Showing posts with label Frequency. Show all posts
Showing posts with label Frequency. Show all posts

Saturday, January 23, 2010

New Y-DNA Indactor of "First Neolithic Farmers" coming into Europe?

Reviewing: A Predominantly Neolithic Origin for European Paternal Lineages, by Balaresque et al., 2010.   

The present study does not really challenge, nor does it appear to be the intended goal at any rate, the oft implicated recent African ancestry component in "first Neolithic farmers" of the "Near East" and "Europe", generally represented by Hg E1b1b markers, in tandem with in situ "Near Eastern" genealogical component generally represented by Hg J markers. Rather, the case made here is one of presumably a new revelation, which is that yet another marker appears to have been in the move, presumably alongside Hgs E and J, amongst the "first Neolithic farmers" diffusing into Europe from the "Near East". The idea here, is to explain why there seems to be disconcordance between the extent of the spread of uniparental nuclear (Y-DNA) markers and the relative far reaching and magnitude of the spread of the Neolithic farming subsistence economy across Europe. Here is how the authors at hand framed this observation: low contribution of incoming Y chromosomes to the European Neolithic, despite its antiquity and impact, has appeared anomalous. So, what do the authors' findings reveal to us? Our interpretation of the history of hgR1b1b2 now makes Europe a prime example of how expansion of a Y-chromosomal lineage tends to accompany technological and cultural change. The idea here therefore, is that the seemingly low contribution of "incoming Neolithic farmers" into Europe stems out of not taking into account, until now, the hg R1b1b2 component of these incoming "first farmers". This leaves the impression that the "first Neolithic farmers" coming into Europe had left a fairly modest patrilineal trail, in contrast to the magnitude of their cultural influence. Hg R1b1b2 findings here are supposed to now show that these "first farmers" had in fact left a much stronger Y-DNA mark than that previously imagined. As a matter of observation, the authors are essentially making a mole hill out of hg R1b1b2 distribution, which they base on microsatellite variation and their age estimations. When one looks at their microsatellite network, it is hard not to notice the relative heightened diversity of Iberian clades against that of the Turkish examples. This observation could be off, but let the viewer verify it for themselves below...


Click on the image for greater resolution

Even their geographical plots, while it does show the most intensified concentration in Turkish territory [for microsatellite variance but not frequency; heightened frequency is most concentrated in the Iberian peninsula and parts of far western areas north Europe], one notices a sharp dip in concentration as one proceeds westward south—i.e. past Italy, and then picks up concentration in the Iberian peninsula. A similar trend is observed going south to north, again west of Italy. The concentration drops from that seen in Iberia and then starts to pick up somewhat in the northern-French and Dutch region.


Click on the Image for greater resolution. Image footnote: Geographical distribution of microsatellite STRs variance within hg R1b1b2.


Click on the image for greater resolution. Image footnote: Geographical distribution of frequency of hg R1b1b2.

Guess what, their observations are not that far out from that seen by Cinnioglu et al. 2004. [around the clade R1b3, which now essentially the R1b1b2] Earlier, as pointed out here before,...
"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)."
- Cinnioglu et al. 2004
It's worth noting that while Cinnioglu et al. (2004) took into consideration the data for nearby "southwest Asian" region (Georgia/Iraq) outside of Turkey, the present study limits its focus on mainly Europe, with Turkey being the geographical extent or the sole representative of the "Near East". While Cinnioglu et al. (2004) also took into consideration the hg R1b1b2-linked TaqI RFLP haplotype distributions respective to haplotypes 15 and 35, there is no indication in the present study that these haplotypes' distribution patterns were taken into consideration. As for the TMRCA ages cited in the present study,  the estimates all generally fall within the 5,460 and 7,900 year bracket, and interestingly, the Turkish samples ages here are based on published data undertaken by Cinnioglu et al. (2004), which the present study cites as its reference-source for those Turkish samples. Turkish sample age estimations are not the only ones to go over 7,000 years, which should all be taken into consideration along with the cited confidence intervals. The likely wisdom here, in relation to the case being put forward in the present study, is that these "spurts" [of the higher-end age estimations] deep into the western corner of Europe may just be serving as relics of the earliest segments of new "first farmer" settlers in the European population in question. This would suggest that the earliest farmers shortly upon arrival, penetrated deep into Europe, straight to the northwestern corner of the subcontinent through central Europe, and then, possibly made their way down southward in western areas of Europe, thereby reaching the Iberian peninsula (?) or else, a two-pronged situation upon reaching central Europe, wherein some migratory group(s) headed straight to the western corner and the others, southwestern corner [which would have to be the scenario, given the erratic distribution of age estimations given to designated regions, with those in Iberia generally being older than those further north in the western areas, save for the aforementioned spurts in the northwestern corner around northern France area]? However, the conventional estimation is one of a expansion southwestward, following regions along the northern boundaries of the Mediterranean sea, from where in the southeast areas, diffusions into central and then north thereof would have been facilitated, with age estimations of Neolithic sites in Europe reported along the order of earliest to latest, and not in such a short time or fast-paced time span upon arrival from the "Near East" [as suggested by the aforementioned scenarios; there are considerable temporal differences between the earlier sites in southern Europe, esp. southeastern areas and relatively later ones in northwestern and other areas of northern Europe], so that one goes from first southeast Europe, then central Europe, and then northwestern Europe; this is also what's indicated by the traditional "first Neolithic farmer" paternal markers of hgs E and J:


Click on the image for greater resolution. Semino et al. (2004) Hg E distribution.


Click on the image for greater resolution. Semino et al. (2004) Hg J distribution.

Of course, it is not inconceivable that Hg R1b1b2 markers arrived along with Hgs J and E carriers during demic difusion, but it is just as likely, as the above observations suggest, that these supplemented preexisting Hg R1b1b2 carriers who spread earlier from certain refugia at end [as noted above via Cinnioglu et al. (2004)] of the LGM or early Holocene, independent from the expansion ensuing from the Neolithic farming subsistence complexes in the "Near East", and subsequently expanded in their new found refuges. That would explain the distinctive geographical patterns seen Hg R1b1b2-linked TaqI RFLPs.

Monday, April 27, 2009

DE* as "Last Refuge" of Sects so psychologically troubled by African Ancestry?

The purported finding of DE* paraphyletic haplotypes in only 2 Tibetan sample candidates appears to have caused hysterical excitement in certain quarters, specifically amongst sects of individuals who are psychologically and emotionally tormented by the prospect of African ancestry in their "homelands". But this excitement is emotionally driven, and just that. As such, intellectual engagement gives way to religious cultism as the medium of self-expression. But let's just examine how much or what really lies herein that is worth being hysterically excited over:
  • DE* is a descendant clade of M168. M168 is undoubtedly African; this fact alone makes it more than probable that this place [Africa] is also likely where DE* emerged.
  • DE* is more common in Africa than outside of it -
It has been identified in African samples in more than one accasion in separately-conducted studies, having been identified in 5 Nigerian sampling candidates in one study, *1 in an Egyptian sample [see "Miscellaneous notes" below] and 1 Guinean individual in another . On the other hand, it had purportedly been identified in only 2 Tibetan sampling candidates. So we have 6 to 7 African cases vs. 2 Asian cases.
  • DE*'s internal phylogeny is more diverse and widely distributed in Africa -
Considering the greater internal phylogenetic branching of haplogroup E vs haplogroup D, it can be suggestive of either 1) longer time-depth for haplogroup E explosion/expansion, and hence, implicating DE* being around longer in Africa, as the homeland of haplogroup E ...

Or

2) that the haplogroup E lineage experienced an explosion that the D counterparts did not achieve in more or less the same time depth. The question becomes: What could account for this?

Either way, with fact being that African Hg E internal phylogeny is more elaborate than Hg D, the end result suggests that the intensity of such intra-E phylogenetic explosion seems to have had some level of erasing effect on DE* distribution. Given the greater pressure, due to greater demic explosion brought to bear on preexisting DE* in Africa — mainly by its own sub-phylogeny — than that which would have been the case in Asia by the YAP+ counterpart sub-phylogeny there, it's amazing that DE* is relentlessly visible enough in the African gene pool, as demonstrated by its greater chance detectability here than elsewhere, including Asia. This suggests that DE* would have been more widely distributed in Africa than in Asia, having been able to withstand greater pressure from greater subsequent demic expansion of Hg E phylogeny than that involving Hg D phylogeny, respectively in Africa and Asia.

The distribution and internal branching of Hg D suggests, on the other hand, that it involved lower scale dispersal of Hg D*, which were relatively more controlled in their subsequent expansion. The distribution pattern for instance, shows that the major subclades of D in different territories are highly differentiated and generally sharply geographically-structured, being confined to territorial spheres. At least that is the image reflected, if one goes by what's professed in the ISOGG.org website, whatever may be said of the credibility:

Sub-group D1 (D-M15) is seen in Tibet, Mongolia, Central Asia, and Southeast Asia, and the sub-groups D* (D-M174) and D3 (D-P47) are seen in Central Asia. The sub-group D2 (D-M55) is seen almost exclusively in Japan.

Hg D* is presumably also identified in the Andaman Islands.
  • A hypothetical Hg DE* back-to-Africa migration seems to have been elusive in leaving genetic tracks behind, presumably from south Asia to Africa -
The supposed back-migrants would seem to have left no genetic tracks behind in a hypothetical destination from southern Asia via the Arabian peninsula, eastern Africa through to African interior, in a hypothetical back-to-Africa migration scenario. If they did, then it had been thoroughly erased by multiple demographic shifts. Hg D's distribution in south Asia, with rare to no presence in territories between that region and Africa, is however explained by founder effect of OOA migrants, already carrying Hg DE* amongst them.

Chandrasekar's speculation is highly questionable for the same reasons just stated above; see:

Some of the YAP insertion chromosomes without the M174 mutation reached the Mediterranean via Central Asia and gave rise to the E lineage with mutations at M40 and M96 (~31 000 years ago; Hammer et al. 1998). This E lineage back-migrated to Africa through the Levant as hypothesized by Hammer et al. (1997) and Altheide and Hammer (1997).

Hg D is rare to absent in the Levant, and conversely, Hg E is virtually rare to absent in populations that do carry Hg D.

Furthermore, Hg E's presence in the so-called Near East, including the Levant and Europe, serves as gene flow from Africa, because Africa is where the entire Hg E phylogeny occurs, not the Levant. All upstream Hg E markers are exclusively found in Africa, and essentially none in the Levant.

The so-called Near East has far much lower frequencies of Hg E than in mainland Africa, and all of these happen to be subclades of African counterparts. Much of these subclades are relegated to the P2 (PN2) phylogeny. Upstream PN2 clades as generally known, only occur in Africa.

Revisiting Chandrasekar's post again,...

Some of the YAP insertion chromosomes without the M174 mutation reached the Mediterranean via Central Asia and gave rise to the E lineage with mutations at M40 and M96 (~31 000 years ago; Hammer et al. 1998).

It is also of note that Chandrasekar conveniently ignores that DE* has been found in Africa as well, but in even greater frequencies than his personal favored region [as noted in the second point above], i.e. Asia, not to mention that it is essentially non-existent in the so-called Mediterranean or the Levant. With DE* being in Africa, it is not necessary for Hg E to have come from the Levant, for reasons just mentioned and the ones immediately above this last Chandrasekar citation. Instead, Chandrasekar relies heavily on outdated studies, when Hg E phylogeny, as with many others, were in their early stages of being resolved.

His statement above, about "some of the YAP insertion chromosomes without the M174 mutation" has also implications that Chandrasekar seems to have overlooked:
  • Common sense intimates that any hypothetical DE* back-to-Africa migration — and it would have to have been major enough — would have been pooled from a newly situated migrant group. The keywords here: "newly situated".
Recalling Weale et al....

the presence of the DE* haplogroup has the effect of forcing an earlier date for the most recent common ancestor of all African YAP chromosomes. This reduces the possible time window within which a back-migration to Africa could have occurred under the scenario of an Asian origin for YAP. - Weale et al. 2003, Rare Deep-Rooting Y Chromosome Lineages in Humans.

Indeed! The presence of DE* in Africa suggests that this lineage was in place very shortly after its emergence. The OOA migrants had just recently left Africa for a reason; what on earth would these folks, who had just arrived, go back to Africa for, and at such a gruesomely long distance from a south Asian refuge? Pending tangible evidence of a compelling motive, it makes little sense.

And even if one were to take a hypothetical Asian origin of DE* for granted, based on skin pigmentation allele examinations, the original carriers of these markers would have closely resembled contemporary "black Africans", and even then, Hg E would still not be Asian [considering points above].

Let's face it; it's really not all that complicated: It just so happens that Hg D exists in Asia, while Hg E plays a dominating role in Africa, well, because DE* markers were present in both. Simple enough, isn't it?!

Neither territory has the other respective sub-clade lineage, because these emerged after OOA migrations, understandably.

Not sure why finding DE* therefore, surprises anyone. It's the only way D could have arrived in south Asia sans E; thus, DE* chromosomes brought in from Africa would have to have been around, in order for D to emerge, there is no other way around it. It is also the reason one finds DE* in both Africa, the origin point of destination, and Asia, the destination. However, instead of looking at it that way, some complicate things for themselves, and say that in order for DE* to be in Asia, it surely must have emerged there, and that there is no other way around that.

The most parsimonious explanation generally tends to reduce the number of questions for each answer that it provides than the alternative. In this case, an African origin entailing DE* dispersal in a OOA migration event, paving way for a founder effect situation in southern Asia is the most parsimonious. All things considered [from above], there really is little for the aforementioned sects to be cheerful about, at least from the intellectual side of things, as opposed to the religiously-motivated or plainly wishful end!
_________________________________________________________

Miscellaneous notes:

A lost gem?

The following recently grabbed the attention of the present author of this blog; the abstract goes like this:

The geographic location of Egypt, at the interface between North Africa, the Middle East, and southern Europe, prompted us to investigate the genetic diversity of this population and its relationship with neighboring populations. To assess the extent to which the modern Egyptian population reflects this intermediate geographic position, ten Unique Event Polymorphisms (UEPs), mapping to the nonrecombining portion of the Y chromosome, have been typed in 164 Y chromosomes from three North African populations. The analysis of these binary markers, which define 11 Y-chromosome lineages, were used to determine the haplogroup frequencies in Egyptians, Moroccan Arabs, and Moroccan Berbers and thereby define the Y-chromosome background in these regions. Pairwise comparisons with a set of 15 different populations from neighboring European, North African, and Middle Eastern populations and geographic analysis showed the absence of any significant genetic barrier in the eastern part of the Mediterranean area, suggesting that genetic variation and gene flow in this area follow the "isolation-by-distance" model. These results are in sharp contrast with the observation of a strong north-south genetic barrier in the western Mediterranean basin, defined by the Gibraltar Strait. Thus, the Y-chromosome gene pool in the modern Egyptian population reflects a mixture of European, Middle Eastern, and African characteristics, highlighting the importance of ancient and recent migration waves, followed by gene flow, in the region.

Source: Y-chromosome analysis in Egypt suggests a genetic regional continuity in northeastern Africa

by Manni et al. - 2002

For the complete journal, click here

The piece has raised some questions as to whether the YAP+ chromosomes in "some East Asian populations, such as the Japanese and Tibetans" is the same one identified in the Egyptian sample, i.e. essentially "Hg D", since this is largely the only YAP+ type found in said groups. The answer: Not necessarily, since the authors tested for YAP+, which is shared between Hgs D and E. The Egyptian YAP+ was very likely a paraphyletic chromosome that did not test positive for Hg E*, you know, just like how Hg DE* is devoid of the downstream characteristic markers of Hg E*. The 12f2 marker tested here more than likely refers to Hg J, which in this journal is designated as Hg 9. The nomenclature used here is apparently outdated [after all, this is a 2002 study we're dealing with here], but the finding of an upstream YAP+ chromosome that didn't belong to Hg E (as denoted here by SRY8299) is interesting nonetheless, because it adds to that theme of the unparalleled richness of Hg DE and derivatives on the African continent, as well as the distribution of the upstream DE* clade being *predominantly* an African 'thing'. So, in light of this, Egypt can now be added to the list of African territories wherein rare Hg DE* chromosome appears, a list which has no peers anywhere else where Hg DE* is concerned!

"haplogroup CF and DE molecular ancestors first evolved inside Africa and subsequently contributed as Y chromosome founders to pioneering migrations that successfully colonized Asia. While not proof, the DE and CF bifurcation (Figure 8d ) is consistent with independent colonization impulses possibly occurring in a short time interval."

Source: Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations

by Peter A. Underhill , Toomas Kivisild - 2007

A nutshell!...of what has essentially been more elaborately demonstrated about said markers on this site. The present author of this blog has not yet come across a single genetic journal that says differently about haplotype CF origin.

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 isogg.org 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. - isogg.org

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 isogg.org

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: isogg.org]

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---

Sunday, March 23, 2008

"Ethno-specific" markers?

Is it possible to trace a marker to a single specific designated ethnic group, by DNA motifs alone?

Well, it is plausible that certain markers can be relatively more frequent in some highly culturally-"conservative" and relatively socially-isolated ethnic group—that just so happens to have marital customs which generally discourage exogamy with other ethnic groups—but rarer in other groups outside the said socially-isolated ethnic group. In such a scenario, it would mean that the said rare marker had in all likelihood emanated from a mutational event within a lineage that was inherited from TMRCA, but only occurred in the said population after it diverged from the source population to which the said TMRCA belonged. The resulting cluster in such a scenario could be inflated in its distribution in the said socially-isolated ethnic group as an after-effect of random but neutral genetic drift. However, is it possible even in such a scenario, for such an ethnic group to have always been completely isolated from nearby populations, or potential "invading" populations from far-off lands, throughout the lifetime of such a "unique" or one-time mutational event?

Even if one were to accept that possibility, then it would in reality be an issue of frequency and distribution pattern of the marker or cluster in question, rather than an issue of some kind of "ethnic" mark or tattoo of some sort on the cluster. That issue would be one that is centered on the observation of high frequency in one group and rarer distribution elsewhere.

From personal encounter, the present author is reminded of an exchange in a discussion from the past, wherein someone spoke of "maternal Tuareg ancestry" in African Americans. The obvious question here, is what constituted maternal ancestry from Tuareg or Tamasheq kels/groups, for it should be obvious to anyone who is remotely familiar with the Tamasheq, that they aren't exactly an isolated group of people, and have been interacting and living with other west African groups for a great deal of their history. Here is how that exchange went:

Originally posted by MyRedCow:

Al Takruri and Supercar,

This is the Kayser study:
http://www.genome.org/cgi/content/full/13/4/624

There is another .pdf file with the latest data with more Haplogroups. But, I've never once seen an African American man with the Berber E3b Y chromosome on any chart. The main Y chromosomes are always E3a and R1b. I said that the African Americans have maternal Tuareg ancestry. The slavetraders did not alway take the men and women from the same place. There maybe and African American maan out of about 17 - 20 million men who has the Berber E3b Y chromosome. But, I haven't seen one yet.

My response was thus:

That may well be the case, but the point is that Tuareg females in all likelihood share markers that you deem "Tuareg" with their west African neighbours. At least that is what I understand from the study cited in your post in the thread centered on the Fulani. Maybe there is a "Tuareg" specific maternal marker, in which case, it won't hurt to know what that is. — Mystery Solver

...and of course, the poster "MyRedCow" never followed through with that request, because in all likelihood, the present author reckons, he could not dig out the answer from anywhere, what would characterize a "Tuareg"-only maternal marker, and so, only traceable to Tuaregs/Tamasheq of the west African Sahel. As noted, the Tuaregs in all likelihood share markers with their neighbors north, south, west and east to their territorial expanse.

By the way, the study that the present author was talking about in the citation above, is this:

From
http://www.biomedcentral.com/1741-7007/4/34

Among the AFDIL sequences with more than five matches to various African ethnic groups, most language diversity was within the various subfamilies of the Niger-Congo family. These subfamiliesinclude Atlantic Congo (e.g., the ethnic groups Fula, Yoruba, Wolof, Balanta) and Mande (e.g., the ethnic groups Mandingo, Mende, Bambara). However, in some of the sequence matches, different linguistic families were represented altogether, including the Afro-Asiatic (e.g., the Tuareg ethnic group) and Nilo-Saharan (e.g., the Dinka ethnic group) families, along with members of the Niger-Congo family.

What one can take from the above...is that the samples from the said groups fall into said sequence patterns [yet to be identified] found in the intra-West African region, from which I infer that this could be due to geographical proximity and corresponding inter-ethnic miscegenation. It says nothing of ethno-specific maternal markers. However, if I missed it somewhere, I would welcome the prospect of it being brought to my attention. — Mystery Solver

As an illustrative example, let us consider Salas et al.'s examination of L1a mtDNA:

Haplogroup L1a (fig. 4a) is common (∼20%–25%) in East, Central, and southeastern Africa, and is almost absent in North, West, and southern Africa. The main subclade, L1a1, is ∼33,350 (SE 16,600) years old and is quite starlike, with a predominantly East/southeastern African distribution and a root type that is common in East Africa.

...L1a seems likely to have been brought to southeastern Africa by the eastern stream of the Bantu expansion, having been picked up in East Africa...

...The analysis of Soodyall et al....They showed an association between an intergenic COII/tRNALys 9-bp deletion and a subset of L1a types lacking the transitions from the CRS at both 16129 and 16168—that is, within L1a2. This deletion is common in southeastern African Bantu speakers, as well as some East and Central African groups. It was absent not only in all Khoisan groups but also in virtually all southwestern African Bantu speakers (with the exception of three Ambo individuals from Namibia, for whom a southeastern Bantu origin was proposed; see also Soodyall and Jenkins Soodyall and Jenkins, 1993). They propose a Central rather than an East African origin for the deletion; we concur that, although L1a seems most likely to have originated in East Africa, L1a2 may have emerged in Central Africa.

...A predominantly East African origin for L1a types also explains its relative scarcity in America, in comparison with other African types. Most American representatives of L1a, in fact, match types from southeastern Africa, and probably derive directly from that region. — by Salas et al. 2002

As observed from the above, Salas et al. trace the likely American representatives of L1a markers back to a particular region in Africa; in this case, southeastern Africa. To demonstrate this, it came down to frequency and distribution pattern of the sub-types examined. First it was stated that haplogroup L1a is rare in North, West and Southern Africa. Then, it is demonstrated that certain mutational events common in the east, central, and southeast African L1a2-bearing groups were rarer in southwestern African Bantu speaking groups. Finally, as already mentioned, the American representatives of L1a2 are said to match those of southeast African subtypes. The point that should be taken away, is one from the general understanding that a major portion of African American ancestry comes from western Africa, where haplogroup L1a is said to be rare; it is thus no wonder, according to the authors, that L1a representation in America is relatively scarce as well...BUT, the little representation that does appear therein, happen to match the southeast African subtypes, i.e. examples more frequent in southeastern Africa than elsewhere. Notice as well, that no attempt was made to implicate a singular ethnic group, but rather, a somewhat general but specific intra-African region. As the piece above suggests, the subtypes in southeastern Africa transcend a singular ethnic group; so, short of finding and sharing the micro-locus/loci details of "unique" subtypes in an even smaller geographical unit within southeastern Africa, tracing the American L1a examples back to southeastern Africa is as specific as the authors can get!