Monday, March 2, 2009

Working hypothesis around haplogroups IJK, I, J, K, P, R, and Q

The newly uncovered Y-DNA clade, given the moniker of 'IJK' at the moment, is defined by UEPs designated as S137 (L15) and S138 (L16) at rs9786139 and rs9786714 respectively.

* The site recently provided additional locus information, in the form of L69.1/S163.1:

L69.1/S163.1 is shown as L69(=G) in IJK. L69/S163 appears in multiple locations. -

And adds that:

The DE haplogroup appeared approximately 50,000 years bp in North East Africa and subsequently split into haplogroup E that spread to Europe and Africa and haplogroup D that rapidly spread along the coastline of India and Asia to North Asia. The IJ haplogroup characterizes part of the second wave of emigration from Africa that occurred via the Middle East 45,000 years bp and defines two branches I and J that emigrated northwards and eastwards into Europe. The J branch subsequently split again and contributed to the current North African population... - Courtesy of

For its part, the International Society of Genetic Genealogy doesn't inform us on its website of either by whom or what circumstances were involved in the study responsible for the finding; rather, said finding was supposedly brought to attention by way of private communication [see:]

Does this clade say anything about haplogroup K (M9), and add anything to either of the two probable scenarios provided earlier here about clade R1*-M173 origins [which recalling, was either African or "Southwest Asian"]?

Unfortunately, everything that is publicly known about this clade at the moment has been outlined above.

Notwithstanding this, what the mere announcement of clade IJK indicates, is the strong possibility of Hg K being part of the male gene pool involved in the earliest peopling events of Europe and "south western Asia" by anatomically modern humans, before either clade I or R came about and thereafter become noticeable and/or dominant in the region. This would have been anywhere between ca. 40,000 and 35,000 years ago, and would likely have been the case, regardless of where clade IJK originated.

Wherever clade IJK emerged, be it in the vicinity of southern Asia or the Great African Rift Valley areas, it appears that the expansion of the lineage occurred in the latter general region, on either side of the Red Sea. The downstream markers of this lineage, R1* in particular, show a general geographical structuring wherein clade R1b is heavily scattered on western Europe, while the clade R1a sibling is more widely dispersed as one moves eastward.

As a unique case, clade R1*-M173 is thus far more widely distributed on the African continent, with the remainder being found in isolated cases in the so-called "Near East" [Jordan Dead Sea area and Oman in particular]. Clade I is more widely dispersed in western Europe, while clade J in the so-called "Near East", followed by Northern Africa. The K clade seems to be relatively more concentrated on the Great Rift Valley geographical confines, with highest frequencies showing up in certain eastern African areas, particularly in the African Horn, followed by certain areas in the so-called "Near Eastern" half of the Great Rift Valley.

The overall picture here is one where it seems that clade IJK reached its expansion peak in the Great Rift Valley region, regardless of where the lineage ultimately emerged, with portions of it spilling over to nearby areas. It is highly likely in this region, the Great Rift Valley, that clades I, J, and K split.

It's plausible that clades I (M170, M258, P212, P38, P19, U179) and J (12f2.1, M304, S35, S34, S6) diverged in the northern areas of the Levant, with clade I, shortly after, spreading westward into western Europe, while clade J largely remaining largely localized then and expanding in situ. From several works, it appears that the J2 (M172) clade emerged first, and then later, J1 (M267) [See Ekins et al., An Updated Worldwide Characterization of the Cohen Modal Haplotype; and Nebel et al. 2001, The Y Chromosome Pool of Jews as Part of the Genetic Landscape of the Middle East]; the former likely emerged in the confines of the more northerly area of the Levant, while the latter, likely in a more southwardly region of the Levant [see Nebel et al. 2001].

According to Ekins et al., the bearing of the Cohen Modal Haplotype (CMH) STRs locus in the divergent clades of J2 and J1 implies that perhaps a derived haplotype cluster fundamental to CMH emerged some time before the divergence of either J2 and J1 from a shared ancestral lineage...

It is possible that the originally defined CMH represents a slight permutation of a more general Middle Eastern type that was established early on in the population prior to the divergence of haplogroup J. Under such conditions, parallel convergence in divergent clades to the same STR haplotype would be possible. - Ekins et al.

Could such a candidate clade have been a "IJ" (M429, S2, P129, P127, P126, P125, P124, P123) clade, or a derivative of "IJ" that has largely drifted out since? Worth pondering. Recently a possible east African origin, as one of the two possible scenarios, for haplogroup J1-M267 DYS458.2 allelic variant had been explored [See "Could Y-DNA J-M267 possibly have an African Origin? Taking a look at the DYS458.2 Locus"]. It is yet another indication of the richness of IJK subclades in the Great Rift Valley neighborhood.

Clade K on the other hand, could have diverged in the northeastern Africa vestiges [including Sinai, for example] or the nearby areas in the Levant, but it need not necessarily have diverged in the same area as clade I or J. However, some clade K carriers who were situated in the so-called "Near Eastern" areas may well have at some point early on, as noted above, i.e ~ 40 ky ago or so, dispersed into Europe, representing one of the earliest male Y-DNA lineages in that region, around the said time frame. These though, were likely modest in numbers, relative to clade K bearers in say, the so-called "Near East" or Eastern Africa on the African Rift.

Given the distribution patterns noted, it seems plausible that somewhere along expansion events of clade K bearers, the few that made their way to central Asia, somewhere around where the modern nation of Afghanistan [or neighboring regions to its north thereof] lies, the clade P (M45) emerged or else simply reached its peak expansion [albeit limited] in that area, in what could possibly be characterized in a founder effect scenario. This though as just noted, does not negate the emergence of clade P in the Great Rift Valley, whether it's on the northeastern African vestiges or the Levantine areas.

It appears that the clade P-bearing populations were likely dispersed in modest effective population sizes in many of the places they were situated. If clade P emerged in central Asia, as noted in one scenario above, then in its westward flow into the Great Rift Valley [actually a piece of Africa] must have spurred clade R1*-M173 somewhere in the latter region. On the other hand, clade P's emergence in the Rift Valley regions would simply mean that amongst those clade P-carriers who remained localized, clade R1*-M173 emerged, wherein it would quickly start spreading deeper into Africa and areas nearby Africa, likely amongst a nomadic-life style oriented group.

In either scenario, those clade P-carriers who made it to central Asia, would become the basis for the downstream clade Q (M242). The newly emergent clade Q carriers would disperse, with sections notably taking the Siberian corridor route. These latter group would become ancestors of some of early American settlers, likely the wave that followed the relatively early "tropical" elements that arrived in America in the late Upper Paleolithic.

Then comes the LGM [Last Glacial Maximum]. By then of course, it's highly likely that some clade R1*-M173 carriers from the Great Rift valley region made their way westward into western Europe by way of the Asian Minor corridor. Like their clade K fore-bearers, these initial migrant would have likely represented fairly modest effective population sizes in Upper Paleolithic Europe, but this would change with the receding of the LGM.

During the LGM, several populations in the northern latitudes, namely in Europe, sought refuge in certain refuge centers. It appear there was one in southwestern Europe [Iberian peninsula region in particular] and the others in the Asian Minor region [see: Cinnioglu et al. for example] and eastern Europe [vicinity of Russia].

The subclade R1b itself seems to have emerged before the LGM, but was initially modestly distributed in Europe. Some of these clade R1b bearers seem to have found their way to these refuge centers, from where many would disperse across Europe upon the recession of the LGM, with the clade reaching its expansion peak in western Europe. Others of course, dispersed to regions nearby the refuge centers. [See: "R1*-M173 bearing chromosomes in Cameroon" for further reading]

The clade R1a (M17) seems to have largely come to the scene as another possible after-effect of the LGM dispersal events, involving mutation amongst remnant R1*-M173 bearers who did not bear the R1b signature markers, including namely M343. From the distribution pattern of this R1 subclade, it appears that the center of [even if not actual point of origin, which is not ruled out either] that dispersal was somewhere likely where the modern state of Iran now lies [perhaps via the northwestern region of Iran, if for example, either the "Ukranian LGM refugium" or the "Asian Minor LGM refugium" model is considered, but also, and more importantly, predicated on the idea that ancestral R1*-M173 arrived from westward, the Great Rift Valley region in particular via its associated so-called "Fertile Crescent" and/or Levantine areas. The alternative would be, as others have suggested, surrounding regions — vis-a-vis Iran — like northern areas of Pakistan, India or thereof].

From there, clade R1a bearers would flow further east, but also moving further southward, into southern Asia, if R1a is presumed to have a western Asian provenance. On the other hand, again, it would flow from the Iranian region into Europe via the Asian minor and its eastern surrounding areas thereof. Perhaps some visual aids are in order, to provide clarity; let's take a look at distribution maps located in easily accessible so-called "encyclopedic" websites and elsewhere on the net...

The Red highlights in the circles reflect R1b, while the purple highlights reflect R1a. The substantive basis of this distribution map (click for hi res) isn't clear, but it seems to be corroborated to some extent by the one below (click for hi res) ...

Note that the top distribution map shows exclusive presence of R1a clade in southern Asia, which would tend to lend some support to the introduction of R1a clade bearers into Iran from nearby regions in say, Pakistan or India, from R1*-M173 clade carriers who arrived from the so-called "Near East". Under such a scenario, it's plausible that the marker spread northward via central Asia and then onto eastern Europe, from where it would spread further west, or could have involved a bi-directional-pronged movement, one via 'southwestern" corridor, and one via the central Asian one.

The question then becomes, what could have sparked such major demographic processes. It is less likely to have involved a LGM in southern Asia (for which we have information on the "Near Eastern" and "European" counterparts), unless information is brought to the fore about such a situation. Then again, as noted, it could be said that shortly after arrival from or emergence in "southwestern Asia" [likely via the Iranian region], R1a clade bearers quickly situated in southern Asia, where they would expand. This would mean that the ancestral R1a* clade bearers started out nomadic [perhaps indicated by mtDNA distribution pattern; according to Richards et al. 2000, Europeans shared few clades with populations rich in R1a clade within south Asia — like India, and eastward, like Siberia. See below, Ref *], with a portion, if not much of it, of the ancestral R1a* clade bearers quickly situating themselves in southern Asia.

This would have entailed what is dubbed as a "founder effect" scenario, which would explain virtual absence of R1b markers, which if were present in the midst of the R1a* clade bearing group, must have largely drifted out. From the said map, R1b clade frequency is relatively low even in the Iranian region, and it visibly starts to fade away as one moves eastward. With the so-called "Near East" closer to Europe, it is not surprising to see some dispersal of R1b markers therein, which could have involved independent demographic expansions [in association with a "Near Eastern" LGM refugia — as that implicated in Anatolia for example; again see: "R1*-M173 bearing chromosomes in Cameroon" for further reading] from that of R1a* clade carriers.

Another caveat: If R1a* emergence occurred somewhere along the dispersal path, somewhere in the neighborhood of Iran or surrounding territories, i.e. from a migratory origin point in the more westward "Near Eastern" refugia locations, which as noted, could have involved parts of the Asian Minor, then it is conceivable that a few R1a* clade bearers moved northwestward via the "Asian Minor" corridor and some possibly through the Caucasus, while others dispersed south and a little eastward, from where they'll further disperse northward into central Asia and beyond thereof.

Ref * [for clarity for the above, as noted]: From Richards et al. 2000, Tracing European Founder Lineages in the Near Eastern mtDNA Pool...

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...

There are even fewer eastern-Eurasian lineages represented, amounting to ∼2% in total: 3 individuals with haplogroup A, 4 with B, 7 with C (or pre-C), 2 with F, 1 from N*, 1 with Y, and 10 additional potential members of the eastern-Eurasian haplogroup M, some of which may be D (Torroni et al. 1993b). As in the case of Africa, these are probably attributable to fairly recent gene flow. Most of them would imply incursions from central/eastern Asia, and their occurrence in Turkey, Greece, Bulgaria, and the Caucasus, as well as in both the Saami and northeastern Europe, implies that they may be the result of historically attested migrations into these areas.

As always, this narrative is subject to ongoing modification as updates in research modify the status quo, and as additional material come to attention.


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":

Exchange #1

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. The said authors conclude that the previous R1*-M173 are likely to be R1b1* chromosomes, since that is what they found in their sample. It's 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 similar patterns of R1*-M173 frequency in Hassan et al.'s Sudanese Fulani sample and those of a number other research teams in the past, 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 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. It may well imply that R1b had more time to expand and overshadow ancestral R1* or R*, which would have largely experienced negative drift.]

-- Exchange ends --

Exchange #2

A poster by the pseudonym of something along the lines of "DMX", writes:

The possible migration routes that article raised seem to suspiciously focus on Africa's prominence.

My response:

While an African origin for R1* therein has not been ruled out, as R1* markers have been found in Africa itself, it does leave R1* origin also open to a possible "Middle Eastern" origin; therefore your suspicion is unfounded, unless of course, you can specifically point out the specifics in question.

"DMX" writes:

Perhaps you can cite something other than (what I'm going to assume is) your blog for these over-complicated population movements?

My response:

The scenarios put forward were not done so in a vacuum, which is why illustrations from studies had been posted. I based the summary off what I've read about the distribution patterns of the lineages in question. If there's anything you find questionable therein, please point it out, and I'll be more than willing to discuss it with you, provided that censorship here allows it.

"DMX" writes:

The views expressed on that blog are just that; views, and not a scientifically credible (or even logical) explanation for Haplogroup dispersal.

My response:

Like which specific points. Please point it out.

"DMX" writes:

Further, they do not explain why almost every variant of the R Haplogroup can be found in Eurasia (let alone Central Asia) and not Africa.

My response:

It does account for such; you must have missed the sections of the post where links to related topics were provided, to expound on the theme at hand, as was done for example, with this link: R1*-M173 bearing chromosomes in Cameroon

In fact, if you like, I can invite you to another board where we can freely debate this issue mano a mano, as it is very impossible here, with all the defensive censorship going on in here.

---Exchange ends---


Too Tall Jones said...

Excellent roundup. did the faux "DMX" ever actually yield any SPECIFIC criticisms or point to specific points to debate or at least clarify or did he simply scurry back to the defensive confines of the HBD "amen corner"?

Anyway some questions on "J" if you feel inclined..

1) Wikipedia contains typically contradictory information- it states that Haplogroup J arose in East Africa according to Semino 2004 yet presents a map with a caption claiming a "Near Eastern" origin. What's the real story?

2)Where does "J" occur most in Africa? and what are its frequencies- say a top 5?

3) Where are the oldest occurrences of J in Africa?

4) Could the presence of J in Africa derive from its original presence in Africa, without the need for any "backflow" theories to explain why?

Mystery Solver said...

Too Tall Jones writes:

Excellent roundup. did the faux "DMX" ever actually yield any SPECIFIC criticisms or point to specific points to debate or at least clarify or did he simply scurry back to the defensive confines of the HBD "amen corner"?

Anyway some questions on "J" if you feel inclined..

1) Wikipedia contains typically contradictory information- it states that Haplogroup J arose in East Africa according to Semino 2004 yet presents a map with a caption claiming a "Near Eastern" origin. What's the real story?

2)Where does "J" occur most in Africa? and what are its frequencies- say a top 5?

3) Where are the oldest occurrences of J in Africa?

4) Could the presence of J in Africa derive from its original presence in Africa, without the need for any "backflow" theories to explain why?

I never looked back on the matter with the "DMX" character, because shortly after I was sensored for good -- i.e. banned for not towing the accepted lines of the forum regulars, like Lancaster for instance, who looks to be the [rather childish] moderator as well, but going by a pseudonym. At any rate, getting to your points: There are some mouthpieces out there who attempt to play word games as form of scamming their way through undetected; in this case, northeastern Africa is simply claimed to be part of the "Near East", and henceforth, tacitly implied in that term, leaving an unsuspecting rookie to think that "Near Eastern" is used in the "southwest Asian" context. National Geographic provides a good example of this scam, with their claim of "Near Eastern" origin of hg E, while paradoxically acknowledging its "northeast" African origin.

Hg J is mostly concentrated on the coastal north African territories and eastern Africa, though there are spots in other areas -- think for example, the Buba clan of the Lemba. As I have noted in other posts, the eastern African examples of hg J1 for instance, are reportedly phylogenetically older than the prevalent examples of the so-called "Near East". See my notes on E-M34 and on the Cro-Magnon, not to leave out the topic on the origins of hg J1-M267. The links to these topics should be in that "one-stop referential" list I provided recently. Therein too, I raise the points about the origins of eastern African examples, including those pertinent to the questions you've raised.

Anonymous said...

You might want to update this information because how can R1b be more ancestral than r1a. common sense that a comes before b and scientist recently have proven Indian region to be original carriers of R1a which spread to central Asia then throughout Europe

Mystery Solver said...

'Anonymous' poster writes:

You might want to update this information because how can R1b be more ancestral than r1a. common sense that a comes before b and scientist recently have proven Indian region to be original carriers of R1a which spread to central Asia then throughout Europe

Anonymous poster, you might want to *carefully* re-read the passage; and links are provided therein for a reason, not to be ignored, only to then ask questions that are already answered by all that's been provided. Don't mix up haplotype designations or "a" and "b" designators to mean that "a" is older than "b"; this is not the alphabet -- these are haplotypes. As for hg R, I've discussed that numerous times on this blog, and discuss the possibilities for its place of origin. With regards to age, R1b is generally understood in genetic circles to be the older branch between R1b and R1a. See the following link, for examples: