Introduction:
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| Image Caption: A rendition of an Ethiopian male, featuring what can be considered an average look among the major Cushitic and Semitic speaking populations of Ethiopia. Click on the image to expand! |
As the authors start of their notes with laying out the goals of their research, they point out the supposed shortcomings of previous publications, particulary as it concerns Ethiopian DNA. In doing so, the authors lament on the supposed infrequency of DNA studies—involving African samples—that focus on Ethiopians in contrast to African samples from central and western Africa. This is right after the authors tell the reader that, because Ethiopia has proven to be relatively rich in human paleontological record, and in their words, "because of Ethiopia’s geographical position between Africa and Eurasia, its capital, Addis Ababa, is often used in genetic studies as a proxy embarkation point for modern human range expansions."
This smacks of double speak, when one considers that the subject of "human range expansions" figures quite a lot in population genetics research undertaken by 'western' research teams, and these seldom avoid including eastern Africa, the African Horn in particular, because its often implied rep of being a "cradle" to modern humanity. On top of this, Ethiopians have often served as "props" by Eurocentric ideologues, both in amateur and academic circles, to effect some ideologically-expedient wedge or another between continental Africans, whereby they feel at liberty to isolate what they either presume to be the source of "their kind" (Europeans) from the "others", who are generally lumped together and dismissed as being "inferior" and/or "undesirable", or use the target group—like Ethiopians—to explain away, and importantly, diminish natural African diversity as that made possible primarily because of foreign contribution.
The authors instead complain that genetic studies often tend to focus and extensively cover western and central Africans. In actuality however, western and central Africans are among the least studied African groups, if not possibly one of least studied from a global context, and in cases where they are studied, they have often been unrepresented in samples, usually in the form of sampling taken in just one or two, or around about there, to represent the entire swath of geography from western Africa to central Africa.
The explanation for such sampling tactics have often tacitly or overtly been that western and central Africans are supposedly more homogeneous in the biological profile than eastern Africans or whatever other African group that is taken out of the immediate domain of "sub-Saharan Africans"—especially those "sub-Saharan" Africans closer to the equatorial regions. Examples of this have been cited on this very cite, like for instance, the lone Ivory Coast sample that was used as the proxy of "sub-Saharan" Africans—a term that is tacitly relegated to mainly western and central Africans—in the study of coastal northern African samples.
In this undertaking, geography is played around with, as have been noted on this site before, to effect the desired outcome in research findings. For instance, to recap, the portion of western Africa that is above the equator is partitioned into coastal northern Africa (aka Maghreb, including some areas in the Sahara) and "sub-Saharan Africa", while the eastern Africa portion that is above the equator, and covering Ethiopia, and in even Somalia in some cases, are all treated as "northeastern Africa" as opposed to sub-Saharan Africa.
This kind of unspoken sampling protocol ultimately has the effect of breaking clinal genetic transitions in western Africa, while basically doing the opposite on the eastern section of the continent, and other places, such as the so-called "Near East" and Europe.
With that briefing, there is no reason not to start moving onto other aspects of the study that stand out. These will be spelled out in the ensuing discussion segment.
Discussion:
What's immediately striking about the authors' procedure, is that they utilized Utah residents with European ancestry, and the Yoruba (from Ibadan, Nigeria) as their primary choice of "ancestral" populations vis-a-vis the global samples they considered in their analysis. Seriously?
Modern European-derived populations are hardly the sort of populations ideal for representation as ancestral-appropriate to global samples; the same rings true for Yoruba, although perhaps not as anomalous a choice as that of some European-derived group. If anything, core European populations are among those which diverged relatively late in the OOA phylogeny. The justification given for this, is the purported "extreme" positions that these sample partook in the authors' PCA (S4 in their supplementary material) plot:
We used as putative ancestral populations either CEU (Utah residents with ancestry from northern and western Europe) and YRI (as previously described39) or CEU and Ari, chosen because of their extremal positions in a PC plot (Figure S4).
The so-called "Ari" group from eastern Africa, which was picked as an alternative to the Yoruba in their second choice—using the same Utah residents, perhaps makes a relatively better fit as some would-be "ancestral" group than either the Utah residents or Yoruba. If there's any indication as to how this could be, then perhaps consider this, concerning the so-called "Ari Blacksmiths" in particular:
Of particular interest is the distinctiveness of the Omotic groups, whose position in Figures 1A and S3 is intriguingly compatible with being a putative ancestral Ethiopian population. One insight provided by the ADMIXTURE plot (Figure 1C) concerns the origin of the Ari Blacksmiths. This population is one of the occupational caste-like groups present in many Ethiopian societies that have traditionally been explained as either remnants of hunter-gatherer groups assimilated by the expansion of farmers in the Neolithic period or as groups marginalized in agriculturalist communities due to their craft skills.51 The prevalence of an Ethiopian-specific cluster (yellow in Figure 1C) in the Ari Blacksmith sample could favor the former scenario; the ancestors of this occupational group could have been part of a population that inhabited the area before the spread of agriculturalists. Further study of multiple groups comparing agriculturists and caste-like groups would reveal whether there is a pattern of a greater Ethiopia-specific genomic profile associated with caste-like occupations, an observation which would support the absorption rather than the exclusion hypothesis.
While the observation is still reasonably tenuous, it does open up that possibility of the aforementioned better candidacy. This is what's said of some of the other populations considered in the analysis:
the ROLLOFF algorithm was recoded in-house (details available upon request) from the description provided, following advice kindly provided by its authors, and was shown to give similar age estimates (r2 > 0.9, data not shown) for a set of test populations previously analyzed with the use of this approach (African Americans, Palestinians, Sardinians, Bedouins, and Druze; all treated as a mixture of CEU and YRI).
"all treated as a mixture" of the Utah residents and the Yoruba? What kind of objective assessment can come of this; it would be absurd to think of say, Palestinians, as some hybridized product of Utah residents and the Yoruba, as they do not derive from either! The same would be equally absurd, if the Ethiopian samples were treated as such.
The relative fringe positioning of the CEU, YRI or even the Ari, at best, says that they have been relatively isolated from those other groups considered in the sample. Geographically-proximate groups are likely to align relatively closer to one another than those with greater distance between them. Cultural conservatism/isolation can also serve as either an additional factor or a driving one, in considerably differentiating populations. The aforementioned [i.e. being compelled to use a Utah or Yoruba series as one that can serve as an ancestral gene pool to groups which would otherwise have no such link to the Utah or Yoruba people] is but a symptom of the very sort of DNA marker assignment into gratuitous grouping of genomes under either "African" or "non-African" that the authors use. Ethiopian samples are given this dubious treatment throughout the analysis, and reports from the authors reflect the corresponding shortcomings of this protocol in several instances.
With regards to the aforementioned possible impact of cultural-related barriers to free gene flow between different groups, consider this:
we observe strong genetic structuring in East Africa, including a strong match between the linguistic and genetic structures. This is exemplified by the three distinct PC clusters (Omotic, Nilotic, and Semitic Cushitic), confirming Ethiopia as one of the most diverse African regions.
This is coming from populations that are supposed to be geographically-proximate!
With regards to the aforementioned possible impact of cultural-related barriers to free gene flow between different groups, consider this:
we observe strong genetic structuring in East Africa, including a strong match between the linguistic and genetic structures. This is exemplified by the three distinct PC clusters (Omotic, Nilotic, and Semitic Cushitic), confirming Ethiopia as one of the most diverse African regions.
This is coming from populations that are supposed to be geographically-proximate!
The Ethiopian gene pool too was assumed to be a derivative of the Yoruba (YRI) gene pool, so as to conveniently isolate what the purported to be the "African" component (amounting to an archetypal rendition of "African" ancestry], whereupon from which, any genetic element that doesn't seem to fit in and perhaps seems to display similarities with groups from outside the continent, was separated and treated as "non-African'. The supposed 'non-African' component is compared against the Utah residents—mentioned earlier—and the French, i.e. European/European-derived samples which were both treated as archetypes or ancestral "templates" for supposed "non-African" ancestry.
It is little wonder then, that the authors could not help but notice that Ethiopian gene pool also contained elements that seemed to neither align with the supposed "African" component and the supposed "non-African" component. One such composition turned out to be what the authors would call "Ethiopian-specific" component, treated as special group of "African" ancestry.
The other African group that served as an "ancestral"—as noted earlier—gene pool for the Ethiopian gene pool, was the so-called Ari Cultivator and Blacksmith groups, no doubt partly stemming from an observation, whereby these groups simply formed their own eastern African cluster away from the Yoruba and western African or central African clusters. Of course, these patterns should have served as clear clues against simplistic grouping of genome into "African" vs. "non-African". To put the just-mentioned into perspective, consider this, for example:
Ethiopian populations, considered as a combination of West Africans with non-Africans or East Africans with non-Africans, depending on their position in the PC plot (Figure S4).
Certain eastern African groups simply could not be pigeonholed into an archetypal "African" component that is modeled after a Yoruba sample from Ibadan. It could not be done:
when looking for correlations between the Nigerian-Congolese component (blue in Figure 1C) and the first three PCs in the Nilotic populations, we found a much weaker correlation (Figure 1F) than observed for the Semitic-Cushitic component. The Ari-Yoruba cline observed for the Nilotic samples cannot therefore be explained as a simple admixture event between Ethiopians and Nigerian-Congolese populations.
This would also be the more likely scenario in cases concerning the non-Nilotic eastern African groups considered in this study. That is to say, seeming inclination in positioning (in the PCA plots) towards clusters predominated by western or central African samples may actually be reflective of either lingering elements of common ancestry and/or convergences in genomic evolution, rather than some recent gene flow from the so-called "Nigerian-Congolese" gene pool into Ethiopian or eastern African gene pool. Perhaps the following could be serving as an indirect indication of this:
Both plots confirmed the high diversity in Ethiopia characterized by a strong (40%–50%) non-African component (light blue in Figure 1C) and an African component split between a broad East African (purple in Figure 1C) and an apparently Ethiopia-specific component (yellow).
The same could well also be at work in the seeming inclination in positioning towards clusters dominated by groups from outside of Africa, i.e. reflective of lingering gene pool from an ancestral source common to said eastern African groups and non-African groups, and/or convergences in evolution of elements of the genome. As will become clear, there is indication of this in several observations noted in the study.
Closer inspection shows that the so-called "non-African" component of Ethiopian gene pool is actually relatively closer to those found in coastal northern Africans than it is to those outside of the continent, a finding that's consistent with the pattern observed in the mtDNA gene pool of Ethiopians (see: Following Trails of the Cro-Magnon I & II ). This is necessary to point out, since elements of 'western researchers' and ideologues from elsewhere have long sought to link not only Ethiopian Semitic languages, but also what they call "Eurasian" lineages in Ethiopian samples, to a historic south Arabian origin. The following could serve as an example of this phenomenon:
We explored this finding further by calculating the minimum pairwise difference (see Material and Methods) between Africans and non-Africans for their whole genome, and for the non-African component only. The results are concordant with the results of the FST analyses in showing that the Egyptians are closer than Yemeni to Ethiopians in their non-African component (Table S3).
The authors go onto explain this off with reasoning that gene flow from Egypt and the Levant, as opposed to south Arabia, may account for the above-mentioned observation, even though, in their own words, they could not say "whether the gene flow was episodic or continuous". However, as noted on this blogging site some 3 years ago or so, the more likely reason is that the ancestors of the major Afro-Asiatic speaking populations in Ethiopia were at one time situated in a more northerly clime on the African continent itself than they now currently reside, likely in the central and/or eastern Saharan areas that now form part of Egypt, and possibly Libya, and/or yet, the northernmost areas of Sudan, wherein said supposed "Eurasian" lineages would have been heavily concentrated prior to the resumption of intense aridity.
As the above scenario goes, the ancestors of said Ethiopians would have been in the Sahara all along, or at least by the early Neolithic time frame, as opposed to coming from some historic migration originating in south Arabia. Under the above scenario, as noted in previous publications here, the seeming similarities that are observed between Ethio-Semitic languages and South Arabian language (particularly Sabean) would have likely been the outcome of cultural exchange (e.g. trade) between the Ethiopian complex and the south Arabian complex, at the height of the Sabean kingdom.
Accordingly, it should be noted that even prior to the noted cultural exchange, the aboriginal language of Ethio-Semitic speakers would have had characteristics of a Semitic language, or to put it another way, would have had tendencies commonly associated with the Semitic language family! As such, resemblances between Ethio-Semitic and Sabean would have only been attained after Ethiopians came into contact with the Sabeans, which would have entailed the use of a lingua franca or trade language—likely Sabean at the time, on top of the already Semitic-like tendencies of the aboriginal Ethiopian language(s), thereby giving the [misleading] impression of a direct monophyletic connection between Ethio-Semitic and south Arabian Semitic.
The use of a south Arabian language as a trade language—and there is archaeological indication of this—which was likely used in tandem with a south Arabian Semitic script, said to be a derivative of the so-called "proto-Sinaitic", would have made it attractive to modify preexisting aboriginal languages in ways that can allow them to accommodate the writing attributes of said script. Additionally, in the urban and sub-urban centers, it is not uncommon for features of a trade language to filter into some preexisting primary language, provided that the trade language isn't the same one as the primary local language [also noted in E-M34: Designation as "African" presents a Dilemma?].
It should not really be an astonishing prospect, for an aboriginal Ethiopian language family to have autochthonously evolved with "Semitic-like" tendencies prior to any contact with the outside world, since after all, Semitic is really nothing more than an offshoot of the so-called "proto Afro-Asiatic"—the theoretical common ancestor determined to have its roots in the African continent itself—which just so happened to subsequently diversify in Red-sea bordering areas adjacent to eastern Africa.
Continuing with the aforementioned theme of a prehistoric residence of Ethiopian groups in northern Africa, i.e. the Sahara, as opposed to the Arabian peninsula, or even the Levant at that, we come across several clues that tacitly surface in Pagani et al.'s report; consider the following, for instance:
The strong PC1 and PC3 correlations therefore seem to indicate that the proportion of non-African admixture is the main driver of the Ari-Egyptian cline formed by the Semitic-Cushitic samples in the PCA plot, regardless of their population of origin.
Results from a study into within-group heterozygosity are in keeping with an ongoing common theme between Ethiopian groups and coastal northern African groups:
The Semitic-Cushitic and North African populations showed the highest values of heterozygosity worldwide, which may reflect a combination of SNP ascertainment bias and the mixture of African and non-African components in these populations.
Perhaps mapping demonstrates the trends in heterozygosity better; on map E in particular, average values when taken and plotted, create a window for the observation made above, with regards to high values reported for the said Ethiopian groups and coastal northern African groups. Notice how there seems to be a trend in concentration of relatively high values of heterozygosity in regions or areas that seem to have traditionally served as "highways" (crossroads) for human movement between major continents or landmasses which are otherwise generally separated by physical barriers.
Also, the smaller the distance of separation of one block of landmass per continent to the next block , the better it seems, a prospect for high heterozygosity attainment; notice for instance, heavier concentration of heterozgyosity around the equatorial and in the northern climes thereof on say, the African continent. There is a generally trend in heavier concentration across areas north of the equator.
On the African continent, the areas most further away from the next concentration of landmass outside the continent's mainland, like southern Africa for instance, seem to show lower concentration of heterozygosity, and the trend seems to surface elsewhere in the world map, as shown below. Perhaps this is partially coincidental, as an artifact of populations sampled; for example, relatively small, simple, somewhat isolated and culturally conservative egalitarian-inclined communities, like say the San hunter-gatherers, are likely to show relatively lower heterozygosity than the more socioculturally complex communities which are surrounded by other complex societies.
This trend also seems to surface elsewhere in the globe; indeed, the San, the Hadza, Mbuti and Biaka pygmies, the Papuan New Guineans and Melanesians for instance, seem to among the groups in the lower end heterozygosity values, as signaled in the map [also see the supplementary table S2 for estimates]:
While the Ethiopian and the coastal north-African samples feature fairly high heterozygosity levels, at nearly similar values, this in itself does not specify the relationship between these samples, perhaps because of the aforementioned issue of geographical location (e.g. being at the crossroad of intercontinental human movement), which may factor into how diversity in some locations manifest; it does however, play into the theme of common qualities about said samples.
The samples of the Ari people of Ethiopia, which reportedly show "little evidence of recent non-African gene flow", feature high heterozgyosity values as well, comparable to those of the Semitic-Cushitic block and coastal north African samples. Pairwise Fst estimates, which will be the subject of the ensuing passages shortly, show interesting qualities about these people as well.
The Fst values from pairwise comparisons between groups on the other hand, are more concise about relationship, mappings for which can also be located in the image above. Like heterozgyosity, there is some geography factor at play in Fst values; the more distant two groups are (likely in the accompaniment of substantial divergence time-depths from a common recent ancestor), barring a fairly recent divergence event, the more likely a higher pairwise Fst value reported respective to the two groups. Conversely, neighboring groups are expected to report smaller values in a pairwise comparison, absent extraordinary occasions of cultural isolation due to socio-cultural barriers between neighboring groups.
The Ari Cultivator and Ari Blacksmith samples are apparently genetically close, but interestingly, it is the Ari Cultivator samples that produce closer (supplementary table S3) pairwise Fst values with the Ethiopian Cushitic-Semitic block. The interesting thing here, is that the reported geographical distance between the Ari Blacksmiths and said Semitic-Cushitic block is much smaller than that reported between the Ari Cultivators and the Semitic-Cushitic block.
The estimated geographical distance between the Ari Blacksmiths and the Semitic-Cushitic block is virtually zero km, while that reported between the Ari Cultivators and the Cushitic-Semitic block is 250km. The genetic distances between the Ari samples and the Nilotic groups (Anuak and the unspecified south Sudanese) are generally close, and so are genetic distances of both groups more or less similar with respect to northern coastal Africans and non-Africans, but the Anuak and the south Sudanese show smaller genetic distances with Niger-Congo samples from western Africa. This, if one recalls, is not easily explained off as "admixture" from Niger-Congo populations.
The closer relationship between the Ethiopian Anuak and the south Sudanese samples than either are to the Ethiopian Ari samples is not all that surprising, and so is the closer relationship between the Omotic Ari Cultivator and Blacksmith than either are to aforementioned Nilotic samples. It is fairly likely that the Anuak diverged relatively more recently from a shared ancestral group with the south Sudanese group than did with the aforementioned Omotic groups.
