Mitochondrial DNA and Y-Chromosome Variation in the Caucasus

Mitochondrial DNA and Y-Chromosome Variation in the Caucasus

We have analyzed mtDNA HVI sequences and Y chromosome haplogroups based on 11 binary markers in 371 individuals, from 11 populations in the Caucasus and the neighbouring countries of Turkey and Iran. Y chromosome haplogroup diversity in the Caucasus was almost as high as in Central Asia and the Near East, and significantly higher than in Europe. More than 27% of the variance in Y-haplogroups can be attributed to differences between populations, whereas mtDNA showed much lower heterogeneity between populations (less then 5%), suggesting a strong influence of patrilocal social structure. Several groups from the highland region of the Caucasus exhibited low diversity and high differentiation for either or both genetic systems, reflecting enhanced genetic drift in these small, isolated populations. Overall, the Caucasus groups showed greater similarity with West Asian than with European groups for both genetic systems, although this similarity was much more pronounced for the Y chromosome than for mtDNA, suggesting that male-mediated migrations from West Asia have influenced the genetic structure of Caucasus populations.

An older paper, but one I hadn’t taken a look at.

Unfortunately there isn’t as much detail on the mt DNA.

From one long ago read text, I can remember that one North Caucasus late neolithic site had a tendency to have Mediterranean male crania with the more robust local females. This could support that  population movements into the area from the Iran/Turkey area (birthplace of the Neolithic) may have been male lead, which might give a clue as to how each the Caucasus population has such a heterogenous Y chromosome profile.

Ancient descriptions of ancient Egyptians.

I had a go at this a few years ago, but since then I’ve got better access to the information, so this page should be more comprehensive. This was inspired by reading through the Alain Froment book from a couple of posts ago, that rather ripped Diop a new one. I’ll go and delete the older entry now.

Let me start with the endlessly repeated… ‘Herodotus said the Egyptians had black skin and woolly hair’.

The full quote from Herodotus …

“For the fact is as I soon came to realise myself, and then heard from others later, that the Colchians are obviously Egyptian. When the notion occurred to me,  I asked both the Colchians and the Egyptians about it, and found that the Colchians had better recall of the Egyptians than the Egyptians did of them. Some Egyptians said that they thought the Colchians originated with Sesostris’ army, but I myself guessed their Egyptian origin not only because the Colchians are dark-skinned and curly-haired (which does not count for much by itself , because these features are common in others too) but more importantly because Colchians, Egyptians and Ethiopians are the only peoples in the world who practise circumcision and who have always done so.

Source, The histories By Herodotus, Robin Waterfield, Carolyn Dewald

You will find translations where ‘black skinned and woolly haired’ are used, but the term melanchroes, which was translated to mean black in some versions, was used to describe any skin tone from bronzed to black, and through usage translates as ‘dark’. As is seen in this piece of text from Homer’s Odyssey.

With this, Athena touched him [Odysseus] with her golden wand. A well-washed cloak and a tunic she first of all cast about his breast, and she increased his stature and his youthful bloom. Once more he grew dark of color [melanchroiês], and his cheeks filled out, and dark grew the beard about his chin.

And the term ulotrichous  meant curly. As this Herodotus book commentary points out:

Despite the efforts of Armayor and English, there is no linguistic justification for relating this term to negores. Melanchroes could denote any colour from bronzed to black, and negroes are certainly not the only physical type to show curly hair. These characteristics found in many Egs., ancient and modern, but they are at variance with what we should expect to find amongst the inhabitants of the Caucasus area. To Hippocrates the Phasians of Colchis were sallow (ochros) whilst the complexions of the modern-day Georgian population have been described as fair, sallow or ruddy. On the other hand, Arab geographer Istakhri describes an element of the Khazar people dwelling east of the Caucasus from at least the 6th century AD ” as if they were a kind of Indians.”

The Colchians lived by the South East of the Black sea, and although there have been some attempt to claims this means there were black Africans living in the area of modern-day Georgia, believing this requires a suspension of disbelief on a par with that necessary to watch a Harry Potter film, as there’s never been any evidence a black skinned population living there. So Herodotus didn’t say Egyptians looked like black Africans, he actually said they looked like the people in Georgia.

