Cruciani et al. 2007: Sorting Out a Complex Network of Clusters

E-M78 (E3b1) network:

Introduction
Both E3a and E3b are found outside of their African homeland, but '''E3b''' is relatively more frequent in Europe and western Asia than its sister clade E3a, thanks to gene flow from North Africa and to a lesser degree, from the African Horn in sub-Saharan East Africa [to the other side of the Red Sea], where E3b bearing chromosomes appear to be the most prevalent. The most commonly distributed E3b sub-branch is '''E-M78'''. The flow of E3b can be summarized into about four main episodes, based on geographic and quantitative analysis of haplogroup and micro satellite diversity:

• Sometime in the Upper Paleolithic, between 23.9 and 17.3ky ago, E3b (M215) bearing chromosomes were introduced to northeast Africa from sub-Saharan East Africa.
  

• The M78 mutation ('''E3b1''') then occurred in the E3b chromosomes distributed in Northeast Africa, to be followed by a back-migration episode to sub-Saharan East Africa, sometime between 18ky and 5.9ky ago. Some chromosomes which had acquired the M78 mutation in Northeast Africa undoubtedly also made their way westward in North Africa.
  

• Sometime around 13ky ago, these M78 bearing E3b chromosomes were introduced to Europe directly from northern Africa.

• Between 20 and 6.8ky ago, M78 bearing E3b chromosomes were introduced into western Asia from Northeast Africa. [Cruciani et al. 2007]
  

Discussion
Sorting E-M78 chromosomes into well defined clusters, while there are certainly strong correspondances between binary markers and microsatellite clusters in certain cases, is anything but simplistic.

What Cruciani did in his efforts to place microsatellite clusters into clearly defined sub-clades more precisely, and identification of new sub-clades in the process, was to muddle up what is presently known about E-M78 macrohaplogroup demographic and biohistoric specificities, and he, himself, has taken note of this fact:

Thus, even though they represent only 5% of the total E-M78 chromosomes analyzed, their inclusion into the respective haplogroups/paragroups **heavily affects inferences** about time and place of origin of these haplogroups/paragroups. — Cruciani et al., 2006.

...taken from the following extract:

Discrepancies between micro satellite clusters and haplogroups/paragroups

Despite the major congruence between E-M78 microsatellite clusters and binary haplogroups, there are important discrepancies between the trees generated by the two types of markers. First, the large majority of the delta chromosomes belong to the clades E-V22 and E-V12*, but a few representatives of both clades are found outside the delta cluster.

Within delta, E-V22 and E-V12* chromosomes are intermingled and not clearly differentiated by their microsatellite haplotypes.

Second, all of the cluster beta chromosomes belong to paragroup E-M78*. However, E-M78* also includes some non-beta chromosomes which are highly differentiated in their microsatellite haplotypes.

Third, there is a striking correspondence between the microsatellite clusters alpha and gamma and the binary haplogroups E-V13 and E-V32, respectively (Fig. IB). However, while all alpha cluster belong to E-V13, some E-V13 chromosomes are not contained in such a cluster. Conversely, all of the E-V32 chromosomes fall within cluster gamma (defined by the rare DYS19 11-repeat allele), but two gamma chromosomes are members of paragroups E-V12* and E-M78*.

Taking into account the above data, the previously described European cluster alpha and the northern African cluster beta are indeed confirmed as monophyletic groups of chromosomes, that, very likely, have their own binary markers yet to be discovered. Cluster alpha chromosomes constitute a major branch of the binary haplogroup V13, which, in turn, includes also a few, highly differentiated chromosomes - previously classified either in cluster delta or unclassified. All 29 chromosomes within cluster beta belong to the paragroup E-M78*, which is relatively rare and almost exclusively restricted to a single geographic region (i.e. northern Africa), thus a common origin for at least a large part of these is likely.

Different scenarios characterize clusters delta and gamma.

The presence of three E-V13 chromosomes within cluster delta and the exclusion of some E-V12 and E-V22 chromosomes demonstrate that cluster delta cannot be regarded as a monophyletic unit.

As for cluster gamma, we have established close phylogenetic relationships of its members - now classified as E-V32 chromosomes - with those belonging to E-V12* within the E-V12 clade (Fig. 2) These relationships go undetected through the micro satellite network (red and pink chromosomes in Fig. 1B), most likely due to recurrent mutations at micro satellite loci. An alternative explanation would be that V12 is within a terminal branch of the Y chromosomes tree; moreover, it was never found by sequencing 18 Y*(xM78) chromosomes representing deep branches of the Y chromosome phylogeny (data not shown). Thus, the new markers we have detected now offer the opportunity to explore in a better defined phylogenetic context the origin and distribution of the chromosomes belonging to haplogroup E-M78.

Also it is worth noting that twelve chromosomes that we were unable to assign to any cluster in the previous network analysis are now classified within four different haplogroups/paragroups (see Table 2 and Fig. 1B) as highly divergent microsatellite haplotypes. Thus, even though they represent only 5% of the total E-M78 chromosomes analyzed, their inclusion into the respective haplogroups/paragroups **heavily affects inferences** about time and place of origin of these haplogroups/paragroups.

Finally, although there is a strong correspondence between cluster gamma - defined by the rare DYS19 11-repeat allele - and haplogroup E-V32, the presence, in cluster gamma, of haplotypes belonging to the binary paragroups E-M78* and E-V12* can only be explained by admitting either a paraphyletic or a polyphyletic origin for the chromosomes in the cluster.

Overall these findings indicate that caution is needed when using the microsatellite alleles as surrogates of UEPs (e.g. Malaspina et al., 2001; Cruciani et al., 2004’ Di Giacomo et al., 2004; Sanchez et al.; 2005). — Cruciani et al., 2006; Molecular Disection of the Y chromosome Haplogroup E-M78 (E3b1a): A Posterior Evaluation of a Microsatellite-Network-Based Approach Through Six New Biallelic Markers

He correctly notes [in the very last piece of this extract] the futility of treating clusters as lineages, for reasons made apparent already in the body of the extract.

Essentially, as noted above, all the 29 beta clusters fall into the E-M78* paragroup found predominantly in Northwest Africa, along with a few other clusters [gamma and unclassified clusters]. In his 2007 study, however, Cruciani had this to say:

It is also worth noting that the rare paragroup E-M78* has not been observed in eastern Africa; moreover, the two north-western African E-M78* chromosomes are well differentiated from the two north-eastern African E-M78* chromosomes (supplementary table 1) adding a new argument for a higher haplogroup diversity in northern Africa. — Cruciani et al., Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-chromosomal Haplogroups E-M78 and J-M12, 2007.

Thus, the paragroup essentially consists of clusters sharing TMRCA, but didn't test positive for any known downstream mutations. So, the likely differences seen here by Cruciani, were of microsatellite cluster differences. It can happen, and has happened as noted above, when newly identified binary markers are stumbled upon in paragroups. The general assumption is that, in whichever population there is the highest concentration of the paraphyletic group of a clade, generally taken into consideration with considerable frequency and diversity, the high probability is that this is the 'representative' group wherein the clade was initially acquired and then spread out, and transmitted through the generations. Clades differentiated by microsatellite clusters in a paraphyletic group, could therefore be seen in the context of having undergone differentiation at the microsatellite level, but likely before downstream potential UEP mutations were acquired in the respective clusters [i.e. polyphlyetic clusters], that is—if we rule out independent parallel microsatellite mutations in the case at hand. So, generally speaking, a paraphyletic cluster of a clade with, i.e. no known downstream mutations of its sub-clades, are viewed as ancestral markers—no news here.

Another exemplary case, would be that of V12* paragroup, wherein clusters have yet to be differentiated into clearly identified V12 sub-clades:

Taking into account the above data, the previously described European cluster alpha and the northern African cluster beta are indeed confirmed as monophyletic groups of chromosomes, that, very likely, have their own binary markers yet to be discovered. — Cruciani et al. 2006.

So, why?, because as noted in the extract, for example...

there is a striking correspondence between the microsatellite clusters alpha and gamma and the binary haplogroups E-V13 and E-V32, respectively (Fig. IB). However, while all alpha cluster belong to E-V13, some E-V13 chromosomes are not contained in such a cluster. Conversely, all of the E-V32 chromosomes fall within cluster gamma (defined by the rare DYS19 11-repeat allele), but two gamma chromosomes are members of paragroups E-V12* and E-M78*. — Cruciani et al.,2006

This strong correspondence between certain clusters and binary markers, but NOT total correspondence, goes back to the point made about the polyphyletic clusters that Cruciani alluded to and that the present author briefly illustrated in a scenario above, concerning the paragroup.

Wherever V12 may have arisen [in Africa], it seems to be the ancestral lineage to E-V32, which has almost all of the gamma clusters identified and is found mainly in east Africa, particularly in the African Horn.

Earlier, the present author wrote:

"Clades differentiated by microsatellite clusters in a paraphyletic group, could therefore be seen in the context of having undergone differentiation at the microsatellite level, but likely before downstream potential UEP mutations were acquired in the respective clusters [i.e. polyphlyetic clusters], that is - if we rule out independent parallel microsatellite mutations in the case at hand. So, generally speaking, a paraphyletic cluster of a clade with, i.e. no known downstream mutations of its sub-clades, are viewed as ancestral markers—no news here."

And so, when looking at this...

there is a striking correspondence between the microsatellite clusters alpha and gamma and the binary haplogroups E-V13 and E-V32, respectively (Fig. IB). However, while all alpha cluster belong to E-V13, some E-V13 chromosomes are not contained in such a cluster. Conversely, all of the E-V32 chromosomes fall within cluster gamma (defined by the rare DYS19 11-repeat allele), but two gamma chromosomes are members of paragroups E-V12* and E-M78*. — Cruciani et al.,2006

...since, it appears that the clusters above are both monophyetic group of chromosomes, it would appear that the V13 was a potentially unique mutational single-event that occurred prior to the mutational events [in tandem repeat nucleotide sequences] characterizing the microsatellite cluster 'alpha', so that it would appear in association with two different microsatellite clusters. Essentially, V13 assumes the role similar to that characterized by the "clade" which identifies the paraphyletic group in the above mentioned scenario. Conversely, it would appear that cluster gamma came to being sometime after the M78 mutation, but before V12 mutation. This would likely explain why an M78 chromosome, which appears to be devoid of any known downstream M78 mutations, would have this microsatellite cluster as do V12* and its derivative V32. The V12 chromosomes that have the delta cluster, may well be the product of multiple mutational events—that is, convergent "parallel mutations". See:

The presence of three E-V13 chromosomes within cluster delta and the exclusion of some E-V12 and E-V22 chromosomes demonstrate that cluster delta cannot be regarded as a monophyletic unit

Now of course, in the event that the present author may have overlooked something here or there, the information herein is subject to modification.

NRY Haplogroup E3a: A Multidisciplinary Proposal of Its Origins

Having touched on this matter in an earlier posting but in a broader topic involving more lineages, this post will focus on one lineage—haplogroup E3a.

Geological and geographical evidence

~23 ky ago: Ogolian aridity takes hold, and renders much of north Africa desertified.

The advent of Hg E3a's TMRCA essentially coincides with rise of the Ogolian aridity.

• PN2 clade (E3) bearers in the vicinity of the general expanse straddling Sudanese-Central African Republic -Ugandan-Kenyan region [get a map aid, if necessary] give rise to E3a ~ between 21 and 18 ky ago [see Semino et al. 2004 for TMRCA dates, pending additional or new info]; E3b-M35* would have likely arose relatively earlier than E3a* [as evidenced by its near absence in some the populations that carry this], sometime prior to the Ogolian and the LGM period.

Hence, indications are that the initial territory of an ancestral Hg E3a bearing group would have likely started south of the Sahara, at a time when:

• The Ogolian aridity rendered much of North Africa with adverse weather conditions, turning much of that general region into desert. The Sahara at this time, extends south beyond its current boundaries to a certain point, likely as far as a little beyond the Niger bend.

• The above mentioned geological conditions in the aforementioned geography indicate that the population density in those arid regions would have been quite sparse—meaning, that most populations would have then been concentrated south of the broad desert region.

Reference to the geographical extent of this desertification is laid out here in maps: AFRICA DURING THE LAST 150,000 YEARS [clickable]

Archaeological evidence
Archaeology indicates that much of west Africa during the height of the Ogolian aridity was abandoned, with many of the populations living therein in the pre-Ogolian periods seeking refuge in the last vestiges of vegetation beyond the desert, which at the time - as noted above, extended to as far as beyond the Niger River bend, and possibly few moving to the far northwestern coast of Africa, if not crossing over to the Iberian or Southwestern European region [perhaps to this end, possible case can made from findings in Goncalves et al. 2005?], which was then a major refuge center for European groups trying to cope with the side-effects of the LGM in their neck of the woods. Vivid archaeological indicator of this comes from:

• "After a favourable climatic period, characterised by relatively dense and diversified Palaeolithic occupations, the arid Ogolian begins locally around 23000 years BP and is represented at Ounjougou by a significant depositional and archaeological hiatus." — Aziz Ballouche [see: Link ]

Incidentally, when this was going on in west Africa, arid conditions extended all the way to the horn-shaped coast of the African Horn, possibly encouraging populations to reside relatively more inwards—that is, away from that aridified horn-shaped coastal region; rather, populations of that region were likely encouraged to seek refuge in the general region straddling southern Sudan, Ethiopia, Kenya and Uganda or even further—i.e. region straddling Uganda, Kenya, and Tanzania. [See AFRICA DURING THE LAST 150,000 YEARS, for visual aid—geology conditions via geography in the Ogolian period]

It is again, from archaeological evidence, that we get a picture of when repopulation events make their appearance, and in what pattern they occur, i.e. things which are all relevant to understanding the circumstances and nature of how the Hg E3a bearing group makes it appearance in west Africa:

• Consequently, it has to be seen in the context of heavy rainfalls and a resettlement of the vegetation cover, during the 10th millennium BC, that a **new population** arrives on the Plateau of Bandiagara." — Human population and paleoenvironment in West Africa [see: Link ]

...and we see how these repopulation events occur sequentially from archaeological record, showing a movement from an east-to-westward direction, and thereafter a south-to-northward movement in west Africa itself:

• From 30,600 to 10,000 BC: "A cultural flow, from the southeast of Subsaharan Africa and to the Sahara, could explain the diffusion of the microlithic industries all the way through West Africa. We observe them initially in Cameroon at Shum Laka (30.600-29.000 BC), then at the Ivory Coast in Bingerville (14.100-13.400 BC), in Nigeria in Iwo Eleru (11.460-11.050 BC), and finally in Ounjougou (phase 1, 10th millennium BC)." — Human population and paleoenvironment in West Africa [see: Link ]

This east-to-west movement shows that a new group of people moved into west Africa, because the "microlithic traditions" that appear at Shum Laka had been in existence for as long as ~ 30 ky ago, and yet didn't show up in west Africa proper until ~ 14 ky ago, a late date which works well within the confines of the TMRCA age of Hg E3a. So the people originally responsible for that "microlithic tradition" at Shum Laka were not the people who likely brought that tradition to west Africa, but by a new group of people who passed through Shum Laka. These new group of people first appeared in vegetation holdout regions beyond the Niger bend, and gradually moved northward, eventually reaching to regions as far as that of Ounjougou, as evidenced by the above carbon-dated archaeological finds. It should be remembered that the Ounjougou region was abandoned in the intense desertification period.

*Details of the "microlithic traditions" had been provided in a related earlier post: P2 Clades: The Arrival of E3a and E3b Haplogroups [clickable]

Genetic evidence
The east-to-west movement of new groups [the candidates being E3a bearing group] into west Africa observed above, seems to be lent further support from genealogical finds.

Observations of genetic differentiation within contemporary E3a bearing populations, suggests that the earliest Hg E3a bearing groups, carrying mainly M2, P1 and M180 mutations devoid of the M191 mutation, had moved to the far west region of Africa...from an eastern-oriented origin:

Consider for one,

• Although haplotypes 22, 24, and 41 were probably all involved in the Bantu expansion, the processes that determined the current distribution of these haplotypes in the Sudanese belt (a region south of the Sahara extending from western to central Africa) seem to have been more complex and perhaps involved a separate expansion.

• In particular, haplotype 24 and its derivative, haplotype 22, harbor opposite clinal distributions in the region, a finding that is at odds with the hypothesis of a parallel dispersion of these two lineages in the area.

• Haplotype 22 has a frequency of 23% in Cameroon (where it represents 42% of haplotypes carrying the DYS271 mutation), 13% in Burkina Faso (16% of haplotypes carrying the DYS271 mutation) and only 1% in Senegal (Semino et al. 2002), whereas haplotype 24 reaches its highest frequency (81%) in Senegal (Semino et al. 2002).

• A possible explanation might be that haplotype 24 chromosomes were already present across the Sudanese belt when the M191 mutation, which defines haplotype 22, arose in central western Africa. Only then would a later demic expansion have brought haplotype 22 chromosomes from central western to western Africa, giving rise to the opposite clinal distributions of haplotypes 22 and 24.

Source: Cruciani et al. 2002, A Back Migration from Asia to Sub-Saharan Africa

This piece shows that the oldest Hg E3a bearing populations, characterized by high frequencies of haplotype 24 and relatively modest frequencies of haplotype 22, remain localized in West Africa; the contrasting distribution and frequency patterns of these haplotypes suggest that the higher the population with haplotype 22, the less older it is in its genetic composition relative to those bearing less haplotype 22 in a gene pool dominated by the relatively older haplotypes, like haplotype 24. Senegal appears to have the highest concentration of haplotype 24, and interestingly, the lowest concentration of haplotype 22...thus, making it likely the oldest Hg E3a bearing group.

The Senegalese samples also have other peculiarities that further support the aforementioned idea of their being the oldest Hg E3a bearing group:

• Hg E3 (P2 or PN2 clade):
  
  Bantu (South Africa) - E3* = 1.9%, Senegalese - E3* = 2.9%, Ethiopian (Amhara) - E3* = 10.4%, Ethiopian (Oromo) - E3* = 12.8% in the ascending order.
  

...the 'older' groups appear to have relatively wider distribution of E3, as the Senegalese sample in particular seems to indicate vis-a-vis other Niger-Congo speaking groups elsewhere; a lineage which has by far the highest frequencies and distribution in Ethiopia [which is in East Africa fyi]

The Senegalese sample shows considerably more E-M35* than that from other Niger-Congo speaking groups of sub-Saharan West Africa, which are not immediately neighbouring major "ancient" African groups in East Africa or like Khoisans.

Hg E-M35* lineages:

• In descending order…Ethiopian (Oromo) - E-M35* = 19.2%, KhoiSan (South Africa) - E-M35* = 16.7%, Ethiopian (Amhara) - E-M35* = 10.4%, Berber (North-Central Morocco) - E-M35* = 7.9%, Berber (Southern Morocco) - E-M35* = 7.5%, Senegalese - E-M35* = 5%, Tunisian - E-M35* = 3.4%, Algerian - E-M35* = 3.1%, Arab (Morocco) - E-M35* = 2.3% , Burkina Faso -E-M35* = .9%
  

The Senegalese group is also the only sub-Saharan 'predominantly-Niger-Congo' speaking group that shares the rare microsatellite motif with Ethiopians on the E-M78 bearing chromosome:

It is interesting that both E-P2* and E-M35* and their derivatives, E-M78 and E-M123, exhibit in Ethiopians the 12-repeat allele at the DYS392 microsatellite locus, an allele scarcely seen (Y-Chromosome STR Database), especially in other haplogroups and other populations (A.S.S.-B., unpublished data).

In addition, the Ethiopian DYS392-12 allele is usually associated with the unusually short DYS19-11 allele, which is typical of this area. These findings are not easily explained. One possible scenario is that an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11). Alternatively, the microsatellite motif may be due to homoplasy.The first scenario is more likely, since this unique microsatellite haplotype occurs in E-P2*, E-M35*, and E-M78 but is almost *absent in all other haplogroups and populations*.

In addition, the high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere.

Moreover, the observation that the derivative E-M78 displays the DYS392-12/DYS19-11 haplotype suggests that it also arose in East Africa. This is illustrated by the microsatellite network (fig. 3, shaded area), which reveals that the Ethiopian branch harboring DYS392-12 is not shared with either Near Eastern or European populations. — Semino et al. Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

The Ethiopian sample may not share the said allele with those populations mentioned, including the northwest African samples as far as the present author can tell, but it does share the said allele with the Senegalese sample [see fig. below], which would suggest that the Senegalese M78 derivative didn’t come from interaction with its northwest African neighbors; rather, they may well be relics of ancient migrations from east to west.

For larger image, click on this link: Source

So what do all these genetic indicators say?

Senegalese sample has the highest concentration of haplotype 24 and the lowest concentration of haplotype 22 - making it the most likely ancient Hg E3a bearing group, it also has higher Hg E3 vis-a-vis other Niger-Congo speaking group of west Africa, has the higher Hg E-M35* vis-a-vis other Niger-Congo speaking groups not neighbouring major "ancient" populations of east Africa or south Africa [aka KhoiSans], and has the rare Ethiopian/East African 12-repeat allele at the DYS392 locus.

The advent of Hg E3a itself coincides with the rise of the Ogolian aridity, which rendered much of North Africa to as far as beyond the Niger River bend largely inhabitable, inducing populations to be densely populated south of the Sahara, which is therefore the likely region of the rise of TMRCA of Hg E3a bearers.

Bearing "rare" lineages predominantly found in east Africa - i.e. the likely point of origin, along with sequential archaeological evidence for [east-to-west and thereafter, in situ west African south-to-north] repopulation events in west Africa, much of which was abandoned in the Ogolian desertification, show that the earliest Hg E3a bearers— which finds expression in Senegalese samples - could not have arose in situ west Africa, but originated in an eastward oriented geography and migrated to west Africa, as the Ogolian aridity relaxed, bringing along with them new microlithic traditions picked up from the Shum Laka region, settled therein and thereafter underwent demic expansion, resulting in the "high diversity and frequency" of the Hg E3a distribution in west Africa.

All this becomes even more apparent, when one realizes that Hg E3 (PN2 clade) is quite rare even in sub-Saharan west Africa, but even rarer in the Sahara. It has the highest frequency in sub-Saharan east Africa [Ethiopia], where it is deemed to have originated— and so, the likelihood of the emergence of Hg E3a in a region with significantly higher frequencies of Hg E3 makes more sense than vice versa.

The above are all the reason the present author found it particularly simplistic in a discussion that he was a part of in the past, a strange question asked by a discussant, as to how one could possibly reconcile 'high diversity and frequency' of Hg E3a in west Africa with the prospect of its origins outside of west Africa; that question was no doubt a mentality born out of lack of familiarity with genetics and how multidisciplinary science works.

Update!

Getting back to the point raised earlier about the rare 12-repeat allele at DYS392 by Semino et al...

It is interesting that both E-P2* and E-M35* and their derivatives, E-M78 and E-M123, exhibit in Ethiopians the 12-repeat allele at the DYS392 microsatellite locus, an allele scarcely seen (Y-Chromosome STR Database), especially in other haplogroups and other populations (A.S.S.-B., unpublished data). 

In addition, the Ethiopian DYS392-12 allele is usually associated with the unusually short DYS19-11 allele, which is typical of this area. These findings are not easily explained. One possible scenario is that an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11). Alternatively, the microsatellite motif may be due to homoplasy.The first scenario is more likely, since this unique microsatellite haplotype occurs in E-P2*, E-M35*, and E-M78 but is almost *absent in all other haplogroups and populations*.

In addition, the high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere.
Moreover, the observation that the derivative E-M78 displays the DYS392-12/DYS19-11 haplotype suggests that it also arose in East Africa. This is illustrated by the microsatellite network (fig. 3, shaded area), which reveals that the Ethiopian branch harboring DYS392-12 is not shared with either Near Eastern or European populations. — Semino et al. Origin, Diffusion, and Differentiation of Y‐Chromosome Haplogroups E and J, 2004.

To which the present author responded...

The Ethiopian sample may not share the said allele with those populations mentioned, including the northwest African samples as far as I can tell, but it does share the said allele with the Senegalese sample [see fig. below], which would suggest that the Senegalese M78 derivative didn’t come from interaction with its northwest African neighbors; rather, they may well be relics of ancient migrations from east to west.

Cruciani et al. in their 2007 publication, Tracing human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12, had this to say about the 12-repeat allele in question:

“An eastern African origin for this haplogroup was hypothesized on the basis of the basis of the exclusive presence in that area of a putative ancestral 12-repeat at the DYS392 micro satellite , found in association with E-M78 chromosomes (Semino et al. 2004). North-eastern African populations were not represented in that study.

In order to test this hypothesis, we analyzed for DYS392 a geographically widespread subset of the E_M78 chromosomes here identified. We observed that the DYS392 12-repeat allele is associated with the majority of the chromosomes belonging to the north-eastern African E-V12* (15 out of 18) and to the eastern African E-V32 (21 out of 23), with about half (9 out of 21) of the E-V22 chromosomes (both in eastern and north-eastern Africa), with a few of the European E-V13 (2 out of 23) and with some north-African E-V65 (3 out of 16) chromosomes.

These findings show that the DYS392 12-repeat allele is common in different regions characterized by high frequencies of E-M78, and suggest that it was most likely generated by multiple mutation events occurring in different UEP-defined sub-haplogroups. Thus, the DYS392 allele distribution is not informative to infer the place of origin of E-M78 chromosomes.”

Cruciani et al. point out that Northeast Africa wasn't represented in the 2004 Semino et al. study, presumably to emphasize the point that its detection therein would have shown that the 12-repeat allele in question wasn't confined to sub-Saharan east Africa, particularly Ethiopia. It is certainly true that northeastern Africa was not represented, but in fact, a close examination of Semino et al.'s 2004 study, shows that the 12-repeat allele wasn't confined to sub-Saharan east Africa; it makes single or very low appearances in the "Near Eastern" and "European" samples, and interestingly none in north African [sans northeast Africa] samples.

Cruciani et al. on the other hand, did detect the 12-repeat allele in north African [sans northeast Africa], but still in relative low frequency (3 out of 16). The same applies to their findings in European samples, where it appears to be yet rarer than that of the north African samples. Considerable frequency is however noted in their northeast African sample, and consistently, in sub-Saharan east African samples. So, even going by Cruciani et al.'s findings, the greater distribution of the 12-repeat allele in eastern Africa in general, would argue for its introduction from eastern Africa.

Cruciani et al. reckon that simply because the 12-repeat allele is not confined to east Africa, it therefore doesn't allow one to infer the place of origin of E-M78 bearing chromosomes. This ignores the point just made about its relatively rare occurrence outside of east Africa. Cruciani et al. reach this conclusion on the understanding that the 12-repeat allele's appearances in distinct sub-clades invokes homoplasy or parallel mutational events, and indeed, Semino et al. 2004 did not rule out that possibility, but unlike Cruciani et al. they took additional material into consideration:

1) "It is interesting that both E-P2* and E-M35* and their derivatives, E-M78 and E-M123, exhibit in Ethiopians the 12-repeat allele at the DYS392 microsatellite locus, an allele scarcely seen..."

So while there is notable presence of 12-repeat allele bearing E-M78 chromosomes in northeast Africa as well, only in sub-Saharan east Africa does one come across not only considerable frequencies of E3-P2 [PN2 clade], but also the more immediate precursor of Hg E-M78, i.e.— Hg E-M35*, which bear this 12-repeat allele. As far as the present author can discern at this point, pending introduction to studies that suggest otherwise, the ensemble of at least three different PN2 macro-clades—including the ancestral ones—bearing the said "12-repeat allele" only occurs in sub-Saharan east Africa. Case in point:

"...first scenario is more likely, since this unique microsatellite haplotype occurs in E-P2*, E-M35*, and E-M78 but is almost *absent in all other haplogroups and populations*."

2) "One possible scenario is that an ancient differentiation of the E-P2 haplogroup occurred in loco (East Africa). However, this also implies a low mutability of the associated microsatellite motif (DYS392-12/DYS19-11)...

In addition, the high stability of the DYS392 locus (Brinkmann et al. 1998; Nebel et al. 2001) and of the shorter alleles of DYS19 (Carvalho-Silva et al. 1999) has been reported elsewhere."

So again, while not ruling out independent parallel microsatellite mutational events across different PN2 clades, the repeat occurrence of the 12-repeat allele across different PN2 clades, including the ancestral ones, coupled with the possibility of "low mutability", which translates into "high stability" of the locus in question, indicates that the 12 repeat could well have also been inherited from a precursor PN2 clade(s). If the latter is the case, certainly sub-Saharan East Africa as the likely place of origin for the allele, can be put forward as a strong argument. And in getting back to the appearance of this allele in sub-Saharan or Sahelian west Africa, in the Senegalese sample for instance, would tend to favor an east African origin at some point in history, rather than as a remnant of interactions with coastal northwest Africans, where the allele is rare, even going by Cruciani et al.'s findings.

Sickle Cell Disease by the HbS haplotype

HbS of African derivation...some parties almost always associate its presence in non-African locations, or else what is perceived to be "non-Sub-Saharan" Africa locations, with historic slavery. How accurate is this observation?

Before one gets into the details about the issue of legitimacy of the above mentioned perception, it is perhaps necessary to know some basic things about HbS:

It is essentially an altered beta-globin (b-globin) cluster of the Hemoglobin A, a cluster which is located at position 15.5 away from the centromere of chromosome 11 on its short arm; the specific alteration that gives rise to HbS instead of the "normal" HbA, is a "point mutation" [*1] in GAC codon at position 6 of the b-globin cluster, which converts GAC to GTG, resulting in the replacement of glutamic acid amino acid by valine. Several haplotypes are associated with this mutation; there are supposed to be some 475 identified allele variants of the b-globin gene, of which the HbS haplotypes are a subset. This includes the African derivatives, namely; the Senegalese, Benin and Bantu haplotypes. Outside of African derivatives, there is the Asian haplotype, mainly found in Arabia and the Indian sub-continent.

Now, since it is difficult to age HbS variants with respect to one another, due to selective pressure acting on the extent of its availability, the distribution pattern becomes worthy of noting, as well as geographical origin. Apparently, the African haplotypes have the highest prevalence among African subjects and recent African descendants. Of the African variants, the Benin haplotype appears to have wider geographical reach, perhaps because it originated in the vicinity of the Niger River Valley, and spread through ancient contact in the Sahara. So, treating African HbS haplotypes unanimously as the product of slave trade is not only simplistic, but also erroneous. Consider the fact for example, that there are locations where African slaves had historically been brought as "pick up points" for trade between the trading parties, after having been picked up from their home region in some other geographical location, but are nonetheless virtually free from the sickle cell disease; the African Horn comes to mind as an example, and yet HbS has hardly penetrated that region. Some may be tempted to attribute this phenomenon to the environment of that region, but that assessment would be oblivous to the fact that Bantu-speaking populations neighbouring the populations of these regions, have high prevalence cases of HbS variants [i.e. Bantu haplotype]. This point is especially relevant, when its presence in Egypt is merely explained off as the product of that region being a historic corridor for slave trade. Additionally, it is necessary to note documented cases of HbS outside of sub-Saharan Africa, in order to realize that the antiquity of its heritage in those regions precedes historic slave trade involving slaves brought from sub-Saharan Africa. For examples, we have the following:

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.

Objective
This study was conducted with two objectives: to determine the b-globin gene haplotypes associated with Hb S in Arabic-speaking populations from different countries (Egypt, Syrian Arab Republic and Jordan), and to compare the results with those of Saudi SCD patients from different regions of Saudi Arabia, where both mild and severe forms of the disease exist.

Patients and methods
The study group of 126 SCD patients comprised 14 Egyptians, 9 Syrians, 10 Jordanians and 93 Saudis. Some of the Egyptians, Syrians and Jordanians were living in Riyadh, while others were living in their own countries, from where buffy coats were received. The Saudis were from three areas of Saudi Arabia where the sickle-cell gene has been reported at a high frequency, these being eastern (22 patients), south-western (67) and north-western (4) regions...

Buffy coat was used to extract DNA [18]. Portions of DNA were first subjected to polymerase chain reaction (PCR) amplification, and the PCR product was restricted using Ava II, HindIII, HincII, Hpa I and Xmn I, following the procedure published earlier [19,20]. The presence or absence of each site (shown in Figure 1) was identified, based on the size of the fragments produced (Table 1).

Results
"We collaborated with researchers from Egypt, Syrian Arab Republic and Jordan in a study of patients with sickle-cell disease from those countries, and from various parts of Saudi Arabia, in order to investigate the influence of genetics on the clinical presentation of the disease, and to attempt to determine the **origin** of the sickle-cell gene in Arabs. Our results suggest that beta-globin gene haplotypes influence the clinical presentation of sickle-cell disease, and that there are at least two major foci for the origin of the sickle-cell gene, one in the eastern part of Saudi Arabia, and the other in the populations of North Africa and the north-western part of the Arabian peninsula…

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."

Source: East Mediterr Health J. 1999 Nov;5(6):1154-8 http://www.emro.who.int/Publications/EMHJ/0506/10.htm

From the above, one gets the impression that the Benin haplotype is dominant over the other haplotypes wherein it appears in a heterozygous case. Not sure how that specifically goes on a case by case basis, wherein the Benin haplotype would appear with the other African variants, but at the least, this study demonstrates that it is the more likely dominant haplotype over that of the Asian haplotypes; the present author takes this to be the case [with the understanding that from the African side, only the Benin haplotype has notably penetrated the regions under discussion, while the others mentioned are of the Asian type], because it has always been identified with the severe cases of SCD in not only the homozygous cases, but also in the heterozygous cases...that is to say, what are the chances of heterozygous cases, especially in areas like eastern Saudi where the Asian haplotype is the prevalent HbS haplotype, being inclusive of Benin-Asian haplotype pairings? Quite likely—albeit to varying degrees, notwithstanding the discernable distribution patterns of these haplotypes as mentioned in the study. On the other hand, as noted, and to reiterate:

one in three Syrians and one in five Jordanians had a milder disease, and the Saudi-Indian haplotype was identified.

...this even when it occurred in either homozygous or heterozygous cases, not involving the Benin haplotype [which consistently appeared in severe cases of SCD, regardless of whether it was a heterozygous or homozygous case].

Another noteworthy case, is that SCD appears in the remains of predynastic subjects, and the only HbS haplotype noted in Egypt today is the Benin haplotype. As we will shortly see, the Benin haploype also accounts for all the known HbS cases outside of Africa, save for the Asian haplotype, largely confined to eastern Saudi Arabia and the Indian sub-continent.

Use of the amplification refractory mutation system (ARMS) in the study of HbS in predynastic Egyptian remains.

Marin A, Cerutti N, Massa ER.

1999 May-Jun

Dipartimento di Biologia Animale e dell'Uomo, Università degli Studi di Torino.

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.

PMID: 11148985 [PubMed - indexed for MEDLINE]

The interesting thing about the study, is that it too talks of severe cases of SCD, which as we've just seen, is the case with the Benin haplotype as well, and it takes us to a period that precedes any known documentation of slave trade involving sub-Saharan Africans.

Let's take a look at the distribution pattern and type of HbS haplotypes present in global samples:

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

The African type in the above regions appear to be exclusively the Benin haplotype, in contrast to...

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, Kingstom.

It is of no coincidence that the other African haplotypes outside of the Benin haplotype, have found their way into the Americas, regions that have been affected by the historic slave trade, and have large size settler populations of recent common ancestry from sub-Saharan Africa.

What all these show, when taken together, is that blanket attribution of African HbS variants solely to historic slave trade events is a blatant distortion of reality.

Ps - A good map showing the geographical range of HbS haplotype variants:

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:

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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
(Morocco)

“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

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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)

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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

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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.

And...

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 Gérard 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.

RFLPs: Lucotte et al., A case study — Pt. 2

Continuing with Lucotte et al. 2006, North African Berber and Arab Influences in the Western Mediterranean Revealed by Y-Chromosome DNA Haplotypes.

Link to the first part of this topic:
RFLPs: Lucotte et al., A case study — Pt. 1[clickable]

There is the question of haplotype V corresponding to more than one binary marker—which is why it is important for one to understand the *context* of the specific study in question, rather than assume that one group of researchers' context per designator is the same as the other. Many a times, researchers use a standardized designation like the Y Chromosome Consortium nomenclature, applying the same context to facilitate cross-reference between researchers, and hence, compare the results at hand, but not every researcher adheres to the most popular standardized nomenclature system—some researchers use one or another system of nomenclature, dependent on the methods applied to discern haplotypic differentiation.

From what the present author can tell, Lucotte et al. didn't run their haplotypes for binary markers for the earlier studies, as exemplified in their 2001 study in "A case study — Pt. 1", but given that Lucotte et al. this time around [i.e. in the present study] proclaimed to have not only used the same sequencing methods used by them in the earlier studies [namely the 2001 and 2003 studies for example], but also the DNA polymerase chain reaction used by Underhill et al. to test for binary markers M81 and M78, presumably using samples already tested by Lucotte et al. in previous studies, they were able to verify that Lucotte et al.'s 2001 and 2003 haplotype V [which they deemed to be 'a characteristic Berber haplotype' and ' of predominantly Berber origin'] were mainly M81 chromosomes, after having further discerned haplotype V into at least two discernable groups: Vb and Va, using Gonçalves et al.'s PCR method. All the Moroccan bearers of the sub-group Vb, turned out to be M81 carriers, including *all* the 'Berber' designated speakers of this bunch and 21 of the 59 'Arab' designated North Africans; the remaining 38 'Arab' designated north African bearers of the sub-group Va either tested positive for M78 or they didn't. To be specific, 31 of the 38 Arabic speaking North African bearers of haplotype V [sub-group Va] tested positive for M78, while the rest didn't. This results confirm the sub-group Vb to be M81, and Va to be partly M78. Going by this, the majority of what Lucotte et al. refer to as a 'characteristic Berber haplotype', are M81 chromosomes.

In that Lucotte et al.'s haplotype V appears to be largely of M81 [all Vb subgroups in the intro study] and partly M78 [sub-group Va], with the remaining [sub-group Va] yet to be identified by other markers, it is obviously associated with E3b macrohaplogroup. Additionally, according to Keita, haplotype XI also turns out to be Hg E3b affiliated. Thus, alerting oneself to the context at hand, is warranted!

As to the question of whether the authors in the present study were able to genetically differentiate Moroccan "Berbers" and "Arabs" into distinct genealogical camps, the answer is that they were probably going by self-ethnic identifications of the contributors of the samples in question. Apparently much of north African populations were really 'Arabized' populations, not original ethnic Arabs. However, as the present author noted before, there is something to be discerned here:

• All* subgroup Vb individuals are either "Berber" identified Tamazight individuals [47 individuals] or what appears to be "Arabized" Tamazight individuals [21 individuals], testing positive for E-M81, whereas...

• ...out of the 38 remaining "Arabic" identified individuals who tested positive for the subgroup Va, 31 turned out to be positive for E-M78. The remaining 7 individuals of this 38 "Arabic" identified individuals didn't test positive for either E-M81 or E-M78. Those individuals *could* [but not necessarily] possibly turn out positive for a non-M78 and non-M81 marker like "R1a"; however, **if** J happens to have the same combination of RFLPs , then it could well be a possible candidate here, as it is the next frequent paternal line which isn't M35 derived, but still quite less frequent than the aboriginal E-M81 marker. Other non-M81 and non-M78 E-M35 [E3b] derived lineages could just as well still be a candidate.

• Four Moroccan "Berber" individuals out of the 51 tested, appear to be unaccounted for here. They probably fell into the Va subgroup, and likely didn't test positive for either E-M81 or E-M78. These individuals could just as well test positive for the aforementioned non-M78 and non-M81 possible candidates.

In any case, non-M81 and non-M78 lineages appear to be in the minority. The majority of Moroccan "Berbers" are M81, while the majority of the Moroccan "Arabs" are largely of subgroup Va E-M78 lineage [31 individuals], but carry a significant amount of subgroup Vb E-M81 [21 individuals]. So clearly, the "Berber" group, while they share lineages [largely E-M81] with their Moroccan "Arab" counterparts, can clearly be discerned from the said "Arab" counterparts, in that the later seems to have relatively more M78 lineages, as well as relatively more non-M81 subgroup Va lineage [7 individuals] than their "Berber" identified counterparts [possibly the unaccounted for 4 "Berber" individuals].

RFLPs: Lucotte et al., A case study — Pt. 1

From Lucotte et al., we have:

North African Berber and Arab Influences in the Western Mediterranean Revealed by Y-Chromosome DNA Haplotypes

Nathalie Gérard, Sala Berriche, Annie Aouizérate, Florent Diéterlen, Gérard Lucotte. Human Biology. Detroit: Jun 2006. Vol.78, Iss. 3; pg. 307, 10 pgs

During the 7th century A.D., Muslim people coming from the Arabian peninsula and the Middle East invaded North Africa. The most important population movement relating both sides of the Mediterranean Sea was the conquest of the Iberian peninsula by North African populations (with recruited Berbers), soon after the first Muslim invasion. More than eight centuries (8th to 15th centuries) of Muslim domination in the southern part of Iberia imparted an important cultural legacy (Conrad 1998) and probable gene exchanges between North African and Iberian populations.

Variations in DNA sequences specific to the nonrecombinant part of the Y chromosome, relating to paternal ancestry, are particularly interesting from a human population genetics point of view. The first published and most informative probe used in Southern blots for this objective is p49 (locus DYSl), which is able to identify at last five TaqI male-specific fragments (A, C, D, F, and I) that are polymorphic between individuals (Lucotte and Ngo 1985). Sixteen main corresponding haplotypes (numbered I-XVI) were identified using the p49 probe on DNA samples of unrelated males living in France (Ngo et al. 1986). Only recently has the molecular basis of the p49 TaqI polymorphisms been established (Jovelin et al. 2003); the polymorphisms correspond to variable TaqI sites located in the four DAZ genes located in the AZF-c region of the Y chromosome.

In fact, the conventional p49 TaqI polymorphisms were the most popular markers used in various populations because of their ability to detect more than 100 different haplotypes [for a compilation on the subject until the end of 1995, see Poloni et al. (1997)]. Haplotype XV (A3,C1,D2,F1,I1) was the most widespread haplotype in our initial study (Ngo et al. 1986). Haplotype XV was also predominant in the first European study we published (Lucotte and Hazout 1996), with elevated frequencies in French Basques. The geographic distribution of haplotype XV in Europe reveals a gradient of decreasing frequencies from this Basque focus toward eastern peripheral countries (Lucotte and Loirat 1999) but also toward southwestern countries. According to the Y Chromosome Consortium (2002) nomenclature, haplotype XV corresponds to the M173 lineage (Diéterlen and Lucotte 2005).

Haplotype V (A2,C0,D0,F1,I1) is the most frequent haplotype in North Africa (Lucotte et al. 2000), with a particularly high frequency (55%) in the populations with a relative predominance of Berber origin. Our previous study on the subject examined the relative frequencies of haplotype V in four Iberian populations compared with a Berber population living in North Africa (Lucotte et al. 2001). The highest frequency of haplotype V (68.9%) was observed in Berbers from Morocco, and the geographic distribution of haplotype V revealed a gradient of decreasing frequencies with latitude in Iberia (40.8% in Andalusia, 36.2% in Portugal, 12.1% in Catalonia, and 11.3% in the Basque Country) (Lucotte et al. 2001); such a cline of decreasing haplotype V frequencies from the south to the north in Iberia clearly established a gene flow from North Africa toward Iberia.

According to the Y Chromosome Consortium (2002) nomenclature, haplogroup E is characterized by the mutations SRY4064, M96, and P29 on a background defined by the insertion of an Alu element (YAP + ). The third clade, E3 (defined by the mutation P2), of haplogroup E is further subdivided into two monophyletic forms, the second one (E3b) being characterized by mutations M35 and M125. All of the 110 p49 TaqI haplotype V subjects from Morocco (51 Berbers and 59 Arabs) that we had previously tested correspond to haplogroup E3b.

In the present study we have subdivided haplotype V into its Berber (Vb) and Arab (Va) components in order to distinguish the relative contributions of these two ethnicity-specific markers in the gene pools of the populations living in Iberia and in other populations in the northern part of the western Mediterranean area.

Materials and Methods
DNA Samples. This study concerns 2,196 unrelated male DNA samples (Table 1). We collected 904 new unrelated males subjects, from three different countries (Portugal, France, and Italy): 79 from North Portugal and 59 from South Portugal; 243 from the Marseilles region of France; 192 from Genoa, 64 from Rome, and 128 from Naples in continental Italy; 39 from Sicily; and 100 from Sardinia. All these new samples correspond to adult males, whose origin is based on the local birthplace of their fathers and (at least) grandfathers. We have obtained informed consent from each of the French subjects studied.

We add for comparison the following subjects, already tested as bearing haplotype V in previous studies: 11 subjects from Mauritania, 51 Berbers from Morocco, 59 Arabs from Rabat, 80 subjects from Algeria, 39 subjects from Tunisia, and 17 subjects from Libya (Lucotte et al. 2000); 29 Spaniards from Sevilla (Lucotte et al. 2001); 4 Spaniards from Barcelona and 9 French Catalans from Perpignan (Lucotte and Loirat 1999); 11 French Basques, 1 subject from Montpellier, and 7 subjects from Grasse in France and 6 subjects from Milan in Italy (Lucotte and Hazout 1996); and 44 subjects from Corsica (Lucotte et al. 2002).
Figure 1 indicates the representative geographic points in the western Mediterranean area for each of the 22 populations studied.

Genetic Analysis. Blood samples were collected by venipuncture using EDTA as an anticoagulant. Genomic DNA was extracted as described by Gautreau et al. (1983), using proteinase K and phenol-chloroform extractions.

Y-chromosome haplotypes were obtained using Southern blot analysis by hybridizing TaqI-restricted DNA successively with the p49f,a-specific probes, oligolabeled by random priming, according to the method described by Lucotte et al. (1994). Subdivision of haplotype V detected by Southern blot analysis into subhaplotypes Va and Vb was realized by polymerase chain reaction (PCR), using the assay published by Gonçalves and Lavinha (1994); the presence of the "low" XY275 allele (275G) defines subhaplotype Vb, and the other allele defines subhaplotype Va.

To compare subhaplotypes Va and Vb with the E3b1 and E3b2 subhaplo-groups [according to the Y Chromosome Consortium (2002) nomenclature], we further analyzed our Berber and Arabic DNA samples from Morocco for biallelic markers M78 and M81 using PCR (Underbill et al. 2000).

Realization of the Isofrequency Haplotype Maps. The maps of subhaplotype Vb and Va isofrequencies have been drawn with the Spatial Analyst program (Arcview software) using the Kringing procedure. We have used the inverse distance weighting method (with a power of 2), which is well adapted to scarce data in coastal areas and on islands in the western Mediterranean area. Five neighbors are calculated for each quadrant.

Results
Table 1 summarizes the frequencies we obtained for haplotype V and sub-haplotypes Vb and Va in the 22 study populations. For the 2,196 males typed, 491 (22.3%) bear haplotype V. The frequency of haplotype V is 35.5% in Portugal, with a more elevated proportion in the south (49.2%) than in the north (25.3%). The frequency of haplotype V in the Marseilles region (11.1%) has a value similar to the mean value in continental France (9%). In Italy the highest frequency is attained in Sicily (28.2%), followed by Naples at 17.2%. As previously shown (Lucotte et al. 2000), haplotype V is found at the highest frequency (68.9%) in Berbers from Marrakech in Morocco; an apparently increasing east-west cline in haplotype V frequencies is shown in North Africa from Libya (44.7%) to Rabat (57.7%), with intermediate values for Tunisia (53.4%) and Algeria (56.7%). In Spain haplotype V is much more frequent (40.9%) in the south of the country [in Andalusia (Sevilla)] than in the north (12.9%) [in Catalonia (Barcelona)].

Subhaplotype Vb is the Berber subhaplotype because its most elevated relative value (63.5%) is obtained for the Berber population of Marrakech. In the non-Berber population of Rabat in Morocco, the frequency of subhaplotype Vb is only 20.6%, whereas the frequency of subhaplotype Va (Arab) is 37.3%. In order of decreasing values, the subhaplotype Vb frequencies are 40% in Mauritania, 35.9% in South Portugal, 25.4% in Andalusia, and 15.8% in Libya. Low frequencies of subhaplotype Vb are found in Sicily (5.1%), Algeria (2.8%), Tunisia (2.7%), and North Portugal (2.5%); frequencies less than 2% are found in French Basques (1.9%), in Naples (0.8%), and in Corsica (0.6%), Subhaplotype Vb is absent in Catalonia (Barcelona and Perpignan), in the south of France (Montpellier, Grasse, and the region of Marseilles), in continental Italy (Milan, Genoa, and Rome), and in Sardinia.

Table 2 summarizes the frequencies of subhaplotype Vb in North Africa, Iberia, the south of France, and Italy. The maximum value (63.5%) concerns the Berber population, but this frequency is notably lower (9.3%) for other populations from North Africa. In southern Iberia an elevated value (30%) is observed, but the frequency of subhaplotype Vb is only 1.8% in northern Iberia. These frequencies are less than 1% in France and Italy.

Figure 2 shows the isofrequency map of subhaplotype Vb in the western Mediterranean area (coordinates on the map: x = longitude, y = latitude). From the Berber focus in Berbers from southern Morocco, the frequencies of subhaplotype Vb decrease in North Africa to the north of Morocco and to the east in Algeria and Tunisia. For Iberia the most elevated value of subhaplotype Vb frequencies is in southern Portugal; relatively elevated values are observed in Andalusia, moderate values are observed in the southern part of Spain, and low values are seen in Catalonia.

In the present study all haplotype V non-subhaplotype Vb subjects are termed subhaplotype Va (Arab) subjects. Their maximum relative frequencies are 53.9% (Algeria), 50% (Tunisia), and 37.3% (Rabat) in North Africa. Table 3 summarizes the frequencies of subhaplotype Va in North Africa, Iberia, southern France, and Italy. The maximum value (45.8%) is found in North Africa. In northern Iberia a slightly more elevated value is observed (20%) compared to southern Iberia (14.6%). A frequency of 10.3% is seen in France, and in Italy the 14.6% value observed in the south is relatively more elevated than in the north (3.4%)

Figure 3 gives the isofrequency map of subhaplotype Vb. In North Africa frequencies decrease from east to west and southward. For southern Europe the map shows the relatively higher percentages observed in the south of Italy versus the north and (to a lesser degree) in the north of Iberia versus the south.

In our PCR assay the 68 Moroccan subjects with subhaplotype Vb (47 Berbers and 21 Arabs) were tested for the M81 marker: All subjects were positive for the M81 marker, so subhaplotype Vb is homologous with subhaplogroup E3b2. The 38 Moroccan non-Berber subjects were further tested for the M78 marker: Only 31 of them (80.8%) were positive for the M78 marker; we conclude that, in Morocco at least, subhaplotype Va corresponds only partly to subhaplogroup E3b1

Discussion
P49a,f TaqI haplotype V, which is homologous with haplogroup E3b according to the Y Chromosome Consortium (2002) nomenclature, is the predominant Y-chromosome haplotype in North Africa (Lucotte et al. 2000), where its geographic distribution shows an east to west cline. In the present study we have extended the research of haplotype V frequencies (Lucotte et al. 2001) in various European populations located in the western Mediterranean basin to include France, Portugal, and Italy. The frequency of haplotype V in the Marseilles region is 11.1%, a value similar to the main value we obtained previously for continental France (Lucotte and Hazout 1996). In continental Italy we observed the highest haplotype V frequency in Naples (17.2%); Sicily, with a frequency of 28.2%, corresponds to the most elevated value we observed for Italy. In South Portugal the frequency of haplotype V is very high (49.2%); we had previously obtained a similar value for Libya and for Mauritania. The frequency of haplotype V for North Portugal (25.3%) is similar to the value we obtained for Sicily in the present study.

To better divide haplotype V into its ethnic components, we have subdivided it into subhaplotypes Vb (Berber) and Va (Arab). We have established that subhaplotype Vb is the Berber haplotype, because it is present at very elevated frequencies (63.5%) in our Berber population from Morocco but at relatively low frequencies (20.6%) in our non-Berber population of Rabat. Such a distinction of a Berber component was also realized by Scozzari et al. (2001), because they observed that the haplogroup they named 25.2 was also more frequent in the Berber population from Morocco than in Arabs. Our present results show that subhaplotype Vb frequencies in North Africa decrease from west to east, starting from the Berber focus in Morocco; in the western Mediterranean area subhaplotype Vb is at low frequencies along the south coast of Europe but occurs at relatively elevated frequencies in southern Iberia (peaking at 35.9% in South Portugal). Flores et al. (2004), in their important study of various locations in Iberia, observed that subhaplogroup E3b2 is more frequent in southern Iberia, attaining a maximum value of 11.5% in the region of Málaga.

In the present study all the non-subhaplotype Vb subjects bearing haplo-type V are classified as subhaplotype Va (Arab); they probably correspond to a heterogeneous group representing various ethnicities (our results concerning the incomplete correspondence between subhaplotypes Va and E3b1 in Morocco suggest that). We have shown here that in North Africa the focus of subhaplotype Va frequencies is in Algeria (53.9%) and Tunisia (50.6%); from this focus frequencies of subhaplotype Va decrease in the south and the west of the region.
Subhaplotype Va attains substantial frequencies along the southern coast of Europe; these frequencies reached relatively elevated frequencies in France (Perpignan, 11.8%) and in southern Italy (Naples, 16.4%; Sicily, 23.1%). For Iberia, relatively more elevated values are attained for Andalusia (15.5%) and for North Portugal (22.8%). Brion et al. (2004) also showed relatively higher frequencies of haplogroup E* (xE3a) (up to 18.3%) in their study concerning northern Iberia.

We had previously established (Lucotte et al. 2001) that haplotype V showed a gradient of decreasing frequencies with latitude in Iberia, and we interpreted this pattern as a consequence of the historical Islamic occupation of the peninsula (Conrad 1998). The results reported in the present study concerning subhaplotypes Vb and Va (subhaplotype isofrequencies maps given in Figures 2 and 3) have again shown both of these gradients. From this perspective, the opposite pattern of gradient frequencies observed in Iberia for the western European haplotype XV (Diéterlen and Lucotte 2005) is reconciled with the slow reconquest of the Iberian peninsula from the north by the Christians, which lasted seven centuries and ended in Granada in 1492

Examination of the above, with the assistance of references to older Lucotte et al. studies:

With regards to Lucotte et al.'s earlier reference to RFLP haplotype V as "Arab", Keita is right about the "Arabic" label being misleading, but in fact, if one reads Lucotte et al. later work, it is clear that they associate this haplotype with North Africans. Lucotte et al. refers to North Egyptians, as Egyptian "Arabs", and makes reference to groups in other parts of North Africa as "Arabs" as well. So, in actuality Lucotte et al. were associating haplotype V with what they perceived as "Arabized" north Africans. And so, as one can see, they refered to haplotype V as "Arab" and "Berberian", and made note of the fact that the Falasha had a high frequency "haplotype V and XI", which attests to their African provenance.

Keita associates haplotype V and XI with African origin, but so does Lucotte et al. Keita associates V and XI [barring his reference to other contexts used by other researchers] with M35/215, but if Lucotte et al. associate these with "North Africans" and Ethiopian Jews, and proclaim that is of African provenance, they too must be associating it with M35/215. M81 is the predominant "Berber" variant of M35. So the question is, if haplotype V is predominantly "Berber" and associated with "Berber origin", and haplotype XI is noted to have high frequencies in Eastern Africa, and decreases as one moves west of the African continent, then what is haplotype V and haplotype XI, as presented by Lucotte et al.?...In the meantime from Keita's publication:

Some TaqI 49 a,f variants have multiple associations; for example VIII is affiliated with several lineages (Al-Zahery, 2003). So far research indicates that haplotype V in Africa is associated with the M35/215 (or 215/M35) subclade, **as is XI**, and IV with the M2/PN1/M180 lineage, both of the YAP/M145/M213 cluster. These lineages that in Africa that affiliate with haplotypes V, XI, and IV (called “sub-Saharan”), are joined by a transition mutation: “(M)ost notably the PN2 transition…unites two high frequency subclades, defined by M2/PN1/M180 mutations in sub-Saharan Africa, and M35/215 in north and east Africa…” (Underhill et al., 2001, p.50; see also Cruciani et al., 2002).

Hence, Lucotte et al.'s 'Arab' and 'Berber' appellations to V haplotypes in north Africa, appear to be what they deem 'Arabic' speaking North Africans and 'Berber' speaking North Africans. On another note, it also appears that haplotype XI is also affiliated with E-M35 in the Lucotte et al. data Keita used. To be certain about any of this, one might as well examine primary texts from Lucotte et al. themselves:

Y-chromosome DNA haplotypes in North African populations

Abstract:
The frequency distribution of Y-chromosome haplotypes at DNA polymorphism p49/TaqI was studied in a sample of 505 North Africans from Mauritania, Morocco, Algeria, Tunisia, Libya, and Egypt. A particulary high frequency (55.0%) of Y-haplotype 5 (A2,CO,DO,F1,11 ) was observed in these populations, with a relative predominance in those of Berber origin. Examination of the relative frequencies of other haplotypes in these populations, mainly haplotype 4 (the "African" haplotype), haplotype 15 (the "European" haplotype), and haplotypes 7 and 8 (the "Near-East" haplotypes), permit useful comparisons with neighboring peoples living in sub-Saharan Africa, Europe, and the Near East.

The highest frequency of haplotype 5 (68.9%) was previously observed in Berbers from Morocco, and it has been established that this haplotype is a characteristic Berber haplotype in North Africa....

Haplotype 5 (A2, C0, D0, F1, I1) has a particularly high frequency (55%) in North Africa (Lucotte et al. 2000), and is of predominantly Berber origin. — Lucotte et al.; North African genes in Iberia studied by Y-chromosome DNA haplotype 5; 2001.

At least based on this, with caution, it is strongly suggestive of M81 derivatives. The authors note that it is supposed to be a characteristic Berber haplotype in North Africa, and is of predominantly Berber origin. However, we also know that the Lucotte et al. data cited by Keita also shows V haplotypes in Egypt, along with XI haplotypes. V haplotype in Egypt has a gradient that increases as one moves from south to north, while that of XI is the opposite, with a gradient increasing as one moves from north to south. So in the Egyptian context, does this mean that V is still suggestive of E-M81 chromosomes? Who knows; but M81 is certainly attested to in Egypt. What about XI? Could that be suggestive of an M78 derivative? Plausible, given its high frequencies in sub-Saharan Africa, particularly east Africa. One has to ascertain this plausibility. **To be certain, one would have to be familiar with the specific binary markers that Lucotte et al. would have searched [usually done, once a restrictive digest [by restrictive enzyme] is undertaken to cut DNA into fragments] and amplified [PCR] for haplotype V in the 2001 study above and their 2003 study cited by Keita, to see if they continued to be in the same exact contexts or if variant binary markers were used in respective studies. As noted in the linked discussion, in Lucotte et al.'s case, this doesn't appear to be the case. However, the authors of the current head topic have addressed this issue, reassuring us with relatively more precision, what specific V haplogroups were involved in Lucotte et al.'s several studies.

To be continued.

Link to part 2:
RFLPs: Lucotte et al., A case study — Pt. 2 [clickable]