Between the Ari Blacksmith and the Ari Cultivator samples, plurality goes to the Ari Blacksmith—which are reportedly more geographically proximate to the Cushitic-Semitic block analyzed in this study—in terms of similarities with the Anuak samples, when the profile of heterozgyosity estimates and pairwise Fst values with other groups are considered; yet, the Ari Cultivators report smaller average pairwise Fst values with the Anuak and the south Sudanese samples respectively, than the Ari Black samples do.
Coupling the above-mentioned qualities with the fact that the Ari Cultivator samples report a higher heterozgyosity value than the Ari Blacksmith and said Nilotic groups, and that in essentially every case of a study into the pairwise Fst estimation with other groups—including the Semitic-Cushitic block, the Ari Cultivator samples produced relatively lower values than the Ari Blacksmith samples, raises the prospect of the Ari Cultivator gene pool serving as potential example of an ancestral east African gene pool; the smaller Fst values with the Semitic-Cushitic block, despite its greater geographical distance with this block than the Ari Blacksmith samples, may speak to the possibility of the Cultivator sample serving as a surviving remnant of an eastern African gene pool that may be ancestral to the Semitic-Cushitic block.
Pairwise Fst values also indicate that the Hadza more closely approximate the San than the Sandawe do, when the aforementioned Omotic, Nilotic, Semitic and Cushitic samples are used as samples to be compared against. This seems to be the case as well, when some of the other samples outside the latter are used. This may be a sign that the Sandawe have more content of a gene pool with contemporary eastern African profile than the Hadza do.
On average, the San and the Pygmies appear to be the most differentiated group from the Ethiopian samples among the African samples, when the latter are applied as the reference sample to be compared with. This seems to be the prevailing trend when the other African samples are considered, and indeed, non-African samples, although the differences with respect to African samples are generally not as acute as those with respect to relatively far-flung regions outside of the continent. Outside of Africa, the Melanesian and the Papuan samples appear as the most differentiated from other samples, both African and non-African; in some cases, even outdoing the San or the pygmies.
In the above context, the Khoisan from south Africa seem to be comparatively less differentiated, perhaps because they have been relatively less isolated in recent times. When the San are used as the reference sample to be compared against, a somewhat different image emerges, whereby some Ethiopian groups appear to be the genetically closest, seemingly with other exceptions—i.e. involving samples other than Ethiopians.
The PCA plot above is another means for studying into the relative positioning, and hence distance, of African groups with respect to other African groups. In the case of the PCA plot above, the primary goal was to deduce relative diversity between African blocks. Another PCA plot was undertaken to gauge this diversity, with the Ethiopian group being the main targets apparently, using a global-wide sample this time around:
The plot above was applied to gauge Ethiopian relative diversity, and it does confirm the substantial diversity of the Ethiopian block [especially vis-a-vis the "Africa" samples; note that all other groups in the plot are treated as continental blocks, except for the "Ethiopian" and the "African-American" samples, which are treated as nationalities], comprising all the respective Ethiopian groups considered in the analysis. However, the plot appears to have an additional value, which does not appear to have been its focal point: Ethiopian samples still lean towards the African clusters than they do the outside groups. If anything, it's elements of the "Eurasians" that scatter in almost all sides.
In general, as also observed by the authors of the present study, pairwise Fst values appear to assume more or less steady increases with incremental geographical distance from centers picked in the African continent:
The observed pattern of uniform decline of FST values away from North,West, or East Africa is consistent with previous interpretations of a single exit, followed by ‘‘isolation by distance.’
It's apparent what the authors were getting at here, although it should be pointed out that Fst values themselves actually steadily increment away from North, West or Eastern Africa, as opposed to a "uniform decline". What the authors probably meant to say, was that there was a decline in genetic similarity with distance, as they do elsewhere:
Consistent with previous studies’ reports of a steady decline in genetic similarity among non-African populations as a function of geographical traveling distance from East Africa, we found that the FST values estimated between either Ethiopian or North African populations and non-African populations followed the same pattern (Figure 2, Table S2).
In the Fst maps above, particularly: C which uses an Ethiopian Semitic-Cushitic sample as the reference sample, followed by that of A which uses an Egyptian sample as the reference sample to be compared against, coastal northern African samples appear to be amongst the closest to the Semitic-Cushitic groups. The redder the area of a test sample away from the reference samples, the more distant is the said sample from the reference sample.
The same story is more or less conveyed in the following Fst plotting, but this time using "ten haploid genomes" and "ten haploid" so-called "non-African" genomes of test samples:
In the image on the left, i.e figure 2A, Fst values with respect to the Egyptian, Moroccan and Yemeni samples appear to be smaller than those reported for elsewhere, using the Semitic-Cushitic Ethiopian samples as the reference samples to be compared against. This is so in what appears to be a test involving some 12 samples—three of which are African—outside of the Semitic-Cushitic samples.
In the image on the right, the one concerning the "ten haploid" so-called "non-African genome", one notices that it is the Egyptians and the Moroccans which show smaller Fst values than those reported elsewhere, with respect to the Semitic-Cushitic samples. Yet again, the test appears to have involved the same 12 international samples.
The color scale applied here, in the two Fst maps above, appears to be the reverse of that applied in the preceding Fst plots; the redder the area of a sample, the smaller is the Fst value or genetic distance, with respect to the Semitic-Cushitic samples. This again, speaks to that recurring theme of the said Ethiopian samples showing their closest relationship with coastal north Africans than any other group, with respect to their supposed "non-African" gene pool!
While the authors' supplementary table S2 appears to show similar Fst values between Semitic-Cushitic Ethiopian samples and Moroccan, Egyptian and Yemeni samples, the reported values in supplementary table S3 convey a somewhat different story, that is more concordant with an observation made in the preceding passages. Table S2 only reports the rounded-up estimates, while table S3 shows the actual values, and thereby revealing that the Egyptians are indeed the closest group to the Ethiopian Semitic-Cushitic block than the Yemeni. In the whole-genome analysis, even the Moroccans attain genetic proximity to the said Ethiopian groups before the Yemeni do, while in the study around the so-called "non-African" component, Bedouin and Druze samples from the Levant follow the Egyptians in genetic proximity before the Yemeni samples do.
The last phenomenon mentioned above is congruent with the theme that emerges from mtDNA analysis. It was certainly the case noticed (see: Following Trails of the Cro-Magnon - I, Following Trails of the Cro-Magnon - II, and E-M34: Designation as "African" presents a Dilemma?) in a study [4] released in 2004. mtDNA show that plurality goes to coastal northern Africa, when Ethiopian Cushitic-Semitic mtDNA affinity is considered. Head to head comparison of mtDNA between Ethiopian samples and the coastal north African counterparts vs. those outside them had not been a focal point of this study; however, they do note a certain other theme emerging from their analysis:
A minimum-pairwise distance measure based on the African component of the genome found that the Ethiopian mtDNA component was closer to non-African populations than was the Egyptian mtDNA component, as previously reported, but that the autosomal genome of non-Africans was closer to the African component of the Egyptian rather than Ethiopian populations. This could be interpreted as supporting a northern exit route.
They caution:
However, the 80% non-African proportion of the Egyptian genome (Figure 1C) reduces the power of our comparisons and, taken together with the requirement for the African state in at least ten chromosomes, means that this conclusion is based on just ~1,800 SNPs (compared to 18,960 for the Ethiopians, 30,798 for the Mozabite, and 5,920 for the Moroccans). Therefore, the question requires further investigation beyond the scope of the present study.
This could be interpreted as the Ethiopian samples better preserving the ancestral "African" component to the non-African gene pool, in terms of the maternally-mediated gene pool. Consider the fact that the authors report an even lower average pairwise difference between the Omotic samples and select non-African samples than Ethiopian Cushtic-Semitic block did with said samples (.0021 vs. .0027; see table 2). Even though the idea is not particularly popular among those with thinking that is Euro-centered leaning, this could also be a signal that some elements of so-called "African" mtDNA among non-Africans may well be serving as lingering relics of OOA migration...
when we first partitioned the mtDNA lineages into African and non-African (i.e., L and non-L) and considered only the L component, a different pattern emerged: Ethiopians were the closest population to the non-Africans (Table 2B), consistent with inferences drawn from more detailed mtDNA analyses.
Egyptian mtDNA could also have been influenced by some occasional migrations to the region from the inner areas of Africa, which would otherwise have been relatively rare to Ethiopia. Among such, for instance, are migrations driven by the desire to reach Mecca in Saudi Arabia, particularly some time in the post-Dynastic periods, since Egypt sits on the pathway to the Levant and the north areas of the Arabian peninsula. Some migrants do subsequently decide to stay in the Nile Valley instead of heading back to their actual territorial origin, although it's fairly questionable whether such settler migrants necessarily have had a sizable impact on the native locals. Still, relatively recent gene flow of Ethiopian mtDNA into some "non-African" gene pools more so than from Egypt, cannot be excluded in the final analysis.
On the other hand, when other mtDNA were considered, transcending the supposed "African" component, a different theme emerges; the Egyptians and Moroccans assume relative genetic proximity to non-Africans:
With the full set of 18 mtDNA SNPs used in our genome-wide data set, Egyptians and Moroccans proved to be the closest African population to any non-African population examined (Table 2A)...
Note that the arrangement of mtDNA into "African" vs "non-African" [briefed on earlier] by the authors looks to be largely arbitrary, since it appears to be driven by little else than simply grouping mtDNA into either "L", which was exclusively treated as "African", or grouped into "M or N" which were effortlessly and gratuitously taken for granted as "non-African". In-depth and careful assessment makes it apparent that mtDNA phylogeny do not simplistically or objectively conform to that protocol, as popular as it may be among 'western' research teams.
The picture emerging from the autosomal component, as the authors describe above, could be more anomalous to some extent. It could be, as the authors noted, the artifact of substantial disparity between the available size of Egyptian SNPs (i.e. from the supposed "African component") and those of other samples analyzed, or it could just be reflective of the relatively greater time-depth of divergence of Ethiopian atDNA vis-a-vis non-African gene pools, by comparison [i.e. to Egypt]; the latter could tacitly parallel (and hence, be reaffirmed by) the relatively closer genetic distance between the Egyptian and Moroccan samples to non-African samples in the mtDNA analysis. Genome-wide analysis of atDNA, it should be noted, conveys the same theme as the so-called "African" component of atDNA...
Applying the same principle, we then calculated the shortest distance between the African and non-African populations on the basis of either full genome data or the African component of this data set. In contrast to the mtDNA results, the Egyptians proved to be the closest to the non-Africans in both cases (Tables 2A and 2B).
As another sign that the authors' simplified assignment of markers into either "African" or "non-African" is fairly questionable, consider the findings noted in the following, with regards to the SLC24A5 gene:
The other African group that served as an "ancestral"—as noted earlier—gene pool for the Ethiopian gene pool, was the so-called Ari Cultivator and Blacksmith groups, no doubt partly stemming from an observation, whereby these groups simply formed their own eastern African cluster away from the Yoruba and western African or central African clusters. Of course, these patterns should have served as clear clues against simplistic grouping of genome into "African" vs. "non-African". To put the just-mentioned into perspective, consider this, for example:
Ethiopian populations, considered as a combination of West Africans with non-Africans or East Africans with non-Africans, depending on their position in the PC plot (Figure S4).
Certain eastern African groups simply could not be pigeonholed into an archetypal "African" component that is modeled after a Yoruba sample from Ibadan. It could not be done:
when looking for correlations between the Nigerian-Congolese component (blue in Figure 1C) and the first three PCs in the Nilotic populations, we found a much weaker correlation (Figure 1F) than observed for the Semitic-Cushitic component. The Ari-Yoruba cline observed for the Nilotic samples cannot therefore be explained as a simple admixture event between Ethiopians and Nigerian-Congolese populations.
This would also be the more likely scenario in cases concerning the non-Nilotic eastern African groups considered in this study. That is to say, seeming inclination in positioning (in the PCA plots) towards clusters predominated by western or central African samples may actually be reflective of either lingering elements of common ancestry and/or convergences in genomic evolution, rather than some recent gene flow from the so-called "Nigerian-Congolese" gene pool into Ethiopian or eastern African gene pool. Perhaps the following could be serving as an indirect indication of this:
Both plots confirmed the high diversity in Ethiopia characterized by a strong (40%–50%) non-African component (light blue in Figure 1C) and an African component split between a broad East African (purple in Figure 1C) and an apparently Ethiopia-specific component (yellow).
The same could well also be at work in the seeming inclination in positioning towards clusters dominated by groups from outside of Africa, i.e. reflective of lingering gene pool from an ancestral source common to said eastern African groups and non-African groups, and/or convergences in evolution of elements of the genome. As will become clear, there is indication of this in several observations noted in the study.
Closer inspection shows that the so-called "non-African" component of Ethiopian gene pool is actually relatively closer to those found in coastal northern Africans than it is to those outside of the continent, a finding that's consistent with the pattern observed in the mtDNA gene pool of Ethiopians (see: Following Trails of the Cro-Magnon I & II ). This is necessary to point out, since elements of 'western researchers' and ideologues from elsewhere have long sought to link not only Ethiopian Semitic languages, but also what they call "Eurasian" lineages in Ethiopian samples, to a historic south Arabian origin. The following could serve as an example of this phenomenon:
We explored this finding further by calculating the minimum pairwise difference (see Material and Methods) between Africans and non-Africans for their whole genome, and for the non-African component only. The results are concordant with the results of the FST analyses in showing that the Egyptians are closer than Yemeni to Ethiopians in their non-African component (Table S3).
The authors go onto explain this off with reasoning that gene flow from Egypt and the Levant, as opposed to south Arabia, may account for the above-mentioned observation, even though, in their own words, they could not say "whether the gene flow was episodic or continuous". However, as noted on this blogging site some 3 years ago or so, the more likely reason is that the ancestors of the major Afro-Asiatic speaking populations in Ethiopia were at one time situated in a more northerly clime on the African continent itself than they now currently reside, likely in the central and/or eastern Saharan areas that now form part of Egypt, and possibly Libya, and/or yet, the northernmost areas of Sudan, wherein said supposed "Eurasian" lineages would have been heavily concentrated prior to the resumption of intense aridity.
As the above scenario goes, the ancestors of said Ethiopians would have been in the Sahara all along, or at least by the early Neolithic time frame, as opposed to coming from some historic migration originating in south Arabia. Under the above scenario, as noted in previous publications here, the seeming similarities that are observed between Ethio-Semitic languages and South Arabian language (particularly Sabean) would have likely been the outcome of cultural exchange (e.g. trade) between the Ethiopian complex and the south Arabian complex, at the height of the Sabean kingdom.
Accordingly, it should be noted that even prior to the noted cultural exchange, the aboriginal language of Ethio-Semitic speakers would have had characteristics of a Semitic language, or to put it another way, would have had tendencies commonly associated with the Semitic language family! As such, resemblances between Ethio-Semitic and Sabean would have only been attained after Ethiopians came into contact with the Sabeans, which would have entailed the use of a lingua franca or trade language—likely Sabean at the time, on top of the already Semitic-like tendencies of the aboriginal Ethiopian language(s), thereby giving the [misleading] impression of a direct monophyletic connection between Ethio-Semitic and south Arabian Semitic.
The use of a south Arabian language as a trade language—and there is archaeological indication of this—which was likely used in tandem with a south Arabian Semitic script, said to be a derivative of the so-called "proto-Sinaitic", would have made it attractive to modify preexisting aboriginal languages in ways that can allow them to accommodate the writing attributes of said script. Additionally, in the urban and sub-urban centers, it is not uncommon for features of a trade language to filter into some preexisting primary language, provided that the trade language isn't the same one as the primary local language [also noted in E-M34: Designation as "African" presents a Dilemma?].
It should not really be an astonishing prospect, for an aboriginal Ethiopian language family to have autochthonously evolved with "Semitic-like" tendencies prior to any contact with the outside world, since after all, Semitic is really nothing more than an offshoot of the so-called "proto Afro-Asiatic"—the theoretical common ancestor determined to have its roots in the African continent itself—which just so happened to subsequently diversify in Red-sea bordering areas adjacent to eastern Africa.
Continuing with the aforementioned theme of a prehistoric residence of Ethiopian groups in northern Africa, i.e. the Sahara, as opposed to the Arabian peninsula, or even the Levant at that, we come across several clues that tacitly surface in Pagani et al.'s report; consider the following, for instance:
The strong PC1 and PC3 correlations therefore seem to indicate that the proportion of non-African admixture is the main driver of the Ari-Egyptian cline formed by the Semitic-Cushitic samples in the PCA plot, regardless of their population of origin.
Results from a study into within-group heterozygosity are in keeping with an ongoing common theme between Ethiopian groups and coastal northern African groups:
The Semitic-Cushitic and North African populations showed the highest values of heterozygosity worldwide, which may reflect a combination of SNP ascertainment bias and the mixture of African and non-African components in these populations.
Perhaps mapping demonstrates the trends in heterozygosity better; on map E in particular, average values when taken and plotted, create a window for the observation made above, with regards to high values reported for the said Ethiopian groups and coastal northern African groups. Notice how there seems to be a trend in concentration of relatively high values of heterozygosity in regions or areas that seem to have traditionally served as "highways" (crossroads) for human movement between major continents or landmasses which are otherwise generally separated by physical barriers.
Also, the smaller the distance of separation of one block of landmass per continent to the next block , the better it seems, a prospect for high heterozygosity attainment; notice for instance, heavier concentration of heterozgyosity around the equatorial and in the northern climes thereof on say, the African continent. There is a generally trend in heavier concentration across areas north of the equator.
On the African continent, the areas most further away from the next concentration of landmass outside the continent's mainland, like southern Africa for instance, seem to show lower concentration of heterozygosity, and the trend seems to surface elsewhere in the world map, as shown below. Perhaps this is partially coincidental, as an artifact of populations sampled; for example, relatively small, simple, somewhat isolated and culturally conservative egalitarian-inclined communities, like say the San hunter-gatherers, are likely to show relatively lower heterozygosity than the more socioculturally complex communities which are surrounded by other complex societies.
This trend also seems to surface elsewhere in the globe; indeed, the San, the Hadza, Mbuti and Biaka pygmies, the Papuan New Guineans and Melanesians for instance, seem to among the groups in the lower end heterozygosity values, as signaled in the map [also see the supplementary table S2 for estimates]:
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| Click on the image to read the accommodating caption and details of the map! |
The samples of the Ari people of Ethiopia, which reportedly show "little evidence of recent non-African gene flow", feature high heterozgyosity values as well, comparable to those of the Semitic-Cushitic block and coastal north African samples. Pairwise Fst estimates, which will be the subject of the ensuing passages shortly, show interesting qualities about these people as well.