This is occasionally backed up by the description of Colchis as being a ’second Ethiopia’ from the fourth century, but it has to be remembered that Napoleon once referred to the Spanish as Negroes, and this was a common kind of insulting description  for any population darker than Northern Europeans. A darker, Indian-looking Khazar population would have come into this category. So far there is zero biological evidence  for any black population having lived in the Georgia area.

Herodotus is actually very specific about the Ethiopians (black Africans) getting control of the Nile at Elephantine, and differentiates between them and Egyptians.

After this man the priest enumerate to me from a papyrus the names of other Kings, three hundred and thirty in number; and in all these generations of men eighteen were Ethiopians, one was a woman and the rest were men and of Egyptian race.

Other Ancient Greek and Roman quotes.

The Ethiopians stain the world and depict a race of men steeped in darkness; less sun-burnt are the natives of India; the land of Egypt, flooded by the Nile, darkens bodies more mildly owing to the inundation of its fields: it is a country nearer to us and its moderate climate imparts a medium tone.

 Manilius, Astronomica 4.724

The appearance of the inhabitants is also not very different in India and Ethiopia: the southern Indians are rather more like Ethiopians as they are black to look on, and their hair is black; only they are not so snub-nosed or woolly-haired as the Ethiopians; the northern Indians are most like the Egyptians physically.

 Arrian, Indica 6.9

As for the people of India, those in the south are like the Aethiopians in color, although they are like the rest in respect to countenance and hair (for on account of the humidity of the air their hair does not curl), whereas those in the north are like the Egyptians.

Strabo, Geography 15.1.13

Black people resided not in the Nile valley but in a far land, by the fountain of the sun.

Xenpohanes (Hesoid, works and says, 527-8)

… the men of Egypt are mostly brown and black with a skinny desiccated look.

Ammianus Marcellinus

A little explanation required for this one, the term ‘brown’ means tanned. About 1/3 modern upper Egyptians would certainly have been called black by the Romans.

subfusucli {“somewhat dark/swarthy”)

Ammianus Marcellinus 22.16.23- from Black Athena revisited

 And finally, of lower Nubians:

 It was a market place to which the Ethiopians bring all the products of their country; and the Egyptians in their turn take them all away and bring to the same spot their own wares of equal value, so bartering what they have got for what they have not. Now the inhabitants of the marches (Nubian/Egyptians border) are not yet fully black but are half-breeds in matter of color, for they are partly not so black as the Ethiopians, yet partly more so than the Egyptians.

Flavius Philostratus: c.170 to c.247,

So the evidence suggests Egyptians looked like Georgians and the Pakistanis (formerly Northern India area). Not exactly as surprise, as the DNA and physical evidence supports very little immigration or change in appearance over the past few thousand years in Egypt.

Biological influences on criminal behavior

Really a set of study links for me to reference. It seems that persistent criminal behaviour is strongly hereditary, and a tendence to criminal behavior is a bit more inherited than something learned. So, something to ask about if you are adopting a baby would therefore be ‘what are the parents like? In particular ‘what is the mother like?’ As criminality seems to be even more inherited from the mother’s side from a couple of these studies.

Biological influences on criminal behavior

Criminal behaviour: a psychological approach to explanation and prevention By Clive R. Hollin

Psychopathology and violent crime

Genetic influences in criminal convictions: evidence from an adoption cohort

Criminal behavior

Genetic epidemiological studies

Reading through the studies the general impression is that yes, a tendency to criminal behaviour is hereditary, and that your DNA has more effect on your chances of becoming a criminal than your environment does, particularly for the sort of repeat offender that commits non stop offences their whole life.  Something to think about.

I’m ill again…

Swine flu this time- along with the rest of family. Excuse me not not clearing comments. I’ll get around to it sooner or later.

Y chromosomes are against an African origin for Afro Asiatic.

I used to agree with the old Ehret/Kieta model for the E3b1 Y chr as a marker for Afro Asiatic, but its become apparent that all the population movements into the near East involving this Y chromosome are too ancient to be tacked on to any modern language group. A few months of rolling this idea around, and the DNA evidence and dating seems to support an Asian origin a lot better.

Against an African origin-

The Genetics

Once it  became apparent that Omotic as an Afro Asiatic language was dubious, with it being shown to be a language isolate by several linguists- it turned out all the African Afro Asiatic speakers show Neolithic Y chromosome input from the near East, in some cases overwhelmingly. The main examples for this are the Ouldeme and other Chadic speaking tribes in Cameroon, who have tested as having an outstandingly high percentage of the Y chromosome R1b, a Eurasian Y chromosome that fits the spread of Chadic languages like a glove. As far as I can tell, the ultimate point of origin for this seems to be SE Turkey, which is within the origin area of the agricultural Neolithic expansion. So, most Chadic male ancestry traces back to the origin point of the Neolithic, which is a big supporter of an Asian origin for Afro Asiatic.

Another Y chromosome that shows a population movementthat tracks Afro Asiatic is from the Nile delta – the M81 Y chromosome. The advent of this mutation is extremely close in time to the entry of R1b’s entry into North East Africa, and it appears to have spread out into North Africa with the Neolithic farmers, and also as far as Somalia, where it is found at a very low rate, but just enough to confirm a Neolithic movement from North to South along the Nile.

 

The language and its dates

Mainly my gripes are based on Dr Ehret’s work on AA languages. His inclusion of Omotic as an Afro Asiatic language was always speculative, and now it appears that it shows no more than a chance relationship to the Cushitic languages (Theil). I suspect he was keen to include it as an AA language as it shores up the African origin by providing him a pre agricultural Afro Asiatic language in East Africa- which now seems to be wishful thinking on Ehrets part.

Looking at Dr Ehret’s dates for the Afro Asiatic group, one major flaw leaps out. He dates proto Cushitic at 10,000 BP, which he describes as an African pastoralist language with goats and sheep. This is impossible, as goats and sheep do not enter Africa until 2,000 years after this date.  If it were correct as a date, this would locate proto Cushitic in the North of the Levant. Assuming that the Cushitic branch is native to East Africa, the arrival of ovicaprines to the area is first known about 5,500 BP in the Sudan. Assuming that the Cushitic branch moved along the coastal areas ( the joining dialects between Egypt and East Africa later wiped out by Asian Semitic languages, and a Nilo Saharan block to them in Nubia), a date of about 6,000 BP for the separation of Cushitic in East Africa would be more likely. This casts major doubt on Ehret’s dating methods for all his work, and really casts a big shadow over his dating of technologies by dating the proto language (the basis of most of his claims for early pastoralism in Africa). This would probably mean Nilo Saharan was the indigenous language group of East Africa prior to the Neolithic.

The dates for proto Cushitic mean his 14,000 BP date for proto Erythraic (ditching the older 15k date for PAA as the Omotic Branch is now defunct) corrects to 10,000 BP assuming his rate of miscalculation is stable at 40%. As a minor note, I’ve seen text books place a maximum date of 10k for any language family, which makes me query Ehret’s work on dates for yet another reason. This 10k age limit would also support all his dates being 40% too old, which would also re-date Cushitic to about 6,000 BP- which agrees with my own estimation.

All the known population movements in this 10k time frame are into  Africa, matching the expansion of the Neolithic, which also matches the expansion of the Y chromosomes R1b and M81 in Africa. There’s no known cultural expansion out of Africa  that could fit this time frame or  movements of African Y chromosomes/mt DNA dated to this era in the near East.

The ancient presence of Semitic in Asia.

Then there is the proximity of Semitic and proto Indo European languages. Numerous agricultural terms turn up in PIE, words for barley, bull etc, that are all suggestive of the Semitic family being present close to the origin point of IE languages when they adopted farming (I’m not ignoring that they may possibly have had the same root dialect at one time). After reconciling the ‘Turkish’ and ‘North of the  Black sea’ origins for proto Indo European (the older IE languages seem to be Anatolian, the last node was ‘Kurgan’) this would place Semitic in contact with older PIE dialects around 9,000 BP. Bearing in mind the age for PAA is needs to be about 10,000 BP for at least two good reasons, this is also not supportive of an African origin for Afro Asiatic.

Theorised tree for Afro Asiatic (my fifth revision)…

The population movements suggest to me that the African AA languages all came from a common tongue at the Nile delta, and then split up from each other and differentiated very quickly as the pastoralist groups moved away more swiftly than the farmers. This might explain why proto Afro Asiatic has been such a bugger to reconstruct; it’s right on the maximum age, and some of the root words for crops and farming implements etc could have been lost by the rapidly moving pastoralist groups who never grew crops.

The main reason I’ve focused on the R1b is the ’sore thumbness’ of its presence in central/West Africa, and the M81 because of its Neolithic age and Egyptian place of origin. I’ve steered clear of the J1 and J2 Y chromosomes in this entry, as at present it isn’t very clear what entered East And North Africa in the Capsian, what with the Neolithic and what with the Arabs. J seems to have arrived in  Africa in three waves. Really it needs an in-depth going over by a specialist study to untangle it, but some papers do discuss J arriving into Africa with the Neolithic, and it is seen in East Africa as far as Somalia, so it’s not impossible one minor J hg also matches the distribution of AA languages in Africa too.

My main objections to a recent out of Africa date.

Also known as the ‘I’m not typing this out in the comments anymore‘ entry. I keep seeing the 40k for the out of Africa date in print, and it’s starting to get on my nerves just a bit. Some of sites these don’t have bones, but modern human associated industries. This is not including any sites in or South of the Sahara.

I’ll start with the oldest first.

Skhul, Israel.

Dates ranging from 130,000 -100,000 BP on assorted remains.  The crania shown is Skhul V, roughly dated to 105,000 BP. Many archaic traits, but anatomically modern humans. The in theory is that the 130,000  year old colonisation of Asia failed due to climate conditions, although it didn’t seem to bother the Neanderthals in the area. There’s a gap in the record from 92,000 BP to about 45,000 BP, which only has Neanderthal remains (so far).

Qafzeh, Israel

Modern human remains about 92,000 BP. The best known is of a 12 year old boy.

Jebel Irhoud, Morocco.

Estimated dates range from 160,000 to 90,000 BP. More modern humans with archaic traits-so archaic they were mistaken for Neanderthals for years.

Frontal view of cast of adult male Homo sapiens from Jebel Irhoud in Morocco. Link.

 

Taforalt, Morocco.

Aterian shell beads  found dated from 110,000 BP to 82,000 BP. The Aterian was continuous in North Africa until the Dabban and IberoMaurassian industries 40,000 and 20,000 BP.

Henan province, China.

Modern human teeth dated to around 94,000 BP, and the Xuchang/ Liujiang skull dated to at least 68,000 BP and possibly as old as 159,000 BP.

Pdf.

 

 Nauwalabila I, Australia.

 Oldest thermoluminescence date of 60,300+6,700 years on stone tools .

Malakunanja II, Australia.

Thermoluminescence dates of prior to 50,000 BP. There’s also a claimed but very poorly provenenced date of 116k in a site in Kimberly.

Topper site, S. Carolina, USA.

Site dated  ~50,000 BP with C14.

Pedra Furada, Brazil.

Oldest date for site occupation 60,000 BP ,according to the archaeologist.

Kota Tampan, Malaysia.

Pebble tools associated with modern humans dating back to 75,000 BP. The pebble tools were found in a later burial with a modern human (Perak man).

Niah Cave, Borneo.

Skull dated to 40,000 to 42,000 BP.

Üçağızlı Cave, Turkey

EUP site about 43,000 BP.

Ksar ‘Akil, Lebanon.

EUP site dated to 45,000 BP

 And Dr Stephen Oppenheimer has worked out it woukd take about 20,000 years for modern humans to work their way into Australia from Africa. so add that on to any Australian and American sites for a minimum OOA date.

There are probably a few I’ve missed. Some of the Indian sites under the Toba ash are claimed as modern human sites, but there’s a lack of bones so I won’t include those, although I suspect they are right. Some are on this pdf, with more detail from this paper, Modern Human Origins and the Evolution of Behavior in the Later Pleistocene Record of South Asia. From this a few snippets..

A number of mtDNA lineages (specifically U2i, M2,and R5) share coalescence dates of 50,000–70,000 yearsago (Kivisild et al. 2000, Metspalu et al. 2004) and may represent an India-specific subcladerelated to the initial dispersal of modern humans into the peninsula.

A Middle Paleolithic scraper-based industry from Patpara in the Middle Son Valley is dated to~103,000 years ago (Blumenschine, Brandt, and Clark 1983, Williams and Clarke1995), while dates of 75,000 and160,000 years ago areassociated with artifacts recovered from Samnapur (Nar-mada Valley) and Balotra (Luni River valley) (Mishra etal. 1999, Misra et al. 1990). The dating of miolites in the Hiran Valley places assemblages classed as Middle Paleolithic at 69,000–56,000 years ago (Baskaran et al.1986). The earliest assemblage classified as Upper Paleolithic is currently Site 55, Pakistan, where the loess overlying the occupational horizon has been dated to ca 45,000 years before present(Dennell et al. 1992).

One of my main objections to a more recent OOA date is that it doesn’t make sense with the dates of the backmigration mt DNA into Africa and the mt DNA in early Europeans. In a nutshell, there was a back migration of mt U and M1 from Asia, which appears to have been accompanied by Y chromosome R1, somewhere from 40,000 to 35,000 BP- supported by stone tool cultures and later dates of mt DNA in the same area matching the cultural epxansions. The problem with a more recent OOA date is that you have to skip impossibly quickly from L3 to U if the exit date is around the 40,000 mark. The same is true for the migrations into Europe where much later haplotypes are found relatively quickly in time and it just wouldn’t allow enough time to get from L3 to pre HV. There’s also not enough time for Y chromosome R1 to appear with the more recent OOA dates. The estimated dates on the mt DNA make a lot more sense when compared to an OOA date of 100k, and the Y chromosome date estimates are starting to get old enough to be an acceptable match. Which is why I’m taking the side that supports humans being on the other side of Asia when the Toba eruption occurred.

I’m in good company at least. Cavalli Sforza’s estimated date for the separation of African and non African populations was 146,000 BP.

The first estimate gave a separation time of the first migrants out of Africa of 146,000 years ago

I’ve seen at one other paper where the date was 120,ooo. My guess would be that modern humans were inhabiting North Africa and particularly the Nile delta (which as far as I know never dried out) for a while before a move into Asia was made. The structure of this Aterian population was wiped out by the later backmigrations from West Asia, and no North African mt DNA dates back prior to this era.

And now I have an evil headache. I’ll have a better look at the Petraglia pdf later…

Y chromosome J quick reference page

My blogging lately has been slowed down by my MS flaring up and my boy discovering Lego Indiana Jones online – my  apologies to anyone I haven’t responded to in the comments.

A basic page for reference on J1 and J2 so I don’t have to root through multiple papers and blog entries every time I want to find something.

This is a homemade table and mainly from Cruciani’s 2004 figures and Hassan 2008  for a one-glace overview . The Egyptian figures are my own from several combined sources and are about as accurate as you’ll get for that country. The other countries are from single paper sources and probably aren’t as accurate overall, but it’s a decent rough guide.

The actual Cruciani table, another chart (can’t remember which paper).

 

From Giacomo 2004 and Battaglia 2008

 

 

   

Greece, From Martinez 2007. Turkey; Cinnioglu 2003 and  Semino 2002.

    

Iran, from Cadenas 2006, from Al-Zahery 2002 and Luis 2004

From Giacomo 2004

 

While not the neatest page, it should be useful for quicker referencing. A good look through the J hg’s around the near East has reinforced a Neolithic or older entry date for the J2 in North Africa as far as I’m concerned, as the ratio of J2 to J1/other hg’s is incompatible with it having a historical arrival from any of the known invading areas. I’m also wondering if upper Egypt is the switch over  area from Arab J1 to Capsian J1.

Reference list.

• Semino 2002
• Al-Zahery 2002
• Cinnioglu 2003
• Cruciani 2004
• Giacomo 2004
• Luis 2004
• Cadenas 2006
• Battaglia 2008
• Hassan 2008

If anyone else finds a Y chromosome J reference for the near East, Europe, North Africa or India/Pakistan that I haven’t included leave the name of the paper ( I expect there’s a few) in the comments, as I’ll be adding to this one as I go along. Also a decent recent tree of J would be nice – if anyone find one send me a link!

Y chromosome J’s tangled past in Africa.

Just something I’ve done to help me get a better grip of the history of the Y chromosome’s presence in North Africa. Firstly, I need the J tree and it’s distribution from Cruciani 2004.

And some more detailed information on the distribution in the places relevant. Most important to this are J-m267 /J1, (typical of Arabs and common in East Africa) and J-m172/ J2, (which maps the expansion of the Neolithic into Europe and apparently into Pakistan (J2e) and North Africa).

J1 is typically seen as the marker for the Arab tribes expanding into North Africa, and this accounts for somewhat more than half of the J in North Africa. However, the J1 in East Africa is lacking a alteration in the historical-Arab specific Y chromosomes, and the latest paper I have seen dates the entry of this to Africa at the Iberomaurusian-Capsian- (pre neolithic) transition-or possibly a little later- which would require an entry date about  of about 12k ago.

Cruciani’s Bedouin sample was free of  J2 - as you can see from the maps there seems to be a break in it’s distribution pattern. A look at Italy and Greece (looking for other possible source of J possibly from the Romans and Greeks) showed it at levels low enough that for the Greek and Romans to have made any impact on the J Y chr of North Africa they would had to have left way more European specific haplotypes (the highest J observed in Italy is 29%, overall it’s a lot lower) and the same is true for other middle Eastern countries- to have added any extra J2 into North Africa a lot of other non-J Y chromosomes would have to have accompanied it. The North African Y chromosomes (Lower Egypt as the prime example)  just aren’t that varied and mainly show ‘ancient in Africa’ Eurasian and African specific Y chromosomes, with J making up most of the difference, which makes Europe and the recent near East as a source for the J2 unlikely. 

The distribution of J2 and J1 in North and East Africa, and whatever near Arabian populations I can find.

From Cruciani 2004

Egyptian

From Luis 2004 in Lower Egypt and Oman.

• Egyptian Arabs… J1 20%   J2 12%
• Oman Arabs…..    J1  38%   J2 10%

From Lucotte 2003

• Lower Egypt…. J1  10.5%  J2  8.6%
• Upper Egypt….  J1  3%        J2  4.5%

From Arredi 2004

• Lower Egypt… J1  9%,  J2 9%
• Upper Egypt     J1  21% J2 3.5%

I’m omitting the other studies I have on file as they don’t differentiate between the two, or lack clarity on which is which.

As the other studies are either a bit vague or very small I stick to these. The average amount of J for lower Egypt seems to be 25% (average of 5 studies) with about 10% being J2. Bearing in mind about 10% of the North African J1` is pre Neolithic, about 13.5% of the Egyptian Y chr are ‘Arab’ J1-possibly. J2 from the recent Arab expansion into North Africa probably does contribute to the J2 in NE Africa, but not in the main. The argument against this is that J2 is a minority in the Palestinian Arabs and Bedoiuns , and that to get J2 up to the levels you find in Egypt you’d need to have a lot more J1 and other Eurasian male ancestry- which would make the other African/ancient EurAfrican types way less more common. J2 is also common in Persia (who also invaded Egypt), but again it isn’t dominant and you would have to expect large amounts of other Y chromosomes to have accompanied it, which has not been observed (same argument against a European origin for Egyptian J2).

If the J2 had come in with the Arabs you’d expect a very obvious overweight of J1 in the ratio-as in the Sudan. It’s not even clear if the J1 there is all ‘Arab’ in origin, as the most of the J1 in East Africa is the pre Arabic J1- which makes Hassan’s 2008 choice of description as ‘Arabic’ for all the J1 in the Sudan a little confusing. As Cruciani wrote..

According to this interpretation, the first migration, probably in Neolithic times, brought J-M267 to Ethiopia

Although, I have to say; Hassan’s calling the Sudan Copts a living record of the Egyptians is strange considering how low they were on African Y chromosomes- particularly the Egyptian m78; and that 13 of 33 samples were J1.

While large scale historic movement of Arabic tribes into the Sudan is well documented, a lot of J1 is showing up in groups like the Nubians. When you bear in mind Arab culture is very patriarchal, I can’t understand how the non-Arab groups in the Sudan seem to have about the same amount of J1 as the Arab tribes in the Hassan study. Did more Arabs move into the Sudan than North Africa or is the recent and ancient J1 just getting lumped together in these studies?

I’m sure I’ll add to this post after my regulars have corrected/added whatever info they feel is necessary, but I think mainly but not entirely the J2 in North East Africa is a result of the Neolithic expansion, as it does seem to form a neat radial pattern from Turkey/Iran which is seems to track along with the R1b/p25, which also seems to be Turkish/Iranian.

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.

Gurna

• 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

Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup

Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup

Chad Basin, lying within the bidirectional corridor of African Sahel, is one of the most populated places in Sub-Saharan Africa today. The origin of its settlement appears connected with Holocene climatic ameliorations (aquatic resources) that started ~10,000 years before present (YBP). Although both Nilo-Saharan and Niger-Congo language families are encountered here, the most diversified group is the Chadic branch belonging to the Afro-Asiatic language phylum. In this article, we investigate the proposed ancient migration of Chadic pastoralists from Eastern Africa based on linguistic data and test for genetic traces of this migration in extant Chadic speaking populations.

Results
We performed whole mitochondrial genome sequencing of 16 L3f haplotypes, focused on clade L3f3 that occurs almost exclusively in Chadic speaking people living in the Chad Basin. These data supported the reconstruction of a L3f phylogenetic tree and calculation of times to the most recent common ancestor for all internal clades. A date ~8,000 YBP was estimated for the L3f3 sub-haplogroup, which is in good agreement with the supposed migration of Chadic speaking pastoralists and their linguistic differentiation from other Afro-Asiatic groups of East Africa. As a whole, the Afro-Asiatic language family presents low population structure, as 92.4% of mtDNA variation is found within populations and only 3.4% of variation can be attributed to diversity among language branches. The Chadic speaking populations form a relatively homogenous cluster, exhibiting lower diversification than the other Afro-Asiatic branches (Berber, Semitic and Cushitic).

Conclusions
The results of our study support an East African origin of mitochondrial L3f3 clade that is present almost exclusively within Chadic speaking people living in Chad Basin. Whole genome sequence-based dates show that the ancestral haplogroup L3f must have emerged soon after the Out-of-Africa migration (around 57,100 ± 9,400 YBP), but the “Chadic” L3f3 clade has much less internal variation, suggesting an expansion during the Holocene period about 8,000 ± 2,500 YBP. This time period in the Chad Basin is known to have been particularly favourable for the expansion of pastoralists coming from northeastern Africa, as suggested by archaeological, linguistic and climatic data.

Thank you for posting this Igbo. I do feel obliged to point out an impossibility in the text..

According to linguistic analyses of Afro-Asiatic branches, the common ancestors of extant Chadic and Cushitic peoples inhabited East or Northeast Africa ~7,000-8,000 years before present

Because for various reasons to do with goats and sheep there’s no way Cushitic is older than 5,500 BP. The evidence does speak to Chadic being a younger arrival in the area. Is the R1b associated with it from the North?

Another interesting observation (I’ve being trying to get hold of come Chadic Mt DNA) is the amount of L3 in the area. I suspect these are the surviving remnants of the North African L3 branches that got wiped out by the Eurasian back migrations across the Maghreb about 30-35k ago. I shall have another read of this later when my kids aren’t bugging me so much. Sigh.