Tuesday, December 30, 2008

Could Y-DNA J1-M267 possibly have an African Origin? Taking a look at the DYS458 .2 Locus

This was the subject of an interesting board discussion that the present author thought would be nice to add to the collection of postings here.

Molecular characterisation and population genetics of the DYS458 .2 allelic variant

G. Ferri, C. Robino, M. Alu, D. Luiselli , S. Tofanellid, L. Caciaglid, V. Onofri, S. Pelotti, C. Di Gaetano, F. Crobu, G. Beduschi, C. Capelli

Abstract

We recently found a number of intermediate DYS458 alleles, indicated as .2. This allelic variant is distributed in several populations, but currently no information is available regarding the molecular structure and the genealogical correlation of chromosomes with this variant. The molecular characterisation of such allele, its worldwide distribution and the correlated evolutionary history are the subject of the present paper. Molecular and genealogical data are suggestive of a single origin for the .2 variant. Phylogeographic analysis points to either a Middle East or East African origin, but additional data is necessary to clarify this point. Our results suggest that the .2 variants is a stable polymorphism and that it could be used for population studies.

Copyright 2008 Elsevier Ireland Ltd. All rights reserved.

From the full text:

"The molecular organisation of allelic variant was investigated by sequencing a number of different DYS458 .2 alleles from individuals having different geographic origin (Table 1). These variant alleles show an incomplete repeat caused either by a AA insertion or GA deletion in front the third repeat form the last. Initial SNPs analysis identified these chromosomes as derived at the M267 markers, placing them on the J1* cluster. J1 sub-lineages were additionally tested (J1a–e) and in all cases the .2 chromosomes resulted ancestral at these additional markers. The DYS458 .2 Y chromosomes were then consequently identified as part of the J1 branch (Fig. 1). The shared molecular structure and the inclusion in the same Y chromosome genealogy branch were considered as supportive to a common origin for the .2 allelic variants."

"Network analysis was conducted as described in Section 2. Fig. 1 shows that two main clusters can be identified: one composed by individuals from the Caucasus (having DYS458*20.2 as modal allele) and a more heterogeneous one containing a well defined North-African clade (DYS458*18.2 modal allele) and other minor clades with European or Ethiopian origin. Only the North-African clade shows a star-like structure, signature of an associated demic expansion. Notably, within each meta population no haplotype structure can be identified except for the Caucasus, due to the rigid apportionment of these populations in groups with different patrilineal descent (data not shown). Some controversies exist about J1 coalescent times [8,9]. However, there is general agreement in recognizing a recent phase of expansion to North Africa that well fit our data: the star-like pattern in the network with Galilee and Palestinian Modal Haplotypes [15] as central nodes."

"The .2 variant shows its frequency peaks in Africa (North and East) and Caucasus. Data from the middle East is scanty and we are currently investigating various populations from this region to gather more information on the distribution in this area (data not shown). The presence in Europe is limited and the occurrences in both US and Asia (India and Malaysia) can be considered as the result of a recent introgression of African and/ or European haplotypes. Given the current set of data it is difficult to establish the ultimate place of origin of such mutation. However, the limited genetic diversity shown by either the Caucasus and North Africa suggest a combination of drift and founder effect (followed by rapid population expansion) in these areas."


So in summation, they are essentially basing their intro-reckoning at this time...

1)on frequency peak of the paragroup of DYS458 .2 alleles in East Africa, as do North Africa and the Caucasus, but [see point #2 below about North Africa and the Caucasus]...

2)on ruling out a European origin on the one hand, due to the general relative rarity therein of both the microsatellite DYS458 .2 allelic variants and the haplogroup [J1-M267] that they belong to, and on the other hand, ruling North Africa and the Caucasus out due to their relatively more rigid microsatellite-haplotype allocations into clusters within their respective paraphyletic units than the case is for the other population samples. In the North African network, the main recurring sequence is the DYS458*18.2 allele, while that of the Caucasus is reported to be DYS458*20.2. This phenomenon occurs in tandem with the relatively 'lower diversity' of both North African and the Caucasus paraphyletic units than those observed for the other samples.

3)on observations 1 & 2 leaving the so-called Middle East out as the alternative origin to East Africa, even though data available to these authors was limited, a priori extrapolation on the authors' part, likely due to the region's ("Middle East") "reputation" as a host to frequency peaks for this haplogroup.

In the course of the discussion, it was noted:

What we do know, which has already been confirmed numerous times, is that J1-M267 in North Africa represents a more recent introgression from so called Arabs, but maybe a small one because founder effect and drift could have elevated its frequency, which would also explain why its far less diverse in North Africa. - Charlie Bass

To this, it was emphasized [by present author of the blog]: Which is why the authors have ruled out origin in both the North African and the Caucasus populations, even though the lineages in question are part of a paraphyletic ensemble [but respective to both]. The difference here between North Africa and the Caucasus, is that the North African paraphyletic unit displays a star-like arrangement when phylogenetically reconstructed, while—as it appears from the authors' language—the Caucasus pharaphyletic unit displays discernable within-paragroup monophyletic relationships not necessarily from a single node, but a few discrete nodes. It appears that the paraphyletic units of the other sampled populations were relatively more phylogenetically scattered at the sub-clade level than the aforementioned two, i.e. showing less discernable within-paragroup monophyletic clustering between the chromosomes.

While in this study, the paraphyetic family of DYS458 .2 chromosomes showed frequency peaks in North African, East African and the Caucasus samples, they differ in their within-paragroup phylogenetic arrangement. The East African pattern is likened to the latter pattern just mentioned, while North African and the Caucasus paraphyletic arrangements are just as mentioned above respectively, showing relatively more discernable within-paragroup [sub-clade] monophyletic relationships. The point of inquiry now, is to see if any potential "Middle Eastern" paraphyletic family of this haplogroup compares with that of the East African family both in terms of frequency peak and loose within-paragroup monophyletic relationships between the chromosomes.

52 comments:

J2 M172 is African also said...

J (Y-DNA) itself more than likely originated in East Africa

J1 moved into Yemen, While J2 spread from Egypt into the Levant

J1 were Nomads similar to the Beja & nubians, While J2 were farmers connected to the Nile early farmers

Areas like Socotra (near Africa) still have the highest % of J*

Ofcourse Near Eastern populations especially in areas like Israel, Syria or Lebanon will reject this & favor anything Non-African due to the stigma attached to being of African origin (European influence)

Mystery Solver said...

Unnamed poster writes:

J (Y-DNA) itself more than likely originated in East Africa

J1 moved into Yemen, While J2 spread from Egypt into the Levant

J1 were Nomads similar to the Beja & nubians, While J2 were farmers connected to the Nile early farmers

Areas like Socotra (near Africa) still have the highest % of J*

Ofcourse Near Eastern populations especially in areas like Israel, Syria or Lebanon will reject this & favor anything Non-African due to the stigma attached to being of African origin (European influence)


I don't rule out possible origin of J, particularly J1*, in Eastern Africa either, but it is necessary to note that this paper is specifically referring to the paraphyletic variants with motifs designated as "DYS458" with "*X.2", so that the clade defining locus or segment of the Y-DNA in question is read as "DYS458*X.2", where "*X" [using my emphasis here, not the authors of the study at hand] is a cluster [of motifs] that may vary from one region to another. To give an example of what I'm talking about here, consider this from the study:

Individuals from the Caucasus have DYS458*20.2 as modal allele, where "20" = my "X" notation above.

Similarly, as per the study, North-African clade is defined by DYS458*18.2 as the modal allele, where "18.2" equals my "X" notation above.

The markers, thus far, by indication of the absence of well-known and assigned downstream SNPs, appear to be older than known J1 subclades. The authors say:

Initial SNPs analysis identified these chromosomes as derived at the M267 markers, placing them on the J1* cluster.

J1 sub-lineages were additionally tested (J1a–e) and in all cases the .2 chromosomes resulted ancestral at these additional markers.


If there are J1* markers supposedly more ancestral at nucleotide sequences designated by M267, I'd like to know about them sequentially, and their geographical whereabouts. Until then, I'd have to assume that such could be a reconstructed hypothetical ancestral sequencing, reconstructed from known data from existing subclades and paraphyletic J1 clades. If so, I'd have to also assume that the paraphyletic J1 clades represent the empirical ancestral markers to date, as noted in respective geographies. This would make a case, as the authors note, pending any modifications of our present knowledge by future findings, for an eastern African origin for J1* clades, as indicated by the allelic group with the ".2" designation.

Both J1 and J2 have African origins said...

J*(xJ1, J2) is the oldest form of J ever found, it was found very close to Africa.

70% J* in Socotra Yemen (Cerny)
7.7% J* in Oman (Di Giacomo)

both nations are very close to Africa, so J* more than likely came from Africa -where else?-

J* intial dispersal gives origin to 30% of Egypt (misleading since Egypt is a big nation that makes 30% seem less than the 50% of a small nation like nations with 5% its population ie Lebanon or Oman)

Please make more studies on this subject, I am very certain that J originated somewhere around modern Sudan, with J1 moving South to Yemen & J2 moving north to the Levant.

J1 & J2 originated in Asia! said...

To the guy with no name, you need to read:

A predominantly Semitic origin of Halpgroup J1 (M267) in North Africa (Yonan et al. 2008)

http://thegeneticatlas.com/study_yonan.htm

Mystery Solver said...

Unidentified poster writes:

J*(xJ1, J2) is the oldest form of J ever found, it was found very close to Africa.

70% J* in Socotra Yemen (Cerny)
7.7% J* in Oman (Di Giacomo)

both nations are very close to Africa, so J* more than likely came from Africa -where else?-

J* intial dispersal gives origin to 30% of Egypt (misleading since Egypt is a big nation that makes 30% seem less than the 50% of a small nation like nations with 5% its population ie Lebanon or Oman)

Please make more studies on this subject, I am very certain that J originated somewhere around modern Sudan, with J1 moving South to Yemen & J2 moving north to the Levant.
.
.
.

What is the title of the study you are referencing here? One has to use caution when approaching these studies, because J* could imply that the sequencing resolution of the study at hand was not sharp enough to place the J clusters at hand into well-established downstream J clades, OR that these happen to be new J subclades awaiting their place in the J macro-haplogroup phylogeny. I'm not ruling out that these "J*(xJ1, J2)" could well be clusters of *upstream*/ ancestral J clades, but just advising on the need for caution, pending specific information provided to this end. To that extent, it would be nice to know what study we are dealing with. And of course, as you all probably know, the post at hand deals with the J1-M267 branch of the J phylogeny.

Doctoris Scientia said...

Has their been any more findings in regard to the origins of J1-M267 and Haplogroup J itself.

I can't remember where, but I read somewhere that the J found among Ethiopians and Sudanese isn't recent or historic, and that they don't match those found in Yemen nor Arabia, therefore they can't be due to direct admixture but parallel evolution.

Also, isn't J most highly found among Yemeni populations, in particular populations who resemble Africans, like Eastern and Southern Yemni people, and Socotra populations.

If J1-M267 is indeed Africa, whats happened in regard to it's expansion?

Mystery Solver said...

Doctor Scientia writes:

Has their been any more findings in regard to the origins of J1-M267 and Haplogroup J itself.

I can't remember where, but I read somewhere that the J found among Ethiopians and Sudanese isn't recent or historic, and that they don't match those found in Yemen nor Arabia, therefore they can't be due to direct admixture but parallel evolution.

Also, isn't J most highly found among Yemeni populations, in particular populations who resemble Africans, like Eastern and Southern Yemni people, and Socotra populations.

If J1-M267 is indeed Africa, whats happened in regard to it's expansion?


Not so much as a "parallel" evolution, but rather, that the Ethiopian hg J markers are not derivatives of south Arabian examples, going off on molecular evidence. As noted above, the Ethiopian samples have their own unique paraphyletic group. If one is to assume that hg J1 arrived in Ethiopia from outside the continent, then the logical conclusion would be that it had to have been shortly after the clade's emergence when it was still fairly new in its distribution, so that that its expansion within Ethiopic population would lead to sub-clades that differ noticeably from the south Arabian examples, like those described for the Yemeni sample. On the other hand, the unique paraphyletic clades of eastern Africa, not to mention the older clades therein when compared with the phylogenetically more recent--and also the most prevalent examples therein--of the south Arabian samples, could very well be suggestive of the emergence of hg J1 clade somewhere on the African side of the Great Rift Valley, and then again, very shortly after its emergence, it spread to nearby territories. Some folks might balk at the possibility of an African origin, but evidence as that described above, in addition to other material noted elsewhere, says that that very possibility is very much scientifically plausible; to say that hg J1 origin in the so-called "Southwest Asia" is unequivocal and beyond doubt, is to engage in politics. It is not driven by thorough objective assessment of scientific data. At any rate, you can read more on the distinctions between the Ethiopian and south Arabian hg J markers in the following:

E-M34: Designation as "African" presents a Dilemma?, link: http://exploring-africa.blogspot.com/2009/09/e-m34-designation-as-african-presents.html

Following Trails of the Cro-Magnon - II, link: http://exploring-africa.blogspot.com/2010/01/following-trails-of-cro-magnon-ii.html

As for a possible scenario of how how hg J expanded, I've spoken about the issue here:

Working hypothesis around haplogroups IJK, I, J, K, P, R, and Q, link: http://exploring-africa.blogspot.com/2009/03/working-hypothesis-around-haplogroups.html

Maju said...

To those who say that Y-DNA J as whole originated in Africa, I must say that it does not look likely at all. I understand that we can pretty safely track the origin of F in South Asia (or Persian Gulf maybe?), IJK probably in the same area, IJ in West Asia not too far from SE Europe and J in West Asia. Large amounts of J* (J3?) in Southern Arabia do not change anything but rather emphasize the West Asian origin of this haplogroup.

However the case for J1 is more intriguing because there is indeed a major clade, or maybe more, with an African personality and the expansion of J1 may be tentatively associated (as that of E1b1b1) to that of Afroasiatic languages, which originated in East/NE Africa without doubt.

Personally I'm tempted to think J1 as Palestinian and E1b1b1 as Sudanese/Egyptian, getting both mixed in various ill-understood interactions, maybe since the backflow from Eurasia into North Africa in the early Upper Paleolithic (Dabban industries). The presence (in North/East Africa) of some surely very old Eurasian mtDNA lineages (M1, X1, U6) could support this model but we'd have to accept very old age for Y-DNA J1, what is at least controversial.

An alternative scenario is that J1 penetrated in Africa (Egypt essentially at first) later, and expanded with the Afroasiatic languages, what in NW Africa surely means Capsian culture (late UP).

Of course, some will argue for Neolithic flows but I must ask within which archaeological cultures? AFAIK, all North African Neolithic is Capsian in culture (excepted a few Cardium Pottery settlements by the coasts), what implies that there was no demic expansion in North African Neolithic.

Then you can also argue for Phoenicians or Bedouins but the impact looks too large for these historical groups and also Phoenicians at least should have carried a good deal of J2, nowhere to be found in Africa. Arabs should have carried some J2 as well (less but still some), along with other lineages maybe.

So I think that the time-frame must be pre-Neolithic in any case. This makes total sense if you consider IJ coalescing at the colonization of West Eurasia some 50 Ka ago. In fact, IJ, J and even J1 and J2 maybe too should have coalesced as founder effects in the early colonization of West Asia, with its offshoot to North Africa.

Mystery Solver said...

Maju writes:

To those who say that Y-DNA J as whole originated in Africa, I must say that it does not look likely at all. I understand that we can pretty safely track the origin of F in South Asia (or Persian Gulf maybe?),...

What empirical evidence do you have to suggest the clade F originated in Asia?

Maju writes:

IJK probably in the same area, IJ in West Asia not too far from SE Europe and J in West Asia. Large amounts of J* (J3?) in Southern Arabia do not change anything but rather emphasize the West Asian origin of this haplogroup.

As I have noted elsewhere, the origin of IJK in "southwestern Asia" is plausible on the grounds of distribution patterns of its downstream clades, namely; I, J, and K. However, on the same grounds, it is equally plausible that it originated on the Great Rift Valley section of or northeastern part of Africa. And no, hg IJK's ancestor need not necessarily have originated in either territory for this to be the case, since human population are not static. What are you going by to adjudge that it must have originated in "south Asia" or the "Persian Gulf"? Likewise, the same for IJ.

There is a strong possibility that hg J originally emerged in the Levant, and I'm basing this primarily on the understanding in some circles that hg J1-M172 is relatively, if not slightly, the older clade of the two major J clades -- hg J1 and hg J2. Had it not been for this, I would have considered it that the jury is still out on hg J origin [hg J2 has smaller distribution in Africa than hg J1].

Maju writes:

Large amounts of J* (J3?) in Southern Arabia do not change anything but rather emphasize the West Asian origin of this haplogroup.

If we consider southern Arabia alone, as I have pointed out, with support from data contained in published journals, the internal diversity of hg J1 clades in inbreeding populations in particular, does not make any unequivocal case for hg J origin in "western Asia". For instance, northeastern African and Ethiopian hg J1 clades are more internally diverse. Only if one were to pool southern Arabian gene pool with that of the northern parts of the Arabian plate, then one might see diversity that rivals those of the northeastern African and African Horn (Ethiopian) hg J1 clades. As a matter of fact, both northern Africa and Ethiopia have paraphyletic clades that are endemic to those regions alone. I've commented on published material on this, in another topic on this very site, and it can be retrieved with the search function.

Maju writes:

Personally I'm tempted to think J1 as Palestinian and E1b1b1 as Sudanese/Egyptian, getting both mixed in various ill-understood interactions, maybe since the backflow from Eurasia into North Africa in the early Upper Paleolithic (Dabban industries).

As I noted elsewhere, it is certainly plausible that hg J1 initially arrived from the Levant, although there is nothing unequivocal about it at this point, and if we consider this to be the case, then one would have to recognize that it came to Africa very shortly after its emergence, and hence, resulting in African territories having their own sets of paraphyletic hg J clades.

Mystery Solver said...

Maju writes:

The presence (in North/East Africa) of some surely very old Eurasian mtDNA lineages (M1, X1, U6) could support this model but we'd have to accept very old age for Y-DNA J1, what is at least controversial.

Your theory is highly questionable, because hg M1 is African in origin, as I have amply demonstrated time and again here, with molecular breakdown. This information too can be retrieved via the search function. The same applies to hg U6, although unlike hg M1, it is not clear whether hg U6's immediate ancestor also originated in Africa. Hg U6 is considered an autochthonous northern African marker, particularly the Maghreb. So, when one talks of hg U6 outside of Africa, the marker is primarily serving as African ancestry in said region.

Maju writes:

Then you can also argue for Phoenicians or Bedouins but the impact looks too large for these historical groups and also Phoenicians at least should have carried a good deal of J2, nowhere to be found in Africa. Arabs should have carried some J2 as well (less but still some), along with other lineages maybe.

hg J2 is found in northeastern African areas, although not as considerable as hg J1. I've also broken down the molecular specifics of why a considerable portion of northern African, as opposed to say, Ethiopian, hg J clades are primarily of historic origin, rather than pre-historic. There is certainly a pre-historic element, as suggested by unique northern African paraphyletic hg J1 clades, but there also strong evidence that these were supplemented by younger hg J clades, that expanded with Arabic contacts.

On that note, I would like to see the molecular specifics for how you come to your conclusions, not merely opinions of what you think might have occurred. Thanks for commenting and keeping the tone respectful.

Maju said...

"What empirical evidence do you have to suggest the clade F originated in Asia?"

Highest basal diversity by far: all subclades (F1, F2, F3, F4, G, H, IJK and the paragroup F*) are clearly centered in Asia, actually in either South Asia (most) or West Asia (G, arguably IJK too).

"the origin of IJK in "southwestern Asia" is plausible on the grounds of distribution patterns of its downstream clades, namely; I, J, and K".

The basal downstream clades of IJK are (in spite of the name) only two: IJ and K. I and J are in the phylogenetic hierarchy comparable to K sublineages: L, MNOPS and T.

"... since human population are not static".

This logic can only bring you to an absolute uncertainty because, by it, you render all the extant evidence meaningless.

Populations migrate, sure, but they also stay. And those who stay put in more or less fertile regions should absorb in most cases the newcomers, who should be far less in number than the older inhabitants. You can only argue this solidly for areas where there is evidence of depopulation.

"There is a strong possibility that hg J originally emerged in the Levant, and I'm basing this primarily on the understanding in some circles that hg J1-M172 is relatively, if not slightly, the older clade of the two major J clades"...

This is highly speculative IMO. I do not give credence to molecular clock conjectures and also you should consider also their close relative I, which is unmistakably European. This should place in my understanding the origin of IJ in "highland West Asia" (but Levant is a possibility too) and, as J is its only local descendant, J probably has the same origin. Instead J1 looks more Palestinian, so to say, with an early branch towards North Africa.

While the data is a little incomplete, Semino 2004 has a nice network of J1 haplotypes (fig. 4) and we can spot clearly what looks like a North Africa-centered subclade (shaded in grey), with back-expansion towards West Asia. It's difficult to say for sure anyhow.

We can agree, I guess, that J1 (but only J1, not J2 nor J overall) appears to have an origin between West Asia and North Africa.

In any case, J1 is not any ancestor of J2 so it says nothing about the origin of J2 and only says something about the origin of J overall (J2 and J* should also be factored in equal terms and the upstream phylogeny, J<IJ<IJK<F cannot be ignored either).

...

Maju said...

...

"the internal diversity of hg J1 clades in inbreeding populations in particular, does not make any unequivocal case for hg J origin in "western Asia"".

I'm not sure about what exact papers you are talking about but I understand that Yemeni J1 is abundant but of low diversity. So Yemen looks as a colonized area and never the origin. I am uncertain about Ethiopia and the East Caucasus, but for North Africa and the Fertile Crescent, I rely on Semino 2004 and the haplotype structure looks West Asian by origin, though I would not discard a backflow from North Africa as well.

"As a matter of fact, both northern Africa and Ethiopia have paraphyletic clades that are endemic to those regions alone. I've commented on published material on this, in another topic on this very site, and it can be retrieved with the search function".

Ok, I'll check it up later (no time right now) but careful with paraphyletic clades. I would not be too surprised if J1 ends up having an African origin (as it looks mostly overlapping with E1b1b) but this does not change much in regard to J overall (it might pull southwards the overall centroid but still within West Asia).

"... one would have to recognize that it came to Africa very shortly after its emergence, and hence, resulting in African territories to have their own sets of paraphyletic hg J clades".

I have no problem with that, but I'd replace J with J1 specifically, as J2 and J* seem not to be present in any meaningful way in Africa.

"hg M1 is African in origin, as I have amply demonstrated time and again here"...

You must excuse my ignorance about your work (I'm a newcomer to this blog). I'll look that up. In any case mtDNA M overall is clearly of Asian (South Asian) origin and M1 is a derived clade, so back-migration is still necessary.

And what I said about U6 and X1 stands.

"... it is not clear whether hg U6's immediate ancestor also originated in Africa".

The immediate ancestor of U6 is U and U is clearly of West Eurasian origin, probably with a geographical tendency towards South Asia, where several subclades are also found (mostly of the U2'3'4'7'8'9 variant but also U1 and U5, i.e. all but U6, which indeed looks like coalescing in North Africa).

