Monday, January 28, 2008

Skin pigmentation gene alleles — Part 2

Reviewing H. Norton, R. Kittles et al, 2006 - Part 2:

Link to the part 1: Skin pigmentation gene alleles [clickable]

Additional notes:

For those who are curious, the authors of the aforementioned skin pigmentation study [Kittles et al.] don't specifically point out the TMRCAs for the identified genes in question, but apparently ancestral lineages were delineated from their derived counterparts. From extrapolation though, it makes sense that mutations that occurred after divergence of any given groups, would be relatively rare in the common ancestor of these recently diverged groups. On the other hand, certain mutations that were present within the common ancestor may be expressed more acutely later on in one or the other group that diverged from this ancestral population, while dying out or becoming relatively rare in another progeny group. Still these developments are able to assist one in delineating the frequency and mutational particulars of the genes controlled by natural selection and/or the pressure of genetic drift.

As for "Southwest Asian" populations, they generally fall into ranges contained within the Saharo-tropical Africans, while some northerly groups of this region apparently have relatively paler skin shades as a product of more recent migrations into the region. Kittles et al. at least in part, attribute such developments to gene flow from Northern Eurasia and perhaps, in some areas, East Asia. See again, from my last post:

Concerning the "derived" SLC24 A5 gene...

In contrast, the SLC24 A5 11*A-derived allele is found at low frequencies in several sub-Saharan populations including the West African Mandinka and Yoruba, the Southern African San, and South West Bantu.

The relatively **high frequencies** of the derived allele in **Central Asian, Middle Eastern, and North Africa** seem likely to be **due to recent gene flow** with European populations.

Similarly, the presence of the derived allele (albeit at low frequencies) in some sub-Saharan populations may be due to recent gene flow from European and Central Asian populations. Alternatively, the derived allele may have lost in the ancestors of modern East Asians but retained in the ancestral European populations. The allele then rose to high frequency in Europeans following the divergence of Europeans and East Asian ancestral groups.

Many places outside of Africa, for instance, harbor the 'derivative' counterparts of several "pigmentation" genes [a variety of which have been associated with relatively lighter pigmentation], while ancestral alleles [many of which have generally been associated with relatively darker pigmentation] are commonly found in Africa and amongst direct descendants of earliest out-of-Africa ancestors of modern non-Africans, as is the case with OCA2 gene...

In general, the derived allele (associated with lighter pigmentation) is most common in Europeans and East Asians, and the **ancestral allele** predominates in **sub-Saharan Africa** and **Island Melanesia.**

...and this quite likely applies to "southwest Asians" harboring "derived" OCA2 which has been associated with playing a role in lightening skin phenotype, for example.

Lightening effect was apparently a gradual process, as populations started expanding to low UV radiation latitudes. This is readily seen in the intermediary situations between adaptations on opposite poles of empirical tests; see for example:

High Fst values [concerning the three genes TYR, MATP and SLC24A5] between Europeans and darkly pigmented populations such as West Africans and Island Melanesians are not unexpected if these genes have functional effects. However, the notably elevated pairwise Fst values relative to East Asians (the population in our panel that is the most similar to Europeans in pigmentation phenotype) is striking. Populations intermediate in pigmentation (Native Americans and South Asians) also exhibit Fst values falling in the top 5th percentile of their relevant Fst distributions with Europeans for these three loci. In the case of SLC24A5 A111G, South Asian pairwise Fst values also fall in this top 5th percentile when compared to both Europeans (Fst = .389,  p < .01) and East Asians (Fst= .519, p < .01), but not when compared to any other population. At all three loci Europeans have the highest frequency of the derived alleles relative to the other five populations.

The South Asians being referred to here, comprised of east Indian samples, which are claimed to be 'intermediate' along with the Native American samples. The phenomenon described above, seems to suggest that the alleles at the three said loci in the said 'intermediate' groups predate those attained in both East Asians and Europeans; as noted, their Fst values are not quite as high when compared with any other population [which would essentially be the dark populations]. Apparently, the pigmentation distribution in these 'intermediate' groups reflect demographic events distinct from those that produced the more dramatic pigment-oriented phenotypic manifestations in Europeans and East Asians respectively; being that they possess alleles that post-date OOA migration events, and yet those that predate extreme pigment-related adaptations sported by Europeans and East Asians, they are bound to report intermediary patterns. One might recall that the Native American OCA2-derived allele frequency was said to be comparatively lower than that of East Asians...

Interestingly, derived allele frequencies at this locus are quite different between Native American (15%) and East Asian populations (45%), suggesting that perhaps the derived allele at this locus did not reach very high frequencies in East Asians until after the colonization of the Americas

And might also recall that KhoiSans on the other hand, reported high frequencies of OCA2-derived...

The lightly pigmented hunter-gatherer San populations of Southern Africa is exceptional in having a high frequency of the derived allele relative to geographically proximate and more darkly pigmented African populations (Jablonski and Chaplin 2000), further supporting the importance of OCA2 in regulating normal variation in pigmentation. The widespread distribution of the derived allele in the CEPH-Diversity Panel suggests that it is not necessarily a new mutation, nor has it been restricted to a specific geographic area.

So yes, the derived version of OCA2 likely predates the often-talked about Upper Paleolithic OOA migration in varying frequencies in different populations, but likely did not pick up in distribution dramatically in East Asian and European populations, until after a section of central-East Asian had left for America, in a wave(s) following that of the first Paleo-Americans. This suggests that one drift episode [perhaps amongst the earliest for this type] raised its frequency considerably in at least one African group [the Sans], another drift episode raised its distribution in vicinity of central and/or east Asia to reasonably visible levels, but yet another drift episode raised its distribution even further in east Asia at a later time. All this paints gradual evolution in skin pigmentation relaxation temporally, in tandem with territorial shifts amongst populations.

And recalling...

The discordance between our Fst -based divergence values and allele frequencies in the Melanesian CEPH populations at ASIP largely stem from the relatively low frequency of the ancestral allele in the 2 CEPH Island Melanesian populations relative to our original Island Melanesian sample. These discrepancies make it difficult to determine if ASIP truly underlies broad pigmentation differences between darkly and lightly pigmented populations or instead inter-population variation at this locus can largely be explained by differences between Africans and non-Africans

The answer is rather obvious, no? It reflects the basal phylogenetic position of Melanesians, which is why they'd share ancestral ASIP alleles with continental Africans. The difference then here, would be one of the basal phylogenetic position of Africans vis-a-vis OOA-derived populations, with the deepest-clade bearers of all OOA-derived groups carrying over basal African alleles outside of Africa.

More on the "derived" SLC24 A5 gene...

On the above piece, in one personal encounter, a question had come up along the lines of:

...because one of the authors says not enough time has passed for mutations? And just how is it the author would know this? Since the author, or one of the authors didn't specifically say how much time
has to pass for mutations then I'm asking explain to me what you know they meant by this.

The natural answer to that question, as the present author put forth, was this:

Yes, the authors reckon that "not enough time has passed for mutations" and don't specify "how much time has to pass for [new] mutations" to occur, nor need to, because they determined this from the fact that the DNA flanking the gene in question lacked variation in the samples they studied; the tacit idea here, is that the DNA locus in question not only indicates selective pressure of the gene SLC24A5, where by the flanking DNA in question must have been part of a selective sweep, but its lack of variation suggests that not enough time has accumulated since such a selective sweep would have occurred; otherwise, more variation, however modest, would be expected of a designated DNA locus that has been around for a considerable length of time. And oh, it must be suggestive of some linkage disequilibrium in the inheritance of this assemblage of DNA.

On Jablonski :

The weaker the ultraviolet light, the fairer the skin. Jablonski went on to show that people living above 50 degrees latitude have the highest risk of vitamin D deficiency. "This was one of the last barriers in the history of human settlement," Jablonski says. " Only after humans learned fishing, and therefore had access to food rich in vitamin D, could they settle these regions." — The evolution of race was as simple as the politics of race is complex, By Gina Kirchweger

And to that, the present author says:


Side notes:
The very "relaxed" eumelanin concentration in the skin of 'pale skin' individuals is the expression of their relatively "recessive" alleles, vis-a-vis the more "dominant" counterparts of those that instruct for more production, to produce the considerable skin eumelanin concentration of dark skin individuals. The present author has come across comical claims about the aforementioned "recessive" counterparts "masking" the effects of the more "dominant" skin pigmentation alleles, no doubt from individuals who are in the dark about the basics of genetics. The case in humans, whereby one comes across skin tone gradients, from extreme dark to extreme paleness, can best be described as one of the interplay of "incomplete" dominance of the 'wild types' over their "recessive" counterparts in subjects of "intermediate" skin tones, via polygenic inheritance—wherein the individual effects of "dominant" or "wild" alleles that produce greater eumelanin dosage, will mask those of the relatively "recessive" counterparts in normal "heterozygous" [so to speak, for simplification purposes] subjects, while the "wild" or "dominant" allele types will simply instruct for considerable skin eumelanin in "homozygous" dark skin subjects, and that of the relatively "recessive" allele types instruct for little dosages in "homozygous" pale skin subjects. Now of course, common sense should tell one that these terms "recessive" vs. "dominant" are relative terms, for we know that even in individuals where 'pale skin' is product of natural selection, as opposed to genetic mishap or disorder, the alleles which instruct for only modest eumelanin dosage, if we had two copies of the same alleles from each parent, then neither is dominant or recessive to the other; however, one such allele in the presence of a "wild type" from a darker skin parent, will tend to be "recessive" relative to the said "wild type". All the said alleles in this case, will instruct for eumelanin dosage, but the 'wild type", and hence more "dominant" type, will instruct for bigger dosages than the other allele, the "recessive" counterpart. For those needing basic illustrative demostration, check this site out:

Gist: If one is recessive, it has to be recessive relative to another, and likewise, if one is "dominant", it has to be so over another. It is just common sense.

Skin pigmentation gene alleles

Reviewing H. Norton, R. Kittles et al, 2006:

Besides the variations in the “SLC24A5” gene, as mentioned in the intro article, the “TYR” gene, the “OCA2“, the “ASIP“, and to some extent those seen in the MC1R gene, Kittles et al. have noted other genes "MATP C374G", “ADAM17“, “ATRN“, and “DCT” the mutations of which are deemed to have to had influence in promoting paleness…

Taken together (with the results of previous admixture mapping studies), these results point to the importance of several genes in shaping the pigmentation phenotype and a complex evolutionary history involving strong selection. Polymorphisms in 2 genes, ASIP and OCA2, may play a shared role in shaping light and dark pigmentation across the globe, whereas SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans but not in East Asians. These findings support a case for the recent convergent evolution of a lighter pigmentation in Europeans and East Asians…

Pairwise Fst estimates for the ASIP A8818G and OCA2 A355G SNPs tentatively suggest a pattern of divergence between 4 populations (Europeans, East Asians, Native Americans, and South Asians) and the relatively more darkly pigmented populations of West Africa and Island Melanesia, or possibly only between West Africans and all other populations. At both loci, West Africans and Island Melanesians have higher frequencies of the ancestral alleles than the other 4 populations. Pairwise locus-specific Fst values falling in the top 5% of the empirical distributions are observed between West Africans and 3 other populations (South Asians, Native Americans, and Europeans) at ASIP A8818G. Fst values between West Africans and East Asians at this locus are elevated but do not reach our cutoff value of 5% (Fst = .489, P = .065). At OCA2 A355G, only West Africans and Europeans show Fst values falling into the top fifth percentile of relevant comparisons (Fst = .516, P<.05). The low pair wise Fst values and higher frequency of ancestral alleles at both SNPs studied in these loci between West Africans and Island Melanesians hint that dark pigmentation associated with both loci in these populations may have a common evolutionary origin (Mean Fst (WA-IM) = .182; ASIP A8818G Fst (WA-IM) = .260, P = .282; OCA2 A355G Fst (WA-IM) = .101, P=.525).

Continuing with regards to OCA2 gene, we are told…

In contrast, the ancestral allele associated with dark pigmentation has a shared high frequency in sub-Sharan African and Island Melanesians. A notable exception is the relatively lightly pigmented San population of Southern Africa where the derived allele predominates (93%), although this may be simply due to small sample size (n=14).

The distributions of the derived and ancestral alleles at TYR A192C, MAPT C374G, and SLC24A5 A111G are consistent with Fst results suggesting strong European specific divergence at these loci. The derived allele at TYR, 192*A (previously linked with lighter pigmentation [Shriver et al. 2003]), has a frequency of 38% among European populations but a frequency only 14% among non-Europeans. The differences between Europeans and non-Europeans for the MAPT 374*G and SLC24A5 111*A alleles (both derived alleles associated with lighter pigmentation) were even more striking (MAT [European] = 87%; MATP [non-European] = 17%; SLC24A5 [European] = 100%; SLC24A5 [non-European] = 46%). The frequency of the SLC24A5 111*A allele outside of Europe is largely accounted for by high frequencies in geographically proximate populations in northern Africa, the Middle East, and Pakistan (ranging from 62% to 100%).

By way of negative Tajima D values, which when strongly negative, indicate selective pressure, or more specifically—“directional selection”, especially when taken into account with both high locus-specific branch length and strongly negative heterozygosity values, the authors continue...

These data confirm the unusual European-specific patterns at MATP and SLC24A5. Both genes display long range (consecutive windows) and significant indications of positive selection for all 3 statistics. In contrast, there is little evidence of a European-specific pattern in the TYR locus although the non-synonymous TYR A192C SNP does individually show a strongly significant CEU-LSBL (P<.003) in the HapMap data as in our original findings. The contrast may be explained by the limitations of our HapMap sliding windows analyses, whereby adjacent SNPs are averaged using a method that does not consider Haplotype structure.

East Asians showed relatively stronger selection for a different set of genes…

…In particular, 2 genes (ADAM17 and ATRN) showed East Asian-specific signatures comparable in strength with those observed for MATP and SLC24A5 in Europeans.


The ADTB3A gene also shows a strong and focused signature of positive selection in Africans...

Many hypotheses predict that natural selection will eliminate genetic variants associated with lighter skin in the regions of high UVR as a protection against photo damage (e.g., sunburn, melanoma, and basal and squamous cell carcinomas) (Blum 1961; Kollias et al. 1991) and folic acid photo degradation (Branda and Eaton 1978; Jablonski and Chaplin 2000). The photo protective properties of a highly melanized skin and the recent African origin of modern humans suggest that the ancestral phenotype is one of the relatively dark skin (Jablonski and Chaplin 2000; Rogers et al. 2004). If dark skin is the ancestral phenotype, then we may assume that the first migrants out of Africa were relatively darkly pigmented…

There are 2 primary explanations for the evolution of lighter skin in regions of low UVR:

—1)The first suggests that light skin is merely due to the relaxation of functional constraint and that derived alleles associated with lighter pigmentation may have simply drifted to high frequency in the absence of strong purifying selection (Brace 1963).

—2)The second explanation suggests that in lower UVR regions, positive selection would have favored mutations leading to lighter skin as a way to maximize cutaneous vitamin D synthesis (Rana et al. 1999; Jablonski and Chaplin 200). Given the relatively recent arrival and divergence of humans in and across Europe and Asia, the most parsimonious evolution of light skin would involve such mutations arising in a proto-Eurasian population soon after humans left Africa.

Consequently, these mutations should be shared between modern Asian and European populations. Alternatively, if separate existing functional variants were driven to high frequency in East Asian and Europeans or independent de novo mutations arose and were selected in each population after divergence of Europeans and Asians, then these would be obvious as high allele frequency differences between modern European and East Asian populations. Reduced levels of heterozygosity surrounding the SLC24A5 A111G polymorphism in the European, but not East Asian, HapMap populations support the latter hypothesis (Lamason et al. 2005), as do reduced polymorphism levels based on full resequencing data from MATP in populations of European descent (Soejima et al. 2005).

So basically, while “SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans,” the ADAM17, ATRN, and DCT appear to play a dominant role in the evolution of light skin in East Asians.

Current archeological evidence suggests human presence in Island Melanesia by at least 40ky ago and in other parts of Sahul by at least 45ky ago (O’Connell and Allen 2004). If the original migrants to Oceania arrived there via a corridor of relatively high UVR, then we might expect their descendants to share ancestral pigmentation variants with African populations. However, if the ancestors of modern day Island Melanesians spent a significant amount of time in low-UVR, then it is possible that mutations associated with lighter pigmentation could have accumulated and a readaptation to high-UVR conditions would have been necessary, leading to potential divergence between Island Melanesians and Africans at functional pigmentation loci. In actuality, both of these scenarios may apply, as we know that modern Island Melanesian populations are descended broth early migrants (arriving 40ky ago) as well as later proto-Austronesian-speaking peoples from a southeast Asian homeland ~ 3,200 years ago (Spriggs 1997).

The discordance between our Fst -based divergence values and allele frequencies in the Melanesian CEPH populations at ASIP largely stem from the relatively low frequency of the ancestral allele in the 2 CEPH Island Melanesian populations relative to our original Island Melanesian sample. These discrepancies make it difficult to determine if ASIP truly underlies broad pigmentation differences between darkly and lightly pigmented populations or instead inter-population variation at this locus can largely be explained by differences between Africans and non-Africans. The discordance between the frequencies of the ASIP ancestral allele in our original Island Melanesian sample and the Melanesian samples from the CEPH panel may be indicative of both the complex demographic history of Island Melanesia (involving several migratory events (Spriggs 1997) and probable extensive genetic drift (Friendlaender 1975, 1987) as well as the importance of multiple loci in determining pigmentation phenotype…

Thus possible further extensions of variations detected amongst Melanesians can be explained by successive demographic events After their African ancestors migrated over 40ky ago. The “original Melanesian sample” appears to have more ancestral pigmentation genes in common with tropical Africans, which is to be expected given that they are direct descendants of the earliest Eurasians, as demonstrated as follows with the OCA2 gene…

In general, the derived allele (associated with lighter pigmentation) is most common in Europeans and East Asians, and the ancestral allele predominates in sub-Saharan Africa and Island Melanesia.

The mutations in the OCA2 gene may well have implications on imparting paleness, as demonstrated in the south African San people…

The lightly pigmented hunter-gatherer San populations of Southern Africa is exceptional in having a high frequency of the derived allele relative to geographically proximate and more darkly pigmented African populations (Jablonski and Chaplin 2000), further supporting the importance of OCA2 in regulating normal variation in pigmentation. The widespread distribution of the derived allele in the CEPH-Diversity Panel suggests that it is not necessarily a new mutation, nor has it been restricted to a specific geographic area.

While it seems plausible that the “derived” OCA2 gene came to being before the out-of-Africa migration that give rise to modern Eurasians, it doesn’t appear that this derived allele was necessarily widespread, and may well have been later on selected for in European and East Asians…

Interestingly, derived allele frequencies at this locus are quite different between Native American (15%) and East Asian populations (45%), suggesting that perhaps the derived allele at this locus did not reach very high frequencies in East Asians until after the colonization of the Americas

Contrast the situation with OCA2 gene with that of the MATP 374*G allele…

The virtual absence of MATP 374*G-derived allele in the sub-Saharan African populations that we examined in the CEPH-Diversity Panel is consistent with the origin of this mutation outside of Africa AFTER the divergence of modern Asians and Europeans.

Contrasting that of the “derived” SLC24 A5 [as in the case with the “derived” OCA2 allele], where two possible scenarios arise…

In contrast, the SLC24 A5 11*A-derived allele is found at low frequencies in several sub-Saharan populations including the West African Mandinka and Yoruba, the Southern African San, and South West Bantu. *The presence of the derived allele (albeit at low frequencies) in some sub-Saharan populations may be due to recent gene flow from European and Central Asian populations...

—1)The relatively high frequencies of the derived allele in Central Asian, Middle Eastern, and North Africa seem likely to be due to recent gene flow with European populations.

—2)Alternatively, the derived allele may have lost in the ancestors of modern East Asians but retained in the ancestral European populations. The allele then rose to high frequency in Europeans following the divergence of Europeans and East Asian ancestral groups.

The different mechanism of the evolution of light skin in Europeans and East Asians apparent from genetic examination, supports the understanding that evolution of pale skin came very late, because if had occurred prior to the divergence of the Europeans and East Asians, then it seems highly plausible that they would share more in common with one another the dominating alleles in playing a role in skin lightening…but as demonstrated, different set of alleles play dominating role in the lightening effect of the skin in Europeans and East Asians…

These results simultaneously and strongly suggest that Europeans and East Asians have evolved lighter skin independently and via distinct genetic mechanism, as there is an absence of any unusual pattern of diversity at SLC24A5, MATP, and TYR in East Asians.

The interesting part of the study, is this about the MC1R gene about its…

The MCIR gene was the only locus examined in detail that did not show any signal of potential positive selection. Previous sequence-based studies have reached conflicting conclusions about whether or not MC1R has been subject to positive selection outside of Africa (Rana et al. 1999; Harding et al. 2000; Makova et al. 2001).

Although MC1R’s association with red hair, fair skin, freckles, and melanorma risk in European and European-derived populations primarily from the British Isles (Box et al. 1997; Smith et al. 1998a; Schioth et al. 1999; Flanagan et al. 2000; Bastiaens et al. 2001) clearly demonstrates the important regional role that it plays in pigmentation, MC1R may have (with some exceptions [John et al. 2003; Nakayama et al. 2006]) little effect on variation outside of Europe (Myles et al. 2006). Consequently, no signal will be detected using our approaches.

Although the 2 SNPs that we typed in MC1R are not strongly associated with the red hair and fair skinned phenotype for which MC1R is so well known (Sturm et al. 2003), both are polymorphic in global surveys of populations (Rana et al. 1999; Harding et al. 2000). In addition, the MC1r G92A SNP may have a ”mild” effect on pigmentation phenotype (Motokawa et al. 2006). The 92*A allele at this site is known to have a lower affinity for alpha-MSH than wild-type MC1R alleles (Xu et al. 1996), which suggests that it may contribute to **normal** variation in pigmentation. However, if positive directional selection has acted on MC1R, we would expect variation at linked sites to be affected. As such, even if have not assayed the relevant SNP, we should still have observed some signal selection, especially given the small size (~3 kb) of this gene.

So polymorphisms in the MC1R gene seem to have had relatively more impact in Europeans than other populations. Perhaps this might have something to do with the effects of MCIR mutations in Europeans having an "exacerbating effect", i.e. in addition to those of other “pigmentation”-influencing alleles therein…or maybe to some degree, tenuously linked to the effects of one or the other, or a few of those lightening alleles in Europeans.

Finally, the seem to be a strong case for the ASIP and OCA2 genes in playing a role as a tale-teller [by way of ‘ancestral‘ genes and their ‘derived’ counterparts ] of the derivation of non-Africans from Africans, the populations wherein polymorphisms at these loci could well have played a role in skin tone variation to some degree or another…

The pattern of diversity at ASIP 8818*G allele (the ancestral allele associated with darker pigmentation) indicates a role primarily in African/non divergence (sub-Saharan African frequency; 66%, all other populations; 14%) rather than between darkly and lightly pigmented populations. At OCA2 355, the derived allele (linked with lighter pigmentation) occurs at its highest frequencies across Europe and Asia, but is also relatively common among Native American populations (18-34%) and is present at much lower frequencies (0-10%) among Bantu-speaking African groups. In contrast, the ancestral allele associated with **dark** pigmentation has a shared **high frequency** in sub-Saharan African and Island Melanesians...

Observed patterns of global skin pigmentation diversity and their correlation with environmental UV exposure suggest an adaptive response. Although we cannot rule out a role for sexual selection, our results support multiple genetic mechanisms for evolution of skin color. We provide evidence that at least 2 genes, ASIP and OCA2, probably played a shared role in shaping light and dark pigmentation across the globe.

Aside from non-sequitur about the need for “uniformity” in dark hue in ancestral humans, considering that not even a single immediate family or household will necessarily pass for such a ridiculous test, all in all, Kittles et al.’s analysis lend strong support to the claims made by the likes of Jablonski, about dark skin being the original or default state of Homo Sapien Sapiens!

As a matter of fact, this paper discredits Frank Sweet's claim on his "Onedroprule" site, about the "default" human skin tone being light brown of the likes of Khoisan, and the "supposed dark tone of Bantus being more recent", as others and the present author himself have demonstrated in "" discussions. There is no evidence that Africans in their ancestral skin tone state were uniformly dark skin, but preponderance of evidence does show that dark skin was the ancestral state of human skin pigmentation. As noted already, the ancestral alleles appear to be shared between dark skin populations like Melanesisans and tropical Africans.

This posting above, is itself a slightly modified repro of earlier posting in the following link: White race very young [clickable Egyptsearch link]

Referenced source: Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians, by Rick Kittles et al. , 2006.

Link to part 2: Skin pigmentation gene alleles — Part 2 [clickable]

R1*-M173 Chromosomes in Africa

R1*-M173 bearing chromosomes in Cameroon

Thus far, the highest frequencies of these R1 lineages devoid of any known downstream mutations that characterize other R1* sub-haplogroups, is in Cameroon, to be followed by that detected in Jordan. On average R1*-M173 distribution seems to be relatively more common in African samples, than those outside of it, with detections in Cameroon as already mentioned, Egypt, Sudan [*see below: Hassan et al. 2008] and Rwanda. Outside of Africa, besides the Jordanian samples, detection of relatively lower frequencies was only in the Omani sample. It is certainly plausible that the presence of R1* chromosomes in Africa are relics of very ancient back-migration, but not conclusive as of yet.

The points thus far argued for back-migration has generally been formed around the idea that R1 macrohaplogroup has relatively lower intra-macrohaplogroup diversity of downstream lineages in areas like Cameroon than those in Eurasia, and while M9 lineages are prevalent in Eurasia, no ancestral markers of these lineages have been uncovered in there to the present author's [of this blog] knowledge. What this fails to take into account, is that Cameroonian populations need not necessarily bear intra-macrohaplogroup diversity of R1, so as to be plausible direct descendants of the founder population for the undifferentiated R1* group. Why? Well, it is plausible that if the founder society was fairly small sized, with a section of this founder community migrating elsewhere, then the former may not necessarily have undergone considerable demic expansion relative to the latter offshoot (branch) which emigrated elsewhere—for some reason or another. The former would therefore experience relatively lower diversity due to smaller effective population size for a certain amount of time than the branch that would have undergone a relatively more rapid demic expansion from the onset. It is only after the small sized community undergoes considerable demic expansion subsequent to a period of relative bottleneck, that chances of greater lineage diversity arise. Indeed, the diversity of R1*-M173 chromosomes—lacking identifiable downstream mutations—in Cameroon suggest that the populations derive from a source population that underwent a relatively recent rapid demic expansion.

The present author has been informed that the R1*-M173 chromosomes in Cameroon appear to be one-step neighbors to those found in the Nile Valley. Perhaps, learning about the distance between Cameroonian R1* lineages and those detected in Omani and Jordanian samples would prove instructive, but at the least, it appears that the Nile Valley corridor played a role in the demic diffusion of R1*-M173. From Flores et al., the present author gets the sense that it is certainly plausible that R1*-M173 bearers diffused from Africa into the Levant via the Nile Valley corridor, likely sometime in the Upper Paleolithic. From Flores et al. we have:

Intrapopulation differentiation in Jordan

As Bedouin tribes had an important role in the colonization of southeast Jordan, it could be that the haplogroup composition of the Dead Sea reflected genetic affinities to them, but that is not the case. The most striking characteristic of the Dead Sea sample is the high prevalence of R1*-M173 lineages (40%), contrasting with the lack of them and of its derivatives R1b3-N269 in Bedouin from Nebel et al. (2001) and its low frequencies in Amman. It is worth mentioning that until now, similar frequencies for R1*-M173 have only been found in northern Cameroon (Cruciani et al. 2002). The possibility that the Dead Sea and Cameroon are isolated remnants of a past broad human expansion deserves future studies.

Interestingly, when the molecular heterogeneity of the G6PD locus was compared between the Amman and the Dead Sea samples, a lower number of different variants and a higher incidence of the African G6PD-A allele was detected in the latter (Karadsheh, personal communication). Another singularity of the Dead Sea is its high frequency (31%) of E3b3a-M34, a derivative of the E3b3-M123 that is only found in 7% Bedouins (Cruciani et al. 2004). Until now, the highest frequencies for this marker (23.5%) had been found in Ethiopians from Amhara (Cruciani et al. 2004). On the contrary, most Bedouin chromosomes (63%) belong to the haplogroup J1-M267 (Semino et al. 2004) compared with 9% in the Dead Sea. All these evidences point to the Dead Sea as an isolated region perhaps with past ties to sub-Saharan and eastern Africa.

Strong drift and/or founder effects might be responsible for its anomalous haplogroup frequencies.

This plausibility [of said northeastern Africa-to-Levantine passage] is suggested by the support provided by the fact that these chromosomes appear relatively more common in Africa, particularly in Cameroon, and other genetic indicators as that provided by the authors above, exemplified by the distribution and frequency pattern of the African-specific G6PD-A allele on the X-chromosomes of Jordanian samples in association with that of the distribution and frequency pattern of R1*-M173. This is what one would expect, due to drift and possibly, selective pressure, if the ancestors of said sampling candidates had first passed through an African "corridor" where relative prevalence of malaria might have jump-started a positive genetic drift to favor those X chromosomes bearing the said G6PD-A allele. Based on previous studies [e.g. Tishkoff et al. (2001)], the Afrian G6PD A- allele appears to have undergone its earliest major expansion around the terminal of the Upper Paleolithic or the beginning of the Holocene epoch; if so, this would be more consistent with the time frame for E-M123 or E-M34 dispersal. On the other hand, the G6PD A+ derivative has much greater TMRCA ages than the A- allele, within which the time frame for R1*-M173 dispersal can be invoked. As a matter of note, the A- variant has a much lower intra-allelic diversity than the A+ variant. In any case, each of these markers show clear post-OOA emigration connections between African groups and the Dead Sea community from which Flores et al.'s (2005) sample set came.

Two possibilities to deduce from R1*-M173 distribution pattern...

Possibility #1

— Originated in central Sahara or northeast Africa amongst a nomadic lifestyle oriented group and spread thereof to the Levant through the Sinai corridor, during the Upper Paleolithic.

— The remnants in Africa trekked down to Cameroonian region and the lower vestiges of West Africa as a place of refuge, with the coming of the Ogolian aridity [ca. between 23 ky ago and 18ky ago]. Sometime between 19ky ago and 15ky ago, some E-M35 bearing nomads would move into the Levant via northeast Africa, perhaps due to growing pressures of progressive Saharan aridity. This may explain R1*-M173 carriers in tandem with E-M34 carriers in places like the Dead Sea, whereas R1*-M173 is absent in sub-Saharan East Africa [but not in northeastern Africa] - the African Horn region - where E-M34 chromosomes are prevalent. It may also explain why the Dead Sea R1*-M173 bearing population also happens to standout from their high-frequency J1 carrying Levantine Bedouin brethren in sporting high prevalence of the African-specific G6PD-A locus on the X chromosome. The presence of both E-M34 and E-M78 derivatives in the so-called Near East make it clear that E-M35 chromosomes did not spill outside of the continent in a single demographic event or even time frame. On the other hand, E-M34 is absent in West and Central Africa where R1*-M173 chromosomes are most prevalent.

— Upon finding a refuge to escape intense aridified conditions of the Sahara, sections [meaning not all] of the previously largely nomadic R1*-M173 carriers began to settle in their new found refugia. The small communities of R1*-M173 would eventually expand, but they would have been overwhelmed by the faster expanding newly arrived PN2 carriers, especially with the receding of the Ogolian aridity. Those who retained their nomadic lifestyle, trekked back and forth the western[mainly] Sahel and the lower geographical vestiges of West Africa, where some of the settled brethren located themselves. These nomad traditionalists would adopt a pastoralist lifestyle [see: the theme centered on the *divergent* C-13.9kbT allele patterns in R1*-M173 carriers], which would modify their diet.

Although, largely tenuous at this point, there might be a link between the C-13.9kbT allele [has been linked to lactose tolerance promotion] and ancestry amongst a section of the groups bearing the ancestral R1*-M173 markers. This phenomenon of one segment of R1*-M173 bearers having the C-13.9kbT allele, while other segments of R1*-M173 bearers have little to none, has only been demonstrated in Africa, the continent where the R1*-M173 marker is so far the most common. Then again, as just another possibility, this phenomenon might be better related by some other line of ancestry or biohistory that portrays a different demographic history from that of the Y DNA marker.

Sticking point(s) for possibility #1:

The only or main one offered for this possibility from those publications which propose otherwise, is the relative greater diversity of the overall K-M9 family outside of Africa, as opposed to that located within continent, even though the presence of Hg K itself [particularly in East Africa] in the continent has been noted; however, even if one were to look at it from that angle, it doesn't necessarily negate a possible African origin for R1*-M173, as its supposed predecessor P-M45 — in particular, the elusive undifferentiated P-M45 — is just as rare in Asia.

Possibility #2

—Originated in the Sinai or the Levantine or northern regions of the Arabian desert, amongst a very small community nomads of that region. Those that trekked between North Africa and the so-called Near East through the Sinai corridor, would give rise to a subset that decided to stay put in North Africa and lead their nomadic lifestyle there. Others went even further north; they went as far as Europe, wherein they'd become ancestors of R1b bearers; on other hand, the demograhic shifts brought upon later by greater expanding groups, like say Hg J carriers, probably urged some remnants of R1*-M173 to spread eastward, central Asia, wherein they'd give rise to R1a carriers, sometime after the LGM or else after a good duration of the LGM had already gone by. The small group of R1*-M173 bearers who moved into Europe would likely have met relatively modest competition, due to smaller isolated groups in the region, as compared to elsewhere in Asia and in Africa.

—With the coming of the LGM, the R1 carriers in Europe would find refugia in southwestern Europe and certain regions in the so-called Near East. This would have coincided with the aridification of the Sahara, wherein R1* bearers there, as the present author has noted above, would have migrated southward, out of the region of the intense aridification of the Sahara. However, when the LGM came to a conclusion, the R1 carriers in Europe, who sought refuge in southern Europe and parts of the so-called Near East, would start repopulating the more northerly regions of Europe, and the subsequent expansion, especially with the advent of farming from the so-called Near East, would result in R1b-rich populations wherein the carriers of the downstream [R1b] carriers would overwhelm any remaining original R1b-predecessor R1* group. In other words, negative genetic drift essentially drifted out the original R1 carriers. Although R1b itself seems to have come to being before the LGM, its numbers likely became much greater after the LGM. As noted above, small group of R1 carriers who populated Europe, were likely fortunate enough to have not met the same competition from non-R1 bearing groups, as they might have been exposed to in Africa and the so-called Near East.

Sticking point(s) for possibility #2:

Naturally with possibility #2, one would have to explain away why the only one of the two places outside of Africa where the rare undifferentiated R1*-M173 marker is present, and where it has been the most substantial [after Africa], that this marker appears to be in a population that stands out in its low Hg J [ 9% J1 in the Dead Sea compared with 63% J1 (Semino et al. 2004) of their Bedouin neighbors , per reference by Flores et al. 2005], while it bears 31% E-M34 compared to the only 7% of Bedouin (Cruciani et al. 2004) [See: Flores et al.2005], and last but not least—it has a lower number of different G6PD locus variants and a higher incidence of the African G6PD-A allele (Karadsheh, personal communication) than the Bedouin, when the molecular heterogeneity of the G6PD locus was compared between the Amman and the Dead Sea samples [Flores et al. 2005]. And even Oman, wherein R1*-M173 markers had been located in low frequency, cannot be ruled out as a recipient of these chromosomes through gene flow from Africa, because it isn't too far from northeast Africa, wherein these R1* chromosomes appear, not to mention the fact that other African ancestry therein [like variant E-M35 lineages and E3a chromosomes] make it clear that Oman has definitely been a recipient of genetic introgression from Africa via multiple and distinct demographic events.


In either cases of possibility #1 and possibility #2, the established downstream R1 derivatives are generally relatively less frequent to absent in the regions that harbor R1* undifferentiated chromosomes figure prominently within the regional hg R1 distribution. Conversely, in the regions where the established downstream R1 chromosomes are prominent, R1* undifferentiated chromosomes are fairly rare or absent. This is simply testament to the possibility that in regions wherein the original R1 carriers [who were likely small to begin with, in terms of effective population size] appear to have expanded the most, the original R1* chromosomes were eventually drifted out by the more downstream hg R1 carriers.

One thing both possibility #1 and possibility #2 converge on, is this: R1*-M173 in Africa are very ancient, and did not come from populations characterizing downstream mutations, like say Europe.

It should be pointed out though, from the looks of data that readers are provided with, that Flores et al.'s (2005) sample were not specifically tested for either the M343 or the M420 nodes of the R haplogroup. In any case, the R1*-M173 chromosomes here would still serve as ancestral markers of chromosomes bearing either marker, since the next identified main downstream nodes respective to the said lineages were not identified in the Dead Sea-sample R1*-M173 bearing chromosomes—namely, P25 and SRY10831.2 respectively.

Research extracts that just lend credence to some of the themes expressed in the above...

In the mtDNA landscape, Richard et al. 2000 tell us:

"We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans."

Neolithic contribution...

"With respect to their Neolithic components, the regions fall into several groups. The southeastern, north-central, Alpine, northeastern, and northwestern regions of Europe have the highest components (15%–22%). The Mediterranean zone has a consistently lower (9%–12%) Neolithic component, suggesting that Neolithic colonization along the coast had a demographic impact less than that which resulted from the expansions in central Europe. Scandinavia has a similarly low value, and the Basque Country has the lowest value of all, only 7%..."

"The principal clusters involved seem to have been most of J, T1, and U3, with a possible H component. This would suggest that the early-Neolithic LBK expansions through central Europe did indeed include a substantial demic component, as has been proposed both by archaeologists and by geneticists."

Late Upper Paleolithic contribution...

"The LUP values are, by contrast, higher toward the west: the western Mediterranean, the Basque Country, and the northwestern, north-central, Scandinavian, and Alpine regions of Europe have 52%–59% LUP, with the central-Mediterranean region having a value of almost 50%..."

"The lineages involved include much of the most common haplogroup, H, as well as much of K, T, W, and X...haplogroup V, the sister cluster of H within HV, appears to have evolved within Europe, possibly in the southwest, and to have expanded with the LUP component (Torroni et al. 1998)..."

"It seems plausible, then, that many founders of haplogroup H—and, possibly, founders from other haplogroups dating to the LUP, such as much of K, T, W, and X—may have (a) arrived prior to the LGM, (b) suffered reductions in diversity, as a result of population contractions at the onset of the LGM, and (c) subsequently reexpanded."

Middle Upper Paleolithic contribution...

"The MUP values are perhaps highest in the Mediterranean zone, especially the central Mediterranean region..."

"The value for the MUP is rather low in the basic fs analysis, at ∼10%–15%, and is highest along the Mediterranean, especially in the central-Mediterranean region. However, after allowance is made for multiple expansions of the H-CRS, it rises to ∼25% overall. The contributing clusters are mainly HV*, I, U4, and (in the repartitioned version) H."

Early Upper Paleolithic contribution...

"The EUP values are highest in Scandinavia, the Basque Country, and northeastern Europe..."

"For the first settlement of Europe, at least, the picture seems to be clearer. The regional EUP component varies 5%–15% and comprises mainly haplogroup U5. The values are highest in southern and eastern Europe, as well as in Scandinavia and the Basque Country."

All in all...

These analyses allow us to quantify the effects that various prehistoric processes have had on the composition of the modern mtDNA pool of Europe. They suggest that < 10% of the extant lineages date back to the first colonization of Europe by anatomically modern humans and that ∼20% arrived during the Neolithic.

Most of the other lineages seem most likely to have arrived during the MUP and to have reexpanded during the LUP. Given the uncertainties associated with the analyses, we should not rule out the possibility of a Mesolithic migration, but we have found virtually no evidence supporting this idea.

The above is essentially relevant for the basic theme of major expansion events with the fading of the LGM, which is consistent with R1b bearers' numbers swelling in tandem with said expansions.

More directly related to the issue of R1 bearers, Cinnioglu et al tell us that: 

"The phylogenetic and spatial distribution of its equivalent in Europe (Cruciani et al. 2002), the R1-M173 (xM17) lineage for which considerable data exist (Semino et al. 2000a; Wells et al. 2001; Kivisild et al. 2003) implies that R1b3-M269 was well established throughout Paleolithic Europe, probably arriving from West Asia contemporaneous with Aurignacian culture. 

Although the phylogeographic pattern of R1b3-M269 lineages in Europe suggest that R1-M173* ancestors first arrived from West Asia during the Upper Paleolithic, we cannot deduce if R1b3-M269 first entered Anatolia via the Bosporus isthmus or from an opposite eastward direction. However, archeological evidence supports the view of the arrival of Aurignacian culture to Anatolia from Europe during the Upper Paleolithic rather than from the Iranian plateau (Kuhn 2002)." - Cinnioglu et a., Excavating Y-chromosome haplotype strata in Anatolia, 2004.

Consistent with the general observation about the role played by the so-called "Middle Eastern" corridor in the initial peopling of Europe involving groups who were to become the main source populations of contemporary native Europeans. This prospect is supported by human paleontological record in Europe, wherein the earliest sufficiently complete anatomically modern human specimens dating to the Early Upper Paleolithic are described as being more "African-like" or "tropical African" body proportions [for example, see Holliday & Hilton (2009)]; one would expect such to be the case, if the earliest Europeans were either directly populated from Africa or indirectly populated from therein via the "Middle Eastern" corridor [the latter seems more likely, given the prevalent Hg HV-derived maternal markers in Europe; also see the works of other analysts like Barbujani et al. 1998 and Cinnioglu et al. 2004], as opposed to peopling from central Asia. One would expect the earliest ancestors of modern Europeans to have lost "tropical body plans", if they had come from the sub-tropical regions of central Asia. This is also in line with minimal central Asian and south Asian component in European maternal gene pool, as observed by Richard et al. 2000:  

mtDNA in the Near East

Table 1 shows frequencies and age estimates of the main mtDNA haplogroups that occur in the Near East and Europe. These clusters are restricted primarily to Europe and the Near East (western Eurasia). Western-Eurasian lineages are found at moderate frequencies as far east as central Asia (Comas et al. 1998) and are found at low frequencies in both India (Kivisild et al. 1999a) and Siberia (Torroni et al. 1998), but, in these cases, only restricted subsets of the western-Eurasian haplogroups have been found, suggesting that they are most probably the result of secondary expansions from the core Near Eastern/European zone.- Richards et al., Tracing European Founder Lineages in the Near Eastern mtDNA Pool, 2000.

The "moderate frequencies" of Western-Eurasian markers that do appear in central Asia, are proposed here to be largely the product of gene flow from "core Near Eastern/European Zone".


variance of 49a,f ht35 related chromosomes are lower in the Balkan, Caucasian and Iraqi representatives than those in Turkey (Table 4). Similarly, the variance is higher in Iberia than in Western Europe.

The decreasing diversity radiating from Turkey towards Southeast Europe, Caucasus and Mesopotamia approximates similar results from Iberia tracing the re-colonization of Northwest Europe by hunter-gatherers during the Holocene as suggested by others (Torroni et al. 1998; Semino et al. 2000a; Wilson et al. 2001)...

Haplogroup R1b3-M269 occurs at 40–80% frequency in Europe and the associated STR variance suggests that the last ice age modulated R1b3-M269 distribution to refugia in Iberia and Asia Minor from where it subsequently radiated during the Late Upper Paleolithic and Holocene. The R1b3-M269 related, but opposite TaqI p49a, f ht 15 and ht35 distributions reflect the re-peopling of Europe from Iberia and Asia Minor during that period.

The R1b3-M269 variances and expansion time estimates of Iberian and Turkish lineages are similar to each other (Table 2) but higher than observed elsewhere (Table 4). Low variances for R1b3-M269 lineages have also been reported for Czech and Estonian populations (Kivisild et al. 2003)." -
Cinnioglu et al. 2004 a wrap up, which is relevant to the idea of the lineages having expanded northwards from west Asia, and then subsequently expanding back to the Mediterranean regions [with southwestern Europe, i.e., Iberia being important, in terms of refuge] and Asian Minor during the last Ice age, and then at the end of LGM, re-peopling of the northward European regions began from these regions.

By the way, previous genetic research work made very enthusiastic attempts to correlate the likes of U6 and possible "Eurasian"-tagged mtDNA with R1*-M173, supposedly as an attempt to buttress a possible back-migration into Africa; all but failed, with results showing considerable African mtDNA gene pool instead, for populations bearing these chromosomes.

If as pointed out by L. Luca Cavalli-Sforza [see: Genes, peoples, and languages] that markers across the human genome from a global sample [presumably, of 42 populations, involving some 120 alleles, i.e. aside from the generally used uniparental paternal and maternal markers], suggest a component of about 1/3 African contribution and 2/3 Asian contribution, then the following would seem to lend support to the African-origin scenario presented above, that is—in light of what is already understood about the genetic markers found in tandem with R1*-M173 chromosomes found in the Dead Sea samples...

One reasonable hypothesis is that the genetic distance between Asia and Africa is shorter than that between Africa and the other continents in Table 1 because both Africans and Asians contributed to the settlement of Europe, which began about 40,000 years ago. It seems very reasonable to assume that both continents nearest to Europe contributed to its settlement, even if perhaps at different times and maybe repeatedly. It is reassuring that the analysis of other markers also consistently gives the same results in this case. Moreover, a specific evolutionary model tested, i.e., that Europe is formed by contributions from Asia and Africa, fits the distance matrix perfectly (6). In this simplified model, the migrations postulated to have populated Europe are estimated to have occurred at an early date (30,000 years ago), but it is impossible to distinguish, on the basis of these data, this model from that of several migrations at different times. The overall contributions from Asia and Africa were estimated to be around two-thirds and one-third, respectively. Simulations have shown (7) that this hypothesis explains quite well the discrepancy between trees obtained by maximum likelihood and neighbor joining. - L. Luca Cavalli-Sforza

Synopsis: Perhaps the jury is still out on Hg R, BUT there is a VERY strong case for an African origin of this clade, and it is one of the two most probable geographic considerations for this origin. This is accessed not only from R1* distribution pattern in the continent, but also from closer examination of the rather unique Hg R family of clades that pervades the continent; if there is any evidence of this, then look no further than to the contradicting reports between Berniell-Lee et al.'s (2009) paper and those of Hassan et al.(2008) and Woods et al. (2005). The reports from the latter two confirm that R1* paragroup finds in earlier journals from the likes of Cruciani et al. (2002) were in fact not a matter of the retrospective state of development of sequencing resolution. This is necessary to note, because cases have been made about the need for not reading too much into the earlier R1* reports of Cruciani et al. (2002), or say Luis et al. (2004), on the premise that these involved insufficient sequencing resolution. Out of comparing these journals, and QUITE importantly, being mindful of their respective sequencing resolution pros and cons, the emerging picture of the African Hg R family of clades is one of a varied and a unique co-existence of paraphyletic clades that has thus far not been seen anywhere else. Where Africa falls short in relative diversity as it pertains to downstream Hg R clades, parts of Asia [including Europe] appears to make up for that. Between the so-called "Near East" and Africa, preponderance of DNA-evidence goes to the latter—i.e. African origin. A case for the so-called "Near East" on the other hand, so says the leading proponents thereof—is trumped by finds in southern Asia, the Indian sub-continent in particular, where diversity of the most upstream examples of Hg R clades are concerned. The so-called "Near East" clearly lacks this feature; this issue however, doesn't crop up when it comes to Africa. The only reservations its dissidents continue to hold against the African origin, boils down to the diversity of the downstream clades, if not reduced to merely wondering how Africa could possibly be a reservoir to unique upstream paraphyletic clades, presumably of "all places".
*Referential notes:

—Hassan et al. 2008, Y-chromosome variation among Sudanese: Restricted gene flow, concordance with language, geography, and history.

Remarks: The R1-M173 [~ 54%] chromosomes of the Sudanese communities of nomadic Fulani pastoralists, not inconsistent with that found in some west African Fulani [esp. in northern Cameroon], is one area of noteworthy, with regards to Hassan et al.2008. These R1 markers are highly likely those familiar undifferentiated R1*-M173 chromosomes found in Cameroon, and yes, Egypt as well. Of course, as noted in the study, these Sudanese Fulani retain their Niger-congo sub-phylum language.

The authors of this study of course do not specifically tell us this, about the paragroup character of these chromosomes, because their intra-phylogenetic resolution for R1 was not too comprehensive or sharp enough to begin with; but we know that those chromosomes didn't belong R1b1, which is the predominant type in western Europe, and which was specifically tested for in this study.

One might recall, again, that Cruciani et al. also come across said paragroup of R1*-M173 in their Fulani samples from Cameroon.

