Haplogroup Assignment; Old Habits that Die Hard

Introduction:

It has become a common theme in DNA research papers dealing with population genetics, particularly those that are either published in the "west" or else rely heavily on references to previous publications by "western" research teams, to dichotomize human phylogeny neatly into two main types: African and non-African. As a result, a good amount of the readership of these papers have also become accustomed to treating human phylogeny accordingly. No doubt that the reactionary segment of that readership have applied such a phylogenetic arrangement synonymously with "races" of humanity.

It's one thing to assign human phylogeny into two main types, but it's another, in terms of how these assignments take form. One would be hard-pressed not to come across a single example, whereby lineage that is given an "L" designation in mictochondrial phylogeny, is automatically treated as "African", while the two main offshoots of the L3 clade are taken for granted as "non-African". Such arrangements tacitly or by design, insinuate non-overlapping phylogeny between the so-named two main groups. The discussion section will deal with this kind of arrangement of human phylogeny further, applying specific examples from published material.

How are the Media and Schools catching up with Scientific Progress? Pt.5

Introduction:

We proceed on from the last segment, wherein we looked at how nationalism and like ideology continues to plague science. No science has infamously suffered from this more than the discipline of human palaeontology. In the "west", the venture into this field started with getting to know remains of the European Neanderthal, and the sparking thereof, the belief that Europe was the hub of human origins.

How are the Media and Schools catching up with Scientific Progress? Pt.4

Introduction:

In the previous segment, a good deal of space was dedicated to a straightforward preliminary look at the portrayal of non-European peoples, especially Africans, in "western" media not merely as a loosely connected hodgepodge of unconscious and conscious underlying motives, ranging from economic considerations to racism, but rather, as a conscious undertaking of "western" imperialism, of which the 'western' establishments are quite mindful.

How are the Media and Schools catching up with Scientific Progress? Pt.3

Introduction:

In the previous segments of the this blog entry, much attention was paid to History channel documentary reenactments of the ancients of Africa, particularly the Ancient Egyptians. Ancient Egypt has been the most popular subject of 'western' fascination and romanticism, but this sort of thing has not been limited to just Egypt. It has been extended to other African complexes, from Timbuktu, the Great Zimbabwe, to ancient Abyssinia (modern day Ethiopia). A good example of this can be seen in the portrayal of an Ancient Abyssinian kingdom in the now 9 year old comedy flick of the title "The Hot Chick".

How are the Media and Schools catching up with Scientific Progress?-Pt2

Carried on from the first entry.

Introduction recap:

The taking up of African historiography by Europeans has long been mired with disinformation, as scholars of European descent sought to accommodate imperialist designs of their governments around the African continent. This matter had been particularly brushed on briefly in an earlier entry discussing the significance of additional Timbuktu chronicles that were brought to light in recent times and the corresponding rush to preserve those relics, whereby we come across the systematic construction of the "Ghana Conquest Theory", at a time when European polities had their eye set on colonizing African territories and fuel their growth with African resources. The historiography of Ancient Ghana, and Western Sudan (otherwise now recognized as "West Africa") in general, was but just one element of this disinformation campaign; the policy had extended to other elements of African historiography, Ancient Egypt being the most popular and enduring example of this. Complexes from Kush, Abyssinia or Aksum to the Great Zimbabwe had all become casualties of European disinformation.

How are the Media and Schools catching up with Scientific Progress?

Introduction:

The taking up of African historiography by Europeans has long been mired with disinformation, as scholars of European descent sought to accommodate imperialist designs of their governments around the African continent. This matter had been particularly brushed on briefly in an earlier entry discussing the significance of additional Timbuktu chronicles that were brought to light in recent times and the corresponding rush to preserve those relics, whereby we come across the systematic construction of the "Ghana Conquest Theory", at a time when European polities had their eye set on colonizing African territories and fuel their growth with African resources. The historiography of Ancient Ghana, and Western Sudan (otherwise now recognized as "West Africa") in general, was but just one element of this disinformation campaign; the policy had extended to other elements of African historiography, Ancient Egypt being the most popular and enduring example of this. Complexes from Kush, Abyssinia or Aksum to the Great Zimbabwe had all become casualties of European disinformation.

Review: Population Relationships in the Mediterranean Revealed by Autosomal Genetic Data (Alu and Alu/STR Compound Systems)

Herein, aspects of a recent publication by E. González-Pérez et al. (2009) under the heading described above, will be revisited and examined respectively.

The abstract goes as follows:

González-Pérez et al.

Am J Phys Anthropol. 2009 Nov 16.

The variation of 18 Alu polymorphisms and 3 linked STRs was determined in 1,831 individuals from 15 Mediterranean populations to analyze the relationships between human groups in this geographical region and provide a complementary perspective to information from studies based on uniparental markers. Patterns of population diversity revealed by the two kinds of markers examined were different from one another, likely in relation to their different mutation rates. Therefore, while the Alu biallelic variation underlies general heterogeneity throughout the whole Mediterranean region, the combined use of Alu and STR points to a considerable genetic differentiation between the two Mediterranean shores, presumably strengthened by a considerable sub-Saharan African genetic contribution in North Africa (around 13% calculated from Alu markers). Gene flow analysis confirms the permeability of the Sahara to human passage along with the existence of trans-Mediterranean interchanges. Two specific Alu/STR combinations-CD4 110(-) and DM 107(-)-detected in all North African samples, the Iberian Peninsula, Greece, Turkey, and some Mediterranean islands suggest an ancient genetic background of current Mediterranean peoples. - abstract ends

A run down of the Alu markers and 3 Alu-linked STRs, is as follows:

18 autosomal Alu markers: CD4, TPA25, APO, ACE, Yb8NBC120, Yb8NBC125, B65, D1, FXIIIB, A25, PV92, HS2.43, Sb19.3, Sb19.12, HS4.32, HS4.69, DM, Ya5NBC221

Tandem Repeats linked to sites identified with specific Alu insertions or deletions designated by three designators: CD4+, DM+ and FXIIIB-. These reportedly represent the "ancestral" states of the sites in question, and the nature of said site-states are indicated by either the "+" or "-" symbols respectively.

Y-chromosome Alu insertion: The YAP+ Y-chromosome Alu insertion, fairly common in African populations, particularly in the form of Hg E, serves as an addition to the collection of Alu markers cited above.

Populations sampled:

Click on the image to get a better resolution.

The study opens with the following lines:

As far as the origin of human populations in the Mediterranean is concerned, it is commonly accepted that their roots can be traced back to the Upper Paleolithic with the expansion of human groups from the Near East or Central Asia, or some millennia later with the westward and northward spread of Neolithic populations from the Fertile Crescent. Although there is little doubt regarding the human entrance route to the Mediterranean, controversy appears when different studies try to determine to what extent their current genetic background preserves traces of Paleolithic people and in which degree the almost continuous cultural and political contacts have influenced present genetic affinities.

Indeed, the authors are correct in their assessment about controversy in terms of how different studies interpret their observations, with regards to the entrance or exit of certain lineages, particularly in relation to the time of event and how extensive. Their own opening assessment attests to this, recalling the bit about origins of "Mediterranean" populations being traced back to the so-called "Near East" or Central Asia. This implies that northern Africa was a barren region for a long period of time, where no autochthonous African population ventured, even as humanity spent the bulk of its socio-biological evolution exclusively on the continent until ca "50-60 ky ago era" when a subset of anatomically modern humans successfully left the African continent for refuge elsewhere. This begs the question: human beings in Africa did not see fit to populate the northern areas of the continent, yet non-Africans were supposedly the first to see fit to do so? As a matter of fact, Maghrebi paleontological record stretches back to as far as the Middle Paleolithic era, preceding anatomically modern human occupation outside of Africa.

