Monday, January 28, 2008

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.

Neutralizers...

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".

Additionally,...

"The
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

...in 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".
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*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

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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.

4 comments:

Saami said...

It is in general a very interesting blog you have.
Nigeria is extremely interesting from my point of view. They have many place names that matches with names in the Buddhist migration routes. I will create maps over some of these names worldwide later.
There is another blog that writes about M173. Take a look in this link:
http://new-indology.blogspot.com/

http://new-indology.blogspot.com/2010/01/contribution-of-recent-genetic-research.html

You can find one of my blogs here:
http://oldgoths.blogspot.com/

Mystery Solver said...

Saami,

Thanks. I'll be sure to check those links out.

Ann said...

I am late to the topic, and do not wish to sound rude, but the state of mind seems to, to be that the entire Y-DNA study centers around proving the European males screwed the Afrikan woman. You know, kind of like proving that the first humans were white to prove that the son of Noah, the descendants of Ham, were cursed to be black! If the genetics proves otherwise then the curse of leprosy is from the skin turning from black to white not white to black!

Does that make sense?

Mystery Solver said...

Ann, the message of the blog entry could not be starkly different from what you gather from it. Nowhere there is any case being made for "white males screwing black women". The blog entry is in fact stating that the original R carriers could very well have been Africans before populating Europe and other parts of Asia. I highly recommend that you go over the blog a few more times, as I suspect its technicality could make it a hard read. If you have questions from that point on, I'd be happy to entertain it, providing that I have time.