Modern Egypt's genetic history

[Dawn2Earth]

This is a scientific thread about any and all lineages now found in the A.R.E. (Arab Republic of Egypt) according to evidence via genetic studies, where they originate and when they seem to have come there and how well (or poorly) this fits in with climatic evidence, documented history, etc. Primarily it's genetic though. In short it's about the any migratory history Egypt's genes reveal.

Mitochondrial DNA (MtDNA), Autosomal, all types of genetic evidence is welcome as a backdrop to and with a bias towards NRY Chromosomal lineages on the basis that paternal lineages are assumed to be founder lineages for the migrant population when they are considered with the native maternal. This isn't a geo-polemical thread about "Africa" (v.s. everywhere else), white v.s. black ethnonyms v.s. mixed "races", Afro-Americans & 'ancient egypt' or any uh that jive-talk. Just the raw genetic markers optionally buttressed with climato-archaeological and documented historical perspectives.

Now, i may need to be updated or refreshed, but as i have it A.R. Egypt's two most common Y-chromosomal haplogroups are Hgs E & J. The J, mostly M267 and the E, for the greater part E-M78. This parent post will mainly deal with Haplogroups E & J and set the stage for discussion of other haps.

*

Major E: E1b-M78

E-M78 likely spreads out North and East from a Nile "Refugium near Lake Nasser" in Sudan 10.5 k years ago at the onset of a humid phase, its Northward-moving rainfall belts, and the Sahara desert's disappearance. This had happand following a hyper-arid phase for the Sahara desert in which it was even larger than it is now and during which it witnessed a complete hiatus of Sahelian human habitation. After the spread, when the Sahara began to re-emerge this population would have moved South. This lineage is pretty common in general in Sudan, Sudanese groups that are not far South today like the Beja of the East and the Fur (of Dar Fur) in the West have this lineages at exceptionally high frequencies:

Haplogroup E-M78, however, is more widely distributed and is thought to have an origin in eastern African. More recently, this haplogroup has been carefully dissected and was found to depict several well-established subclades with defined geographical clustering (Cruciani et al., 2006,2007). Although this haplogroup is common to most Sudanese populations, it has exceptionally high frequency among populations like those of western Sudan (particularly Darfur) and the Beja in eastern Sudan."

- Hassan et. al. 2008, Y-Chromosome Variation Among Sudanese: Restricted Gene Flow, Concordance With Language, Geography, and History

So the M78 is a pre-Pharaonic Nile River Valley lineage. It exists in the primarily Sudanese Beja and also in Kenyan Borana so I wouldn't be surprised to find out it exists in Ethiopian Afar as well. What i wrote specifically above is based on Battaglia et. al. 2008 and the referenced Hassan et. al. 2008 study.

*

Major J: J1-M267

This may not sound very scholarly but according to this map i saw Hg J's highest frequencies seem to be in the South Levantine region just outside of Africa. The majority of Haplogroup J in Africa is J1-M267. The majority of J in greater North Africa according to the below study is of a single motif which is attributed to 7th Century Islamic era Arab expansion from the Arabian peninsula rather than a Neolithic origin such as in Ethiopia.

These results are consistent with the proposal that this haplotype was diffused in recent time by Arabs who, mainly from the 7th century a.d., expanded to northern Africa (Nebel et al. 2002).

- Semino et. al. 2004, Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area

Though the story with J1 (a.k.a. M267) varies by region, in Africa J-M172 (aka J2) is as far as I'm aware uniformly indicative of recent & historic admixture as opposed to being an ancient lineage there. Instead of M172, however, the majority of Hg J lineages in Africa are M267. As Semino et. al. write above, citing Nebel et. al. 2002, J1 in North Africa and the Southern Levant is generally attributed to Arab migrations. I will go more into M267 in another post. The Levant has quite a high frequency and diversity of Hg J lineages in general, here is how Levantines look.

***

I will divulge on Hg J* in general later, and definitely on E1b-M78's (&V68's) ancestor M35 later.

Paternal lineages that folks may not know much about in terms of spread that I will explain include:

Hg J2 which in Africa is almost always indicative of recent / historic admixture.

Another is R-M173 which is archaic and found sporadically, including in Sudanese Fulani who likely come from somewhere around Cameroon.

Another is E1b1a1*-M2 which seems today to emanate from Sahelian West Africa and is the predominant West African and African American lineage -- this one's easily explainable as there was a lot of bidirectional movement during the Middle Ages including Mansa Musa's epic entourage Hajj to Mecca, Mali's generous gesture of recruiting of an Egyptian architect, Muslims, Arabs, Turkish and African slave routes, etc., but there appears to be more to the story than any of those stories recount as is for some reason often suggested and alluded to by many a study, but never divulged. Until now. Well, sorta, ;D in another post anyway.

[Dawn2Earth]

I'd decided to start this thread because i'd noticed [this pattern in evidence from the vast majority of morphology related studies] on ancient Kemetians, which all seem to agree in large part, and aim to make it easier to juxtapose and maybe reconsile these with the another type of hard evidence, perhaps the hardest of all: genetic evidence.

[Dawn2Earth]

Comparable Populations

---

In this quote below and anywhere else in the study where they mention "Egypt" they are referring to 63 samples from the impressive city of Cairo in Lower Egypt - a city over a millenium old coming into being in the early centuries C.E. (current era) - and which houses Africa's largest urban population today.

The Levant versus the Horn of Africa: Evidence for Bidirectional Corridors
of Human Migrations (click here for pdf), J. R. Luis et. al. 2004

"For group E, we observe a geographic gradient from
west to east as well as a partitioning from south to north.
The sample collections from the western sub-Saharan
populations (Benin and Bamileke) are represented exclusively
by group E, whereas the frequencies of these
chromosomes are somewhat lower in the east (94.2%,
85.1%, 81.4%, and 82.8% for the Hutu, the Tutsi, Tanzania,
and Kenya, respectively) and drop sharply in the
northern-most populations of Egypt (39.5%) and Oman
(23.1%)."

[...]

"The microsatellite results for Egyptian and Omani
samples are given in table 3. The variance, continuous
expansion, and median BATWING values of the Egyptian
M35 lineages are considerably larger than those of
Oman. This is also true for K2-M70. However, for either
the collective J-12f2 or J*-12f2, the disparity is not so
large. The expansion times of collective E3b-M35 lineages
of the Egyptian sample are substantially older than
those of the J-12f2, whereas, in Oman, the order is reversed.
On the average, the median BATWING values
based on the 30-year generation time are 20% greater
than those calculated using a generation interval of 25
years."

[...]

"The NRY composition of the Egyptian and Omani
collections exhibits a greater Middle Eastern versus sub-
Saharan affinity. The cumulative frequency of typical
sub-Saharan lineages is
9% in Egypt and 10% in Oman, whereas the haplogroups
of Eurasian origin account
for 59% and 77%, respectively. These profiles
display levels of diversity similar to those of the nine
Turkish populations reported by Cinniog¢ lu et al. (2004)
(an average of 9 groups and 19 haplogroups per population)
and also include polymorphic frequencies of
many of the lineages observed in Turkey (i.e., E3b1-
M78, Eb3-M123, G-M201, the collective J-12f2, J2-
M172, and R1a1-M17). Many of these haplogroups are
common throughout the Middle East and Europe as
well, and several are thought to have arisen somewhere
within this range (Underhill et al. 2001b).

A different study, immediate below, says similar things. Though I didn't check out the sample, it seemed like each was comprehensive:

"Within the plot, the populations of Egypt, Iraq, Yemen, Qatar, Oman, UAE, Syria and Lebanon occupy an intermediate position with populations from Africa to one side and Anatolia, Caucasus, Iranian Plateau, Central Asia and South Asia on the other. Of note, for the observed partitioning is the affinity of Egypt to populations from the Arabian Peninsula. Furthermore, Yemen and Qatar segregate together but separate from their neighboring populations, Oman and UAE particularly along Dimension 2. As expected, the populations from Central Asia group together and away from the South Asian ones, however, there is a segregation of North Pakistan with populations from Central Asia, whereas South Pakistan shares a closer affinity to populations to the west."

[url=http://www.nature.com/ejhg/journal/v16/n3/full/​5201934a.html
]Y-chromosome Diversity Characterizes the Gulf of the Oman (click for full study)[/url],
Alicia M. Cadenas et. al. 2007

More and more though i'm intrigued by Hg J's complex picture. J-12f2 is similar in Egypt and the Oman, but is much older in the Oman whereas E1-M35 is much older in Egypt. Based on a number of studies' tracking of J1-M267 which is common in Southern Arabia a motif that makes up like 70% of Arabia's and 90 % of North Africa's M267 is associated with recent migration like the 7th Century A.D. expansion of Arabs. However J1-M267 its self underwent much older Neolithic expansions in Ethiopia and South Eastern Europe where it is much more diverse, though very rare in the latter (S. E. Europe).

Back to Semino et. al. 2004:

"The E3b1-M78 and E3b3-M123 lineages, as well as the R1*-M173 lineages, mark gene
flow between Egypt and the Levant during the Upper Paleolithic and Mesolithic.

...

The areal diffusion patterns of G-M201 and J-12f2 suggest more recent genetic associations between the Middle East and Africa, involving the Levantine corridor
and/or Arab slave routes."

These, G & J, are common in West Asia and I would say are pretty much Eurasian.

[Dawn2Earth]

On M267 (J1*), in Ethiopia (the below study) only a very minority of J is recent, and the recent stuff is mostly M172 which constitutes like 2% in this study, and this is a study including mixed groups. At any rate this mentions the Amhara, which are of known mixed ancestry including of various Ethio- ethnies:

"Haplogroup J, characterized by the mutation 12f2.1,has been found at a frequency of approximately 18% in Ethiopians, with a relatively higher prevalence among the Amhara, where it has been found to exist at levels as high as 35% , of which about 33% is of the type J-M267, almost all of which was acquired during Neolithic times or earlier, while 2% is of the derived J-M172 type representing admixture due to recent and historic migrations."

- Semino O, Magri C, Benuzzi G, et al. 2004, Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area American Journal of Human Genetics 74 (5): 1023–34. doi:10.1086/386295. PMID 15069642

However J1 may ultimately be Ethiopian / East African.

Basal J1* a.k.a. "the .2 variant" is described as such below:

"We recently found a number of intermediate DYS458 alleles, indicated as .2. This allelic variant is distributed in several populations, but currently no information is available regarding the molecular structure and the genealogical correlation of chromosomes with this variant. The molecular characterisation of such allele, its worldwide distribution and the correlated evolutionary history are the subject of the present paper. Molecular and genealogical data are suggestive of a single origin for the .2 variant. Phylogeographic analysis points to either a Middle East or East African origin, but additional data is necessary to clarify this point. Our results suggest that the .2 variants is a stable polymorphism and that it could be used for population studies

...

Initial SNPs analysis identified these chromosomes as derived at the M267 markers, placing them on the J1* cluster. J1 sub lineages were additionally tested (J1a–e) and in all cases the .2 chromosomes resulted ancestral at these additional markers. The DYS458 .2 Y chromosomes were then consequently identified as part of the J1 branch (Fig. 1).

...

The .2 variant shows its frequency peaks in Africa (North and East) and Caucasus. Data from the middle East is scanty and we are currently investigating various populations from this region to gather more information on the distribution in this area (data not shown). The presence in Europe is limited and the occurrences in both US and Asia (India and Malaysia) can be
considered as the result of a recent introgression of African and/ or European haplotypes. Given the current set of data it is difficult to establish the ultimate place of origin of such mutation. However, the limited genetic diversity shown by either the Caucasus and North Africa suggest a combination of drift and founder effect (followed by rapid population expansion) in these areas."

- Ferri et. al. 2008, Molecular characterisation and population genetics of the
DYS458 .2 allelic variant

Notably according to the above study it is not very diverse in the Caucasus or North Africa.

According to a general study on the haplogroup, immediately below, it's more diverse in Ethiopia and "South East Europe" where it arrives in Neolithic times, compared to in the Middle East and North Africa which, due to low diversity especially in North Africa, they attribute to being due to recent expansion (they said Arab expansion in the 7th Century). It's rare in Europe according to this study.

The lower internal
variance of J-M267 in theMiddle East and North Africa,
relative to Europe and Ethiopia, is suggestive of two different
migrations. In the absence of additional binary
polymorphisms allowing further informative subdivision
of J-M267, the YCAII microsatellite system provides important
insights. The majority of J-M267 Y chromosomes
harbor the single-banded motif YCAIIa22-YCAIIb22
in the Middle East (>70%) and in North Africa
(>90%), whereas this association is much less frequent
in Ethiopia and only sporadically found in southern
Europe.

...

According to this interpretation, the first migration,
probably in Neolithic times, brought J-M267 to Ethiopia
and Europe, whereas a second, more-recent migration
diffused the clade harboring the microsatellite motif
YCAIIa22-YCAIIb22 in the southern part of theMiddle
East and in North Africa.

...

These results are consistent with the
proposal that this haplotype was diffused in recent time
by Arabs who, mainly from the 7th century A.D., expanded
to northern Africa (Nebel et al. 2002).

- Semino et. al. 2004

According to another study, in the Middle East, M267 (aka J1) in general has a much older expansion time in Turkey than in Egypt. It's most common however in Arabia (the Southern Middle East) and North Africa, most of which appears to be due to recent expansion (usually attributed to 7th Century Arabs).

Based on binary and STR markers, the greatest degree of differentiation for J1-M267 is detected in the Levant with two distinct demographic dispersals generating its current distribution. A higher observed STR diversity of this clade among Europeans and Ethiopians in comparison to populations of North Africa points to its arrival to Ethiopia and Europe during Neolithic times with a more recent appearance in the latter.58 Semino et al58 describe a YCAIIa22-YCAIIb22 motif in the North African (>90%) and Middle Eastern (>70%) J1-M267 representatives that is less frequent in Ethiopia and Europe, postulating that the dispersal of the M267-YCAIIa22-YCAIIb22 clade occurred during the Arab expansion in the seventh century A.D.

- Cadenas et. al. 2007

Interestingly: probably because Turkish J1, though rarer (like 9%, compared with 35%-73% going West to East in Arabia, with even Oman having 38%), is dated to be by far the oldest in this study (and if I recall correctly the age is much older than its nearest competitor Yemen and even twice as old as its second nearest competitor Qatar) and probably also because of its diversity in the Levant, it was said verbatim the "data suggests expansion from the north".

---

Check this out though:

Haplogroup J*

Around 14% of the Saudi Arabia Ychromosome
pool is typical of African biogeographic ancestry, 17% arrived to
the area from the East across Iran, while the remainder 69% could be
considered of direct or indirect Levantine ascription. Interestingly, basal E-M96*
(n=2) and J-M304* (n=3) lineages have been detected, for the first time, in the
Arabian Peninsula. Coalescence time for the most prominent J1-M267
haplogroup in Saudi Arabia (11.6 ± 1.9 ky) is similar to that obtained previously
for Yemen (11.3 ± 2) but significantly older that those estimated for Qatar (7.3 ±
1.8) and UAE (6.8 ± 1.5).

It's rare and scattered, notably having been found in the highest percentages that I know of, in an Island quite a ways South of Arabia. (Also, I know there's a theme of migration from the North in Arabia, but "69% Levantine"?)

In any case, by far the highest percentages of "J*" lineages have been found in the Island of Socotra, (which is why I posted the above picture of kids from there) which is South of Arabia (even Yemen may only reach this latitude at its very Southernmost end) and around Central Sudan, Ethiopia, and Northern Somalia. Though, all I can find at the moment are various random quotes on the internet, including Wikipedia, attributed to:

Out of Arabia—The settlement of Island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity, Černý et al. 2008.

And guess what they say in the abstract?:

Recent expansion of the novel lineages is consistent with a Holocene settlement of the island ∼6 kya.

[/i][/color]

*And* they hardly found any African lineages (which, they really may have found ones with undetermined origins). Which would imply what both the original inhabitants of that island and carriers of J* may have looked like, how the "darker skinned" prehistoric folk at the dawn of history may have looked.

---

All in all, I'd have to say there is a theme in Africa of J2 indicating recent admixture, but for J1 the picture appears more complex. This lineage has been around quite a few places and may many times just indicate native inhabitants' remnants of genes that've been there since the Neolithic (or possibly pre-Neolithic in Ethiopia and Turkey's case) and so would likely have gotten absorbed / heavily admixed into the Native population.

The Arab Republic of Egypt's Hg J paternal ancestry is certainly part recent / historic, but since M267 is so old and pre-Neolithic lineages are found to both its South and North, it could have some prehistoric J as well.

I highly doubt by the way that M267 comes from either Europe or the Caucasus (due to low frequency and lower diversity than elsewhere), which I don't think was ever implied, but patterns in the Southern Levant do suggest it might have come from there, so anywhere between there (general region) and Ethiopia is an adequate candidate.

Oh, and one more thing: interestingly, an Abu-Amero et. al. 2009 study on Arabia also date this lineage to the Mesolithic in at least Saudi Arabia and Yemen: it finds a higher diversity and proposes an older age for this lineage in Saudi Arabia and Yemen than in Qatar, the United Arab Emirates and the Oman which if you look on a map shows an early Western orientation. I will post a link to the Arabian study in the next post which is on the West African lineages in the region.

[Dawn2Earth]

dubs

[Dawn2Earth]

This first study is Mitochondrial (that's mtDNA) and doesn't mention M2, it just serves as a prelude to what follows:

Global male inputs from Sub-Saharan Africa and Asia across Iran, not the Levant, into the Arabian Peninsula have been estimated in this study, as 13.4% and 16.6% from both source areas respectively. Recent mtDNA studies on the same Arabian Peninsula countries [7-9,12] have confirmed a notable female-driven sub-Saharan African input with a mean value around 15% for all the Peninsula, although frequencies as high as 60% have been detected in Hadramawt populations of Yemen [9]. Curiously, the Iranian female flow (18%) was also rather similar to that calculated for Africa. Although a slight ratio excess of Sub-Saharan African female versus male gene flow is detected (1.12) we do not found the strong sexual bias proposed by other authors for Arabian populations and attributed to the peculiarities of the recent slave-trade [12,36]. Without dismissing the role mediated by slavery, the geographical distribution of these sub-Saharan African lineages in the Arabian Peninsula seems to indicate a prehistoric entrance of a noticeable portion of these lineages that participated in the building of the primitive Arabian population [8,9].

- Khaled K Abu Amero et. al. 2009, Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions[/color]

***

Thoughts about the comedic effect politics may play in all these studies aside:

Them saying that a portion of this African gene-flow, even being maternal, is prehistoric and not due to the recent African slave trade is significant, because as interesting as that would be, they're not the only ones to say so.

Another study suggests the same, only for paternal lineages:

Y-chromosome diversity characterizes the Gulf of Oman
Alicia M Cadenas1, Lev A Zhivotovsky2, Luca L Cavalli-Sforza3, Peter A Underhill3 and Rene J Herrera1
1Department of Biological Sciences, Florida International University, Miami, FL, USA
2N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
3Department of Genetics, Stanford University, Stanford, CA, USA
Correspondence: Dr RJ Herrera, Department of Biological Sciences, Florida International University, University Park, OE 304, Miami, FL 33199 USA. Tel: [phone]; Fax: [phone]; E-mail: [e-mail]
Received 20 February 2007; Revised 30 August 2007; Accepted 11 September 2007; Published online 10 October 2007.

"Distribution of E3b1-M35 derivatives

The presence of signature sub-Saharan African mtDNA lineages in the south Arabian populations has been attributed to various waves of gene flow to the region, including that associated with the East African slave trade. This is apparent from the exact mtDNA haplotype matches between lineages in Yemen and East Africa, including those associated with the Bantu expansion.20 The presence of the E3a-M2 lineage in Oman (7.4%),4 Yemen (3.2%), UAE (5.5%) and Qatar (2.8%) could lead to the oversimplified conclusion that these chromosomes are also a contribution from the East African slave trade. Mitochondrial DNA analysis of the Yemen Hadramawt indicates recent gene flow (2500 yBP) from Africa to the Arab populations in part through the slave trade, yet an ancient arrival from East Africa is responsible for the Y-chromosome haplotypes."

[/blockquote]

It is also worthy to note that even not all of the recent genetic contribution to the Middle East would have been via slaves. Poor African migrants (and for that matter, any poor people today) may be .. subjugated in the Middle East today (take poor Indian workers in Dubai for instance), but historically this is a major oversimplification.

On Egyptian E1b1a (M2) aka Lucotte's "haplogroup 4":

Haplotype IV, designating the M2/PN1 subclade, as noted, is found in high frequency in west, central, and sub-equatorial Africa in speakers of Niger-Congo—which may have a special relationship with Nilosaharan—spoken by Nubians; together they might form a superphylum called Kongo-Saharan or Niger-Saharan (see Gregersen 1972, Blench 1995), but this is not fully supported. The spatial distribution of p49a,f TaqI haplotypes in the geographically-widespread speakers of Nilosaharan languages has not been fully characterized, but the notable presence of haplotype IV in Nubians speaking the Eastern Sudanic branch is interesting in that this subgroup is in the Sahelian branch of speakers, whose ancestors may have participated in the domestication of cattle in the eastern Sahara (Ehret 2000, Wendorf and Schild 2001). Sometimes haplotype IV (and the M2 lineage) is seen as being associated with the “Bantu expansion” (2000-3000 bp), but this does not mean that it is not much older, since expansion and origin times cannot be conflated. Haplotype IV has substantial frequencies in upper Egypt and Nubia, greater than VII and VIII, and even V. Bantu languages were never spoken in these regions or Senegal, where M2 is greater than 90 percent in some studies.

- Keita, 2005.[/color]

These genes may not be fully expounded upon or characterized, at least not in any studies I'm aware of, *however*, something else has that has been traced back to West Africa: sickle cell disease.

***

Sickle Cell Anemia in the Middle East and Proximate / Other Regions:

The Benin haplotype accounts for HbS associated chromosomes in Sicily,4 Northern Greece,10 Southern Turkey,11 and South West Saudi Arabia,6,7 suggesting that these genes had their origin in West Africa. The Asian haplotype is rarely encountered outside its geographic origin because there have been few large population movements and Indian emigrants have been predominantly from non HbS containing populations. However, it is of interest that the Asian haplotype was first described among descendants of Indian indentured laborers in Jamaica.12

...

From these original foci of the HbS mutation, the gene spread along trading routes to North Africa and the Mediterranean, was transported in large populations to North and South America and the Caribbean during the slave trade, and latterly has spread to Northern Europe by immigration from the Caribbean, directly from Africa to the United Kingdom, France, Belgium, and Holland, and from Turkey to Germany. The relative prevalence of these haplotypes in the Americas reflects the different origins of their African peoples, approximately 70% of HbS associated chromosomes having the Benin haplotype, 10% Senegal and 10% Bantu. Haplotype frequencies in Jamaica are similar to the USA but the Bantu haplotype accounts for the majority of HbS associated chromosomes in Brazil.9

- Graham R. Serjeant, MD, FRCP, MRC Laboratories (Jamaica), University of the West Indies, Kingston.

A good map:

A study on the various types (including Indo-Arabian) in the Middle East (we'll get to how ancient they are after this):

Haplotypes of the beta-globin gene as prognostic factors in sickle-cell disease.

el-Hazmi MA, Warsy AS, Bashir N, Beshlawi A, Hussain IR, Temtamy S, Qubaili F.Medical

Biochemistry Department, World Health Organization Collaborating Centre for Haemoglobinopathies, Thalassaemias and Enzymopathies, College of Medicine, King Khalid University Hospital, Riyadh, Saudi Arabia.

The Benin haplotype was found in patients with severe disease, either as homozygous or in combination with another haplotype. The majority of Syrians and Jordanians had the Benin haplotype, and severe disease. However, one in three Syrians and one in five Jordanians had a milder disease, and the Saudi-Indian haplotype was identified.

All Saudi patients from south-western and north-western areas, where the disease is generally severe, had the Benin haplotype in the homozygous or heterozygous state. Of the Saudi patients from the eastern area, where a mild form of SCD exists, only 9% had the Benin haplotype. The remainder had the Saudi-Indian haplotype, either in its homozygous or heterozygous state…

Restriction endonuclease restriction sites have provided a useful insight into the normal polymorphic variations in the DNA surrounding various gene loci, where a combination of two or more polymorphic sites has led to the identification of specific haplotype patterns [13,14]. This has been of significance in the study of the regions surrounding the b-globin gene (i.e. the b-globin gene cluster), where several polymorphic sites have been identified, and population differences have been found on analysis of the haplotype pattern [9]. An interesting observation is that the sickle-cell mutation has occurred on chromosomes carrying different polymorphic sites and different b-globin gene haplotypes, and this seems to play a role in the clinical expression of SCD [9].

We compared the haplotype pattern of SCD patients from different Arabic-speaking countries. Benin haplotype was the major haplotype in all countries with a severe presentation of SCD and it was present in both the homozygous and heterozygous state. This was true for those SCD patients from south-western and north-western areas of Saudi Arabia, and for those from Egypt, Jordan and Syrian Arab Republic. On the other hand, patients from the eastern part of Saudi Arabia, who present with a significantly milder clinical picture, carried the Saudi-Indian b-globin gene haplotype either in its homozygous or heterozygous state."

- 1999, Eastern Mediterranean Health Journal

Modern Middle Easterners would not be the only ones to have severe anemia, PreDynastic Egyptian mummies have it too:

Use of the amplification refractory mutation system (ARMS) in the study of HbS in predynastic Egyptian remains.
Dipartimento di Biologia Animale e dell'Uomo, Università degli Studi di Torino.

PMID: 11148985 [PubMed - indexed for MEDLINE]

We conducted a molecular investigation of the presence of sicklemia in six predynastic Egyptian mummies (about 3200 BC) from the Anthropological and Ethnographic Museum of Turin. Previous studies of these remains showed the presence of severe anemia, while histological preparations of mummified tissues revealed hemolytic disorders. DNA was extracted from dental samples with a silica-gel method specific for ancient DNA. A modification of the polymerase chain reaction (PCR), called amplification refractory mutation system (ARMS) was then applied. ARMS is based on specific priming of the PCR and it permits diagnosis of single nucleotide mutations. In this method, amplification can occur only in the presence of the specific mutation being studied. The amplified DNA was analyzed by electrophoresis. In samples of three individuals, there was a band at the level of the HbS mutated fragment, indicating that they were affected by sicklemia. On the basis of our results, we discuss the possible uses of new molecular investigation systems in paleopathological diagnoses of genetic diseases and viral, bacterial and fungal infections.

- Massa et. al., 1999

All I have to say to that one is, no wonder! ;D

(No wonder about the previous studies attributing M2's presence not to descent / babies of a slave male Middle Eastern Papa, but to ancients) (and fyi male slave input in Mena / Muslim populations seems to have always been negligable if at all)

[Dawn2Earth]

Coming up next perhaps?:

Perhaps a full list of everywhere the PN2 Clade has been spotted. I wonder about Sudan and Chad maybe. It'd seem weird were it not spotted there and yet spotted only in Ethiopia (and a few outside of one group) and Senegal (West African Sudan/Sahel).

Oh, btw, it wasn't the first time someone talked about the sickle cell thing, it's happened various times, but I brought it over here via a write-up that Supercar did on his blog, just to credit the bloggee.

[sttigray]

I like this will you be available for questions later?

[Dawn2Earth]

Quite possibly so, yeah probably.

[calabooz]

Do you have an EgyptSearch account? This would get more replies there, I'm sure.

[calabooz]

One study not mentioned herein:

Within sub-haplogroup J1, the putative ancestral haplotype is 14-16-23-11-12 (for loci DYS19-DYS388-DYS390-DYS392-DYS393), found in 17 out of 61 chromosomes. This haplotype is compatible with the major haplotype found in the middle-eastern J pool, which in turn contains the so-called Cohen modal haplotype (Thomas et al. 1998). Within J1, the marker DYS388 identifies two interesting subgroups. First, chromosomes with DYS388(17) have been linked with the expansion of Arabian tribes in southern Levant and northern Africa (Nebel et al. 2002). Our data agree with this scenario, as out of 13 instances of DYS388(17), ten are from Oman, UAE, and Egypt. Second, chromosomes with DYS388(13) have been reported by Cinnioglu et al. (2004) with no DYS388(14) intermediate. We have found eight chromosomes of the former type, three of which are from northern Turkey and Azerbaijan, but we have also observed the DYS388(14) intermediate in southern Italy. In addition, this allele is also present on some M172(G) chromosomes. Thus, the geographic clustering observed in Turkey probably represents more a drift or a founder effect than a deviation from the stepwise mutational model."--F. Di Giacomo et al. 2004

[calabooz]

In regards to mtDNA:

"Egypt’s location and amalgam of past ruling populations mixing with the Egyptians has resulted in a heterogeneous make-up. The haplotype breakdown of this dataset is predominantly European (67.5%), followed by African (20.6%) and Asian (11.9%). The breakdown is as follows: European origin (n = 187) including R0 and its subgroups (31.4%), I (3.2%), J (7.6%), K (4.7%), T (9.4%), U (9.0%), W (0.7%), X (1.4%); African origin (n = 57) including L0
(2.2%), L1 (2.5%), L2 (3.6%), L3 (12.3%); and Asian origin (n = 33) including M (6.9%), N (5.1%)."--Source: Mitochondrial control region sequences from an Egyptian population sample