Also of note, K2 & K* incidences in this study, show considerable distribution amongst the Afrisan ("Afro-Asiatic") speaking groups. Though less relevant to this topic, F-M89's distribution is also noteworthy, across populations generally linked with three major African language phylums namely, Nilo-Saharan and Afrisan [Sudanese groups; present authors], and Niger-Congo [Senegalese sample; courtesy Semino et al. 2002].

Other reading:

More on R1*-M173 bearers

R1*-M173 Chromosomes in Africa - II

Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007


Discussion points: Questions & Answers that come up about this subject...

The following is a recounting of questions that came up about a possible African origin of R1*-M173 in a DNA forum run by some Eurocentic-cultist by the name of Andrew Lancaster; he censors the board to ensure dissenting voices [to his subjective opinions] are not heard, and so, this section is being devoted to address such matters, wherein responses are not stifled or edited, as done by such self-professed "discussion boards":

A poster going by a pseudonym "Jafety R1b-U152" writes, having compared a possible African origin to the same sort of logic that places Hg E as an Asian originated marker:

I wanted to say that the view to originate R from Africa seems to be like originating E from outside Africa. There is much more "political" intention than scientific, I guess. Of course your blog do not say Hg E originated outside Africa, and I do not claim it does.

My response:

Whereas R1*-M173 markers were reported across Africa, E* has never been reported in the so-called Middle East, to even begin to compare it an 'inverse' version of Hg E originating in Asia. I make specific points in the blog; if you feel something therein is not right, feel free to point it out *specifically*, and I'll be glad to discuss the point with you.

"Jafety R1b-U152" writes:

R1b has no percentage in the India study because it was not found. Of course, they could not test for downstream SNPs as every sample was M343-

My response:

I know that, as I said so myself.

"Jafety R1b-U152" writes, having been informed about the Fulani sample in Hassan et al.'s (2008) by myself:

I also found the interesting R1* among Fulani in the Sudan study. Vineviz told us in the Sub-Saharan R1b1 thread that P25 is not a stable mutation, and he thinks (I hope I understood correctly) that they probably lost P25, but had it before. I am not an expert, so I can not comment if this is possible.

My response:

Well, Vineviz will have to show evidence of a unique event SNP being lost, if he/she has it. But in terms of the Fulani situation, it is interesting to me, because the Cameroonian Fulani were one of the groups that Cruciani and other research teams had detected undifferentiated R1* chromosomes, with considerably high frequency. Hassan et al.'s study, who did also a test for P25, seems to reaffirm this. Here to, the Sudanese Fulani sport considerably high frequencies. I hear about Bantus in Cameroon have tested positive for P25 markers that were found in those samples, but it is necessary to note that the R1* markers that earlier studies noted in northern Cameroon, happen to be mainly in non-Bantu speaking groups, like the Fulani.

[Note: Emphasis is made here on "non-Bantu", because a recent study by Berniell-Lee et al. claims to have made additional discoveries into where northern Cameroonian R1*-M173 markers may actually fall, where the phylogenetic order of R1 is concerned, presumably by studying Cameroonian Bantu-speaking groups and central African pygmies. However, the R1*-M173 chromosomes located in Cameroonian samples in previous studies, were mainly found in the non-Bantu speaking groups of northern Cameroon in rather considerable frequencies, and virtually rare to absent in Cameroon's Bantu-speaking groups [only the Ewondo were implicated in these markers in Cruciani et al.'s (2002) southern Cameroonian samples @ ~ 3% of that sample]. The said authors (Berniell-Lee et al.) conclude that the previous R1*-M173 are likely to be R1b1* chromosomes, since that is what they found in their sample. This is something worth pointing out, as it seems to not touch the radar of many folks out there. Furthermore, as noted above, the Sudanese Fulani sample of Hassan et al. (2008), obviously tested negative for the P25 marker on their R1*-M173 markers, which again appear in considerable frequencies (54%). This is important, because it contradicts Berniell-Lee et al.'s findings of R1b1*, which does have the P25 marker. Given the recurring theme of R1*-M173 incidence in Hassan et al.'s Sudanese Fulani sample when coupled with those of a number of other research teams in the past, with regards to groups in northern Cameroon, including the Fulani therein, it is not hard to imagine that these are the same markers that the northern Cameroonian Fulanis have too.]

"Jafety R1b-U152" writes:

On Fulani, it is important to see that they are not a monolithic group, for example Senegali Fulani have Hg T while Camerooni not.

My response:

Of course they are not a monolithic group, which is why I said a section of west African Fulani, in my earlier post to you. Please re-examine it. Fulani, save for the isolated cases of these R1* carriers, are largely E-M2 carriers, consistent with other areas of western Africa.

[Note: The above is alluding to genetic composition, of course, but culturally, Fulani is undoubtedly monolithic; in fact, genetically too, for the most part, save for outliers like the R1*-M173, Fulani can be described as largely 'monolithic', in that their gene pool is consistent across the Fulani communities, and with those of the general west African area]

"Jafety R1b-U152" writes:

its African origin is very unlikely.

My response:

Why, when R1*-M173 markers were found there; [what argument is there], besides the argument that Hg R is not as diverse there, which doesn't negate an African origin as I note in the blog?

"Jafety R1b-U152" writes:

A North Indian or Pakistani origin is much more likely if you look at Q, R*, R2, R1a* (xM17), and they have R1* as well. However, R1b (M343) seems to have originated elsewhere, as it is nearly absent from India.

My response:

Like I said in the last post, this rationale is not as unequivocal as you think. R1b is generally rare to absent in Indian populations, and yet, it is generally considered the older branch of the two. If Indian groups are the ancestral groups, one might expect to see a good degree of R1b distribution amongst them alongside R1a, but that's not the case; as you now acknowledge yourself, R1[b] is essentially rare to absent in Indian populations. This means that R1* carriers were still around when R1a mrca emerged, because that is the only way R1a marker could have branched out into its own lineage, independent of R1b. So, the presence of paraphyletic R* markers amongst them can only mean three things: 1) that R1* spread from a western region, where R1b, the older branch, are heavily clustered, to the more eastern areas, in the path of which, R1a would eventual emerge. 2) R* and R1* are relics of this sort of expansion, or 3) R* and R1* in Indian groups are yet more rare R markers whose phylogenetic status is yet to be resolved, because even though they may not match the basic defining markers for established R sub-clades, they could be other newly independent downstream branches that have yet to be identified.

[It should be of note, that the presence of R* and R1* amongst a predominantly R1a carrying groups, can be seen as a sign of its R1a's relatively younger age and expansion than R1b, which again, is mainly seen in western areas. R1b in "Western Asia": It may well imply that R1b had more opportunity to expand and overshadow ancestral R1* or R*, which would have largely experienced negative drift.]

-- Exchange ends --

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

*Last edited on 10/22/2010.

Closer Examination of the Iraqw: Southern Cushitic Speakers of Tanzania

Zeroing in on the Iraqw

Recently, it has been proposed that E3b originated in sub-Saharan Africa and expanded into the Near East and northern Africa at the end of the Pleistocene (Underhill et al. 2001). — Cruciani et al. 2004, Phylogeographic analysis of haplogroup E3b

Between 23 and 18ky ago—Ogolian period begins, which coincides with and is likely connected to the LGM weather situation.

23,000 BP ~ 21,050 BC: "After a favourable climatic period, characterised by relatively dense and diversified Palaeolithic occupations, the arid Ogolian begins locally around 23000 years BP and is represented at Ounjougou by a significant depositional and archaeological hiatus." - Aziz Ballouche [see: Link ]

—Much of North Africa and the Sahara are characterized by adverse weather conditions, with much of the region turning arid. The Sahara at this time, extends south beyond its current boundaries to a certain point, possibly a little beyond the Niger bend. Arid conditions extend all the way to the "horn" coast of the African Horn region, possibly encouraging populations to reside more inwards—away from that horn-shaped coastal region; rather, likely towards the region straddling southern Sudan, Ethiopia, Kenya and Uganda or even further—region straddling Uganda, Kenya, and Tanzania.

—PN2 clade (E3) bearers in the vicinity of the Sudanese-Central African Republic -Ugandan-Kenyan general region give rise to E3a ~ between 21 and 18 ky ago [pending additional or new info]; E3b-M35* would have likely arose relatively earlier than E3a* [as evidenced by its near absence in some the populations that carry this], sometime prior to the Ogolian and the LGM period. At this time, it was likely the M78 derivative that came about ~ between 19 and 15 ky ago. It was also likely during this period, that some E3b-M35 variants spilled over to the "southwest Asia", which would be identified as E-M34. The E-M78* likely arose somewhere in the bidirectional-migration route between Northeast and sub-Saharan East Africa; this location was likely in the region straddling upper Egypt and Sudan of the eastern Sahara, amongst earlier E-M35 migrants from sub-Saharan East Africa. These M78 bearers were increasingly pressured to move further south due to progressive aridity, possibly as far as Uganda-Kenya and/or Tanzanian general region.

Even today, Cushitic-speaking E-M78 bearing groups straddle between Ethiopia and Kenya, namely the Oromos, normally going by the names Oromo and Borana in Ethiopia and Kenya respectively. However, getting back to the matter of those latter Hg E-M78 bearers who would have gone to as far as the Tanzanian region, they would leave descendants in the region, the most notable of whom we recognize as the "Iraqw" today.

These folks, i.e. the Iraqws, seem to be Cushitic speakers who are rarely talked about, in comparison to groups like the Oromo, the Borana and the Somali. Much of this, perhaps has more to do with the fact that most geneticists have focused their attention to the aforementioned African Horn regions, while lesser attention has been afforded to these groups, who dwell in the Tanzanian region.

Some notes on the Iraqw, from various sources:

Iraqw is a Southern Cushitic language with a speaking population of 500,000 (and growing) in the Arusha province of Northern Tanzania in East Africa. It is a language which is thriving, despite the strong presence of Swahili in Tanzania. The success of its modernization process is due to the openness of the Iraqw people, who welcome new ideas and new people into their speaking group — Courtesy of Maarten Mous et al, Cushitic Language Studies volume 18.


The history of the 200,000-strong Iraqw, who occupy much of the area between Karatu and Mbulu town in the south, is a fascinating enigma, though the theory that they originally came from Mesopotamia (Iraq, no less) is too simplistic to be likely.

Nonetheless, the Iraqw language is related to the "southern Cushitic" tongues spoken in Ethiopia and northern Kenya, meaning that at some point in their history they migrated southwards along the Rift Valley, something you can also tell by their facial features, which are finer than those of their neighbours and similar to those of Ethiopians.

Exactly when the Iraqw arrived in Tanzania is not known, but a number of clues offered by their agricultural practices - the use of sophisticated terracing to limit soil erosion, complex irrigation techniques, crop rotation and the use of manure from stall-fed cattle - provide uncanny parallels to the ruined irrigation channels, terraces and cattle pens of Engaruka (see p.437), at the foot of the Rift Valley escarpment

Iraqw oral legend makes no mention of a place called Engaruka, but that's hardly surprising given that Engaruka is a Maasai word. Instead, legends talk of a place called Ma'angwatay, which may have been Engaruka. At the time, the Iraqw lived under a chief called Haymu Tipe. In what is suggestive of a power struggle or civil war, the legend says that Haymu Tipe's only son, Gemakw, was kidnapped by a group of young Iraqw warriors and hidden in the forest. Finally locating him, Haymu Tipe was given a curious ultimatum: unless he brought to the warriors an enemy to fight, his son would be killed. So Haymu Tipe asked the cattle-herding Barbaig, who at the time occupied the Ngorongoro highlands, to come to fight, which they did. Many people were killed, and it seems that the Iraqw lost the battle, as Haymu Tipe, his family and his remaining men fled to a place called Guser-Twalay, where Gemakw - who had been released as agreed - became ill and died. Haymu Tipe and his men continued on to a place called Qawirang in a forest west of Lake Manyara, where they settled. The legend then becomes confusing, but it appears that Qawirang is the same as the most recent Iraqw "homeland", the lrqwar Da'aw valley, 70krn south of Karatu, where the Iraqw settled at least 200 years ago, shortly after Engaruka was abandoned. Subsequently, population pressure in lrqwar Da'aw led to further migrations; the first Iraqw to settle in Karatu arrived in the 1930s — Courtesy of Fink, Jens The Rough Guide to Tanzania 2003

More on the Iraqw mythology: See -


The Iraqw language's place in the Cushitic language family, comprising 47 members in total:

Central (5)
Central-Eastern (1)
Xamtanga [xan] (Ethiopia)

Central-Northern (1)
Bilen [byn] (Eritrea)

Central-Southern (2)
Awngi [awn] (Ethiopia)
Kunfal [xuf] (Ethiopia)

Central-Western (1)
Qimant [ahg] (Ethiopia)

East (34)
Boon [bnl] (Somalia)

Dullay (3)
Bussa [dox] (Ethiopia)
Gawwada [gwd] (Ethiopia)
Tsamai [tsb] (Ethiopia)

Highland (7)
Alaba [alw] (Ethiopia)
Burji [bji] (Ethiopia)
Gedeo [drs] (Ethiopia)
Hadiyya [hdy] (Ethiopia)
Kambaata [ktb] (Ethiopia)
Libido [liq] (Ethiopia)
Sidamo [sid] (Ethiopia)

Konso-Gidole (2)
Dirasha [gdl] (Ethiopia)
Komso [kxc] (Ethiopia)

Oromo (6)
Oromo, Borana-Arsi-Guji [gax] (Ethiopia)
Oromo, West Central [gaz] (Ethiopia)
Garreh-Ajuran [ggh] (Kenya)
Oromo, Eastern [hae] (Ethiopia)
Orma [orc] (Kenya)
Sanye [ssn] (Kenya)

Rendille-Boni (2)
Boni [bob] (Kenya)
Rendille [rel] (Kenya)

Saho-Afar (2)
Afar [aar] (Ethiopia)
Saho [ssy] (Eritrea)

Somali (6)
Dabarre [dbr] (Somalia)
Garre [gex] (Somalia)
Jiiddu [jii] (Somalia)
Somali [som] (Somalia)
Tunni [tqq] (Somalia)
Maay [ymm] (Somalia)

Western Omo-Tana (4)
Arbore [arv] (Ethiopia)
Baiso [bsw] (Ethiopia)
Daasanach [dsh] (Ethiopia)
El Molo [elo] (Kenya)

Yaaku (1)
Yaaku [muu] (Kenya)

North (1)
Bedawi [bej] (Sudan)

South (7)
Aasáx [aas] (Tanzania)
Burunge [bds] (Tanzania)
Dahalo [dal] (Kenya)
Gorowa [gow] (Tanzania)
Iraqw [irk] (Tanzania)
Alagwa [wbj] (Tanzania)
Kw'adza [wka] (Tanzania)

— Language breakdown, Courtesy of

Knight et al, 2003...

M2 is frequent in most African populations, with the exception of Afro-Asiatic-speaking groups (Table 1). The highest frequencies of M2 are observed across Bantu-speaking groups. M35 is rare within Bantu speakers and is widely though nonuniformly dispersed throughout Africa (Table 1). M112 has been observed at highest frequencies within San and peoples of the central African forests (i.e., Biaka, Mbuti, and Lisongo; hereafter referred to collectively as forest peoples)… Two or more Tanzanian populations shared 5 of the 33 resulting haplotypes. One M35 haplotype, for example, was observed in three of four Tanzanian groups (Hadzabe, Iraqw, and Sukuma). Two of four Hadzabe M2 haplotypes were shared with Sukuma… We observed extensive mtDNA and NRY diversity within the set of four Tanzanian linguistic groups. Only one individual with the basal NRY haplogroup A was ob- served, probably reflecting the small number of male Iraqw tested. A linguistically diverse set of Tanzanians fall into the basal mtDNA haplogroup L1a, and L1f haplotypes were observed in Iraqw.

Language family = AA (Afro-asiatic/Afrasan); Language subfamily = S Cushitic, Population = Iraqw, N = 6, Haplogroup A (91) = 17%, Haplogroup E (M35) = 33, Haplogroup E1, E2 and E* (YAP) = 17, 33 [which most likely reflect E1 and E2 respectively; at any rate YAP+ lineages lacking M2 and M35 mutations]

Courtesy Knight et al., source:

Among the groups sampled, the Iraqw is the next ethnic group, after the Nilo-Saharan East-Sudanic speaking Datoga, to show the highest frequencies of the Haplogroup E -M35. The Iraqw are followed by the Khwe!