"So, when one talks of hg U6 outside of Africa, the marker is primarily serving as African ancestry in said region".

Agreed. This is almost totally limited to the Iberian peninsula anyhow and is probably related to the flow in the opposite direction of mtDNA H (and V), which I tend to locate in the Oranian (Iberomaurusian) genesis.

But U overall is Eurasian, West Eurasian specifically. So I understand that U6 (and probably other haplogroups as the said X1) penetrated in North Africa as extension of the colonization of (most of) West Eurasia from Southern Asia by H. sapiens in the 50-40 Ka ago timeframe. The Dabban industries (quite clearly "Aurignacoid") may be the archaeological record of this flow.

"I would like to see the molecular specifics for how you come to your conclusions, not merely opinions of what you think might have occurred".

As I have already mentioned I base my conclusions in diverse data publicly available but specially in Semino 2004, which has some sampling shortcomings, admittedly but AFAIK remains the main reference. I have also discussed this matter in the past with diverse rather knoweldegable people but never with an "Africanist", so I find your viewpoint interesting, different.

I welcome any sort of informative feedback you can provide. My opinions are not set on stone.

"Thanks for commenting and keeping the tone respectful".

Thanks to you for providing this space and your opinions, info, etc. Respect is, of course, always first.

Luis said...

Btw, I just got notice of this new open access paper on U6 by L.
Pereira
. I do not have time to read or discuss it now but I presume
you'll be interested.

Maju said...

PS- I just got this morning notice of this new open access paper on mtDNA U6 (by L. Pereira, who previously researched Cape Verdean genetics), quite focused on chronology, which I find pretty good and I am sure you will be interested in.

Mystery Solver said...

Maju writes:

Highest basal diversity by far: all subclades (F1, F2, F3, F4, G, H, IJK and the paragroup F*) are clearly centered in Asia, actually in either South Asia (most) or West Asia (G, arguably IJK too). . .

Hg IJK theoretically is basal. As for the hg F sub-clades, having diverse downstream haplogroups only speaks to expansion, not origin. As for the paragroup of hg F, please do provide the molecular details on this. I'm interested in examining it.

The basal downstream clades of IJK are (in spite of the name) only two: IJ and K. I and J are in the phylogenetic hierarchy comparable to K sublineages: L, MNOPS and T.

Hgs I, J, and K are distinctive haplogroups. This is obviously what's being referenced. In what order they descend from the theoretical eponymous ancestry of clade IJK is therefore just an argumentative non-issue.


Maju writes:

"... since human population are not static".

This logic can only bring you to an absolute uncertainty because, by it, you render all the extant evidence meaningless. . . .


You cannot approach molecular genetics by ignoring the historically mobile element of human and animal populations. It doesn't make sense. That's what the whole purpose of molecular genetics is in the first place, to track human movements and bio-history thereof. No evidence is meaningless if understood in the proper context.

Maju writes:

Populations migrate, sure, but they also stay. And those who stay put in more or less fertile regions should absorb in most cases the newcomers, who should be far less in number than the older inhabitants. You can only argue this solidly for areas where there is evidence of depopulation. . . .

This is what "expansions" are all about; when populations settle down and grow. Expansionism in itself is not a euphemism nor a substitution for "point of origin" of the base or ancestral group. Likewise, "founder effect" speaks to the potential of a marker to dramatically rise to a population level, but does not necessarily resolve the actual geographical point of origin for the marker at hand, which could well have been present in small numbers in a base population with a markedly different gene pool structure. "bottlenecks" on the other hand, are signs of movement, and/or some adverse situations rendering considerable population reduction, and potentially thereof, reduced genetic diversity. "Ancestral markers"? They tell us that said population is likely the direct remnant of the base core population, as opposed to descendants of a divergent bottlenecked population. "Diversity"? Again, can say two things, depending on empirical data under study: identifying the ancestral core stratum vs. the shallower stratum of population biohistory, and/OR expansion vs. bottleneck. These elements, when working in concert with one another, may allow for extrapolation for the most likely place(s) of origin, and therefore not meaningless. Take for instance, how "diversity" coupled with distance of geography can hint on the most-likely geographical origin, under the context of "isolation-by-distance" models.

Mystery Solver said...

Maju writes:

This is highly speculative IMO. I do not give credence to molecular clock conjectures and also you should consider also their close relative I, which is unmistakably European. This should place in https://www.blogger.com/img/cmt/close.gifmy understanding the origin of IJ in "highland West Asia" (but Levant is a possibility too) and, as J is its only local descendant, J probably has the same origin. Instead J1 looks more Palestinian, so to say, with an early branch towards North Africa . . .

Of course, it is speculative [not the molecular clock estimation bit, but the assessment of hg J origin grounded on age and distribution of hg J2], but so is your own conjectural theory above, if not even more so. Even if one were to assume that hg IJ originated in "western Asia", that is not substitute nor serve as origin determination for either clade IJK or say, hg J1. The appearance of hg I in Europe only tells us that hg IJ carriers once roamed there. Likewise for say, for hg J in the Levant. There is no conclusive evidence that hg J1 is "Palestinian", as paraphyletic clusters of this clade are found as far as Europe and the African horn, each with distinctive network patterns, as noted in the blog post. If hg IJ carriers were in the northeastern section of the African continent, it is fairly plausible that of out this, hg J1 carriers emerged, and then spread to the northern parts of the Arabian plate. Hg IJK sub-haplogroups are generally rich in the Great Rift Valley segments of Africa and the Arabian plate; so either region is a potential candidate for hg J1 origin.


While the data is a little incomplete, Semino 2004 has a nice network of J1 haplotypes (fig. 4) and we can spot clearly what looks like a North Africa-centered subclade (shaded in grey), with back-expansion towards West Asia. It's difficult to say for sure anyhow...

That is not as significant an element than what Semino et a. (2004) noticed about the hg J1 clades in say, Ethiopia vs. that in their "Near Eastern" samples. Do you recall what that was?

We can agree, I guess, that J1 (but only J1, not J2 nor J overall) appears to have an origin between West Asia and North Africa.

Correction: I don't rule out hg J1's origin between the red-sea neighboring eastern African territories and the southern part of the Levant. I hold this same viewpoint for theoretical ancestral clades of IJK and IJ.

In any case, J1 is not any ancestor of J2 so it says nothing about the origin of J2

Obviously. Nobody claimed otherwise.

Maju said...

"Molecular" details of a paraphiletic group? Sorry, I have not clear what you're talking about. F* is described by being F but not any of its derived sublineages, at least not the main ones (G, H and IJK).

Suffice to read Wikipedia's entry (and track the sources if need be):

F(xG,H,IJK) is found in:
1. India (12.5%)
1.1. Tribal Indians (18.1%)
1.2. Caste Indians (9.6%)
1.3. Sinhalese (10%)
1.4. Kurds (7% or more)
1.5. Ailao mts. of Yunnan (China, as dominant specially among a hunter-gatherer tribe)
1.6. Malay archipelago
1.8. Korea (8%)

Unless some error in testing strategies was made (I have no time to review all relevant papers right now), all this F* is F(xG,H,IJK) and probably also excluding F1, F2, F3 and/or F4. But this is more difficult to be sure about because these lineages are seldom tested for. Whatever the case there's more to F than just G, H and IJK, and this F-other is particularly concentrated in Asia along the presumed routes of early human (H. sapiens) expansion.

""Diversity"? Again, can say two things, depending on empirical data under study: identifying the ancestral core stratum vs. the shallower stratum of population biohistory"...

That is why my emphasis is always in basal diversity, not just vague any-kind diversity, which can well be shallower. For any haplogroup, it is basal diversity which can tell us where it coalesced (unless there was a total population replacement which erased all evidence - but I tend to dismiss such ideas).

So for F I do not look at the differences between R1b and R1a for instance, because these are nothing but details of super-common basal subclade IJK. But instead I am interested in F*, even if it is poorly researched, as well as the other, much better known, basal subclades.

It is very clear in the phylogeny and structured distribution that there was one single relevant migration out of Africa involving mtDNA L3 (leading to M and N, that is: pre-M and pre-N) and Y-DNA CDEF (or maybe better: CDEF leading to CF and DE leading to D, let's say pre-CF and pre-D). They stayed in Arabia and the Persian Gulf probably between 90 and 80 Ka ago (Petraglia 2010) and then went on to South Asia and beyond, where they diversified in the haplogroups we can see now.

It's very possible that other L sublineages (notably within L3 and L0) made it to Arabia Peninsula also in that time but they never reached South Asia which was the real "pump" of Eurasian expansion. While not nearly as large as Africa, South Asia is and was large and fertile enough to support a huge demographic expansion, attested specially in the immense basal diversity of mtDNA haplogroup M. SE Asia, including South China, was a secondary "pump".

Eventually some of these Eurasian peoples back-migrated to Africa, specially the North, separated from the rest by a Sahara that is only very rarely "wet", carrying some derived lineages (M1, U6, X1). Other lineages arrived later (notably H and V from Iberia at the Oranian genesis most likely, and K and JT maybe with the Neolithic, from West Asia). None of these lineages ever made inroads into Africa south of the Sahara, the main exception is M1 which is scattered along the Eastern coast.

Maju said...

"Likewise, "founder effect" speaks to the potential of a marker to dramatically rise to a population level, but does not necessarily resolve the actual geographical point of origin for the marker at hand, which could well have been present in small numbers in a base population with a markedly different gene pool structure".

Technically this is correct but quite irrelevant unless it can be demonstrated.

I say it's quite irrelevant because it is not so important for us where the final mutation shaping M arose specifically (I'd say the Persian Gulf, but it's a hunch), what is relevant is where people with such mutation began expanding. After all we are trying to use the lineages to understand human prehistory, right? We cannot get the precision to pinpoint a long deceased woman who first carried such mutation (and it does not matter so much anyhow) but we can find out where the rather close descendants of that woman expanded by exploring the basal diversity of M (for example).

""Ancestral markers"? They tell us that said population is likely the direct remnant of the base core population, as opposed to descendants of a divergent bottlenecked population".

I think that here you refer to basal diversity, which is my emphasis too. As I said before, I don't care too much about "raw diversity", but I do care a lot about where the basal lineages of any haplogroup exist, because that's the only way to reconstruct the history of the clade with some objectivity.

"Take for instance, how "diversity" coupled with distance of geography can hint on the most-likely geographical origin, under the context of "isolation-by-distance" models".

I think I can agree with this, even if we seem to use somewhat different vocabulary. We should not be in disagreement I believe.

"The appearance of hg I in Europe only tells us that hg IJ carriers once roamed there".

They still do. That's precisely what I is: the European variant of IJ, while J is the Asian (and African) variant.

"There is no conclusive evidence that hg J1 is "Palestinian""...

Sadly we cannot conclusive claim that or anything else because the haplogroup is not sufficiently well researched. But Palestine offers a deep archaeological record in the context of "West Eurasian" Upper Paleolithic (Aurignacoid industries) and holds enough numbers and diversity within this clade. Also, geographically it is at the gates of Africa, what makes it a good candidate for the coalescence of haplogroups shared deeply in the phylogeny between West Asia and North Africa (and sometimes The Horn too).

However I cannot discard totally a place like Egypt at the current stage of knowledge. Sadly the archaeology (and even the relevant genetics) of Egypt (and Sudan) are not sufficiently well known AFAIK.

"Hg IJK sub-haplogroups are generally rich in the Great Rift Valley segments of Africa and the Arabian plate"...

I have to protest here what is a vague statement. When you say IJK subhaplogroups you mean surely J1 and maybe R1b1a and the occasional J2, right? This is precisely like talking about "diversity" without qualifiers.

I am surely as puzzled as you are by the occasional presence of rare IJK clades in Africa (such as K* or P*) and I wish this could be researched further. But they do not seem to counterweight the Asian diversity of either K, IJK or F. This is as much as saying that the occasional DE* in Tibet does not seem enough to challenge the African origins of DE overall (I support this last: DE coalesced most likely in Africa, in the Upper Nile, along with mtDNA L3 or L2"6 - just to avoid confusion).

(continues)

Maju said...

MS said: "That is not as significant an element than what Semino et a. (2004) noticed about the hg J1 clades in say, Ethiopia vs. that in their "Near Eastern" samples. Do you recall what that was?"

Maybe you mean this:

"In the absence of additional binary
polymorphisms allowing further informative subdivision of J-M267, the YCAII microsatellite system provides important insights. The majority of J-M267 Y chromosomes harbor the single-banded motif YCAIIa22-YCAIIb22 in the Middle East (70%) and in North Africa (90%), whereas this association is much less frequent in Ethiopia and only sporadically found in southern Europe".

"... we suggest that the
motif YCAIIa22-YCAIIb22 potentially characterizes a monophyletic clade of J-M267".

This is curious but it's difficult to assess what it means. If Semino was correct, what is possible, it may mean that this subclade of J1 experienced a secondary expansion affecting mostly West Asia and specially North Africa.

Still J1 is only common among the Semitic speakers in Ethiopia (Amhara 33% vs. Oromo 2%), so it's really tempting (though maybe wrong) to attribute it to such linguistic flow, which probably originated in West Asia, at the Circum-Arambian Pastoralist Complex (regardless that Afroasiatic languages are indeed overall original from the Nile at an older date).

"Correction: I don't rule out hg J1's origin between the red-sea neighboring eastern African territories and the southern part of the Levant. I hold this same viewpoint for theoretical ancestral clades of IJK and IJ".

I accept this for J1 but I do not see how it can be extrapolated to IJ (considering where J2 and I are found) or much less IJK.

Cheers. It's an interesting debate in any case.

Mystery Solver said...

Maju writes:

I'm not sure about what exact papers you are talking about but I understand that Yemeni J1 is abundant but of low diversity...

I'm making tacit reference to such publications as Semino et al. (2004), Cadenas et al. (2007) and Luis et al. (2004).


So Yemen looks as a colonized area and never the origin. I am uncertain about Ethiopia and the East Caucasus, but for North Africa and the Fertile Crescent, I rely on Semino 2004 and the haplotype structure looks West Asian by origin, though I would not discard a backflow from North Africa as well...

I'm also partially relying on Semino et al. (2004) about the greater internal diversity and molecular peculiarities of Ethiopian hg J1 clades vs the ones noted for their Arabian plate samples. This feature does not speak to a "West Asian origin".

Ok, I'll check it up later (no time right now) but careful with paraphyletic clades.

Careful, what for?


I have no problem with that, but I'd replace J with J1 specifically, as J2 and J* seem not to be present in any meaningful way in Africa.

Well, you ought to know by now that it is J1 we are talking about, as it is the subject of discussion. I therefore feel no need to keep notifying that it is J1 that I'm referring to.


You must excuse my ignorance about your work (I'm a newcomer to this blog). I'll look that up. In any case mtDNA M overall is clearly of Asian (South Asian) origin and M1 is a derived clade, so back-migration is still necessary.


Hg M1 is not a derived clade any more than Asian hg M clades are derived. Hg M1 is clearly not a sub-clade of any Asian specific M clade. So, why should a "back-migration" still be "necessary"?

And what I said about U6 and X1 stands.

What supposedly stands? And elaborate why.


The immediate ancestor of U6 is U and U is clearly of West Eurasian origin, probably with a geographical tendency towards South Asia, where several subclades are also found (mostly of the U2'3'4'7'8'9 variant but also U1 and U5, i.e. all but U6, which indeed looks like coalescing in North Africa).

There is no such thing as "U" in Asia. If such does not exist in Asia, how then can it be "clearly" of "west Eurasian origin". There is however, such as thing as common basal motifs shared across different hg U clades. Proto-U6, as I have noted with citations, has not be located. Nor is it a derivative of any preexisting "west Eurasian" example. In fact, it is the other way around: "West Eurasian" U6 clades are derivatives of Maghrebi examples.

Mystery Solver said...


Agreed. This is almost totally limited to the Iberian peninsula anyhow and is probably related to the flow in the opposite direction of mtDNA H (and V), which I tend to locate in the Oranian (Iberomaurusian) genesis.


That's false. U6 is not "almost totally limited to the Iberian peninsula". It is scattered in the northern areas of the Arabian plate and parts of eastern Africa, like the African Horn. In all cases, the clades are more downstream clades of Maghrebi examples.

But U overall is Eurasian, West Eurasian specifically.

That doesn't make sense for reasons already stated above.

So I understand that U6 (and probably other haplogroups as the said X1) penetrated in North Africa as extension of the colonization of (most of) West Eurasia from Southern Asia by H. sapiens in the 50-40 Ka ago timeframe.

This is false. U6 does not originate in southern Asia. You've got it backwards.


The Dabban industries (quite clearly "Aurignacoid") may be the archaeological record of this flow.


You may need to update your understanding of North African Paleolithic pre-history. The Upper Paleolithic lithic complexes are now understood to be primarily of local origin. Again, it is the other way around, with northern African lithic techniques flowing into western Eurasia in the Upper Paleolithic.

Mystery Solver said...

Maju writes:

Maybe you mean this:

"In the absence of additional binary
polymorphisms allowing further informative subdivision of J-M267, the YCAII microsatellite system provides important insights. The majority of J-M267 Y chromosomes harbor the single-banded motif YCAIIa22-YCAIIb22 in the Middle East (70%) and in North Africa (90%), whereas this association is much less frequent in Ethiopia and only sporadically found in southern Europe".

"... we suggest that the
motif YCAIIa22-YCAIIb22 potentially characterizes a monophyletic clade of J-M267".

This is curious but it's difficult to assess what it means. If Semino was correct, what is possible, it may mean that this subclade of J1 experienced a secondary expansion affecting mostly West Asia and specially North Africa.


Well, that is certainly part of the study I had in mind. The Ethiopian J1 clades generally lack the downstream motifs in question that are common in the Arabian plate and the Levant. That's what the above essentially means. The other matter I had in mind, is the internal diversity of Ethiopian clades vs. the Arabian examples Semino et al, Cadenas et al. and Luis et al. noted. The reported diversity of Ethiopian clades is noticeably greater by comparison, i.e. when the entire Arabian territory is not pooled together, but going by individual populations, as is done with Ethiopians.

Still J1 is only common among the Semitic speakers in Ethiopia (Amhara 33% vs. Oromo 2%), so it's really tempting (though maybe wrong) to attribute it to such linguistic flow, which probably originated in West Asia, at the Circum-Arambian Pastoralist Complex (regardless that Afroasiatic languages are indeed overall original from the Nile at an older date).

I agree with the "tempting, though wrong" assessment. None of key subsistence root words of Ethio-Semitic languages are derived from the "Circum-Arabian Pastoralist Complex" or "Near Eastern" Neolithic. Hg J1's distribution may well, however, be correlative with Semitic language phylum's distribution, and in this regard, its origin in Africa, and then spread into the Levant is very perceivable. Semitic is simply an offshoot of "Afro-Asiatic", which has the rest of its phylogenetic diversity exclusively on the African plate.


I accept this for J1 but I do not see how it can be extrapolated to IJ (considering where J2 and I are found) or much less IJK.


Nobody said that it can be extrapolated to either IJ or IJK clade. You jumped the gun on that.

Mystery Solver said...

Maju writes:

"Molecular" details of a paraphiletic group? Sorry, I have not clear what you're talking about. F* is described by being F but not any of its derived sublineages, at least not the main ones (G, H and IJK).

You are not clear on what "molecular" details of a clade entails? Put in another way, how about characteristic sequences peculiar and distinctive to a paraphyletic F clade? F* need not always necessarily imply an hg F clade that lacks downstream mutations of its derived sub-clades; sometimes, it simply means that that other established mutations were not tested in the study at hand, for a finer resolution analysis, and therefore only being referenced in a generic sense.

Unless some error in testing strategies was made (I have no time to review all relevant papers right now), all this F* is F(xG,H,IJK) and probably also excluding F1, F2, F3 and/or F4.

You've got to do better than that. I need specifics on the loci of these F* that you are alluding to, and independently verify if they are in fact upstream clades. For what its worth, hg F* was implicated in Arredi et al.'s study of northern African samples, but I believe that may have been a matter of sequencing resolution.

But this is more difficult to be sure about because these lineages are seldom tested for.

Precisely my point of asking for loci information.

That is why my emphasis is always in basal diversity, not just vague any-kind diversity, which can well be shallower. For any haplogroup, it is basal diversity which can tell us where it coalesced (unless there was a total population replacement which erased all evidence - but I tend to dismiss such ideas).

If it "basal diversity" you were alluding to, I have not seen any substantiation from you that would suggest "Palestinian" hg J1 clades are more diverse than the Ethiopian examples.


It is very clear in the phylogeny and structured distribution that there was one single relevant migration out of Africa involving mtDNA L3 (leading to M and N, that is: pre-M and pre-N) and Y-DNA CDEF (or maybe better: CDEF leading to CF and DE leading to D, let's say pre-CF and pre-D). They stayed in Arabia and the Persian Gulf probably between 90 and 80 Ka ago (Petraglia 2010) and then went on to South Asia and beyond, where they diversified in the haplogroups we can see now.


Taking the example of hg M, the L3 marker that likely left, would have been the proto-M3 clade. An African L3a clade suggestive and exemplary of this has found identified. No such clade has been located in Asia. In this aspect, a clade little more than L3 would have left. Also, a lot of the times, some folks tend to view DNA marker networks rather simplistically. Like for instance, this notion that all M and N clades are exclusively "Eurasian". This sort of thinking is very simplistic, and usually based on a priori assumption, usually justified on the overall diversification of these clades outside of Africa. In the majority of these cases, no upstream L3 clades representative of their immediate L3 ancestry have been located outside of Africa, yet it is taken for granted, that these markers originate outside of the continent. Such rare examples have however, been located in Africa, only to be dismissed as not being significant. There is some tendency out there, to simplistically look at human genetic structure and imply that only a uni-directional flow can take place most of the time. Hence, you have people claiming that say, any hg M or hg N, can only be indicative of back-migration; it is not possible for certain hg M or hg N clades to be peculiar to Africa, and in a twist, actually be a back-migration into Asia. Population bio-history is rarely that simplistic.

Mystery Solver said...

It's very possible that other L sublineages (notably within L3 and L0) made it to Arabia Peninsula also in that time but they never reached South Asia which was the real "pump" of Eurasian expansion. While not nearly as large as Africa, South Asia is and was large and fertile enough to support a huge demographic expansion, attested specially in the immense basal diversity of mtDNA haplogroup M. SE Asia, including South China, was a secondary "pump".


Well, South Asia may have basal clades for Asian specific M clades, but it does not have it for hg M1, which is noticeably absent or very rare there as well. However, basal clade to all M clades, be it south Asian or African, has been located in Africa, already. Not sure why it surprises anyone for this to be the case. After all, the said Asians derive from Africans, not the other way around. I think much of it has to do with anti-African prejudice amongst non-African folks.

Eventually some of these Eurasian peoples back-migrated to Africa, specially the North, separated from the rest by a Sahara that is only very rarely "wet", carrying some derived lineages (M1, U6, X1).

While I agree with the prospect of back-migration, you generalization here is not grounded on empirical data. You have not offered anything short of casual assumptions about M1 being back-migration derived. Likewise, no evidence offered for a non-African origin of U6. X1 can be treated along the same lines as U6. In fact, all empirical data move in the opposite direction of what you say. While there is a question mark on the territorial origin of proto-U6 [not U6 itself], there is no such situation with hg M1, whose ancestor has already be identified in African sampling. And no, the "northern" Africa has never been separated from the rest by the Sahara; that is a myth. Ever heard of the historic tran-Saharan trade network?

None of these lineages ever made inroads into Africa south of the Sahara, the main exception is M1 which is scattered along the Eastern coast.

Correction:U6, M1 and X1 are found "south of the Sahara". In fact, another U clade implicated in an African origin, is U9. Both U6 and M1 are found in western and eastern Africa. I'll agree with you however, with regards to H and V clades, but not necessarily the more upstream N and M clades.

Maju said...

"Well, you ought to know by now that it is J1 we are talking about"...

Well, you have droped before that all J (and even IJ, IJK and F) could be of African origin. Other than Y(xA,B), I can't see how can be the case.

As for J1, I'd like to see clear data. What I have seen so far is not suggestive of African origin. I'm open to such idea and I even pondered about a North African origin of the clade or a subclade of it but I'd like to be reasonably sure before I take that position.

"Hg M1 is clearly not a sub-clade of any Asian specific M clade".

It's a subclade of M, which is indeed an Asian clade no matter how you look at it. Besides it is now known it is a subclade of M1'51, and its sister clade M51 has only been accounted for in Asia AFAIK.

"And what I said about U6 and X1 stands.

What supposedly stands? And elaborate why".

Sorry that I can't remember the context (I posted that two weeks ago). But I guess essentially I meant that U6 and X1 are derived from Asian or Eurasian lineages as follows: N>X>X1 and N>R>U>U6. So even if U6 and X1 coalesced in Africa, what is not too clear for X1 but is for U6 without doubt, they represent a back-flow from Asia, where their ancestors lived after the OoA (i.e. after the L3 node).

"There is no such thing as "U" in Asia".

There is indeed a haplogroup known as U and defined under R by transitions at the sites 11467, 12308 and 12372. Most U is Asiatic or European, the only exception being U6.

If you mean that there is no underived U anymore, sure: there's no underived U6 either. Everything evolves. But we are talking haplogroups, with emphasis in "group", not prehistorical reconstructed lineages at their basal node.

So U has four basal subclades: U1, U5, U6 and U2'3'4'7'8'9. The center of gravity of these four lineages, as a whole: as U, is by all accounts in West Asia. The lineage as such extends by all West Eurasia, Central Asia, South Asia (U1, U2 and U7) and North Africa (almost only U6 but some U1 in Egypt AFAIK). U6 is therefore the North African specific branch of U. The transition from ancestral U to U6 clearly indicates a migration from West Asia to North Africa, probably associated to the Dabban Industries, considered derived from Palestinian "Aurignacoid" ones.

(continues)

Maju said...

...

"That's false. U6 is not "almost totally limited to the Iberian peninsula". It is scattered in the northern areas of the Arabian plate and parts of eastern Africa, like the African Horn. In all cases, the clades are more downstream clades of Maghrebi examples".

My bad, I obviated the West Asian U6, which we agree that is derived from North African one. Anyhow what I meant is that U6 in Europe is almost restricted to Iberia, with only rare examples elsewhere.

"U6 does not originate in southern Asia".

I know that, what I say is that U does, and U6 is a derivative.

"You may need to update your understanding of North African Paleolithic pre-history. The Upper Paleolithic lithic complexes are now understood to be primarily of local origin".

I am as updated as I can, believe me. The UP complexes, which are several, all look at least partly intrusive, main exception being the Capsian Late UP culture. The Dabban industries of Cyrenaica are generall understood as an offshoot of West Asian ones, the same that Aurignacoid industries in Europe are. The Oranian culture is claimed by some to be of NE African origin but this is inconsistent with the oldest C14 dates being in Morocco, so it seems a pretty awful revisionism without merit. See for example the Pereira paper linked above.

I have given some serious thought to the Oranian issue and to the fact that North African mtDNA H clades (24%, to which V should be added probably) are derived from SW European ones (Cherni 2008). And my only possible conclusion is that there was in fact an interaction between Iberian Gravetto-Solutrean and North Africa at that point. This interaction was not surely a simple migration from Iberia because I think that the U6 in Iberia (and maybe even Y-DNA E1b1b1b) must represent a back-flow from North Africa, affecting particularly the Western parts of the peninsula. Also it is then when Iberian Gravetto-Solutrean adopts back-tipped points, who are a typical North African design and whose origins may well go back as far as Aterian culture.

In any case there is an important SW European layer in North Africa, evidenced by mtDNA H and probably V as well, and the only moment of clear connection is that of the Oranian genesis, which is slightly but significantly younger than the arrival of Gravettian and then Solutrean to Iberia c. 23-22 Ka ago.

My reconstruction of NW African demographic layers is as follows:

1. Middle Paleolithic (Aterian): L(xM,N) (now c. 25% of all)
2. Early UP (Dabban ind.): U6 (now c. 10-15%)
3. Middle UP (Oranian): H and V (now c. 30%)
4. Late UP (Capsian): Nile lineages such as U6a and some L(xM,N)
5. Coastal Neolithic and post-Neolithic arrivals: K and JT (less than 10%)

However I am not so sure about how to read the Y-DNA, though the 5% of R1b1b2a must have arrived with HV mostly as well as the I, which is documented among Canary Islands native mummies in surprisingly high amounts (6.7%). I'd also say that J1 possibly arrived with Capsian culture but the bulk must have been E1b1b, whose fine details I have not been able to unravel yet.

Mystery Solver said...

Well, you have droped before that all J

Where; not the topic under discussion, that's for sure?


(and even IJ, IJK and F) could be of African origin.


Elsewhere, yes I did not rule it out, under a specified context. That has nothing to do with the topic we are now discussing.


Other than Y(xA,B), I can't see how can be the case.

The confusion is all yours, because you are mixing topics, and who knows what you are referring to or not. If you stuck to the topic at hand, you wouldn't be confused about what's being referenced. The topic at hand is paraphyletic J1-M261 clades, not IJ, IJK of F.

As for J1, I'd like to see clear data. What I have seen so far is not suggestive of African origin.

The very topic you are replying to is an example of clear data, or did you forget? I've also repeated myself on references from Semino, Cadenas and Luis et al. about internal diversity quantification and downstream vs. upstream motif matters. Either of these material do not rule out an African origin for the J1 marker. Yet you say that you have seen no clear data. Alternatively, I've seen only speculations as your reactions to these data.

It's a subclade of M, which is indeed an Asian clade no matter how you look at it. Besides it is now known it is a subclade of M1'51, and its sister clade M51 has only been accounted for in Asia AFAIK.

*There is no such thing as "M"; you made it up. Hg M1 does not derive from any Asian-specific non-M1 clade. You disagree? Name the specific name of that clade, instead of simply saying "M", which does not exist.

*A revision in haplogroup terminology does not change this fact. M1 is not a sister clade of M51 any more than it is a sister clade of any other Asian-specific M; that too you made up. You disagree? Point out to me, M1 and M51's immediate stand alone ancestral Asian M clade. Also tell me how this ancestral clade supposedly ties M1 and M51 more immediately with one another but not with other M clades.

*I'd like to see how this supposedly trumps the African proto-M1 clade, which is an L3 clade with basal haplogroup M characteristics.

Sorry that I can't remember the context (I posted that two weeks ago). But I guess essentially I meant that U6 and X1 are derived from Asian or Eurasian lineages as follows: N>X>X1 and N>R>U>U6. So even if U6 and X1 coalesced in Africa, what is not too clear for X1 but is for U6 without doubt, they represent a back-flow from Asia, where their ancestors lived after the OoA (i.e. after the L3 node).

Of course, X1 is ultimately a sub-clade of N phylogeny. Likewise, U6. However, N is not the proto-X1 or proto-U6 ancestor of X1 and U6 respectively. You haven't produced a shred of evidence other than speculative opinion about U6 being anything but of African origin.

There is indeed a haplogroup known as U and defined under R by transitions at the sites 11467, 12308 and 12372. Most U is Asiatic or European, the only exception being U6.

You know very well that I'm not talking about the name of a macro-haplogroup; I am referring to a standalone haplotype that is simply called "U"; you made it entirely up, it doesn't exist!

Fact of the matter is, U6 doesn't derive from any European-specific or Asian-specific U clades. You want to create an imaginative "U" to force such a relationship.

there's no underived U6 either.

I just told you that, like a dozen times now. Yet you insisted that there is such a thing in Asia, under the banner of "U".

Mystery Solver said...

But we are talking haplogroups, with emphasis in "group", not prehistorical reconstructed lineages at their basal node.

YOU must have been referring to "groups". I was specifically referring to the U6 clade, which you profess to be Asian in origin, without a shred of evidence, other than to say that it belongs in the U haplo "group". Matter of fact, we don't even know if proto-U6 is Asian origin, as proto-U6 remains elusive. However, we do know that U6 clade itself is African in origin.

Maju said...

"F* need not always necessarily imply an hg F clade that lacks downstream mutations"...

Not at all what I meant. Ancestors died all long ago. All F is derived, as is any other haplogroup. Just that it's something else than the usual downstream clades, what adds to basal diversity.

"You've got to do better than that".

I wish I could.

"I need specifics on the loci of these F* that you are alluding to, and independently verify if they are in fact upstream clades".

They are not. They are just "other F". They are not G nor H nor IJK however.

"If it "basal diversity" you were alluding to, I have not seen any substantiation from you that would suggest "Palestinian" hg J1 clades are more diverse than the Ethiopian examples".

I cannot substantiate it. Remember that Palestine is an occupied country and that therefore all the data that comes from there is subject to Zionist filtering and no study that I know has researched Palestinian J1 so well.

All I can say is that in Semino 2004, the haplotype structure looks Asian-centered, except for the grayed area, which may well be centered in North Africa (but not too clear).

Also I can say that in Tofanelli 2009, fig. S1, the highest diversity of J1 is detected (quite unexpectedly) in South Portuguese, Iranians and Kurds, all with rather low frequencies however. Ethiopians have rather high diversity indeed but in line (0.30-0.40) with Central Portuguese, Italians, Turks and Lebanese and are not the top ones in any case. No Palestinians were sampled anyhow.

"Taking the example of hg M, the L3 marker that likely left, would have been the proto-M3 clade. An African L3a clade suggestive and exemplary of this has found identified".

The proto-M clade went extinct long ago, only M remains (actually only derived M sublineages, no M-root, logically).

L3a is a different clade from M and N, a "sister" lineage like the other L3 subclades, namely: L3b'f, L3c'd'j, L3e'i'k'x and L3h. M is defined under L3 by transitions at loci: 489, 10400, 14783 and 15043, while L3a has transitions at loci: 152, 12816, 16316. Not a single one is coincident.

"Also, a lot of the times, some folks tend to view DNA marker networks rather simplistically. Like for instance, this notion that all M and N clades are exclusively "Eurasian"".

That's obviously a simplification. Similarly not all L(xM,N) is African. Some (not many but a few) clades are probably of Arabia Peninsula origin, while others must have coalesced in North Africa specifically (sure, part of Africa but a special part anyhow). A lot of authors tend to see all L(xM,N) as in these two areas as product exclusively of the slave trade, something I disagree with. In fact some of those lineages may have been in those areas for many many millennia and in some cases at least they may be a remnant of the OoA migration process.

To my still imperfect understanding these may well be: L0f2, L0a1b, L5c, L3e2, L3i and L6 in the Arabian case. In North Africa I suspect as "Aterian": L2a1j, L3k, L3d1c and L3b1b.

But I have no doubt that M and N coalesced in Asia, specifically in South Asia (M) and SE Asia (N and its largest derivate: R). Regardless that some sublineages like U6 did coalesce back in Africa (what implies a back-migration).

...

Maju said...

...

"There is some tendency out there, to simplistically look at human genetic structure and imply that only a uni-directional flow can take place most of the time".

Well, in some cases at least the flows look rather unidirectional (a small group of immigrants arrived and managed to thrive). In others, as the North Africa-SW Europe one or the North/NE Africa-West Asia ones, they probably imply bidirectional flow (but not necessarily in strictly equal terms).

I agree in any case with your word of caution in this aspect.

"Hence, you have people claiming that say, any hg M or hg N, can only be indicative of back-migration; it is not possible for certain hg M or hg N clades to be peculiar to Africa"...

One thing does not exclude the other: U6 originated in Africa (very clearly so) but its ancestors (U, R, N) were Asians (after older ancestors in Africa, of course). So U6 in Europe or West Asia implies flow from Africa but U in Africa (U6 mostly) implies flow from Asia at an earlier stage.

"... basal clade to all M clades, be it south Asian or African, has been located in Africa"...

No, that's L3: an earlier stage before M. M coalesced in Asia, there is no doubt about that because 44.5 out of 45 basal subclades are located in Asia (or Oceania in some cases).

Similarly we know that L3 coalesced in Africa because 5 out of 7 basal clades are clearly African (even if two are not).

If you think you can argue that M might not be Asian because M1 is partly located in Africa, then someone could also argue that L3 is not African because M or N are located in Asia. Both are wrong and the reason is where most basal lineages are found (basal diversity). There are less clear cases like, say, N2, but when a clear majority of basal sublineages is still found in a region, then that region is surely the origin.

Besides, did you take notice of the new adscription of M1 to M1'51, sharing a transition at 14110? M1 is not anymore even basal within M but second tier derived.

"I think much of it has to do with anti-African prejudice amongst non-African folks".

I agree with this assessment. And believe me that, in spite of being European, it pisses me off a lot. However we have to be objective and when a case of back-migration from Asia or Europe is clear, it is.

But there is more than just that: Africa is clearly undersampled and under-researched (slowly improving but not as much as I'd wish), also, as I said before there is a tendency to attribute every single case of L(xM,N) to the slave trade. However a lot of North African and Arabian L(xM,N) does not fit well with such conjectures and rather looks like very old substrate. There is also a bad understanding of intra-African structure.

...

Maju said...

...

"And no, the "northern" Africa has never been separated from the rest by the Sahara; that is a myth. Ever heard of the historic tran-Saharan trade network?"

Of course, but that's recent (not more than 2000 years or so) and unlikely to have caused the impact some claim.

Otherwise the Sahara was wet and hence easily transitable in two known periods: the Abbassia Pluvial (c. 120-90 Ka) and the end of Ice Age. The Mousterian Pluvial, c. 50 Ka ago, was it seems not intense enough to make the Sahara very transitable, though I'm a bit unsure about this last. You cannot currently cross the Sahara on foot and that was the case through most of Human prehistory (with the said exceptions and the Nile corridor, as well as whatever coastal Red Sea routes there might have existed). Only with the domestication of the dromedary and its arrival to Africa eventually, the vast desert could be tamed a bit.

"... there is no such situation with hg M1, whose ancestor has already be identified in African sampling".

I'm pretty sure you are confused about this. I remember a claim in the line you say but was soon dismissed. So far there's no pre-M anywhere other than L3 (derived L3, of course).

If there would be a pre-M in Africa or anywhere, I'd certainly like to know about it but it seems a case of misinterpretation.

"Correction:U6, M1 and X1 are found "south of the Sahara"".

But where? AFAIK excepting M1, their frequencies are low and clearly derived from North African clades. U6 has important presence in Mauritania and therefore also in Senegal probably but it's a clear case of flow from North Africa, possibly at the end of the Ice Age (and/or Bedouin migrations).

In any case I agree that these three lineages are old in Africa. There's no discussion about that.

"In fact, another U clade implicated in an African origin, is U9".

Maybe. Is this one common in Egypt? In this case we are before a subclade of U2'3'4'7'8'9, which again is clearly West Asian by origin (with important presence in Europe, Central and South Asia, and documented as U2 in Eastern Europe c. 30 Ka ago).

"I'll agree with you however, with regards to H and V clades"...

It's something. :)

Maju said...

"... instead of simply saying "M", which does not exist".

M does exist, of course! It's made up of all M subclades (45 last time I counted them). The same happens with every single haplogroup. M1 is made up of M1a and M1b, M1a is made up of M1a1, M1a2, etc.

Each individual lineage can be different (not necessarily in the case of mtDNA but it's the common thing anyhow). When we talk of haplogroups we talk of hierarchically ordered sets of such individual lineages, which share a common ancestor (and the corresponding mutations).

The ancestors all died long ago, their ancestral lineages do not exist anymore, anywhere. We have to judge based on derived lineages, in all cases.

There is no L3 underived, no L1 underived and no H underived: all actual lineages have derived mutations: they are subclades. I thought you had this basic ABC of population genetics clear, but seems I was wrong.

I'm not coming back until you get that straight, sorry. I am very interested in African genetics (and everything else African or human in general) but I need to discuss with someone who knows what he/she is talking about. Sorry about this but you are never going to find any proto-haplogroup because they are all found as highly derived modern lineages.

You seemed to know that DE* is not DE-root but DE-derived (other than D or E) but now you come with this? Sorry, I can't discuss with such a misconception on your side.

"the U6 clade, which you profess to be Asian in origin".

I do not. I have repeatedly said that U6 coalesced in North Africa. It is its ancestor U which is Asian. But you do not seem to understand what "haplogroup" means.

Mystery Solver said...

Maju writes:

Not at all what I meant. Ancestors died all long ago. All F is derived, as is any other haplogroup. Just that it's something else than the usual downstream clades, what adds to basal diversity.

That's not necessarily true. There are paraphyletic clades, that do lack downstream mutations of the more established clades. But then of course, there are other paraphyletic clades, that are simply poorly understood sister clades of pre-existing clades.

I wish I could.

That's unfortunate, because if you could, you might have a case to stand on.

I cannot substantiate it. Remember that Palestine is an occupied country and that therefore all the data that comes from there is subject to Zionist filtering and no study that I know has researched Palestinian J1 so well.

That is no good enough. Furthermore, that should not stop you from seeking data from neighboring non-occupied Arab populations.

All I can say is that in Semino 2004, the haplotype structure looks Asian-centered, except for the grayed area, which may well be centered in North Africa (but not too clear).

I'm not sure you sufficiently understand what it is you are referring, as the results related by Semino et al. 2004, re: internal diversity [mind you, not of pooled samples, but individual populations] and time frame estimations, contradict what you are saying.

Also I can say that in Tofanelli 2009, fig. S1, the highest diversity of J1 is detected (quite unexpectedly) in South Portuguese, Iranians and Kurds, all with rather low frequencies however. Ethiopians have rather high diversity indeed but in line (0.30-0.40) with Central Portuguese, Italians, Turks and Lebanese and are not the top ones in any case. No Palestinians were sampled anyhow.

Not only is the Ethiopian J1 clades internal diversity high, but also according to the topic you are replying to [in line with data from the three studies I already repeatedly referenced to you], it is stated that unlike the Caucasus chromosomes, the paraphyletic Ethiopian clades have no haplotype structure, and doesn't form the star-like structure as in the northern African counterpart; and post goes onto note [blog post study] >...

"The .2 variant shows its frequency peaks in Africa (North and East) and Caucasus. Data from the middle East is scanty and we are currently investigating various populations from this region to gather more information on the distribution in this area (data not shown). The presence in Europe is limited and the occurrences in both US and Asia (India and Malaysia) can be considered as the result of a recent introgression of African and/ or European haplotypes.

The reason for diversity in places like Anatolia, is attributable to multiple dispersal, and hence founder effect situations, as noted by Semino et al. 2004. This is also likely to be the case in some European territories, as the Caucasus sampling exemplifies, yet again. This is not the case described for the Ethiopian chromosomes.

Mystery Solver said...

The proto-M clade went extinct long ago, only M remains (actually only derived M sublineages, no M-root, logically).

This is grounded in apparent falsehood, as a clade already ancestral to hg M and lacking M downstream mutations but a downstream L3 clade is being specified above. Simply ignoring it, is not a substitute for refuting the empirical evidence.

L3a is a different clade from M and N, a "sister" lineage like the other L3 subclades,

That's because you are choosing not to read the nucleotide specifics of the L3a subclade I'm referring to, as mentioned in the blog post on M1. Instead you want to react with a priori speculations and denials.

Similarly not all L(xM,N) is African.

Give me specific examples, as opposed to Simon-says-so speculations.

Some (not many but a few) clades are probably of Arabia Peninsula origin

Specifics!

while others must have coalesced in North Africa specifically (sure, part of Africa but a special part anyhow).

Creating a pseudo-apartheid zone on the African continent and picking your personal liking of what is supposedly "special" does not elevate your position,. In fact, it makes you look silly.


To my still imperfect understanding these may well be: L0f2, L0a1b, L5c, L3e2, L3i and L6 in the Arabian case.


Let me get this straight: These are supposed to be Arabian specific L clades, right? Tell me you are not entertaining such a thought.

But I have no doubt that M and N coalesced in Asia, specifically in South Asia (M) and SE Asia (N and its largest derivate: R).

Just like your belief in religion, I'm sure you don't doubt what you want to believe about hg M. But to make a scientific case, you'll need to demonstrate your merit of your belief with empirical data, which you lack. I now you lack this, because you reply my posts with denials and speculative reasoning -- nothing hard. Speculative reasoning is not gospel truth.

Mystery Solver said...

Maju writes:

I know that, what I say is that U does, and U6 is a derivative.

There is no such thing as standalone "U" clade. You are imagining things.

I am as updated as I can, believe me.

But your posts, belie you, which makes it hard to believe you are as "updated as you can". Perhaps you need to notch up your effort.

The UP complexes, which are several, all look at least partly intrusive, main exception being the Capsian Late UP culture.

Examples of these "several".

The Dabban industries of Cyrenaica are generall understood as an offshoot of West Asian ones, the same that Aurignacoid industries in Europe are.

Tell me what makes the Dabban industry "Aurignacoid"? Does it not have lithic industry culture peculiar to it? And why?



The Oranian culture is claimed by some to be of NE African origin but this is inconsistent with the oldest C14 dates being in Morocco, so it seems a pretty awful revisionism without merit.


Actually the burden is on you. You are not going to sit there an tell me that the Lithics of the Ornian culture are all duplicitous renderings of far older complexes overseas, are you? If so, let's have the specifics on this.

I have given some serious thought to the Oranian issue and to the fact that North African mtDNA H clades (24%, to which V should be added probably) are derived from SW European ones (Cherni 2008). And my only possible conclusion is that there was in fact an interaction between Iberian Gravetto-Solutrean and North Africa at that point.

When you note haplogroup H, you are in effect relying on living populations. Modern Maghrebi populations are only Holocene era originated. The Maghrebi sub-clades of hg H are of holocene or recent epoch provenance, nothing that goes back to the Paleolithic, less alone the Oranian complex. You cannot use that marker as a substitute for material lithic evidence for your suppositions.

In any case there is an important SW European layer in North Africa, evidenced by mtDNA H and probably V as well, and the only moment of clear connection is that of the Oranian genesis, which is slightly but significantly younger than the arrival of Gravettian and then Solutrean to Iberia c. 23-22 Ka ago.

This is only conjectural talk with next nothing grounded on empirical data. You disagree? Show me the data.

Mystery Solver said...

Well, in some cases at least the flows look rather unidirectional (a small group of immigrants arrived and managed to thrive). In others, as the North Africa-SW Europe one or the North/NE Africa-West Asia ones, they probably imply bidirectional flow (but not necessarily in strictly equal terms).

I agree in any case with your word of caution in this aspect.


I was actually referring to this obsessive tendency to interpret any African LM or LN derivative marker as being suggestive of "back-migration", with little to no material grounding.


No, that's L3: an earlier stage before M.

Let's test your denial. Give me a nucleotide demonstration of an non-M and generic L3 clade that has these nucleotide position substitutions:

Both "DdeI site at np 10394 and an AluI site of np 10397"

M coalesced in Asia, there is no doubt about that because 44.5 out of 45 basal subclades are located in Asia (or Oceania in some cases).

Your reasoning is grounded in faulty logic. It casts doubt on your opinion that you wish to pass for fact.

If you think you can argue that M might not be Asian because M1 is partly located in Africa, then someone could also argue that L3 is not African because M or N are located in Asia.

This is your imagination. You have barely gotten anything I've put in print here correctly, let alone presume to know what I think.


Besides, did you take notice of the new adscription of M1 to M1'51, sharing a transition at 14110? M1 is not anymore even basal within M but second tier derived.

You keep repeating this line, all the while avoiding earlier questioning on it. What's the hold up for?

Mystery Solver said...

Maju writes:

Of course, but that's recent (not more than 2000 years or so) and unlikely to have caused the impact some claim.

Recent, precisely! That's all the more significant, because it has been a desert ever since. That did not prevent interaction between coastal northern African and those south of the Sahara. Even more ridiculous, is the attempt to chop northern Africa off the remainder of Africa in the present era, even though there is no such thing as a barrier between the coastal north and south of Sahara. There is plenty of genetic exchange and interaction going on across the Sahara as I write this post.

I'm pretty sure you are confused about this. I remember a claim in the line you say but was soon dismissed. So far there's no pre-M anywhere other than L3 (derived L3, of course).

My confusion is a figment of your imagination. If you disagree, then tell me why you continue to fail on delivering substantive rebuttal, short of unsophisticated denials, to my nucleotide proof for this, with requested demonstration for a generic hg L3 clade that has the basal nucleotides that are otherwise only characteristic of hg M. Your assessment of my supposed confusion seems to be wishful thinking on your end.

Rather, I think you are either willfully or unwittingly confusing what I'm talking about, and it is not some generic L3 clade, but a specific L3a clade given the nominal name of "AF24". If you bothered reading the blog post, you would not confuse what L3 haplotype I'm referring to, and why I'm referring to it. The problem is, the only way you can diminish the significance of haplotype AF24, is if you were to demonstrate that it does not have the basal motifs generally characteristic of only M clades and not the generic L3 clades. Guess what? Such a rebuttal will be next to impossible, but I await your trial all the same.

If there would be a pre-M in Africa or anywhere, I'd certainly like to know about it but it seems a case of misinterpretation.

From your best efforts here so far, I highly doubt you are all that all-knowing.

But where? AFAIK excepting M1, their frequencies are low and clearly derived from North African clades.

Ever heard of Ethiopia for instance? Does it lie above or below the Sahara?

U6 has important presence in Mauritania and therefore also in Senegal probably but it's a clear case of flow from North Africa

Of course, they derive from the Saharan U6. The point in contention is your claim that the clade is nowhere to be found below the Sahara, which is grounded in myth. Don't try to change the subject to implying that there is contention in northwest/Saharan African origin of U6. The attempt at trickery is doomed to fail, trust me.

Maybe. Is this one common in Egypt? In this case we are before a subclade of U2'3'4'7'8'9, which again is clearly West Asian by origin (with important presence in Europe, Central and South Asia, and documented as U2 in Eastern Europe c. 30 Ka ago).

If you were all-knowing as you profess to be, there would not be a "maybe" reaction about this; you'd know it off the bat as soon as it was mentioned. The logic you seem to apply to African-specific U clades is amazingly faulty; common sense says that a clade which is African-originated cannot be of "West Asian" origin at the same time...unless you think Africa and "West Asia" are one and same.

I'm willing to bet you cannot locate a standalone proto-U9 clade in "West Asia" for me, if pressed. Yet, with this non-existent situation, you will swear that this proto-U9 is also Asian. You are proceeding not from an objective perspective, but from a purely ideological one.

Mystery Solver said...

M does exist, of course! It's made up of all M subclades (45 last time I counted them).

You are confusing a standalone "M" clade, which does not exist, with the haplo group.

There is no such thing as an Asian proto-M1; it is all in your head only. Take a cue from Metspalu et al.


There is no L3 underived, no L1 underived and no H underived: all actual lineages have derived mutations: they are subclades. I thought you had this basic ABC of population genetics clear, but seems I was wrong.


And you are still wrong. The only in the dark about what's being discussed is you. You can't tell the difference between a presenting "M" as a standalone "prototype"/ancestral clade and presenting it, on the other hand, as a haplogroup. I spoke of "proto-M1" and you interpreted it as "M". You are not in a position to be barking about anyone else not knowing the ABCs of anything without getting your own abc basics in check.

Of course, there is such clades that are ancestral, and nominally "underived" for the more downstream clade. If you knew your ABCs in genetic, this would be a no-brainer.


I'm not coming back until you get that straight, sorry.

Cop-out.


I am very interested in African genetics (and everything else African or human in general) but I need to discuss with someone who knows what he/she is talking about.


To do that, you'd need to know what you are talking about first.

Sorry about this but you are never going to find any proto-haplogroup because they are all found as highly derived modern lineages.

That's BS. A prototype clade is standalone clade that lacks the derivative mutations of the more downstream descendent clade. Anyone acquainted with their ABCs with know this by common sense. That you don't have this common sense, is revealing about you.


You seemed to know that DE* is not DE-root but DE-derived (other than D or E) but now you come with this?

And now, a pathetic attempt at accusing me of ideological bias. You are funny. DE* is ancestral to both D and E, so of course, it is prototype clade for E and D. The DE* designated clades DO NOT have downstream mutations of either clade D or clade E. And guess what? They are actual standalone clades in their presently known states, not merely basic motifs shared across hg E or hg D. The problem with your Asian-originated M1 dilemma, is that you cannot find an M1 equivalent of DE* in Asia, because it is non-existent. However, you can find this equivalent in the African L3a haplotype "AF24". It is obvious who is not in the know here, and it is not me. No simpleton writes elaborate notes on neocleotide loci as I do on blog posts here; you'd have to be drunk to jump to that conclusion.


Sorry, I can't discuss with such a misconception on your side.

Undisguised cop-out.

You tried to make phony screw-ups of what I'm saying, just so you can cop-out eventually, by spreading a white tale about my confusion. You know very well what I was asking for when I requested empirical evidence of your supposed Asian-based "Proto-M1". You tried to use "proto-M1" interchangeably with haplogroup "M", saying that "M" is ancestral to M1, and then when called on the absurdity of any such thing as "M" as a standalone ancestral clade, you switched gears to claiming that you were taking "M" to be understood as a "haplogroup". Even if one were to take this latter phony excuse, it does not make any coherent sense for a "haplogroup" to be a "proto-type" clade for M1.

Mystery Solver said...


"the U6 clade, which you profess to be Asian in origin".

I do not. I have repeatedly said that U6 coalesced in North Africa. It is its ancestor U which is Asian. But you do not seem to understand what "haplogroup" means.


You are funny. You are the one who used "haplogroup" interchangeably with "proto-U6", as you did with "M1". When asked for specifics of an Asian "proto-U6", you go onto speak of "U" as the presumed clade. When called out that there is no such thing as a proto-U or ancestral U6 clade as "U", you conveniently switch gears to saying that you meant "U" by a "haplogroup". By your own excuses, you are in effect saying that you don't grasp the difference between a "haplogroup" and a standalone ancestral or prototype clade of either say, hg U6 or hg M1.

Maju said...

A haplogroup is the set that includes all lineages which share a common ancestor. So all L3 lineages, including M and N, share a female ancestor by pure matrilineage at the L3 node.

Similarly all M lineages, including (M1, C, D, etc.) share a common ancestor at the M node and all U lineages (including U6) share a common ancestor at the U node.

I have never claimed that there is any living such ancestral haplotype. That is practically impossible because all lineages evolve. It is you who is making unsubstantiated claims or absurd demands about that.

All I say is that such ancestors existed in the remote past and the area of their existence can only be inferred from where the highest basal diversity exists today (it's most parsimonious and logical). In the case of L3 it is Africa, near Ethiopia or Sudan, in the case of U6 it is NW Africa, in the case of M is South Asia, etc.

All these haplogroups (or clades, because haplogroups are a type of clades) are like matriushka dolls and fit into each other hierarchically (because they descend from each other at the ancestral nodes).

"Take a cue from Metspalu et al."

It's obsolete. It has been this last year when M51 was fit in (PhyloTree is no amateur site). And in any case, M was always the ancestor of M1, exactly the same as L3 is the ancestor of M.

"... there is such clades that are ancestral, and nominally "underived" for the more downstream clade".

Show me one. I have not seen anything like that in my life and I have been reading, discussing and writing on population genetics for many years now.

All present day haplotypes are derived (unless maybe if you are talking of a really recent haplogroup which had no time to accumulate any downstream mutations). There is no M1-root anymore (there can be M1* but that is not the same), there is no U6-root anymore, there is no H-root anymore and of course there's no M nor L3 nor anything that old in its root form anymore. Eventually all descendants accumulated mutations downstream the ancestral node.

"That's BS. A prototype clade is standalone clade that lacks the derivative mutations of the more downstream descendent clade".

Show me one, please. I challenge you to find a single sequence with M1 or anything vaguely that old that is underived from the ancestral node state. Such thing does not exist.

"DE* is ancestral to both D and E".

No. DE* is just other lineages derived from DE-root which fall out from D and E. DE root existed once upon a time in the patrilineal ancestor of all modern DE people, incl. D, E and DE*. The difference is that D and E are monophyletic (they descend from "grandfathers" who had the original D or E state, respectively), instead DE* is paraphyletic by definition because is just all the DE sublineages that never went through either the D or E nodes (they probably have their own unique histories but we do not know much about them, because they are so rare and ill-researched). DE* could be one, two, three or a dozen sublineages of DE (let's say DE1, DE2, etc., even if it's at the moment mere speculation). IMO the Tibetan DE* is probably just one single DE sublineage but the African DE* could be several (at least is more scattered).

"You tried to use "proto-M1" interchangeably with haplogroup "M", saying that "M" is ancestral to M1"...

It is: M-root, the M node underived (not anymore extant) is ancestral (was the ancestor) to M1. Other M sublineages are not (they are horizontal relatives. "sisters"), but they are still informative about where the women who carried the M-root lineage in the deep past lived: in South Asia with all likelihood.

(continues)

Maju said...

...

"Even if one were to take this latter phony excuse, it does not make any coherent sense for a "haplogroup" to be a "proto-type" clade for M1".

This seems a misunderstanding of what I meant. Maybe I expressed myself incorrectly (expecting you to understand what I meant). I did not expect to need to give such complex explanations about phylogeny, as it's the basics.

You still seem to think that ancestral lineages exist in the present day but you are wrong about that. Mutations accumulate generation after generation and, even if the mtDNA is relatively small and therefore relatively stable, mutations must have accumulated in every single M descendant in the 80,000 years or so that have passed since M-root existed in its original form. The same applies to M1 and to every other haplogroup you can think of.