The authors appear to have been influenced in their assessment by the likes of Olivieri et al. (2006), whose work has been a subject of discussion (clickable link) on this site, as it relates to the Upper Paleolithic demic diffusion episodes in the northern sections of the African continent, and by the likes of Arredi et al. (2004), as it relates to theories surrounding Neolithic demic diffusions in that same region. Apparently, the authors are working with outdated concepts in their assessment, as earlier theories about Upper Paleolithic northern African complexes [see for example, the so-called "Ibero-Maurusian"] being manned by people from outside of the continent, based on erroneous assumptions built around archaeological finds on lithic artifacts, have now been rectified and updated with research that link origins of certain Upper Paleolithic lithics-oriented innovations to northern Africa, which were subsequently diffused into neighboring extra-African territories. Other erroneous assumptions about the earliest Upper Paleolithic northern African anatomically modern populations coming from outside had been based on shabby and flimsy reliance on outdated bio-anthropological concepts built around cranio-morphometric examinations. A notable example that immediately comes to mind, is the idea of Mechtoid populations [see: Mechta and Afalou: Do they and the so-called "Mechtoids" constitute a type with the "Cro-Magnon"?] , who were almost considered to be synonymous with the Cro-Magnon of Europe. Outposts of lingering cult-like Eurocentric elements continue to rely on ideological concepts of the Cro-Magnon as some sort of embodiment of "Caucasoids" or "Caucasians", and even that, has been discredited by more recent and refined analysis of cranio-morphometric data [See: Brace et al. (2005) and Chris Stringer (click), for example]. Even earlier bio-anthropologists tacitly took note of differentiations between the African Mechtoid variants and those of the European Cro-Magnon, even as superficially-invoked links were being insinuated. The bottom line is that the authors' presumptuous assessment, that the theory of northern Africa being first populated by people from the so-called Near East is a "commonly accepted" understanding, has little basis to it, as no prevailing evidence backs up such a notion. It implies that this is an understanding that has harmonized the various scientific multidisciplinary applications at our disposal, when no evidence has been brought forth to suggest such status quo. It is certainly not the message harmoniously relayed by either genetics or paleontology, nor by Upper Paleolithic complexes, as just mentioned a few comments ago. Then by what, aside from wishful thinking? Notably, the authors' own data does not lend support to such thinking. On the other hand, the flaws of Olivieri et al.'s (2006) and Ana Gonzalez et al.'s (2007) Upper Paleolithic demic diffusion hypothesis have been touched upon on this site before. U6 is undoubtedly Upper Paleolithic by most accounts, but it makes up very little of the contemporary northern African gene pool, while major M1 expansions are mostly linked with spread of proto-Afrasan or Afrasan-affiliated speaking groups some time in the late Paleolithic and early Holocene Neolithic time frames. Again, Olivieri et al. (2006) are emphasized here, because the authors of the present study appear to be relying on them, with regards to so-called Near Eastern sourcing of Upper Paleolithic northern African populations; see for example:

Recent mitochondrial DNA data (Olivieri et al., 2006) suggest a common Levantine source for the Upper Paleolithic cultures that occupied the European (Aurignacian) and North African (Dabban) shores of the Mediterranean. A more recent origin for these populations associated with the demic diffusion of Middle Eastern groups in the Neolithic has been suggested by studies of Y-chromosome (Arredi et al., 2004) and autosomal data (Myles et al., 2005; Tomas et al., 2008).

The authors of the present study themselves reference research that contradicts the idea of either the Upper Paleolithic or Neolithic sourcing from the so-called Near East; see for example:

A detailed survey of the E-M78 Y-chromosome haplogroup (Cruciani et al., 2007) indicates the Northeast African origin of this variant and its involvement in trans-Mediterranean migrations from North Africa to Europe during the last 13,000 YBP.

The predominant paternal markers of coastal northwestern-central African markers are comprised of E-M78 and E-M35 markers. This being the case for the northern African populations that the authors sampled here, the fact serves as a major contradiction to the so-called Near Eastern sourcing of northern African populations, who have supposedly persisted into contemporary times, if we are to go by conclusions drawn by the authors of the present study. Yet, we are suppose to buy into some presumption of the Upper Paleolithic "Near Eastern" sourcing of northern African populations as some sort of a "commonly accepted" understanding or truth.

It should be reiterated, as explained before on this site, that contemporary Imazighen-groups , who predominate much of northern Africa today, don't have TMRCAs—deemed to be "characteristic" of Tamazight or "Berber" speaking populations—that date to the Upper Paleolithic. Yes, these lineages derive from lineages of Paleolithic provenance, but they themselves, don't—at least not according to patrilineal lineage. The E-M81 mutation of the E1b1b lineage—which is predominantly found in Imazighen populations—has at most, been implicated in expansions that only go back as far as 8 ky or so ago. This falls short of the ages associated with Upper Paleolithic/Epi-Paleolithic or earliest Holocene cranial specimens uncovered in coastal northwestern Africa. Furthermore, none of the cranial specimens tied to contemporary northern African populations remotely tie in with the Cro-Magnon specimens of Europe, as Brace et al. (2005) had found out; whereas we are pressed to believe in ties between the so-called Mechtoid variants and the European-based Cro-Magnon.

Furthermore, the authors note:

Similarly, specific Mediterranean haplogroups or clades (U6 and M1b in the mtDNA; EM78 and EM81 in the Y-chromosome) have also been described for these populations and dated in Paleolithic times.

Nothing in the above supports "Near Eastern" sourcing of northern African populations examined here. None of the above markers are known for being quintessential indications of "Near Eastern" ancestry, as opposed to African ancestry. Not even U6, whose "non-African" ancestor remains ever so elusive, is a marker of the so-called "Near East"; it is quite rare in that region and its presence there can only be spoken of, in terms of back-migration from northern Africa, even if it is assumed that a proto-U6 ancestor was "Near Eastern" in origin. None of the markers above are even confined to the "Mediterranean" regions, so as to justify the use of the moniker of "Mediterranean haplogroups or clades".

One issue that stands out like a sore thumb, is the comprehensiveness of the authors' so-called "sub-Saharan" collection; see:

In search of new insights into these questions, this study analyzes a relevant set of Mediterranean populations including eight European samples (from Spain, France, Greece, and Turkey), seven from North Africa (Morocco, Algeria, and Egypt), plus two samples from Central Europe (Germany) and sub-Saharan Africa (Ivory Coast) as external references.

Granted, the Ivory Coast sample is representative of sub-Saharan gene pool, but it only serves as a part of that gene pool, not the whole of it. It is highly questionable that this Ivory Coast sample will contain all that that is present in sub-Saharan Africa, as opposed to giving a snapshot of what is present in sub-Saharan Africa. Furthermore, what purpose does it serve, to ignore populations situated between Ivory Coast and those in the northern African territories sampled? Common sense intimates that such an undertaking will ensure more abrupt changes in DNA marker distribution trends; but then again, the authors could be gunning for just that. From their frame of thinking, such relative abrupt change in pattern could serve to sift out what they think could be representative of the autochthonous northern African patterns. After all, the authors reckon:

This pattern identifies Mediterranean populations as genetically separate from both sub-Saharans and Central Europeans and allows the identification of a certain genetic structure between the two shores of the Mediterranean region.

There is still a problem with that perception, because while genetic exchange is expected between coastal northern African and the more-inward African populations, their primary ancestry has been liked to northeastern Africa [the Sahel region or southern confines of eastern Sahara; in other words, the belt or areas that seem to have been neglected in the study] and ultimately sub-Saharan eastern Africa. Certain information is bound to escape the authors' observation, with such sampling choices. Let's examine the sampling particulars, visually:


Click on the image for better res.

It is highly questionable that the Ivory Coast sample will be representative of all that which is part of the southern Sahara or Sahel belts. It is any wonder the Siwa sample assumed an "outlier" position on the authors' admixture analysis mapping, even though the Siwa, like the rest of the northern African populations sampled, are largely Imazighen and also live on the coastal areas of northern Africa. The Siwa sample noticeably maintains a good deal of distance from the Ivory Coast sample as well, not withstanding observations that sub-Saharan gene flow appears to be most significant amongst them vs. the other northern African samples.


Click on the image for better res.

Image caption: Multidimensional scaling plot (stress 0.036) applied to the Reynolds’ genetic distance matrix based on 18 autosomal Alu markers.

This sampling choice might account for the seemingly discordant observations in the 18 Alu "admixture" estimations and that of the Alu-STR combination "admixture analysis". The authors note:

In this general view, it is worth noting the particular position of two populations (the Spanish Pas Valley and the Egyptian Siwa Berbers) (see Fig. 2). These two populations have previously been described as genetic outliers (Esteban et al., 2006; Moral et al., 2006; Coudray et al., 2009) due to the orography of the Pas Valley and the desert surrounding the Siwa Oasis. This isolation could explain their differentiation by the action of the genetic drift associated with episodes with low effective population size, which in the case of Siwa Oasis, could have enhanced the effect of sub-Saharan flow (51% from Alu/STR data) through the Nile River (Fakhry, 1973).

Assuming one went by the earlier theory of the so-called Near Eastern Upper Paleolithic origin for coastal northern African populations, shouldn't the basic genetic structure of these populations therefore be the same, even when the effects of genetic drift are accounted for? Not only does the Siwa sample cluster away from the lone sub-Saharan sample of Ivory Coast, but also considerably does so from the coastal north African bunch, just going off on the 18 autosomal Alu markers alone...

MDS representation of the genetic distances (see Fig. 2) based on autosomal Alu data stresses the main differentiation of sub-Saharans, the clustering of Mediterraneans in two different groups corresponding to northern and southern populations, and the distant position of the Egyptian Siwa and the Spanish Pas Valley samples from their corresponding population clusters. The Siwa oasis sample presents a relatively extreme position, with respect to the other populations. In fact, the first genetic boundary in the Mediterranean separates Siwa Berbers from all remaining groups.

For visual aid, we have the following:


Click on the image for better res.

Image caption: Fig. 3. Multidimensional scaling plot (stress 0.049) applied to the Reynolds’ genetic distance matrix based on three Alu/STR compound systems.

Furthermore, if "sub-Saharan" gene flow was able to reach the Siwa, then how could they be considered "isolated"? Certainly the desert areas in northern Africa have not "isolated" the other coastal northern African groups. "sub-Saharan" gene flow reportedly finds expression in many of the coastal northwestern African Imazighen populations sampled, as reaffirmed by the pattern seen in the Alu-STR clusters; however, we are told that in the Siwa sample's case, "sub-Saharan" gene flow is virtually negligible in Alu pattern alone. Yet, the same Siwa sample is supposed to be indicative of the highest "sub-Saharan" gene flow amongst the coastal northern African Imazighen groups, going by STRs linked to certain Alu sites.

As for individual populations, the sub-Saharan gene flow in North Africa based on the Alu data collection ranges between 6 and 17% (Table 3), except the Siwa Berbers where that influence was negligible. Admixture values based on Alu/STR combinations indicate that sub-Saharan flow in North Africa ranged from 16% (North East Moroccan Berbers) to 35% (remaining samples) with the exception of Siwa Berbers who showed the highest admixture value (51%).

How was the relatively lower "sub-Saharan" contribution able to find expression in Alu markers of the other coastal northern African populations, but the more significant "sub-Saharan gene flow"— as communicated in the Siwa Alu-STR combinations— almost not represented at all in the Siwa Alu markers alone? Are we to assume that genetic drift enhanced "sub-Saharan" STR patterns but minimally did the same for Alu markers? The authors attribute this phenomenon of their finds in the following manner:

The disparity between the results from Alu loci and Alu/STR haplotypes, apart from the potential effect of the different number of independent markers examined (18 vs. 3), could be related to different mutation rates and therefore the power to detect ancient or more recent demographic events. Similar disparities between these two kinds of markers were found in the admixture analysis (Table 3).

Now of course, only three types of autosomal Alu loci were selected for examination along with flanking STRs, which tells us little about change in mutation rates across the genome types used here, and to what extent STRs on the other locations are useful enough in determining gene flow, along with whether this is in line with the data provided by the three type of sites used here. Undoubtedly different mutations rates between STRs and Alu markers could be a factor at some level, but the pattern we see in the extent of "sub-Saharan" gene flow across the full range of markers used in this study, may be more explainable in the sense, that 1) if the Siwa sample sufficiently comprised of identical Alu markers on chromosomes that share their immediate TMRCA nodes with sub-Saharan counterparts, then it could be distributed in such a way that it would be hard to ascertain gene flow from "sub-Saharan" populations with any degree of precision, or 2) some differentiation in Alu allele representation and nucleotide manifestation could be the product of within-population mutational events of markers with a "sub-Saharan" background in the Siwa, possibly in an interplay with that "action of genetic drift" that the authors mentioned in a piece cited above and some level of external gene flow from neighboring non-African territories, or yet 3) if the basic genetic structure of the Siwa stemmed from a non-African source, but then got introduced to "sub-Saharan" gene flow in an ancient period, and the population had since then remained relatively isolated from such influences ("sub-Saharan"). Only here, in either scenario, some visible level of Alu allele similarities would have come to the surface within those samples that reportedly tested positive for said "gene flow".

The first scenario doesn't seem to be likely, based on the 18 Alu makers multidimensional plot, given the position the Siwa sample assumes. While the third scenario could be presumptuously insinuated from the 18 Alu markers plot, given the considerable distance between the Siwa and that lone sub-Saharan African sample from the Ivory Coast, not to mention the possible case of the relative narrower distancing from the European clusters when compared to the African counterparts, including the so-called "southern Mediterranean samples" (coastal northern African samples), it is doesn't seem likely either; why? One would have to assume that while the Siwa might have been introduced to "sub-Saharan gene flow" at some point in time, it would have likely been a very occasional affair, and/or a very ancient one in the ethnogenetic history of the population, because this gene flow would otherwise not be negligible from across just the 18 Alu markers standpoint, even if the Siwa were of a small effective-population size subjected to heightened "action of genetic drift", and would therefore find expression as it did, in the other coastal northern African samples and European counterparts. Furthermore, the problem with that assumption is that the Siwa would likely have assumed a position more extreme than that of the "northern Mediterranean" samples in the 18 Alu markers multidimensional plot, from the lone sub-Saharan sample of Ivory Coast. The reason for this, is that elements of the "northern Mediterranean" samples would have become continued recipients of "sub-Saharan gene flow" either directly from sub-Saharan emigrants, and/or indirectly through continued contact with the "southern Mediterranean" populations aka coastal northern Africans. So the inclination here, is to go with the second scenario, and here's why: If the range of Alu markers were one or several step derivatives of autochthonous African counterparts, developed within the Siwa population during its ethnogenesis, then naturally, these markers would stand in contrast to ancestral sub-Saharan counterparts. As such, one would expect some level of persistence in some areas of the genome type selected for this study, particularly given that the sites that were picked for STR analysis happen to be those under linkage disequilibrium, according to the authors. So, while subsequent "sub-Saharan gene flow" cannot be ruled out in this scenario, it need not be the sole explanatory factor for the sub-Saharan inclinations of Siwa Alu-STR combinations, i.e. if the Siwa were treated as group that has been socio-culturally isolated from other external groups for some reason or the other. Possible additional external gene flow from nearby "non-African" territories, again likely ancient, cannot be ruled out under this scenario, in which case, such element would only serve to further contrast the Siwa Alu distribution from the sub-Saharan counterpart examined here...

The Siwa oasis sample presents a relatively extreme position, with respect to the other populations.

Under this scenario (2nd scenario), one can see why the so-called "southern Mediterranean" samples would assume intermediary positions along both types of multi-dimentional plots provided by the authors. The polarity here likely stems from a mix of continued, and hence more recent gene flow from external populations both African and non-African, along with in situ autochthonous within-population evolutionary events in said "southern Mediterranean" populations. Either of these factors would ensure that their socio-cultural and geographic distance from the Siwa would contribute to the differentiations in general Alu marker genetic structure, while at same time clustering them away from European clusters and the lone sub-Saharan sample. See:

the clustering of Mediterraneans in two different groups corresponding to northern and southern populations, and the distant position of the Egyptian Siwa and the Spanish Pas Valley samples from their corresponding population clusters.

 Furthermore,...

This pattern identifies Mediterranean populations as genetically separate from both sub-Saharans and Central Europeans and allows the identification of a certain genetic structure between the two shores of the Mediterranean region. This genetic picture of populations may be related to geographic factors as indicated by the high correlation (P < 0.002) between geographic and genetic distances (based on Alu markers) found under the isolation by distance model. The genetic distinctiveness of Mediterranean populations, as well as the distinction between Northern and Southern Mediterraneans, coincides with results in previous studies (see for instance, Simoni et al., 1999; Comas et al., 2000; Boschet al., 2001).

Furthermore...

The estimates of sub-Saharan gene flow in Southern Mediterraneans oscillated between 12.9% (Alu loci) and 39.5% (Alu/STR haplotypes), a wide range probably related with the different mutational nature of the markers analyzed and with the effect of repeated homoplasic mutation in STRs.

One might expect the effect of genetic drift to pick up these elements in the Siwa as well, if one is to treat said "sub-Saharan" gene flow level as largely the product of action of random genetic drift in a population of small effective-population size.

The presence of sub-Saharan African traces in the gene pool of North Africans supports the idea of the permeability of the Sahara desert to human migrations as reported in other studies for different kinds of markers (see for example, Plaza et al., 2003; Arredi et al., 2004; Myles et al., 2005; Coudray et al., 2006).

In the above, the authors seem to have no problem in acknowledging the fact that a desert environment, of the Sahara, has not restricted or barred gene flow. This means that these groups are not isolated by the desert; so why couldn't the same logic be approached with regards to the Siwa? It may well be the case, that the Siwa have socio-culturally isolated themselves from other coastal northern African Imazighen groups on their own terms, not to mention the considerable distance between them and the other coastal northern African populations sampled, and has little to do with the desert environment. One will note that even as far as neighboring territories go, which here are apparently European territories bordering the Mediterranean sea, the territory that the Siwa are identified with is relatively more distant from the nearest such territory than those associated with the other coastal northern African populations, respective to their nearest neighbor, This could explain the differentiation in genetic structure and their relative "outlier" position. The authors add:

Interestingly, data from mtDNA and Y-chromosome estimates of sub-Saharan gene flow in North Africa are similar to that obtained from our Alu loci set, a value also concordant with that corresponding to Mozabites in the recent survey of Li et al. (2008) based on more than 500,000 SNPs. The interpretation of the disparity in gene flow estimates according to the kind of marker is difficult, but it might be presumably be related to the different mutation rates of Alu and STRs.

The need to confide in uniparental lineage is not obviously underestimated, but the authors allude once again to the unpredictability characterizing their choice of markers, autosomal markers in the form of Alu sites and flanking tandem repeats at certain designated sites. As we have seen in an earlier piece, the chiming in of homoplasic tendencies in STRs does not dampen this unpredictable character. Of course, since we are dealing with autosomal sites, the question of recombination cannot be avoided. We are assured here, at least with regards to the Alu-STR combinations, that these are perceived to be the types in linkage disequilibrium.

Alu/STR linkage disequilibrium was present in all systems and samples.

This is a sure sign of non-random associations here, which means that the odds against random reshuffling by recombination are high and hence, possibly of some selective pressure advantage of the Alu/STR association. This naturally factors further into that matter about "different mutation rates" and no less, contributes to the unpredictability character of the change in mutation rates in different parts of the genome.

Notwithstanding the lone sub-Saharan sample of Ivory Coast, upon revisiting the matter, one notices that it still managed to give a snapshot of the fact that non-African populations are just representative of a subset of African gene pool: 

When STR variation has been analyzed separately in Alu(+) and Alu(-) chromosomes, larger variances are observed in chromosomes carrying the ancestral Alu variant: CD4(+), FXIIIB(-), and DM(+). In humans, the ancestral stage of the CD4 and DM loci is the presence of the Alu insertion, whereas the absence of the insertion is the ancestral stage for the FXIIIB locus (Brook et al., 1992; Nishimura and Murray, 1992; Tishkoff et al., 1996 ). Alu/STR linkage disequilibrium was present in all systems and samples.

The most obvious pattern of haplotype variation is observed in the CD4 system. The ancestral CD4(+) chromosomes show a decreasing pattern of copy number variation from sub-Saharans to Southern and Northern Mediterraneans. Among these latter populations, the 85(+) and 110(+) haplotypes are the most frequent (Supporting Information Table 2). The derived CD4 Alu(-) chromosomes present a lower variation than the ancestral Alu(+) chromosomes, which is statistically significant for Northern Mediterraneans (P < 0.01) and Southern Mediterraneans (P < 0.05), but non-significant for the sub-Saharan sample. This reduction trend is considerable in Northern Mediterranean samples (gene diversity: 0.174 for derived chromosomes vs. 0.554 for ancestral ones), moderate in Southern Mediterraneans (0.458 vs. 0.705), and less marked in sub-Saharans (0.721 vs. 0.778).

The ancestral markers are disproportionately higher in "sub-Saharans", which in this case as we know, is based on that lone sample from the Ivory Coast, and then, they are moderately represented in "southern Mediterraneans", which would be our coastal north African samples here, and least represented of all the groups herein, in the "northern Mediterranean" samples, which here would be the southern European samples. Respectively, greater nucleotide variation is found in "sub-Saharans", as characteristic of the ancestral markers, moderate diversity in coastal northern African, and least diversity in Europe. This seems to find some expression in the general positions assumed by the samples in the plots respective to each marker-format type; in each case, the northern African groups appear to be in the intermediary positions between the African samples in the extremes and the European ones on the other hand. Along the x coordinates of the multidimensional scaling plots provided to us by the authors of the present study, the Ivory Coast sample consistently attains the most extreme position on one end. Please refer back to the plots or maps provided earlier in the body of this post.

Of the derived examples of the Alu-STR clusters, the distributions patterns found in the present study suggest possible "southern Mediterranean" or coastal Northern African origins (or at least, populations ancestral to them) for the following types: CD4 110(-) and DM 107(-)

The highest frequencies of CD4 110(-) and DM 107(-) have been found in the High Atlas region (7 and 5.5%, respectively) of Morocco, reaching polymorphic frequencies in all the North African samples [barring the Mozabites for the CD4 110(-) combination]. They have also been found in the Iberian Peninsula, scattered along the northern Mediterranean shore to Greece and Turkey, and on the main islands of the western Mediterranean (Majorca, Corsica, Sardinia, and Sicily; González-Pérez et al., 2007). The CD4 110(-) haplotype (Flores et al., 2000) and has also been reported in West Saharans and Mauritanians on five of the seven Canary Islands (Flores et al., 2001), as well as in Adygei from the Northern Caucasus (Tishkoff et al., 1996). Assuming from their frequency distribution that the place of origin of these particular haplotypes is located in the westernmost extreme of North Africa (Fig. 4A,B), their current ample distribution along both shores of the Mediterranean most likely reflects the effect of gene flow across the region since ancient times, even though specific ages cannot be accurately estimated with our data. Similarly, specific Mediterranean haplogroups or clades (U6 and M1b in the mtDNA; EM78 and EM81 in the Y-chromosome) have also been described for these populations and dated in Paleolithic times.

Last but not least, in keeping with pointing out the recurring theme of the lingering onto outdated or outmoded and subjective concepts by the authors of the present study, the following serves as further example:

Concerning Northern Mediterraneans, the gene flow from sub-Saharan Africa was inappreciable for Alu markers and swung from 6 to 15% for the Alu/STR haplotypes data calculations. When gene flow in Northern Mediterraneans was tested, taking Central Europe and Southern Mediterraneans as parental populations, the results were statistically inconsistent, indicating the limited power of our markers to discriminate gene flow within Caucasoid populations. Nonetheless, the distributions of frequencies for the Mediterranean haplotypes CD4 110(-) and DM 107(-) (Fig. 4A,B) are suggestive of gene flow processes across this geographical region.

Such recurring themes throughout different parts of the study do not bode well for the authors at hand.

*Keep an eye on possible future updates.
___________________________________________________________________
*References:

— As already cited in the body of the post.

Striving for Clarity and Accuracy

There are various aspects of academia that some of us take for granted, without critical thinking. The driving "wisdom" here, is that if an idea is an oft repeated or recited one in sections of academia, then it must certainly be accurate and doesn't call for further investigation. This almost certainly appears to have been the case in a recent personal encounter with a question dealing with "bovine" taxonomy, one concerning the Fulani cattle in particular. It has generally been the case in "western" academic circles, to casually refer to Fulani cattle breeds as "West African Zebu", and as such, one opinion encountered fairly recently in an internet discussion forum, figured that such a description is fine and dandy, because Zebu happens to be accompanied by the "West African" descriptive, thereby invoking the subspecies' precise African origin. That may well be so, but does that at any rate, necessarily render the Zebu-characterization correct? After all, here, it is not simply the matter of the cattle subspecies' geographical origin, but its actual genealogical heritage. As far as the latter goes, i.e. the genealogical question, this was greeted with an explaining-away that "implicitly" argues that the West African "Zebu" makes sense given the relatively predominant Zebu genetic contribution over those of other bovine lineages [namely the Bos Taurus — either African and/or European] in the West African "Zebu" gene pool. To this end, sources such as that compiled by E. M. Ibeagha-Awemu. et al. 2004 have been offered as evidence; it goes like this:

Click on the image for hi resolution

The argument given based off this piece of information, as it goes, appears to be that most of the Bovine types sampled herein are "hybrid", because of their apparent "inter-subspecies" ancestries, and that notwithstanding, has no bearing on their assigned taxonomic identity; the unspoken "wisdom" here, is that since this piece of information appears to suggest that most cattle breeds out there are rarely "pure", and hence are inclined to be "hybrid", then the condition of having ancestry from divergent subspecies doesn't have any bearing on a cattle breed being assigned to only one of the subspecies. Instead, contribution from the other parental subspecies — whose taxonomic identity had not been assigned to the offspring — is interpreted here as "admixture". The tacit premise—wittingly or unwittingly—that this logic lies on, is that the breeds are assigned their taxonomic identity based on which parental type's contribution to their gene pool supposedly 'predominates' or 'prevails' over others'. Indeed, just reading off of that table above, for example, one comes out with the understanding that many of the African breeds assigned the "Zebu" descriptive appear to have more "Zebu" contribution than their Bos Taurus counterparts. However, further investigation involving other set of markers cautions that the situation is more complex than that imagery.

You see, one has to bear in mind, that we are dealing with domesticated fauna here, which means that whether or not the herders are actively aware of the precise set of phenomena that impart advantageous features to their livestock, awareness of a trend(s) in the success of a breed will lead to every effort [by the herders] at sustaining or maintaining, if not swelling the populations of said breed. The type of markers implicated in the table above, do not necessarily allow one to adjudge the significance or precise magnitude of contribution from the parental inter-subspecies elements involved; and why is that? Because again, the Fulani was the product of domestication, meaning that it was intentionally crossbred to bring out and retain certain advantageous features from the contributing parental bovine subspecies types. These advantageous features would have had to have been encoded in certain DNA nucleotides, rendering certain DNA loci under "selection pressure". Such a situation would therefore make these loci insufficient in ascertaining the actual level of respective contribution from the contributing parental bovine "inter-subspecies" involved. Other loci may well simply be relatively stable in the face of random genetic drift, by chance occurrence. For instance, a largely "hybrid" population comprising Zebu-Taurine individuals might not accurately reflect contribution of the "parental" subspecies involved, because certain loci could, by chance occurrence meted out by "positive" random genetic drift, remain relatively stable in their distribution across the population, simply because the number of "hybrid" individuals which just-so-happen to be homozygous at the locus in question happens to be the relatively overrepresented one than that comprising individuals which are heterozygous at said locus. To demonstrate how all this could be, one only need to look at what uniparental genotyping from the so-called African Zebus thus far reveal: these tests show that in the case of West African "Zebu" breeds, a majority of them have "Zebu" paternal ancestry, but by contrast and almost "exclusively", they have the Bos Taurus maternal ancestry! This is a true definition of a "hybrid" ancestry. It is not as if the West African "Zebu" are largely "Zebu" in both maternal and paternal ancestry, and that only a small segment of their population is "Zebu" and "Bos Taurus" in ancestry, so as to deem the "aberration" as "admixture", but that this is true for virtually all the African "Zebu", that they happen to have both "Zebu (Bos Indicus)" and "Bos Taurus" uniparental ancestry.

Yes, there are hybrids amongst the so-called African breeds of "Bos Taurus" as well, but unlike their so-called "Zebu" counterparts, uniparental genetyping show that there are actually sizable populations of these "Bos Taurus" who have virtually ONLY "Bos Taurus" ancestry both maternally and paternally.

The argument that many herds are likely to have "inter-subspecies" ancestry, and therefore are 'hybrid' and the condition has no bearing on their assigning to one or the other taxonomic [bovine] group, is immaterial to the fact that genealogical and archeological particulars point an "independent" African Bos Taurus domestication, and hence, considered a "true" phylogenetic entity on its own that distinguishes it from the "Near Eastern" or European Bos Taurus and Bos Indicus. Nor is it necessarily the case, as uniparental genotyping attest to, that African Bos Taurus populations are inclined to be breeds of "Taurine-Bos Indicus" lineage; there are considerable populations of African Bos Taurus, particularly in Western Africa, that are still virtually all Bos Taurus in their lineage! This however, as just demonstrated, is not the case with the western African "Zebu" breeds like the Fulani. The following piece, from Blench et al.'s compilation, gives us an illustration of what has just been described, in relation to uniparental genotyping:

And...

Click on the images for better resolution

The other argument made, in addition to the genealogical one just examined, goes like this:

They are zebu, African zebu, as their physical characteristics and their genetics make clear.

Indeed, the present author of this blog is aware of the naming schemes based primarily on morphological traits; that though, says little in actual genetic basis for such terminology. In fact, many of the so-called West African "Zebu" breeds appear to bear traits that are considered "intermediate" in relation to Asian Zebu breeds. This includes things like for example, the less prominent humps on many of the West African "Zebu" breeds when compared to those of their Asian counterparts. It has even led to coining of such terms like "Zeboid"; see, courtesy of Blench et al.'s compilation:

Click on the images for better resolution

Generally, the bovine subspecies have become casually synonymous in dichotomous terms, with hump-less breeds being synonymous with "Bos Taurus" or Taurine descriptive and humped subspecies being synonymous with the "Zebu" descriptive; this, usually regardless of actual genealogical particulars.

The last line of defense for upholding the viewpoints examined and rebuked [or at least challenged] herein, about the justified assigning of West African "Taurine-Bos Indicus" hybrid breeds like the Fulani to just the Bos Indicus taxonomic group, appears to one of logical fallacy 'appeals to popularity'; that is to say, that many in "western" academia circles simply refer to Western African breeds like Fulani as West African "Zebu", and therefore they must necessarily know all and have the last word on the subject matter. Any challenge to this viewpoint or call for further investigation into the subject matter, to iron out potential incoherencies, peculiarities or inadequacies is dismissed out of hand as emotionalism or an attempt at making an argument simply for argument's sake. It matters not, the fact that all the sources cited by its defender (advocate) too agree with the position maintained by the present author of this blog, as well as "materially"-supported [as the plentiful citations herein bespeak] by the present author, that the so-called West African "Zebu" are IN FACT "hybrid" breeds of BOTH "Bos Taurus" and "Bos Indicus", and so from that fact alone, it would actually be inadequate and inaccurate to deem these hybrid breeds as simply "Zebu". Superficial reasonings aside, the taxonomic assignment as such doesn't really reflect the genetic reality at hand, other than its ardent defenders crying that the Zebu do in fact form part of the genealogy; but still the keyword here, is "part"! A defender of the said taxonomic assignment even went as far as using human socio-constructs as the presumably perfect analogy of the situation at hand, pointing out that despite "hybrid" ancestry, humans are inclined to assign themselves to just one "ethnic"/"racial" group or the other. If said defender were not blindsided by ideology, it would have occurred to the person that not only are the socio-contructs in question not regarded as scientific, but also humanity from a biological standpoint, does not comprise of several distinct "sub-species"; our variations have not been that significant to warrant division of humanity to several distinct subspecies. Such is the sort of weight [as it relates to substance] with which the layperson approaches questions relating to the subject matter of this very blog topic. Is it possible that better explanation is afforded by the more informed defenders, lettered in the disciplines of bioanthropology and molecular genetics, than those examined herein? Perhaps, but from accessible material spread over the net and libraries, none has come to attention that adequately and accurately justifies the taxonomic assignment of the West African Bos Indicus-Taurine 'hybrids' to just the "Zebu" phylogen. The quest for accuracy and clarity should not be dismissed as an abomination, but as an opportunity for furthering knowledge, and the specifics demonstrated here thus far go to show just why!

*As always: Lookout for ongoing updates; notes on this site are regularly updated as information comes to attention!

Reviewing: The Genetic Structure and History of Africans and African Americans

This is a carryover from the "miscellaneous notes" of the last blog posting (The Creation of a Fake Controversy: The Fula Origins). It pertains to extracts taken from: The Genetic Structure and History of Africans and African Americans, a publication by Tishkoff et al (2009). that just came out recently. Here, we will examine the work a bit more:

Sampling entailed...

We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties.

And mentions of interest here...

Ethnic groups, sample size, language classification, and subsistence classification are given in Table S1. For the Kenyan, Sudanese, Nigerian, and Cameroonian samples, white cells were isolated in the field from whole blood with a salting out procedure modified from (S1) and DNA was extracted in the lab with a Purgene™ DNA extraction kit (Gentra Systems Inc., Minneapolis, MN). Dogon samples were obtained from blood spots donated by participants in a cohort study of malaria incidence in Bandiagara, Mali. Ghanaian DNA was extracted onsite from whole blood, with the Purgene™ DNA extraction kit. The Juspeaking !Xun (a.k.a.Vasekela) and Khoe-speaking Khwe samples were collected from individuals in the area of Schmidtsdrift in the North-West Cape of South Africa. The Cape Mixed Ancestry (CMA) population, commonly referred to as Cape Coloured in South Africa, was collected in the Western Cape Province. The Dogon sample was collected in Bandiagara, Mali. Nigerian samples were collected in Abuja and Adamawa State districts. Cameroon samples were collected from the Eastern Province (Baka Pygmies and neighboring Bantu groups), Southern and Ocean Provinces (Bakola Pygmies and neighboring Bantu groups and coastal groups), Center Provinces (Medzan Pygmies and neighboring groups, mostly Bantu populations), Western Province (Bamileke and Mbororo Fulani groups), Extreme North Province (Mandara mountains and northern plains; Fulani and Afroasiatic/Nilo-Saharan speaking populations). All Cameroonians were sampled in their native village; the Hausa sample (a population who emigrated mainly from the Kano area two generations ago) was sampled in the city of Yaounde. Samples from Chad, CAR, Congo, DRC and Rwanda were obtained from individuals who recently immigrated to Cameroon. Tanzanian DNA samples were collected from individuals residing in the Arusha and Dodoma provinces of Tanzania. Samples from Kenyan populations of southern Ethiopian origin (Burji, Konso) samples were collected in the Rift valley, Nyanza, and Eastern provinces of Kenya. Sudanese samples were collected in the Khartoum and Kasala provinces of the Sudan. The Yemenite Temani and Ethiopian Beta Israel samples were purchased from the National Laboratory for the Genetics of Israeli Populations (S2) . The South African !Xun/Khoe, Xhosa, Vende, Cape Mixed Ancestry (CMA), Yemenite Temani, Beta Israel, and the Malian Dogon DNA samples were amplified by Whole Genome Amplification (WGA) with Illustra GenomiPhi HY™ kits provided by GE-Healthcare (Buckinghamshire, UK). It should be noted that the DNA for the Dogon population extracted from blood spots appeared to be of lower quality and microsatellite markers did not amplify as well as other samples obtained from whole blood (43% of markers had missing data).

Abstract:

Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, four African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observed high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (~71%), European (~13%), and other African (~8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.

Right off the bat, the first thing that probably jumps at any reader, is the heavy reliance on microsatellite repeats, as opposed to uniparental binary markers. Restricted fragment length nucleotide sequences or polymorphisms [relying on insertions/deletions] can add precision to identifying discrete monophyletic units, but even here, the results are not always as clear cut as the case generally is with "classic" uniparental binary markers of Y-DNA and mtDNA respectively, relying on unique event SNPs. For instance, certain RFLP haplotypes have been linked to two different haplogroups; case studies on RFLP haplotypes on this website have shed light to such occurrences: see Lucotte et al.'s haplotype IV, RFLPs: Lucotte et al., A case study — Pt. 1, and RFLPs: Lucotte et al., A case study — Pt. 2. In the first link of the three for instance, we were told:

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. - 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.

In cases where it might be difficult to link a RFLP haplotype to a specific sub-clade or else superclade, classic uniparental (Y-DNA or mtDNA) SNP and/or UEP markers are called on, as we see in the aforementioned link 2 and link 3 on Lucotte et al. Questionable allocation(s) of ancestral origin based on "shared" microsatellite markers and/or insertion/deletion markers is therefore bound to occur, as one comes across in the study at hand; ancestry, which would otherwise actually be more a reflection of an ultimate shared common recent ancestry prior to the ethnogenesis of the implicated contemporary groups into recognizable ethnic or socio-geopolitical entities they are known today, as opposed to some recent unidirectional gene flow from one designated contemporary group to another.

Moving onto excerpts of interest...

As some have correctly picked up on, and as the authors themselves openly admit, there are issues with their Dogon sample that need to be ironed out...

Detection of relative pairs: Relative pairs and duplicated samples in the dataset were inferred from the pattern of shared genotypes and population allele frequencies with RELPAIR 2.0.1 ( 6-8) . Because the inclusion of closely related individuals can impact population genetic inferences [e.g. (S9)], we took the conservative approach of excluding individuals inferred to be third degree or more closely related, including inferred relative pairs between regional ethnic populations (e.g. all Tanzanian populations). An exception was made in the case of the Dogon as it is difficult to reliably infer relative pairs in a small sample and the Dogon are highly distinctive and could not be readily merged with other populations to improve allele frequency estimates. Merging the Dogon with other non-Pygmy West African populations inferred four unrelated individuals in the sample, but this may be overly conservative given the distinctiveness of the Dogon sample from other West Africans. Also, the Dogon are the only representatives from Mali in our study and since the sample size is already small we did not want to further reduce the sample size in the analyses, especially if the relative pair estimates were questionable. Therefore, RELPAIR inferred relative pairs among the Dogon were not excluded. In total 737 individuals were removed. Networks of relatives, which in some cases were quite complex, were plotted with neato from the GraphViz software package (S10), which was used to select the minimum number of individuals to exclude to break up networks of relative pairs.

Indeed, the Dogon sample size, which to reiterate what the authors tell us — consisted of candidates who could also possibly be closely related and the only sample that represented Mali, was only one of 9 individuals, a fairly modest size. Keeping this in mind, we are told:

The Dogon from Mali, who speak a Niger-Kordofanian language, cluster with the Saharan and eastern Africans in the NJ tree (Fig. 1), consistent with the results from STRUCTURE analysis, showing considerable Saharan (blue) and Afroasiatic (purple) ancestry, and consistent with oral history of a northern African origin (although it should be noted that the sample size for this population, 9 individuals, is very small and many markers did not amplify well) (Fig. S13; Table S9).

"Saharan" without regional specificity is next meaningless. Just about any of the groups on the Sahara, Sahel or adjoining "sub-Saharan" territories have "Saharan ancestry". Furthermore, as has been the talk of this site recently, relics of "fertile-Sahara" era or earlier east African ancestry is scattered along the length of the Sahara, and generally finds expression in Sahelian and "Sub-Saharan" populations in relatively low incidences, if not somewhat patchy distribution. Such shared Saharan ancestry is bound to have some sort of manifestation across bi-parental microsatellite markers as well. As we've just seen, the authors note that "many markers did not amplify well", and indeed, if there is any further indication of an air of dubiousness about the results of the amplifications, then perhaps it is notion of some 45% ancestry, or specifically 45% of the sample identified with an AAC (Associated Ancestral Cluster) , being suggestive of European ancestry in that small sample of Dogon, with 9 individuals [see table S8 of the publication]; and even if one were to remotely entertain the possibility as a hypothetical scenario for argument's sake, it would implicate these individual as essentially "outliers", if anything, based off on previous information published on samples taken from sections of Malian society, including the Dogon. Additionally, with regards to such an outlier situation, one might even ask if this is not a function of "third party" interaction, with that "third party" being coastal north African Imazighen and Arabized groups. The authors themselves base AAC assignment on where said markers are allegedly the most maximum in 'frequency'...

African and non-African Associated Ancestral Clusters (AACs; labeled based on the populations showing the highest levels of ancestry for each inferred ancestral cluster)are highly divergent.

One can suppose 'frequency' could be a telltale sign of geographical origin of certain biparental microsatellite clusters, if only tenuously by itself, but as a matter of precision, it effectively plays that role only when taken into account with other molecular genetics information, like the internal molecular variation of a designated clade, and in association, how much of this variation is paraphyletic, along with definite geographical patterns of distribution. For instance, one might surmise that Hg R1b originated in Europe, merely on the account of the haplogroup's unparralleled prevalence in that region, and place the maximum likelihood of finding ancestral R1b clades in Europe before finding them elsewhere. However, as a matter of merely "frequency", Hg R1b's incidence in Europe in no way allows inference that either Hg R1* or its descendant, the upstream clade R1b* originates there; in fact, R1b* clades bearing upstream SNPs that are nearer to the root of that sub-clade, but lacking the well-known downstream SNPs, have so far only been identified in non-European samples. Interestingly, these non-European samples happen to be African ones. At the same, ironically, R1b itself is relatively rare in Africa, even in the coastal north African areas which are closer to Europe. So frequency as a single factor for adjudging origin can be misleading. Neutral factors like random genetic drift, for example, can elevate a marker's frequency in a designated locale, and yet, this locale in of itself need not be the actual location of origin for said marker. For microsatellite repeats, in absence of binary or UEPs, the assignment of origin based on frequency alone becomes even more uncertain, than the case is for binary or SNP markers. Microsatellite repeats could even be shared both between different and within single monophyletic clades in some occasions, due to homoplasy.

Many questions abound the objectivity of result inferred for the small Malian sample. In a related matter, the Beja samples were implicated in some ~ 32% and ~ 34% AACs [the Banuamir and Hadandawa samples respectively] placed under "European" [see: Table S8 of the journal]. Well, to the extent that ancestry suggestive of "possible" European origin has been implicated in a Beja sample before, it is reasonable to assume that this may render a section of the Beja to display shared clusters with Europeans in a segment of nuclear DNA that is outside uniparental binary markers; however, it is worth noting that the uniparental gene pool, the paternally-inherited one in particular, featured fairly low incidence of ancestry suggestive of ultimate European ancestry. Citing Hassan et al. (2008), the Beja male gene pool comprised of only ~ 5% ancestry that could *potentially* be linked to European origin [Hassan et al. (2008) provide little information on specific downstream clades of Hg R1b]; this is fairly consistent with R1b's general distribution in northern Africa, where it is generally low, in contrast to the fairly considerable representation of European maternal ancestry in coastal northwest Africa. So, the 32 or so % of microsatellite AAC linked to a possible European origin is out of character, when uniparental ancestry information is taken into account. On the other hand, substantial AAC sharing between coastal northwest African samples and the European ones is consistent with uniparental DNA examinations, which to reiterate, mainly finds expression in the maternally-inherited gene pool.

Mitochondrial DNA analysis indicates that Fulani have lineages of predominantly West African origin and that they cluster together and close to the Mandenka population from Senegal [S93].

By contrast, Y chromosome analyses of Fulani sampled in the Sudan indicates shared ancestry with Nilo-Saharan and Afro- Asiatic speaking populations [S89].

The line about the mtDNA is essentially a reversion back to what has been cited in the main post above, as observed by Cerny et al. (2006). The line about the Y chromosome analysis however, is quite misleading; one only needs to refer to Hassan et al. (2008) [see: Y-Chromosome Variation Among Sudanese] to see how: The Sudanese Fula sample here, as noted in the main post above, predominantly featured Hg R1*-M173 markers in the uniparental paternal gene pool. This marker is in fact generally quite rare in "Afro-Asiatic" speaking populations; rather, its highest incidences has thus far been reported in Niger-Congo, Nilo-Saharan and "Afro-Asiatic" (Chadic) speaking groups in northern Cameroon, with smaller occurrences in the rest of central Africa [see Luis et al. 2004]. Nilo-Saharan groups in Sudan itself, it should be noted, did NOT share this ancestry with the Sudanese-based Fulbe at all. This reverts back to what had already put forward in the main post, about the implication being that these Sudanese Fula derived from a section of the northern Cameroonian Fula, wherein the Hg R1*-M173 is featured in a considerable but not the predominant frequency.

The only marker that the Sudanese Fula shared with Nilo-Saharan and Afrasan ("Afro-Asiatic") speaking Sudanese groups was Hg E3b1 (M78). Common sense however, intimates that this aspect of the paternal gene pool was largely picked up from neighboring populations, only after the Fula situated themselves in Sudan. It makes sense, since after all, E3b1 is one of the prominently featured markers found in the Sudanese sample.

To recap, there's something still unmistakable about the Sudanese Fula sample: they retain western African ancestry, as signified by Hg E1-M33, which was absent in all autochthonous Sudanese groups; the only other groups where this marker was implicated in Hassan et al.'s (2008) work, were, well, the well-established west African groups like the Hausa and Wolof. When pressed on to explain away this anomalous feature of the Sudanese Fula's paternal gene pool, dissidents of the west African origin noticeably become mute on the matter.

These results raise the possibility of differential patterns of male and female gene flow into this population.

Whatever may be "differential" about male and female gene flow patterns in Fula sample, no doubt influenced by matters like life style — recalling on nomadic vs sedentary, both the maternal and paternal gene pools communicate the same thing: west African origin!

Our analysis, using genome-wide nuclear markers and STRUCTURE, indicates that the Fulani have distinctive ancestry [fuchsia] at K = 14 in the global analysis [Figs. 3,4] and at K = 9 -14 in the Africa analysis [Fig. S13]. The Fulani cluster with the Chadic and Central Sudanic speaking populations at K <13> They also cluster near the Chadic and Central Sudanic speaking populations in the NJ tree based on population genetic distances [Fig. 1].

Fula samples taken from either central Africa or Sudan are expected to cluster with groups in central Africa-Chad, as the Fula would have arrived in Sudan via a central African and/or Chadic corridor, having experienced a bottleneck [see main blog post]. The central African Fula in turn would have arrived ultimately from Atlantic-coastal regions of western Africa, where their ethnogenesis as the Fula-"proper" likely occurred.

The pattern of the Sudanese Fula's Y-DNA composition is for instance, undoubtedly different from their western African brethren, but continuity still exists via recurring typical western African markers that unite all Fula groups, regardless of where they spread to; e.g. primarily Hgs E1 and E3a, and a lesser extent, Hg E2. Either of these clades are telltale signs of so-and-so Fula groups' western African ancestry.

In the global STRUCTURE analysis, the Fulani show low to moderate levels of European/Middle Eastern ancestry [blue], consistent with mtDNA and Y chromosome [S89] analyses, as well as the presence at low frequency of the -13910 mutation associated with lactose tolerance in Europeans in this population [S94].

Again quite misleading. Yes, understandably, "low" levels of shared ancestry attributable to potential "European" ancestry, might be correlated with "low level" incidences (~1.7 %) of R1b [pertaining the Rosa et al.'s (2007) Guinean sample] or relics of this ancestry attained from coastal northwestern populations [Imazighen] seen on the mtDNA side [Cerny et al. 2006], as cited in the main post. However, in the case of Fula samples, from northern Cameroon through to Sudan, a good degree of presumed shared "European/Middle Eastern ancestry [blue]" may very well actually be linked to common "distant" ancestry, as the paraphyletic R*-M207 and R1*-M173 markers suggest; these latter two are essentially rare to absent in "Middle Eastern" and "European" populations, which are mainly characterized by more downstream markers, especially European populations, who have no upstream markers for R1. Now, because R1b and R1a markers are still 'molecularly' linked to the upstream R*, any group bearing the latter or else any intermediary nodes between the upstream R* and the downstream R1a and R1b will "appear" to share ancestry with Europeans and/or possibly "Middle Easterners", which could misleadingly be misread as ancestry from "European/Middle East". Given the features of northern Cameroonian and Sudanese Fula sample uniparental male gene pool, it is a safe bet that this is the underlying issue at work, especially when the red flag of "moderate" levels is evoked; the Fula uniparental gene pool specifics, whether maternal or paternal, simply do not bear out "moderate" ancestry from "Middle East" or "Europe".