The Fst values from pairwise comparisons between groups on the other hand, are more concise about relationship, mappings for which can also be located in the image above. Like heterozgyosity, there is some geography factor at play in Fst values; the more distant two groups are (likely in the accompaniment of substantial divergence time-depths from a common recent ancestor), barring a fairly recent divergence event, the more likely a higher pairwise Fst value reported respective to the two groups. Conversely, neighboring groups are expected to report smaller values in a pairwise comparison, absent extraordinary occasions of cultural isolation due to socio-cultural barriers between neighboring groups.
The Ari Cultivator and Ari Blacksmith samples are apparently genetically close, but interestingly, it is the Ari Cultivator samples that produce closer (supplementary table S3) pairwise Fst values with the Ethiopian Cushitic-Semitic block. The interesting thing here, is that the reported geographical distance between the Ari Blacksmiths and said Semitic-Cushitic block is much smaller than that reported between the Ari Cultivators and the Semitic-Cushitic block.
The estimated geographical distance between the Ari Blacksmiths and the Semitic-Cushitic block is virtually zero km, while that reported between the Ari Cultivators and the Cushitic-Semitic block is 250km. The genetic distances between the Ari samples and the Nilotic groups (Anuak and the unspecified south Sudanese) are generally close, and so are genetic distances of both groups more or less similar with respect to northern coastal Africans and non-Africans, but the Anuak and the south Sudanese show smaller genetic distances with Niger-Congo samples from western Africa. This, if one recalls, is not easily explained off as "admixture" from Niger-Congo populations.
The closer relationship between the Ethiopian Anuak and the south Sudanese samples than either are to the Ethiopian Ari samples is not all that surprising, and so is the closer relationship between the Omotic Ari Cultivator and Blacksmith than either are to aforementioned Nilotic samples. It is fairly likely that the Anuak diverged relatively more recently from a shared ancestral group with the south Sudanese group than did with the aforementioned Omotic groups.
Between the Ari Blacksmith and the Ari Cultivator samples, plurality goes to the Ari Blacksmith—which are reportedly more geographically proximate to the Cushitic-Semitic block analyzed in this study—in terms of similarities with the Anuak samples, when the profile of heterozgyosity estimates and pairwise Fst values with other groups are considered; yet, the Ari Cultivators report smaller average pairwise Fst values with the Anuak and the south Sudanese samples respectively, than the Ari Black samples do.
Coupling the above-mentioned qualities with the fact that the Ari Cultivator samples report a higher heterozgyosity value than the Ari Blacksmith and said Nilotic groups, and that in essentially every case of a study into the pairwise Fst estimation with other groups—including the Semitic-Cushitic block, the Ari Cultivator samples produced relatively lower values than the Ari Blacksmith samples, raises the prospect of the Ari Cultivator gene pool serving as potential example of an ancestral east African gene pool; the smaller Fst values with the Semitic-Cushitic block, despite its greater geographical distance with this block than the Ari Blacksmith samples, may speak to the possibility of the Cultivator sample serving as a surviving remnant of an eastern African gene pool that may be ancestral to the Semitic-Cushitic block.
Pairwise Fst values also indicate that the Hadza more closely approximate the San than the Sandawe do, when the aforementioned Omotic, Nilotic, Semitic and Cushitic samples are used as samples to be compared against. This seems to be the case as well, when some of the other samples outside the latter are used. This may be a sign that the Sandawe have more content of a gene pool with contemporary eastern African profile than the Hadza do.
On average, the San and the Pygmies appear to be the most differentiated group from the Ethiopian samples among the African samples, when the latter are applied as the reference sample to be compared with. This seems to be the prevailing trend when the other African samples are considered, and indeed, non-African samples, although the differences with respect to African samples are generally not as acute as those with respect to relatively far-flung regions outside of the continent. Outside of Africa, the Melanesian and the Papuan samples appear as the most differentiated from other samples, both African and non-African; in some cases, even outdoing the San or the pygmies.
In the above context, the Khoisan from south Africa seem to be comparatively less differentiated, perhaps because they have been relatively less isolated in recent times. When the San are used as the reference sample to be compared against, a somewhat different image emerges, whereby some Ethiopian groups appear to be the genetically closest, seemingly with other exceptions—i.e. involving samples other than Ethiopians.
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In general, as also observed by the authors of the present study, pairwise Fst values appear to assume more or less steady increases with incremental geographical distance from centers picked in the African continent:
The observed pattern of uniform decline of FST values away from North,West, or East Africa is consistent with previous interpretations of a single exit, followed by ‘‘isolation by distance.’
It's apparent what the authors were getting at here, although it should be pointed out that Fst values themselves actually steadily increment away from North, West or Eastern Africa, as opposed to a "uniform decline". What the authors probably meant to say, was that there was a decline in genetic similarity with distance, as they do elsewhere:
Consistent with previous studies’ reports of a steady decline in genetic similarity among non-African populations as a function of geographical traveling distance from East Africa, we found that the FST values estimated between either Ethiopian or North African populations and non-African populations followed the same pattern (Figure 2, Table S2).
In the Fst maps above, particularly: C which uses an Ethiopian Semitic-Cushitic sample as the reference sample, followed by that of A which uses an Egyptian sample as the reference sample to be compared against, coastal northern African samples appear to be amongst the closest to the Semitic-Cushitic groups. The redder the area of a test sample away from the reference samples, the more distant is the said sample from the reference sample.
The same story is more or less conveyed in the following Fst plotting, but this time using "ten haploid genomes" and "ten haploid" so-called "non-African" genomes of test samples:
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| Click on the image to enlarge and see the details |
In the image on the right, the one concerning the "ten haploid" so-called "non-African genome", one notices that it is the Egyptians and the Moroccans which show smaller Fst values than those reported elsewhere, with respect to the Semitic-Cushitic samples. Yet again, the test appears to have involved the same 12 international samples.
The color scale applied here, in the two Fst maps above, appears to be the reverse of that applied in the preceding Fst plots; the redder the area of a sample, the smaller is the Fst value or genetic distance, with respect to the Semitic-Cushitic samples. This again, speaks to that recurring theme of the said Ethiopian samples showing their closest relationship with coastal north Africans than any other group, with respect to their supposed "non-African" gene pool!
While the authors' supplementary table S2 appears to show similar Fst values between Semitic-Cushitic Ethiopian samples and Moroccan, Egyptian and Yemeni samples, the reported values in supplementary table S3 convey a somewhat different story, that is more concordant with an observation made in the preceding passages. Table S2 only reports the rounded-up estimates, while table S3 shows the actual values, and thereby revealing that the Egyptians are indeed the closest group to the Ethiopian Semitic-Cushitic block than the Yemeni. In the whole-genome analysis, even the Moroccans attain genetic proximity to the said Ethiopian groups before the Yemeni do, while in the study around the so-called "non-African" component, Bedouin and Druze samples from the Levant follow the Egyptians in genetic proximity before the Yemeni samples do.
The last phenomenon mentioned above is congruent with the theme that emerges from mtDNA analysis. It was certainly the case noticed (see: Following Trails of the Cro-Magnon - I, Following Trails of the Cro-Magnon - II, and E-M34: Designation as "African" presents a Dilemma?) in a study [4] released in 2004. mtDNA show that plurality goes to coastal northern Africa, when Ethiopian Cushitic-Semitic mtDNA affinity is considered. Head to head comparison of mtDNA between Ethiopian samples and the coastal north African counterparts vs. those outside them had not been a focal point of this study; however, they do note a certain other theme emerging from their analysis:
A minimum-pairwise distance measure based on the African component of the genome found that the Ethiopian mtDNA component was closer to non-African populations than was the Egyptian mtDNA component, as previously reported, but that the autosomal genome of non-Africans was closer to the African component of the Egyptian rather than Ethiopian populations. This could be interpreted as supporting a northern exit route.
They caution:
However, the 80% non-African proportion of the Egyptian genome (Figure 1C) reduces the power of our comparisons and, taken together with the requirement for the African state in at least ten chromosomes, means that this conclusion is based on just ~1,800 SNPs (compared to 18,960 for the Ethiopians, 30,798 for the Mozabite, and 5,920 for the Moroccans). Therefore, the question requires further investigation beyond the scope of the present study.
This could be interpreted as the Ethiopian samples better preserving the ancestral "African" component to the non-African gene pool, in terms of the maternally-mediated gene pool. Consider the fact that the authors report an even lower average pairwise difference between the Omotic samples and select non-African samples than Ethiopian Cushtic-Semitic block did with said samples (.0021 vs. .0027; see table 2). Even though the idea is not particularly popular among those with thinking that is Euro-centered leaning, this could also be a signal that some elements of so-called "African" mtDNA among non-Africans may well be serving as lingering relics of OOA migration...
when we first partitioned the mtDNA lineages into African and non-African (i.e., L and non-L) and considered only the L component, a different pattern emerged: Ethiopians were the closest population to the non-Africans (Table 2B), consistent with inferences drawn from more detailed mtDNA analyses.
Egyptian mtDNA could also have been influenced by some occasional migrations to the region from the inner areas of Africa, which would otherwise have been relatively rare to Ethiopia. Among such, for instance, are migrations driven by the desire to reach Mecca in Saudi Arabia, particularly some time in the post-Dynastic periods, since Egypt sits on the pathway to the Levant and the north areas of the Arabian peninsula. Some migrants do subsequently decide to stay in the Nile Valley instead of heading back to their actual territorial origin, although it's fairly questionable whether such settler migrants necessarily have had a sizable impact on the native locals. Still, relatively recent gene flow of Ethiopian mtDNA into some "non-African" gene pools more so than from Egypt, cannot be excluded in the final analysis.
On the other hand, when other mtDNA were considered, transcending the supposed "African" component, a different theme emerges; the Egyptians and Moroccans assume relative genetic proximity to non-Africans:
With the full set of 18 mtDNA SNPs used in our genome-wide data set, Egyptians and Moroccans proved to be the closest African population to any non-African population examined (Table 2A)...
Note that the arrangement of mtDNA into "African" vs "non-African" [briefed on earlier] by the authors looks to be largely arbitrary, since it appears to be driven by little else than simply grouping mtDNA into either "L", which was exclusively treated as "African", or grouped into "M or N" which were effortlessly and gratuitously taken for granted as "non-African". In-depth and careful assessment makes it apparent that mtDNA phylogeny do not simplistically or objectively conform to that protocol, as popular as it may be among 'western' research teams.
The picture emerging from the autosomal component, as the authors describe above, could be more anomalous to some extent. It could be, as the authors noted, the artifact of substantial disparity between the available size of Egyptian SNPs (i.e. from the supposed "African component") and those of other samples analyzed, or it could just be reflective of the relatively greater time-depth of divergence of Ethiopian atDNA vis-a-vis non-African gene pools, by comparison [i.e. to Egypt]; the latter could tacitly parallel (and hence, be reaffirmed by) the relatively closer genetic distance between the Egyptian and Moroccan samples to non-African samples in the mtDNA analysis. Genome-wide analysis of atDNA, it should be noted, conveys the same theme as the so-called "African" component of atDNA...
Applying the same principle, we then calculated the shortest distance between the African and non-African populations on the basis of either full genome data or the African component of this data set. In contrast to the mtDNA results, the Egyptians proved to be the closest to the non-Africans in both cases (Tables 2A and 2B).
As another sign that the authors' simplified assignment of markers into either "African" or "non-African" is fairly questionable, consider the findings noted in the following, with regards to the SLC24A5 gene:
we noted one that contained SLC24A5 (MIM 113750). This gene is a major contributor to the pigmentation differences between Africans and Europeans and a strong candidate for positive selection in Europe.
This gene, in its derived form, which is said to be under positive selection in "lightly" pigmented populations, was implicated in the San, who as noted above, tend to generally be isolated, and culturally-conservative hunter-gatherers. "Derived" variants of other pigmentation-associated genes were also cited, with respect to the San ([5]). It is questionable that this gene is serving as a "non-African" marker in the San. The same issue actually surfaces with regards to its presence in Ethiopian groups:
Firstly, the authors were compelled to say:
Although potentially disadvantageous due to the high intensity of UV radiation in the area, the SLC24A5 allele has maintained a substantial frequency in the Semitic-Cushitic populations, perhaps driven by social factors including sexual selection.
Secondly:
Given that SLC24A5 is one of the most highly differentiated genes between African and European populations, we then looked for other highly differentiated genes among the outlier windows, but found none...
To further investigate the effect of admixture on the genetic landscape of skin pigmentation in Ethiopia, we also looked at other genes associated with pigmentation in Europe; however, none were found in our outlier regions.
If this gene, in its "derived" form, was essentially serving as a "non-African" marker in the Ethiopians, then one would expect that other "derived" skin-pigmentation markers would have been introduced along with the SLC24A5 allele, by the foreign "non-African" group(s) that is supposed to have been the source. Skin pigmentation is the byproduct of the consortial work of a number of distinct genes, and so, it's highly unlikely that a "derived" SLC24A5 allele would be introduced without other accompanying skin-pigmentation genes.
No less, it's highly unlikely that only the derived "SLC24A5" allele would survive from a foreign "non-African" source, in a population for which the allele's presence is "potentially disadvantageous", as the authors note, on grounds of the kind of UV-radiation intensive environment they generally reside. Likewise, if as the authors note, the presence of the derived SLC24A5 allele in Ethiopians may be attributable to "socially"-promoted selection, then one would think that other skin-pigmentation genes, which would have accompanied the SLC24A5 allele in an introduction by a foreign "non-African" source, would have likely also survived in some capacity or another, so as to serve the same role that the SLC24A5 may be serving.
While on the subject of suspiciously tenuous findings by the authors, it's worth noting that the introduction—for which the authors insinuate a single-entry—of the so-called "non-African" gene pool of Ethiopian groups is purported to have taken place some 3ky ago; this interestingly coincides with the date generally attributed to the historic Sabean kingdom of southern Arabia; in fact, in a thinly veiled manner, the authors even make a reference to a study (Kitchen et. al. 2009), so as to make it a point that their dates firmly match that of said study:
The estimated time (3 kya) and the geographic origin (the Levant) of the gene flow into Ethiopia are consistent with both the model of Early Bronze Age origins of Semitic languages and the reported age estimate (2.8 kya) of the Ethio-Semitic language group. They are also consistent with the legend of Makeda, the Queen of Sheba. According to the version recorded in the Ethiopian Kebra Nagast (a traditional Ethiopian book on the origins of the kings), this influential Ethiopian queen (who, according to Hansberry, reigned between 1005 and 955 BCE) visited King Solomon—ruler, in biblical tradition, of the United Kingdom of Israel and Judah—bringing back, in addition to important trading links, a son.
The authors of course, conveniently seize on legends of the Kebra Nagast, with little regard to what archeology has to say, because doing so seems to fit into the narrative they want to build. There is a "dark age" period in Ethiopian archaeological record, between the Da'amat complex—a contemporary of the noted Sabean complex—and the Aksumite complex:
A kingdom called D`MT (perhaps to be read Da`mot or Di`amat) is attested in Ethiopian inscriptions at this early date, and, though the period between this and the development of Aksum around the beginning of the Christian era is an Ethiopian `Dark Age' for us at present, it may be surmised that the D`MT monarchy and its successors, and other Ethiopian chiefdoms, continued something of the same *`Ethio-Sabaean'* civilisation until eventually subordinated by Aksum.
"A certain linguistic and religious continuity may be observed between the two periods, though many features of Aksumite civilisation differ considerably from the earlier material." [1]
The Dark period (from archaeological standpoint) between the demise of D'MT complex and the rise of the Aksumite complex gave way to the introduction of Christianity, which would become a regular feature of the Aksumite complex. It is little wonder then, that legends would subsequently develop, long after the demise of the Aksumite complex, which would capitalize on Abrahamic belief, centered on the person of King Solomon and Makeda, i.e. Queen of Sheba, as part of the Kebra Nagast narrative. As such, just as observed elsewhere (click on the link), the narrative of Kebra Nagast seems to proceed from a mythologized period to a more realistic historic era...
The origins of these legends hark back to some unknown time after the conversion of the kingdom to Christianity in the reign of king Ezana of Aksum in the fourth century AD, or in some cases perhaps to an even earlier period when some Jewish traditions had entered the country.
Such legends had their political use in providing pedigrees for national institutions. It was believed in later times that the state offices from the king downwards were descended from the company which had brought the Ark to Aksum from Jerusalem (Budge 1922: 61). Doubtless the Christian priests, searching for a longer pedigree for their religion to impress pagans and unbelievers, would have been interested in developing these tales which connected Ethiopia with Solomon and Sheba.
The Ethiopian kings themselves, anxious to acquire the prestige of ancient and venerable dynastic ancestors, could scarcely have hoped for a more august couple as their reputed progenitors. Even in the official Ethiopian Constitution, up to the time of the end of the reign of emperor Haile Selassie, the dynasty was held to have descended directly from Solomon and the queen of Sheba through their mythical son, the emperor Menelik I.
The real events in Ethiopia's history before the present two millenia are lost in the mists of antiquity, but valiant attempts were made by Ethiopian chroniclers to fill in the immense gap between the reign of Menelik I and the time of the kings of Aksum. The king lists they developed (all those now surviving are of comparatively recent date), name a long line of rulers, covering the whole span from Menelik through the Aksumite period and on to the later Zagwé and `Solomonic' dynasties (Conti Rossini 1909). There is little point in reciting the majority of these names, but some of the most important of the reputed successors of Menelik I are worth noting for their importance in Ethiopian tradition.
With regards to Menelik I, legend says of him...
Tradition says that he was the son of king Solomon of Israel and the queen of Sheba conceived during the queen's famous visit to Jerusalem. Although no information survives in the legends about the ancient Aksumite rulers who really built the palaces and erected the giant stone obelisks or stelae which still stand in several places around the town, these monuments are locally attributed in many instances to Menelik or to Makeda, the queen of Sheba or queen of Azab (the South). Such legends are still a living force at Aksum today; for example, the mansion recently excavated in the district of Dungur, west of Aksum, has immediately been absorbed into local legends as the `palace of the queen of Sheba'. [1]
This phenomenon is not uncommon on the African continent; many groups, be they Muslims, Jews or Christians, tend to build legends around eponymous ancestors which take their community's lineage back to the homelands of these ancestors. These legends, as the notes above indicate, are generally applied to give ruling circles—more than anyone else—legitimacy of power, as well as the ability to macro-manage their societies through prestige bestowed upon religion. The authors of the present genetic study seem to be oblivious of intricacies of this nature.
While there have been long contacts across the Red Sea, it is mainly between 8th Century and 5th century B.C. that we begin to see visible south Arabian influence in the region, in the form inscription, architecture and so forth. As Stuart Munro-Hay put it,...
some sort of contact, apparently quite close, seems to have been maintained between Ethiopia and South Arabia. This developed to such an extent that in not a few places in Ethiopia the remains of certain mainly religious or funerary installations, some of major importance, with an unmistakeable South Arabian appearance in many details, have been excavated. Among the sites are Hawelti-Melazo, near Aksum (de Contenson 1961ii), the famous temple and other buildings and tombs at Yeha (Anfray 1973ii), the early levels at Matara (Anfray 1967), and the sites at Seglamien (Ricci and Fattovich 1984-6), Addi Galamo, Feqya, Addi Grameten and Kaskase, to name only the better-known ones. Fattovich (1989: 4-5) comments on many of these and has been able to attribute some ninety sites altogether to the pre-Aksumite period...
Inscriptions found at some of these sites include the names of persons bearing the traditional South Arabian title of mukarrib, apparently indicating a ruler with something of a priest-king status, not otherwise known in Ethiopia (Caquot and Drewes 1955). Others have the title of king, mlkn (Schneider 1961; 1973). Evidently the pre-Aksumite Sabaean-influenced cultural province did not consist merely of a few briefly-occupied staging posts, but was a wide-spread and well-established phenomenon.
Having acknowledged the extent of Sabean influence, Munro-Hay cautioned:
Until relatively recently South Arabian artefacts found in Ethiopia were interpreted as the material signs left behind by a superior colonial occupation force, with political supremacy over the indigenes — an interpretation still maintained by Michels (1988). But further study has now suggested that very likely, by the time the inscriptions were produced, the majority of the material in fact represented the civilisation of the Ethiopians themselves. Nevertheless, a certain amount of contact with South Arabia is very apparent, and had resulted in the adoption of a number of cultural traits (Schneider 1973; 1976).
The picture that emerges, based on archaeology, is one wherein the late early-Holocene urbanization process of the African Horn was accompanied by cultural interaction—such as trade—with the relatively more established complexes to the north, on the African continent itself (see: Urbanization in the African Horn was the outcome of autochthonous social processes, or was it?, for example). This interaction may well have aided the growth of Ethiopian urbanization, to extent whereupon state formation in the Ethiopian highlands was made possible, and with it, the capacity of Ethiopia's forebears to become worthy trade partners in their own right, i.e. of their counterparts both to their north and across the Red Sea. However, the subsequent rise to regional prominence of the Sabean complex in southern Arabia marked a new chapter in Ethiopian history.
From Fattovich, 2002 [2]:
The late second and early first millennia BC were marked by the decline of Egyptian power, and the rise and expansion of the kingdom of Kush in Nubia, and the kingdoms in southwest Arabia.. Trade along the Red Sea was under the control of the South Arabians, but it is possible , however, that the Phoenicians sporadically visited the Horn (Doe 1971; Adams 1977; Groom 1981; Liverani 1988). In the mid-first millennium BC, the south Arabian commercial expansion was at its peak under the control of the kingdom of Saba. At this time, the pre-Aksumite kingdom of Da’amat was surely an important partner of Saba.…
In the early first millennium BC, the South Arabians penetrated in the western Tigrean plateau, most likely to get a direct access to the resources of the western lowlands, particularly ivory. Quite soon the region was included in the area of political and commercial influence of the kingdom of Saba.. That contacts with the Sabeans gave rise to the local kingdom of Da’amat.. An urban society, reflecting the south Arabian pattern, appeared on the plateau. Yeha become a very important ceremonial center and the possible residence of the kings. The agricultural production to sustain the new state was improved by the use of plough. The need to control the routes to the Red Sea caused the eastwards territorial expansion of the kingdom. Kaskase became another important ceremonial centre. An urban settlement arose at Matara.
In the late first millennium BC, after the decline of the kingdom of Saba in southern Arabia, the kingdom of Da’amat collapsed. The plateau was probably divided into petty kingdoms
The use of Sabean language as a possible trade language, for example, would have a lasting impact on the evolution of Ethio-Semitic language in a certain manner, which was already described briefly in earlier passages. This is not to say that Ethio-Semitic itself comes from southern Arabia, but just that such a trade language would have had an impact on how Ethio-Semitic would evolve; for instance, from Stuart Munro-Hay, one also gets an impression of this, i.e. existence of Ethio-Semitic language prior to contact with the Sabean complex before some 3ky ago:
Semiticized Agaw peoples are thought to have migrated from south-eastern Eritrea possibly as early as 2000BC, bringing their `proto-Ethiopic' language, ancestor of Ge`ez and the other Ethiopian Semitic languages, with them; and these and other groups had already developed specific cultural and linguistic identities by the time any Sabaean influences arrived. [1]
The implied message here, is that the Agaw people of Ethiopia were already "Semiticized" by 2000 BC, long before the appearance of the south Arabian complex in history. At this time however, we are informed that this would have been a proto-Ethiopic ancestor of modern Ethio-Semitic languages. Note that the "Semiticized" (acculturated) Agaw and other Ethiopian groups "had already developed specific cultural and linguistic identities by the time any Sabean influences arrived."
Elsewhere:
The inscriptions dating from this period [Sabean-Ethiopian contact] in Ethiopia are apparently written in two languages, pure Sabaean and another language with certain aspects found later in Ge`ez (Schneider 1976). All the royal inscriptions are in this second, presumably Ethiopian, language. A number of different tribes and families seem to be mentioned by the inscriptions of this period, but there is no evidence to show whether any of these groups lasted into the Aksumite period.[1]
One of the two aforementioned languages was very likely serving as a trade language and possibly for administrative purposes, which from a logical standpoint, would have been the "pure Sabean" noted above; the other language, would have been for the benefit of the locals, so that the message which the ruling circles wanted to get across the public, could be heard widely. This latter language, would have desirably been a language that is more widely accessible to the public than the former, and hence, would have been a local "Ethiopian language", as indicated above. This local language happened to already have "aspects" that would later on be a feature of Ge'ez, which happens to be an Ethio-Semitic language. Remember, this was during the time of Ethio-Sabean contact!
Only the word YG`DYN, man of Yeg`az, might hint that the Ge`ez or Agazyan tribe was established so early, though the particular inscription which mentions it is written in the South Arabian rather than the Ethiopian language (Schneider 1961). Some of the other apparently tribal names also occur in both groups of inscriptions. The usual way of referring to someone in the inscriptions is `N. of the family N. of the tribe N.', possibly also reflected later by the Aksumite `Bisi'-title; `king N. man of the tribe/clan (?) N.' (Ch. 7: 5). [1]
...again, speaking to the already established presence of Ethiopic language with Semitic attributes, prior to contact with the Sabean complex. Furthermore:
Indeed, it may be that the Sabaeans were able to establish themselves in Ethiopia in the first place because both their civilisation and that of mid-1st millenium Ethiopia already had something in common; it has been suggested that earlier migrations or contacts might have taken place, leaving a kind of cultural sympathy between the two areas which allowed the later contact to flourish easily.[1]
Ethio-Semitic language, having been available prior to any contact with the Sabean complex, would fit into this scenario of "something in common".
As noted earlier, south Arabian impact on Ethiopian gene pool would have been limited, and primarily focused in administrative outposts, where Sabean migrants communities would have been more visible, during the Ethio-Sabean contact. So, the south Arabian footprint is nowhere near as considerable as proponents of a south Arabian origin for Ethio-Semitic would like it to be, so as to bolster their theory. As one observation has it, the possible role south Arabian migrants would have served during this time,...
It appears that there were undoubtedly some South Arabian immigrants in Ethiopia in the mid-first millenium BC, but there is (unless the interpretation of Michels is accepted) no sure indication that they were politically dominant.
The sites chosen by them may be related to their relative ease of access to the Red Sea coast. Arthur Irvine (1977) and others have regarded sympathetically the suggestion that the inscriptions which testify to Sabaean presence in Ethiopia may have been set up by colonists around the time of the Sabaean ruler Karibil Watar in the late fourth century BC; but the dating is very uncertain, as noted above. They may have been military or trading colonists, living in some sort of symbiosis with the local Ethiopian population, perhaps under a species of treaty-status.[1]
With regards to the D'MT complex, it's noted:
Its rulers, kings and mukarribs, by including the name Saba in their titles, appear to have expressly claimed control over the resident Sabaeans in their country; actual Sabaean presence is assumed at Matara, Yeha and Hawelti-Melazo according to present information (Schneider 1973: 388).
The Sabaeans in Ethiopia appear, from the use of certain place-names like Marib in their inscriptions, to have kept in contact with their own country, and indeed the purpose of their presence may well have been to maintain and develop links across the sea to the profit of South Arabia's trading network.
Naturally, such an arrangement would have worked also to the benefit of the indigenous Ethiopian rulers, who employed the titles mukarrib and mlkn at first, and nagashi (najashi) or negus later; no pre-Aksumite najashi or negus is known.
It seems that these `inscriptional' Sabaeans did not remain more than a century or so — or perhaps even only a few decades — as a separate and identifiable people. Possibly their presence was connected to a contemporary efflorescence of Saba on the other side of the Red Sea. Their influence was only in a limited geographical area, affecting the autochthonous population in that area to a greater or lesser degree. Such influences as did remain after their departure or assimilation fused with the local cultural background, and contributed to the ensemble of traits which constituted Ethiopian civilisation in the rest of the pre-Aksumite period. [1]
Moving past the addictive history lessons, let's take a look at other weak moments of the Pagani et al. (2012) analysis. They purportedly have been able to get solid dates on "admixture" events, by using some ROLLOFF logarithm coded "in-house".
Short of coming across haplogroups wherein the mutation rate is supposedly steady and non-variable, available dating models, from "strict-clock" inference model, "relaxed-clock" inference models to time-free inference models (like say, the Bayesian model) hardly ever get 100% accuracy on dating (for example, see [3]). Whereas reporting concrete dates, short of using reference fossils or remains of known dates to aid in phylogenetic dating, imply maximum accuracy of the model being applied, likely within the reach of a 100% accuracy, which as noted, is hardly ever attained through available inference models .
Seemingly neutral segments of the genome are not necessarily inclined to conform to uniform or strict-clock rates of mutation, let alone the even more unpredictable segments of the genome that are under selection. Besides, the parameters picked by the authors, such as the translation of generations into years, is largely an arbitrary variable. So, the alleged attainment of precise dates is cause for skepticism.
Conclusion:
Overall look at the genetic data shows that generally speaking, Ethiopian groups which have most frequently been implicated in recent gene flow from outside the continent, like say the main Cushitic and Semitic speaking groups of Ethiopia, tend to assume closer genetic proximity with groups from coastal northern Africa, like say the Egyptians and the Moroccans, before they do with people from the Levant or the Arabian peninsula. The Levantine samples in turn, tend to be relatively closer to the same Ethiopian groups, than those from south Arabia. This pattern does not speak to a historic origin of Ethio-Semitic languages from southern Arabia some 3ky ago, as Pagani et al. (2012) seize upon to bolster their argument.
Inspection of the Cushitic-Semitic block's gene pool suggests that the ancestors of said groups may have once resided in the more northerly climes of the African continent itself, before they moved to the current location(s) where they now reside. In keeping with this narrative, its starts to dawn in why such pigment-associated alleles, like the SLC24A5 in "derived" form, are relatively frequent among said Ethiopian groups, notwithstanding that such allele variants are likely to be disadvantageous in the UV radiation intense areas where these groups now reside; it's because their ancestors must have arrived from the relatively lower UV radiation climes of the African continent, within the Saharan region, likely eastern Sahara, even though the central Saharan region is a next logical possibility. This may explain why other well-known supposed "non-African" pigment-associated allele variants in "derived" form had not been located in Ethiopian gene pool!
Findings in archeology seem to reaffirm the prospect of Ethio-Semitic speakers having already been around, by the time there is close contact between Ethiopians and Sabeans, across the Red Sea. The potential use of Sabean language as possible trade [and possibly, administrative] language, may have inspired the manner in which Ethio-Semitic languages evolved, giving them features that would resemble those of south Arabian language, but this does not mean that Ethio-Semitic languages actually have a south Arabian origin.
*Subject to modification, if and when credible new information comes to attention.
______________________________________________________________
*References:
—Pagani et al., Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool, 2012.
[1]—S. Munro-Hay, Aksum: An African Civilisation of Late Antiquity, 1991.
[2]—Fattovich, The development of urbanism in the northern Horn of Africa in ancient and medieval times, 2002.
[3]—Wertheim et al., Relaxed Molecular Clocks, the Bias–Variance Trade-off, and the Quality of Phylogenetic Inference, 2009.
[4]—Kivisild et al. (2004), Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears.
[5]—Norton et al., Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians, 2006.
—Kitchen et al., Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East, 2009.
—Personal notes from 2005, 2008, 2009 & 2010.
7 comments:
Brilliant. Thank you for writing this, I often hear laymen (and women, etc.) utter these stereotypical notions of Cushitic-Semitic East Africans as "non-African" or "mixed with Yemenis and people from Southwest Asia, and always want to correct them with linguistic, archaeological, genetic, and anthropological evidence. This blog will help do that when I send the link around.
Excellent roundup, exposing the assumptions and methodologies that seek to distort or minimize African diversity.
Under what scenario could the derived SLC24A5 variant have been selected for? Climate zone variations over log time spans?
Differing micro-clime zones spread over a broad Saharan/NE African geographic space?
Research data,
As noted in the entry, the SLC24A5 may have been one of the loci that got selected for in the sub-tropical Saharan area where remote ancestors of Ethiopian Afro-Asiatic speaking elements would have been at some point in time prior to relocating to the region where Ethiopia now lies. The trigger for this selection would have been the relative lower UV radiation environment of the Saharan region in the vicinity of its sub-tropical zone. As such, some of these skin pigment-related mutations would have been brought along during any migration southward, down to the equatorial areas of eastern Africa. Skin pigment relaxation in the sub-tropical area of the Sahara would not have been as acute as that seen in the more northward temperate regions, like say, Europe. The originally dark ancestors of Ethiopians would thus have simply undergone some lightening, but not necessarily to the extremes seen in places like Europe.
Is the supposed "Non-African" component one that emerged before the OOA migration?
Joshua,
From the looks of things, it would appear that a good amount of what is alleged to be the "non-African" component, more than likely emerged right on the African continent, perhaps having most heavily been distributed in the Saharan general region.
Elements of the Saharan inhabitants would eventually make their way to Eurasia, both along the Arabian peninsula corridor, and the Sinai corridor. This would perhaps explain the seemingly two-pronged patterns of the so-called "Eurasian" maternal clades of L3M and L3N. This perspective also puts a dent on the seeming mystery of what appears to be lopsided "Eurasian" component of Maghrebi/coastal "north African" mtDNA gene pool vs. their seemingly lopsided "African" male gene pool...for otherwise, one would have to assume that "Eurasian" males were effectively massacred to a point of non-existence, when there is fairly meager evidence of their arrival in pre-LGM and LGM Paleolithic era in the first place!...and also account for the seemingly "heavy" representation of these alleged "Eurasian" clades in some groups in sub-Saharan Africa, particularly in eastern Africa.
I intend to make a blog entry in the not-so-distance future, about this possibility of so-called "Eurasian" mtDNA clades having fundamentally emerged on the African continent itself!
Is the results the same for Somalis? I mean given their history with us, I am of Ethiopian descent. I have always had Whites openly call me some form of caucasian, and I knew it was ludicrous. I am African and we existed before Caucasians so how the hell could I be one? I am Habesha btw.
articon26@Aol.com,
Thanks for your comment. The results of Somalis used in the study would be different from those of the Ethiopians used in the study, but there are relations. It appears from many studies done on uniparental markers, and at times, autosomal markers, not leaving out cranio-metrics and linguistic analyses, that Somalis and Ethiopians' time of divergence from one another is relatively shallower in depth than either group's divergence is to the more geographically distant and/or distinct linguistic groups.
While the Somali genetic profile has its own distinct pattern from those of Ethiopians, whom by the way--comprise of different groups among themselves, there are some parallels in trends. For instance, one may come across a good amount of those so-called "Eurasian" components in Somali maternal gene pool as well, just as the claim is made for the Ethio Afro-Asiatic speaking groups!
However, if you look at say, the Amhara male genetic profiles, you'll see that hg J1 figures in a considerable way, while it less so in Somalis. Likewise, Somalis have other markers that are less prevalent in the Amhara specimenst. Something similar could be said of a comparison between say, Amhara or some other Ethio-Semitic speaking group and the Oromo. Yet these groups are closely related, and show some parallels in some of their genetic profiles. Linguistic comparisons obviously pit Oromo closer to Somalis than the Ethio-Semitic groups, but a few DNA publications seem to support this idea as well.
From what I gather from research, the possibility that a good amount of these so-called "Eurasian" elements that these groups seem to have, particularly in the mtDNA profile, could have been acquired on the African continent itself, and may have even emerged right on that continent, cannot be ruled out. I realize that this perspective is not exactly popular among "Western" academic circles, but it is just as very real a possibility as any other theory, on grounds I've spelled out elsewhere, and will likely revisit in the future on this site...with updates, of course!
"Westerners", in a bid to assume "ownership" (possibly with the coming of European imperialism and subsequent side-effect of jingoism and narcissism, as in for instance, "white supremacy"), attempt to portray any African diversity, especially those that deviate from the infamously stereotyped "Negro", as those exported to Africans by either "westerners" themselves, or people proclaimed to be close to them "westerners". And so, the narrative is to say that Ethiopians and Somalis look the way they do, because Europeans or people who look like Europeans introduced those looks to them...rather than say, it is from the Africans that Europeans or people who look like Europeans inherited looks that were first acquired on the African continent, and that Europeans and/or people who look like Europeans are essentially but extensions of Africans living on other landmasses!
This narrative is actually an insult to Ethiopians and the like, because it is saying that they would not look the way they do, if it were not for outsiders that were either Europeans, or closely looked like Europeans!
Contrary to what some DNA journals may insinuate, no theory is set in stone when it comes to reality. Almost all of these journals are compelled to delve into a good degree of speculation, mostly offered as "educated" guesses, about genetic history based off--in many cases--small pieces of test-populations...and this is especially true of history that goes well into pre-historic era humanity's existence, where no written material or film capture is handed down!
Hope I have satisfactorily approached your concerns!
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