Jessica L. Saunier et al. 2009

Download link: www.sendspace.com/file/fk714r

Sample consisted of males from Alexandria. So, the heterogeneity can be attributed to the invasions throughout Egyptian history. Aside perhaps for M1 which has an possible/probable African origin


On the mtDNA of Siwa Berbers:

Our results highlighted a clear genetic differentiation between Berbers from the Maghreb and Egyptian Berbers. The first seems to be more related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4∗, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. Probably, such a maternal diversity between North African Berbers would have been the result of a conjunction of several geographical, prehistoric, and historic factors which guided contacts (and thus exchanges) between local populations and migrating groups. First, in addition to the geographical distance, which certainly increases the genetic distance, the geographical location of Berber populations is very peculiar: the Berbers from the Maghreb are at the end of a long migration route, whereas Berbers from Siwa are rather in a crossroads between the Middle East, East Africa, sub-Saharan areas and the North African corridor. Therefore, meetings and exchanges between local and migrating populations were not identical in North West and North East Africa. - C. Coudray et al., The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

The above is very interesting indeed. It also add evidence that M1 is African, as they note how Siwa Berbers are at a crossroads between Middle East and East Africa. Also, is the Gonzalez et al. 2007 tried to claim a parallel distribution of M1 and U6 or something of that sort but we see no U6 in Siwa!

On the Northwest Berber, Siwa Berber distinction noted above, recent articles go into more detail:

The distribution of subsets of haplogroups U6 and M1 also suggests the presence of a discontinuity between Libya and Egypt, separating western North Africa from eastern North Africa. Even if both haplogroups are thought to have been carried by a back-to-Africa migration from the Near East, significant increased U6 frequencies have been detected in the West compared to the East. The network of all U6 sequences found in the database presents two nodes with star-like shape, U6a* and U6a1. In a similar way, M1a1 is the node with starlike topology in haplogroup M1, and the node where most of the eastern sequences are found. Time estimates of these nodes are 13.5 6 3.7, 13.0 6 5.7, and 13.1 6 7.0 kya for haplogroups U6a*, U6a1, and M1a1 respectively. The most plausible explanation of the frequency distribution of M1a, U6, and M1b1 lineages, their coalescence age estimates, and the star-like shape would be an early split in the back to Africa migration followed by a period of stability and a period of expansion. The split would have produced two different migration waves, one westward, represented by U6 and possibly M1b1 in lower frequencies, and the other southward, represented by M1a. Each haplogroup would have increased its frequency by drift and subsequently accumulated diversity over time. Coalescent time estimates point to a possible second expansion of these haplogroups at the end of the LGM, simultaneously with some Eurasian haplogroups, as suggested by Olivieri et al. (2006). Moreover, all but one M1a1 sequence are found in eastern North Africa, which suggests that this subclade might have appeared in the East, and only after that have migrated westwards at this period.- Karima Fadhlaoui-Zid et al., (2011)

[calabooz]

Major E

I would like to your already nice detail of major E in the Nile Valley.

What we can take from the presence of E in the Nile Vally is as follows:

Our findings are in accordance with other studies on Y-chromosome markers
that have shown that the predominant Y-chromosome lineage in Berber communities
is the subhaplogroup E1b1b1b (E-M81), which emerged in Africa, is
specific to North African populations, and is almost absent in Europe, except in
Iberia (Spain and Portugal) and Sicily. Molecular studies on the Y chromosome in
North Africa are interpreted as indicating that the southern part of Africa, namely,
the Horn/East Africa, was a major source of population in the Nile Valley and
northwest Africa after the Last Glacial Maximum, with some migration into the
Near East and southern Europe (Bosch et al. 2001; Underhill et al. 2001)--Frigi et al. 2010

We can see also in Keita (2005) the high presence of PN2 derivatives. Also supported by Cruciani et al. (2007) which states:

"E-M78 belongs to clade E3b (E-M215). On the basis of robust phylogeographic considerations, an eastern African origin has been proposed for E-M215 (Underhill et al. 2001; Cruciani et al. 2004), with a coalescence time of 22.4 ky (95% CI 20.9–23.9 ky; recalculated from Cruciani et al. [2004], see Subjects and Methods). A northeastern African origin for haplogroup E-M78 implies that E-M215 chromosomes were introduced in northeastern Africa from eastern Africa in the Upper Paleolithic, between 23.9 ky ago (the upper bound for E-M215 TMRCA in eastern Africa) and 17.3 ky ago (the lower bound for E-M78 TMRCA here estimated, fig. 1). In turn, the presence of E-M78 chromosomes in eastern Africa can be only explained through a back migration of chromosomes that had acquired the M78 mutation in northeastern Africa."--Cruciani et al. 2007

The Markers Frigi et al. mentions are E-M215/M25. As you showed earlier in this thread, E-M78 did indeed have origins in northeastern Africa, also shown in aforecited Cruciani et al. 2007

[sitabanu]

Origin of the Jews and the Arabs: Date of their Most Recent Common Ancestor is Written in their Y-Chromosomes – However, There Were Two of Them – By Anatole A. Klyosov:

www.google.com/url?sa=t&source=web&cd=7&ved=0CEgQFjAG&url=http%3A%2F%2Fprecedings.nature.com%2Fdocuments%2F4206%2Fversion%2F1%2Ffiles%2Fnpre20104206-1.pdf&rct=j&q=HAPLOTYPE%20VIII%20is%20the%20ancestral%20haplotype%20in%20Jews.&ei=3OJTTpi8MM-EsgLJosWJBw&usg=AFQjCNFGkvNoRpIFdca70H3jEU22FpcjRQ&cad=rja

“The younger,” Jewish only branch on the right-hand side in Fig. 2 had a common ancestor who lived 1,020 +/- 170 YBP or 932 CE (AD) !.

Again, this is within the margin of error with 1,125 +/- 160 YBP obtained for the 37 marker dataset. The data is quite reliable, and calcuations employing the 25, 37, and all 67 marker haplotypes in Fig. 2 gave 900 +/- 195, 1,150 +/- 140 YBP, respectively, to the lifetime of a common ancestor of the Jewish population (the “younger” branch on the right in Fig. 2), all of them having the “Cohen Modal Haplotype.”

:oops:
:oops: J2 lived 3,300 +/- 400 YBP (or 1348 BC)!!!!!

...J2a*-M410 - UAE - 1.23, Yemen - 4.84, Iran - 4, Pakistan 8.52.

"To sum this section up, the most recent common ancestor of the Jews and Arabs of haplogroup J2a-M410* lived 4,175 +/- 510 years ago, and he had the “J2 Cohanim” signature in his haplotype. Again, it is rather “J2 Abraham Modal Haplotype.” From him a split occurred between the Jewish and the Arabic lineages in haplogroup J2. The split is clearly visible on the haplotype tree in the 37 and the 67 marker format (Figs. 3 and 4). Around 3300 YBP, in the middle of the 2nd millennium BC, a line of Cohanim, haplogroups J2a*, split from the lineage and continued with the initial ancestral haplotype. Around 2500 YBP, in times of the Babylonian and Assyrian exiles, the J2 Cohanim-Sephardim lineage split, and continued with the two mutations at DYS385a,b (13-18 compared to the initial 14-17) in the ancestral haplotype. The rest of J2 Cohanim continued with the same ancestral haplotype, and passed a population bottleneck (a genetic drift occurred) in the middle of the 1st millennium AD."

4,175 + 510 = 4,685 – 1952 = 2,733 BC. 2500 YBP = 548 BC.

(For the novice,) YBP = Years Before Present, which in the field of archaeology is 1952 AD/CE.

[Dawn2Earth]

Apr 30, 2011 16:26:18 GMT -5 calabooz said:

In regards to mtDNA:

"Egypt’s location and amalgam of past ruling populations mixing with the Egyptians has resulted in a heterogeneous make-up. The haplotype breakdown of this dataset is predominantly European (67.5%), followed by African (20.6%) and Asian (11.9%). The breakdown is as follows: European origin (n = 187) including R0 and its subgroups (31.4%), I (3.2%), J (7.6%), K (4.7%), T (9.4%), U (9.0%), W (0.7%), X (1.4%); African origin (n = 57) including L0
(2.2%), L1 (2.5%), L2 (3.6%), L3 (12.3%); and Asian origin (n = 33) including M (6.9%), N (5.1%)."--Source: Mitochondrial control region sequences from an Egyptian population sample

Jessica L. Saunier et al. 2009

Sample consisted of males from Alexandria. So, the heterogeneity can be attributed to the invasions throughout Egyptian history. Aside perhaps for M1 which has an possible/probable African origin

Don't you mean females from Alexandria?

As far as the lineages go, Alexandria is a Mediterranean area, almost Levantine, a Metropolitan place with a historic hosting of non-Egyptian populations (from any direction). So I don't even really need an explanation for their heterogeneity -- it doesn't really surprise me.

I am skeptical that there are all those European lineages, although the name itself, "Alexandria", is of European (Greek) provenance. What I mean is, I wonder if some would be attributable to Asian lineages.

And good thing I just noticed you commented on the Asian description of M1 (which is Ethiopian), though I was wondering about the N. It's only been found in Africa in rare cases. I'd say with the presence of L3, undisputably African ancestor to both HGs M & N, the N thing seems unresolved.

Thanks for the post though.

You know what though?

I was surprised at all the European lineages because paternally they descend mainly from Near Easterners in terms of non Africans.

I believe this may reflect the pattern in their region of Africa.

In coastal North Africa (which is where most of the cities, metropolis and populace is) which lies smack on the Mediterranean Sea, you see a lot more European ancestry (Spain and France sit at the Mediterranean Sea, for instance, but they have ancestry ties also as far as the far Northern Saami), compared to the people living on the River Nile.

With Nile Valley (which is East) inhabitants, and actually greater East Africa in general from the Lower Nile (Cairo to Khartoum), to the Rift valley you see more Near Eastern admixture and influence. Depends on where you go though.