Recalling a previous blog post here, R1*-M173 in Africa, we have:

Interestingly, upon revisiting Wood et al. (2005), it should be pointed out that paraphyletic clade of R*-M207 was detected amongst some "Afro-Asiatic" African groups, along with the paraphyletic clade R1*-M173 [it is worth noting that Wood et al. implicate the Egyptian sample here as something other than that of Semitic speakers (Arabic)], while some Niger-Congo groups — though in small frequencies [pooled] — tested positive for the paraphyletic R1b*, lacking the established downstream R1b markers. Henceforth, R*-M207, lacking downstream mutations have been identified in African groups via this study; and yes, the basic nodes of all presently known Hg R's downstream clades had been accounted for, which means that R*, as predicted above, is NOT relegated to the Indian sub-continent. All in all, this suggests that African Hg R pool is actually more diverse than many seem to think.

As for the matter concerning lactose tolerance, it has been pointed out here before, how this has nothing to do with European ancestry. Recap, see: More on R1*-M173 bearers

In summation, the piece essentially rehashes the well-understood facts of primary west African ancestry of the Fula, both in terms of genealogy and language, along with genealogical "admixture" elements picked up over the course of migratory events, but suffers from matters, as laid out in detail in the main blog post, pertaining to idealistic urges for mystification where none is necessary or warranted. To provide an example, consider the following line:

Our analysis, using genomewide nuclear markers and STRUCTURE, indicates that the Fulani have distinctive ancestry (fuchsia) at K = 14 in the global analysis (Figs. 3,4) and at K = 9 -14 in the Africa analysis (Fig. S13). The Fulani cluster with the Chadic and Central Sudanic speaking populations at K <13>Fulani show low to moderate levels of European/Middle Eastern ancestry (blue), consistent with mtDNA (S93) and Y chromosome (S89) analyses, as well as the presence at low frequency of the -13910 mutation associated with lactose tolerance in Europeans in this population (S94). Additionally, we observe moderate to high levels of Niger- Kordofanian ancestry in the Fulani populations (Figs. 3, 4, S13;Tables S8, S9). These results do not enable us to determine the definitive origin of the Fulani, although they indicate shared ancestry with Saharan and Central Sudanic populations and suggest that the Fulani have admixed with local populations, and possibly adopted a Niger-Kordofanian language, during their spread across central and western Africa. The origin of European (possibly via the Iberian peninsula) and/or Middle Eastern ancestry in the Fulani requires further exploration with additional genetic markers.
 
The words "admixed with local populations" is particularly interesting, as it is naturally inconsistent with mtDNA report [and Y-DNA] where western Africa is concerned, recalling Cerny et al. (2006) for example, who point out that their results show a primarily or predominantly west African ancestry of "charasteristic" markers of the Fula, but wherein the gene pool of nomadic Fula samples show very little genetic contribution from neighboring sedentary populations. This, to put it simply, means that the only way for the Fula gene pool to be primarily west African, is if they were autochthonously west African.

Another interesting choice of words, is the mention of "adopt" in Tishkoff et al.'s piece above, in relation to the Fulani language. "adopt" is usually suggestive of one taking on something that wasn't originally his/her's. Supposing one remotely entertained said insinuation of the authors for just a minute, their very idea that a small band of foreigners adopted the "Niger-Kordofanian" language along their migratory path, means that the locals along that path would have had to have already been Fula speakers; that is the only way a wandering group of immigrants/foreigners could have become speakers of a Niger-Congo language — a language family that supposedly did not characterize their own — which by chance, happens to be Fula. In other words, the Fula as an ethnic group was already established on the continent prior to the intrusion of this small band of immigrants; it's just common sense. Henceforth, this band of immigrants cannot be judged as proto-Fula antecedents by any stretch of the imagination; rather, they should be viewed merely as a foreign element that integrated into an already well established ethnic-group, i.e. the Fula, as opposed to assuming the role of a "prototype" for the group into which they allegedly integrated. To somehow use this [unsupported] scenario as something that mystifies Fula origins, is clearly not rational or logical deductive reasoning; at best, it is quite comical. The matter of Fula origins was recently posted here, in detail; recap: The Creation of a Fake Controversy: The Fula Origins

It is interesting to note that while the authors carry themselves as very confused individuals about Fulani ancestry, their own tables (see S8) show very little AAC sharing with Europeans; their Nigerian Fulani sample supposedly shared ~5 % or so AACs placed under "European", while the Cameroonian Fula samples shared about 2.5% and 2.6% respectively. Nothing "moderate" about these.

From language, culture to genealogical heritage, all indicators resolutely point to a west African ethnogenesis of the Fula. This has been supplemented with archaeological evidence, as that from Tassili, on rock art. Here, are renditions of a cattle-rearing group, bearing features reminiscent of contemporary Fula and/or western Sahel groups in general. One scholar often cited on the internet, regardless of how objective or otherwise the sites themselves are, for identifying definite links between the Tassili n'Ajjer rock painting and contemporary Fula, is Amadou Ba. For instance, one site notes:

At the Tin Tazarift site, for instance, historian Amadou Hampate Ba recognized a scene of the lotori ceremony, a celebration of the ox's aquatic origin. In a finger motif, Ba detected an allusion to the myth of the hand of the first Fulani herdsman, Kikala. At Tin Felki, Ba recognized a hexagonal carnelian jewel as related to the Agades cross, a fertility charm still used by Fulani women. With the disappearance of many traditions and other aspects of African culture, works of traditional African art are becoming more and more scarce. - This particular piece is from Jamtan.com

The following are from Andrew Brown Smith [African Herders (2005)], who seemingly attempts to portray himself as a "voice of moderation":

Of note here, is the observation that Smith — as any other person guided by reasoning — could not pass over the significance of linguistics, i.e. recalling the Niger-Congo familial ties of Fula language.

While briefly citing examples of the sort of reception Ba's definite correlations got in certain quarters, mainly amongst "western" observers, even Smith could not resist pointing out that the "coincidences" surrounding the reminiscence of Fula socio-cultural traits in definite features of the rock arts are simply too considerable to not draw a link between the two, i.e. between the figures in the rendition and contemporary Fula. Notwithstanding this openly-admitted acknowledgment, Smith of course, goes onto characterize Ba's demonstrations as "perhaps what they wanted to see to support their thesis", but offers no substantive counter-thesis that puts to question the "specifics" of what Ba "sees", other than a mere opinionated presumption of Ba's "possible" motive behind making the definite links that he made.

Click on the above images to get higher resolution versions.

In the lower images for example, one notices the head gear, which is not unlike that featured on a contemporary Dogon dancer in the image on the right hand side.

Other notes: Fulani cattle are also deemed to be of west African origin, as a sub-phyla of the west African breed of Zebu cattle called the "West African Zebu", and they fall into the following two groups -

The Fulani have been classified further into two groups: the lyre-horned subgroup consisting of Senegalese Fulani (or the Gobra), the Sudanese Fulani, and the White Fulani (or Bunaji); and long-horned subgroup represented by the Red Fulani (or Rahaji). Diali (or Djeli) is a strain of Fulani found on the flood plains of Niger river in Niger and south-west Nigeria (Rege 1999; Rege and Tawah, 1999). - courtesy cdad-is.org

Dictionary description...

Sudanese Fulani cattle
West African, lyre-horned, milking cattle, usually light gray.- Medical-dictionary

Continuing with examination of the study at hand, the authors note:

Individuals from Saharan and Eastern Africa show heterogeneous ancestry, reflecting descent from populations ancestral to non-Africans and/or gene flow from non-Africans into Africa.

Well, "exotic" gene flow as function of said heterogeneity, while reasonably a contributing element to some extent, is really quite trivial in the big scheme of things. African populations would still be quite heterogeneous *regardless* of gene flow from non-Africans. In relation to this, a subset of Africans who formed the basis for non-African groups, would assume an intermediary position in a case study involving a "comprehensive" collection of African and some non-African samples, because quite simply, that subset of Africans only represents a portion of the overall African diversity. Non-Africans in turn, only have a portion of the diversity of the subset of Africans from whom they emanate.

*Watch for occasional updates or modifications of this post in future.


*Last edited on 10/26/2010.