Thursday, November 26, 2009

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.
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).
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.

— As already cited in the body of the post.

No comments: