Wednesday, January 30, 2008

Lucotte et al.'s haplotype IV

So exactly what UEP marker is Lucotte et al.'s haplotype IV associated with?

Lucotte et al. don't exactly tell us which specific NRY monophyletic unit haplotype IV belongs to, but S.O.Y Keita clues us in on it:

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.

Aside from referencing various Lucotte et al. publications from 1996 through to 2003, and relating their findings on RFLP markers to those of Al Zahery et al. 2003, the frequency and distribution pattern of haplotype IV no doubt reinforced Keita's perception of its link with E3a bearing chromosomes. Keita tabulated the frequencies of various RFLP haplotypes across the samples studied in the aforementioned works, and it can be viewed here:

Haplotypes and percentages

                                   IV    V      XI     VII   VIII  XII   XV

Falasha (38)                       0.0   60.5   26.3   0.0   0.0   0.0   0.0

Ethiopians [non Falasha](104)      0.0   40.4   25.9   0.0   23.1  0.0   0.0

Berbers (74)                       1.4   68.9   2.8    1.4   6.8   4.1   0.0

“Sephardic” Jews (381)             8.4   18.6   6.8    19.9  34.1  4.2   2.1

“Oriental” Jews(56)                1.8   8.9    0.0    7.1   78.6  0.0   1.8

“Near Eastern” (27)                0.0   7.4    0.0    7.4   85.1  0.0   0.0

Askenazic Jews(256)                0.0   3.1    15.2*  22.7  24.6  9.0   10.9

1 - Lucotte and Mercier (2003a)
2 - Lucotte and Mercier (2003b)
3 - Al-Zahery et al. (2003); *haplotype XI here is documented from two biallelic lineages
4 - Lucotte et al. (2000)
5 - Lucotte and Smets (1999)

country (n)                     Haplotypes and percentages

                                IV    V      XI    VII   VIII   XII   XV

Egypt(274)                      13.9  39.4   18.9  6.6   7.3    2.2   5.5

Lebanon(54)                     3.7   16.7   7.4   20.4  31.5   5.6   1.9

Palestine(69)                   1.4   15.9   5.8   13.0  46.4   0.0   4.3

Iraq(139)                       1.4   7.2    6.4*  20.1  36.0   1.4   0.7

Egypt(52)                       7.7   40.4   21.2  9.6   7.7    3.8   1.9

Libya (38)                      7.9   44.7   10.5  0.0   5.3    13.2  0.0

Algeria (141)                   8.5   56.7   5.0   1.4   7.1    4.2   5.0

Tunisia (73)                    0.0   53.4   5.5   4.1   2.7    26.0  2.7

Morocco (102)                   0.98  57.8   8.8   4.9   7.8    0.98  10.8

Mauretania (25)                 8.0   44.0   8.0   0.0   4.0    0.0   0.0

Suprasah(composite)(505)        4.4   55.0   7.7   3.2   6.3    7.1   4.2

Ethiopia(composite)(142)        0.0   45.8  26.1   0.0   16.9   0.0   0.0

6 - Lucotte et al. (1996)

— References 2, 4, 5, as in Table 2A.

— *Haplotype XI in groups admixed with northern Europeans is usually affiliated with haplogroup R1; in Africa it is usually associated with haplogroup E (al-Zahery 2003).

The distributions of haplotype 4 in those tables make perfect sense, if they were strongly associated with Hg E3a chromosomes.

As the present author has noted elsewhere, an apparent limitation of just relying on RFLP markers lies with the high probability for re-occurrence of the same RFLP sequences in two, if not more, distinct haplogroups. However, lest one thinks that Keita is alone in his observation, about linking haplotype IV to E3a bearing chromosomes, then consider this:

A total of 21 different 49a,f haplotypes were found and are illustrated in Fig. 4 as a sub-classification of the Iraqi Y-chromosome haplogroups. The most represented haplotype of haplogroup E is haplotype 5 (A 2 C 0 D 0 F 1 I 1 ). This is followed by haplotype 11 (A 3 C 0 D 0 F 1 I 1 ) at a much lower frequency. Haplotypes 5 and 11 were observed both in Africa (Lucotte et al., 2001; Passarino et al., 1998; Persichetti et al., 1992; Santachiara-Benerecetti and Semino, 1996; Spurdle and Jenkins, 1992; Torroni et al., 1990) and Eurasia (Passarino et al., 2001; Semino et al., 2000b) but in Africa they belong to haplogroup E, whereas in Eurasia, particularly in *Northeastern Eurasia*, they belong mainly to the haplogroup R-M17. Interestingly, the proportion of haplotypes 5 and 11 in haplogroups E and R-M17 is reversed, with haplotype 5 prevalent in haplogroup E and haplotype 11 in haplogroup R-M17. By considering that the two haplotypes differ by a single band change and their different proportion in the two lineages, it is likely that haplotype 11 is a derivative of haplotype 5 in haplogroup E and just the opposite in haplogroup R-M17.


It is worth mentioning that in haplogroup E two subjects belong to the African specific E-M2 clade, which is very frequent in the Western and Southern part of the continent (Cruciani et al., 2002; Passarino et al., 1998; Scozzari et al., 1999; Seielstad et al., 1994; Semino et al., 2002; Underhill et al., 2000) and has been related to the Bantu expansion. These two Y chromosomes **harbor haplotype 4** (A 1 C 0 D 0 F 1 I 1 ) which is also African- specific and **shows the same geographic distribution** (Excoffier et al., 1987; Passarino et al., 1998; Spurdle and Jenkins, 1992; Torroni et al., 1990). Within haplogroup J, haplotypes 7 (A 2 C 0 D 1 F 1 I 0 ) and 8 (A 2 C 0 D 1 F 1 I 1 ) are the most represented, but haplotype 7 is observed only in the J-M172 sub-set. This suggests that the 49a,f haplotype 7 arose on a 12f2-8Kb/M172 Y chromosome. — N. Al Zahery et al. 2003, Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations.

To understand how Al Zahery et al. were able to link RFLP haplotypes to SNP markers on the chromosomes under study, it is worth noting that they identified the former by using TaqI restriction enzyme digests and the latter with the likes of PCR and DHPLC analysis; essentially this sort of approach to testing for both RFLP markers and binary markers has been exemplified in the following link—we discussed the methods utilized in relative detail, in the sorting out of RFLP markers into respective sub-clades: RFLPs: Lucotte et al., A case study — Pt. 1 [clickable]

Therefore, E3a in the Nile Valley?

Getting back to Keita's linking of haplotype IV to Hg E3a chromosomes, and as verified above in the Al Zahery et al. study; some parties are perplexed by the detection of the rather considerable frequencies of Hg E3a in the Nile Valley, as denoted by the distribution and frequency patterns of haplotype IV in Lucotte et al.'s study, i.e. if haplotype IV is to be unequivocally accepted as a marker characteristic of Hg E3a-bearing chromosomes - again, as maintained by Keita and Al Zahery above, for instance. Even Lucotte et al. themselves had placed haplotype IV in a context not inconsistent with that maintained by Al Zahery et al. and Keita, for they say:

Haplotype IV, characteristic of sub-Saharan populations, shows a southern geographic distribution in Egypt. — G. Lucotte and G. Mercier

...and they also refer to it as "African haplotype" elsewhere, in contrast to:

Haplotype V is a characteristic Arab haplotype, with a northern geographic distribution in Egypt in the Nile River Valley. — G. Lucotte and G. Mercier, Y-chromosome haplotypes in Egypt, 2002.

If one recalls, it has already been noted that "Arab" here, as used by Lucotte and Mercier, is in reference to "Arabized" north Africans; it is necessary to realize this, for it has the potential of misleading those in the little know.

It is necessary to note, that while haplotype IV has considerable presence in the Upper Nile Valley, which Lucotte and Mercier refer to as "Upper Egypt" and "Lower Nubia" respectively, its average frequency still follows that of haplotype V and haplotype XI, both of which have been linked to Hg E3b-bearing chromosomes:

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 IV has a gradient that decreases as one moves from the so-named Upper Nile Valley regions to Lower Egypt, with higher frequencies in "Upper Egypt" and "Lower Nubia" and lower frequencies in "Lower Egypt". Nonetheless, does haplotype IV's presence in Lower Egypt mean that Hg E3a has been detected therein? Well, if Luis et al.'s work of "the Nile Valley corridor vs. the African Horn" is anything to go by, this should come as no surprise; they show that low frequencies of Hg E3a occur in "northern Egypt", which in itself should be instructive, considering that this is the region of the Nile Valley relatively further away from sub-Saharan Africa [where this haplotype predominates]. So, if lower Egypt can show low frequencies of E3a, as verified by Luis et al., then does it not follow that Upper Egypt could and would have this marker, in relatively higher frequencies?

The aforementioned perplexion that the present author has come across, concerning this E3a presence, was presumably justified by the idea that few other studies that have been done on samples taken from Upper Egypt and Sudan, little to no Hg E3a had been documented. Now of course, the results of samplings can be affected by choice of sampling, in terms of its ethnic diversity and geographical range, the type and number of markers typed and methods used to amplify or detect them. The present author recalls a discussion wherein he was told that Arredi et al.'s study, "A Predominantly Neolithic Origin for Y-Chromosomal DNA Variation in North Africa", was one such study which studied samples from the Upper Nile Valley of Egypt, but found no E3a markers therein. It goes back to the sample issues just mentioned, and this is what the present author had to say about that issue:

"Arredi et al.'s study primarily focuses on E3b and J lineages, not E3a. Their samples, as far as I know consist of candidates from two locations: 44 candidates from Mansoura and 29 from Luxor. Of these samples, 14 binary markers were identified in the 44 candidates from Mansoura, while the 37 identifications were done by tandem repeats, and likewise, of the 29 candidates, 9 binary markers was identified amongst them while 27 markers were defined only by tandem repeats. It is also of interest that this study also shows E3a detection in the Ethiopian sample. Whereas in the Luis et al. sample, more diverse speaking groups in northern Egypt were sampled, namely Arabic and Tamazight speakers. So it is the question of sampling selection, sampling size, and ability to detect as much binary markers along with STR markers as possible."

Yet, what's interesting in all this, is that the individual who raised the issue of lack findings of Hg E3a in the aforementioned Arredi et al. study, didn't and perhaps was not capable of demonstrating that RFLP haplotype IV corresponds to any other but Hg E3a chromosomes. To top that, the frequency and distribution pattern of haplotype IV—which would make sense if it is associated with E3a, in terms of sporting the aforementioned decreasing south-to-northward gradient, was not taken into consideration; nor was the correspondence between the frequency of haplotype IV in Lower Egypt, as noted by Lucotte et al., and that of Hg E3a in Lower Egypt, as noted by Luis et al. (2004), taken into consideration.

As it stands, pending new information to the contrary, haplotype IV is linked to E3a bearing chromosomes, not to mention the other peculiarities specific to and shared by haplotype IV and Hg E3a, and as such, one would have to concede that Hg E3a is present in the Nile Valley [and there is no doubt about that], with a south-to-north gradient showing higher frequencies in the Upper Nile Valley, that progressively decreases as one goes further down the Nile, and finally reaching the lowest frequencies in northern Egypt.

Last but not least, of note:

One Y-specific DNA polymorphism (p49/Taql) was studied in a sample of 469 African males coming from twelve populations of sub-Saharan Africa. An high frequency (62.5%) of the Y-haplotype IV was observed in these populations, the most elevated percentage of this haplotype being observed in Mossis (from Burkina-Fasso). The “Arabic” haplotype V is present in these populations at a mean frequency of 8.7%. The “oriental” haplotype XI is present at a mean frequency of 11.3%, the most elevated percentage of this haplotype being observed in Songhaiis (from Niger).—Lucotte G. and GĂ©rard N. 2000, Haplotypes of the Y chromosome in some populations of west Africa
Brief references:

*As noted by Keita 2005, Explanation of the Pattern of P49a,f TaqI RFLP Y-Chromosome Variation in Egypt:

1 - Lucotte and Mercier (2003a)
2 - Lucotte and Mercier (2003b)
3 - Al-Zahery et al. (2003); *haplotype XI here is documented from two biallelic lineages
4 - Lucotte et al. (2000)
5 - Lucotte and Smets (1999)
6 - Lucotte et al. (1996)

*Lucotte et al.; North African genes in Iberia studied by Y-chromosome DNA haplotype 5; 2001.

*G. Lucotte and G. Mercier, Y-chromosome haplotypes in Egypt, 2002.

*N. Al Zahery et al. 2003, Y-chromosome and mtDNA polymorphisms in Iraq, a crossroad of the early human dispersal and of post-Neolithic migrations.

*Luis et al. 2004, The Levant versus the Horn of Africa: Evidence for Bidirectional Corridors of Human Migrations.

*Arredi et al. 2004, A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa.