Saharan African populations and is derived from Hg 4, has been associated with the Bantu expansions 3000-4000 years ago (Hammer et al. 1998). Here, we found Hg 8 in only one individual from Egypt and in 4%-6% of the Moroccan samples, indicating minimal gene flow from sub-Saharan Africa. We also detected low levels of another sub-Saharan Y-chromosome lineage in Egypt, Hg 7, supporting the findings by Karafet et al. (1999). Although Hg 7 is typical of Khoisan populations, it has been observed in East Africans, Gambians, and East Bantus, and its presence in Egypt is probably due, once again, to limited gene flow from East Africa, perhaps through the Nile Valley.

Our analyses suggest that migration patterns and gene flow between the southern and northern shores of the Mediterranean Sea have been very different in its western extreme (Gibraltar) compared to the eastern region (Egypt). The topology of the minimal spanning tree (Figure 1), which connects NW Africa to the Middle East and Europe through Egypt, indicates a low level of gene flow through the Gibraltar Strait. This scenario is in agreement with the spatial pattern of genetic variability described elsewhere using Y-chromosome markers, autosomal Alu-insertion polymorphisms, and autosomal STR markers (Bosch et al. 2000a, 2000b, 2001; Comas et al. 2000), where a sharp genetic discontinuity between NW Africa and the Iberian Peninsula was reported. Geographic analysis of genetic variation (Figure 2) supports a genetic barrier between SW Europe and NW Africa, the intensity of which decreases from the western to the eastern part of the North African continent. In contrast with the pattern observed in the western Mediterranean region, the MDS plot (Figure 1) indicates an intermediate genetic position of Egypt between North Africa, southern Europe, and the Middle East. In addition, the geographic analysis of genetic variation (Figure 2) provides no evidence for the existence of a genetic barrier between the southern and northern shores of the eastern part of the Mediterranean basin. The isolation-by-dislance model may well explain the genetic relationships between Egypt and the surrounding African, European, and Middle Eastern populations. This is an opposite pattern to that observed in NW Africa, where the presence of a genetic barrier is incompatible with this model. This conclusion is reinforced by Mantel-test correlations between genetic and geographic variability, since the correlation index almost doubles (0.494 –> 0.820) when populations encompassed by the first genetic barrier (defined by the Gibraltar Strait, Figure 2) are withdrawn from the analysis.

In conclusion, our analyses have identified a genetic regional continuity between the northeastern part of Africa (Egypt), the Middle East, and southern Europe. In agreement with the ethnohistorical connections between NE Africa and the Middle East, the genetic data confirm that Egypt, occupying an intermediate position along these routes, has been an important contact zone between the three continents. This is in sharp contrast with the pattern observed between NW Africa and the Iberian Peninsula where no regional continuity along the Gibraltar Strait is observed. However, the previous observation of a continuum of gene flow in another African strait, the Bab-el-Mandeb Strait (Quintana-Murci et al. 1999) highlights the need to consider each geographic feature independently, rather than to extrapolate general conclusions on their influence on gene flow. Moreover, given the absence of recombination for most of the Y chromosome, which behaves effectively as a single genetic locus, the direct inference of population processes from Y-chromosome variation is not without risks. Different factors, such as different effective population sizes, differences in male vs. female cultural and social habits and selection, could affect Y-chromosome variation and distribution in human populations. Future studies integrating data from multiple independent loci (mtDNA, autosomal markers) may reveal additional information on the population structure and the peopling processes of North Africa.

Egyptian Y chromosomes

Y-chromosome Haplotypes in Egypt

G. Lucotte *, G. Mercier
International Institute of Anthropology, Paris, France


We analyzed Y-chromosome haplotypes in the Nile River Valley in Egypt in 274 unrelated males, using the p49a,f TaqI polymorphism. These individuals were born in three regions along the river: in Alexandria (the Delta and Lower Egypt), in Upper Egypt, and in Lower Nubia. Fifteen different p49a,f TaqI haplotypes are present in Egypt, the three most common being haplotype V (39.4%), haplotype XI (18.9%), and haplotype IV (13.9%). Haplotype V is a characteristic Arab haplotype, with a northern geographic distribution in Egypt in the Nile River Valley. Haplotype IV, characteristic of sub-Saharan populations, shows a southern geographic distribution in Egypt. Am J Phys Anthropol 121:000-000, 2003. © 2003 Wiley-Liss, Inc.


As for mtDNA (Krings et al., [1999]), the present study on the Y-chromosome haplotype shows that there are northern and southern Y-haplotypes in Egypt. The main Y-haplotype V is a northern haplotype, with a significantly different frequency in the north compared to the south of the country: frequencies of haplotype V are 51.9% in the Delta (location A), 24.2% in Upper Egypt (location B), and 17.4% in Lower Nubia (location C). On the other hand, haplotype IV is a typical southern haplotype, being almost absent in A (1.2%), and preponderant in B (27.3%) and C (39.1%). Haplotype XI also shows a preponderance in the south (in C, 30.4%; B, 28.8%) compared to the north (11.7% in A) of the country. In mtDNA, sequences of the first hypervariable HpaI site at position 3592 allowed Krings et al. ([1999]) to designate each mtDNA as being of northern or southern affiliation, and proportions of northern and southern mtDNA differed significantly between Egypt, Nubia, and the Southern Sudan.

It is interesting to relate this peculiar north/south differentiation, a pattern of genetic variation deriving from the two uniparentally inherited genetic systems (mtDNA and Y chromosome), to specific historic events. Since the beginning of Egyptian history (3200-3100 B.C.), the legendary king Menes united Upper and Lower Egypt. Migration from north to south may coincide with the Pharaonic colonization of Nubia, which occurred initially during the Middle Kingdom (12th Dynasty, 1991-1785 B.C.), and more permanently during the New Kingdom, from the reign of Thotmosis III (1490-1437 B.C.). The main migration from south to north may coincide with the 25th Dynasty (730-655 B.C.), when kings from Napata (in Nubia) conquered Egypt.

Concerning less frequent Y-haplotypes in Egypt, haplotype VIII is characteristic of Semitic populations, originating in the Near East (Lucotte et al., [1993]). For example (Lucotte et al., [1996]), the frequency of haplotype VIII is 26.2% among North African Jews (where it represents the majority haplotype) and 77.5% among Jews from the island of Djerba (Tunisia), reaching 85.1% among Oriental (from Iraq, Iran, and Syria) Jews. Similarly, haplotype VII had a general geographical distribution fairly identical to that of haplotype VIII (which it often accompanies as a secondary haplotype); haplotype VII distinguishes itself by increased preponderance north of the Mediterranean and in Eastern Europe (Lucotte et al., [1996]). Haplotype XV is the most widespread Y-haplotype in Western Europe (Lucotte and Hazout, [1996]), where its frequency decreases from west to east (Semino et al., [1996]; Lucotte and Loirat, [1999]). Haplotypes VIII, VII, and XV are less common haplotypes in Egypt (7.3%, 6.6%, and 5.5%, respectively), and tend to be located in the north of the country, near the Mediterranean coast. Possibly haplotypes VIII, VII, and XV represent, respectively, Near East, Greek, and Roman influences.

Life would be so much easier if they just put down the recognised name for the haplotypes. Now I’ll actually have to engage my brain. V is M81(68.9% among Moroccan Berbers where it is in the wide majority) and XI is M78.