When we say "haplogroup" we mean that (as far as we can tell) all members share a common ancestor at the shared root: all M people share a common "grandmother" (by pure matrilineage) in the person who first evolved that series of mutations defining M. But all descendants have accumulated mutations, these mutations indicate other haplogroups (other "grandmothers" of each sublineage, for example M1 was one of those "grandmas" who had M as "grandma" herself, the same as did M2, M3, M8, D, etc.)

This is basic and that's why I am having difficulties when discussing with you, because I expected you to understand all this.

"When asked for specifics of an Asian "proto-U6", you go onto speak of "U" as the presumed clade".

U6 is a descendant of U (U-root, a lineage that existed once upon a time, maybe 50 Ka ago) it is not descendant of other U sublineages such as U5, etc. U5 and U6 are "sisters" (many generations apart, of course: distant cousins).

"When called out that there is no such thing as a proto-U or ancestral U6 clade as "U", you conveniently switch gears to saying that you meant "U" by a "haplogroup"".

I do not switch gears: I meant that all the time. U as haplogroup means that all U people share an ancestor at the U node (this is real, but the ancestor lived long ago - logically: that's why she is an ancestor).

So how can we decide where that U ancestor or her "tribe" lived? By joining the dots of where her descendants live now: some live in North Africa, others in Europe, in West Asia, in India, etc. The first thing that comes to mind is West Asia, which is right in the middle. Careful discernment of the various subclades, where basal diversity is greater, etc. does not seem to indicate differently, so for me it's pretty much confirmed.

Similarly with U6 I concluded already in 2006 or 2007 (with Maca-Meyer's data but against her conclusions) that U6 must had coalesced in or near Morocco. A couple of weeks ago a new paper comes out that says exactly that (I appreciate that confirmation of what I already thought, really, because since then I can refer to an authority instead of just explaining once and again why I think so).

But I'm having to give to many basic explanations and we are getting bogged down in a circular discussion, because we have clearly different foundations (and I think that yours are somewhat confused).

So my question is: do you really believe that ancestral lineages still exist in living people? If so, do you have an example? (link please)

Mystery Solver said...

Maju writes:

A haplogroup is the set that includes all lineages which share a common ancestor.

Glad you looked up the definition after our exchange. Now, look at the difference between an "ancestral" or "proto-clade" and a "haplogroup", and then report back.

Similarly all M lineages, including (M1, C, D, etc.) share a common ancestor at the M node and all U lineages (including U6) share a common ancestor at the U node.

*Name* the "common ancestor" clade of hg M and hg U *respectively*. I hope you know what a "clade" is.

I have never claimed that there is any living such ancestral haplotype.

Haplotypes don't live. People carrying them live.

That is practically impossible because all lineages evolve. It is you who is making unsubstantiated claims or absurd demands about that.

I'm guessing English is not your first language. I demanded that you produce the "proto-clade" or "ancestral" clade of M1 and U6 respectively, since you keep telling me fairy tales about how M1 and U6 originated in Asia. Demand for substantiation is a no-brainer and can only be dismissed as absurd by one who is spreading emotional-driven propaganda rather than fact.

All I say is that such ancestors existed in the remote past and the area of their existence can only be inferred from where the highest basal diversity exists today (it's most parsimonious and logical).

In the case of hg M1, the ancestral clade does not have to be inferred, because it has been identified. I tried to ram that into your head to no avail. You insist that U6 is of Asian origin, yet you don't even know the ancestral-clade for this lineage. You are a joke.

There is no M1-root anymore (there can be M1* but that is not the same)

Pure BS. As outlined in the blog post, which you seem too scared to address head-on, M1's basic motifs are outlined. Let me teach you:

Hg M is defined by 10400 C->T transition, as well as DdeI site at nucleotide position 10394 and an AluI site of nucleotide position 10397.

The only, and I mean only, hg L3 clade that has *both* mentioned restriction and insertion sites [@ np 10394 and @ np 10397], is the African L3a "AF24" haplotype. This haplotype is a downstream clade of L3, but it is upstream vis-a-vis haplogroup M. This clade therefore serves as a "prototype" clade for the entire M haplogroup.

Therefore, a proto-clade for hg M1 and the rest of the M family has already been located...in Africa!

Haplotype "AF24" is not simply a generic L3 clade, as you insisted ad nauseam, when I was trying to teach you earlier. It serves as an L3-derived basic node for the entire M haplogroup.

Additionally, as I was trying to teach you, only to have you fool around, even if this prototype haplotype were not found, there is still a subset of African L haplogroup gene-pool that has yet another node that could create conditions for an M-type clade to emerge. This is represented by the transition 10873C. Haplogroup M is the ONLY non-African mtDNA family that retains this transition along with the African L types.

But I suspect that all this is too much for your mind, and you'll in all likelihood react with emotional, irrelevant made up stories of how I supposedly don't know what I'm talking about. Cheap cop-out.

Mystery Solver said...

Continued...

Maju writes:
and all U lineages (including U6) share a common ancestor at the U node.

Name the "common ancestor" of U.

All I say is that such ancestors existed in the remote past and the area of their existence can only be inferred from where the highest basal diversity exists today (it's most parsimonious and logical). In the case of L3 it is Africa, near Ethiopia or Sudan, in the case of U6 it is NW Africa, in the case of M is South Asia, etc.

Goobledygook. Ancestral clades for several L3 respective sub-clades have been located [while others may just be in the paraphyletic stage]. Likewise for haplogroup M, as I elaborately demonstrated in the last post. U6's proto-clade or ancestral clade, on the other hand, remains elusive. It is only tied to other U sub-clades via certain basal motifs, which cannot be deemed as an actual common ancestor, since there is no specific empirical clade that characterizes only the said basal motifs and nothing further downstream.

It's obsolete. It has been this last year when M51 was fit in (PhyloTree is no amateur site). And in any case, M was always the ancestor of M1, exactly the same as L3 is the ancestor of M.

Metspalu et al.'s assessment is not obsolete. Take a cue from . That M1 does not derive from any Asian-specific M clade, still stands. That south Asia essentially lacks M1, still stands. That no proto-M1 or M-like ancestral L3 clade has not been located in south Asia, still stands.

I keep telling you that there is no such ancestral-clade called "M", only for you to turn around and make an excuses for yourself, in that you are referring to the "haplogroup" that is called "M", not a clade. This is how you start confusing yourself, and then covering it up by making up stories about my supposed confusion. This is what Metspalu & co. were trying to penetrate into your head; there is no such thing as an ancestral-clade going by the name of "M". It is just a figment of your imagination.

You speak of M51 as a supposed "sister clade" of M1, going by some mere reshuffling of nomenclature on "PhyloTree". First of all, all recent publications don't even agree on the nomenclature standards, making matters worse. You can take a cue from Chandrasekar et al.'s (2009) note of that fact. I also noticed that your supposed source, "PhyloTree", only links the M51 clade to the M1 family via the singular 14110 nucleotide position. This does not make this clade M1's sister clade any more than it makes any other south Asian-specific M clade M1's sister clade. This nucleotide substitution has been implicated in a few other distinct M clades and not just a single other clade, and in fact, appears to be nothing more than a recurrent mutation. In other words, the substitution doesn't appear to be a UEP. It is found in for example, singular extreme sub-clade of one M monophyletic unit and then it appears as a basic transition in another M monophyletic unit. This suggests recurrent mutation, as opposed to a unique event.

Mystery Solver said...

Maju writes:

"... there is such clades that are ancestral, and nominally "underived" for the more downstream clade".

Show me one. I have not seen anything like that in my life and I have been reading, discussing and writing on population genetics for many years now.


That is because basic molecular genetics is way over your head. It is not for everyone, you included. You are not the all-knowing, so you are not the be-and-all of what is supposed to be known. You are expected to not know certain things in all your life -- basic genetic stuff being an example.

You want an example of an ancestral clade? Simple, here is one: Clade DE*. It is ancestral to hg E and D!

Here, is another: Clade R*. Found in samples, wherein the basic nodes of every known downstream R haplogroup had already been accounted for.

Yet another...

"Two mutations (M122 and P198) now define the large O3 clade, which is subsequently divided into a major subclade (O3a) that is defined by five mutations (M324, P93, P197, P199, and P200) and an underived lineage (O3*), which is found at low frequencies in China, Taiwan, and Indonesia." - Karafet et al. 2008

No. DE* is just other lineages derived from DE-root which fall out from D and E.

You are trying to say DE* (YAP+) is a sister clade of the more downstream clades of D and E, which is quite comical, and just goes to show how much you know about molecular genetics. Using your logic, the upstream YAP+ clades found in African samples, that lack either of haplogroup E and haplogroup D downstream basic nodes, is simply a derivative of these same clades nonetheless. What planet do you come from? It ain't earth, that's for sure. LOL.

Mystery Solver said...

Maju writes:
The difference is that D and E are monophyletic (they descend from "grandfathers" who had the original D or E state, respectively)

...and DE* clades are not monophyletic? What a joke.

My friend, DE* form a monophyletic unit with hgs D and E, since these clades test positive for YAP+, a UEP, but just do not test for any of the basic nodes respective of hg D and hg E.

, instead DE* is paraphyletic by definition because is just all the DE sublineages that never went through either the D or E nodes (they probably have their own unique histories but we do not know much about them, because they are so rare and ill-researched).

Your logic is faulty and simply a priori speculation. It is not a rebuttal. Can you demonstrate to me that the DE* clades at hand have accumulated substitutions on comparable levels as those of the established DE-descended haplogroups of E and D respectively?

Do you realize that ancestral loci are determined from cross-reference between distinct haplogroups from divergent monophyletic units, or is this news to you, as well?

It is: M-root, the M node underived (not anymore extant) is ancestral (was the ancestor) to M1.

I rest my case. You don't know the difference between a "proto/ancestral" clade and a "haplogrou", LOL. This exchange was a dead-end from the start. You cannot reason with anyone who is this confused about the simplest of things in genetics.

Mystery Solver said...

Maju writs:

Maybe I expressed myself incorrectly

That, you sure did. Plain "M" cannot be the name of a "haplogroup" and serve as the name of proto-clade for each and every sub-clade of haplogroup M, with their distinctive bio-histories and most recent common ancestry.

And no, your abysmal self-expression is a fault that lies with you, not the reader. Your "blame the reader" attitude is foolish, or comical at best.

This is basic and that's why I am having difficulties when discussing with you, because I expected you to understand all this.

That's cheap. You screw up, and it is the other person that is making "difficult" for you. When was the last time you went outside for a breath of fresh air? It looks like you need one.

Maju said...

M is defined by transitions at the following sites (under L3): 489, 10400, 14783, 15043 (per PhyloTree), specifically (per Ian Logan's M1 page):

T489C C10400T T14783C G15043A

Where the first letter refers to the CRS and the last one to the M clade. All people under M have those mutations in their mtDNA (excepting maybe some back-mutation in some specific sublineage).

This is somewhat different than your claim of "Hg M is defined by 10400 C->T transition, as well as DdeI site at nucleotide position 10394 and an AluI site of nucleotide position 10397".

Nobody seems to be using DdeI or AluI as markers anymore. Only transitions (single nucleotide changes or SNPs) but I'm unsure why is this.

"Glad you looked up the definition after our exchange".

I did not look up anything. I popped it out from my head knowing it is a correct description.

"*Name* the "common ancestor" clade of hg M and hg U *respectively*. I hope you know what a "clade" is".

It is, for our purposes, the same as a haplogroup (per Wikipedia: "a group consisting of an organism and all its descendants"). So, your request has the following answers: L3 and and R, "respectively".

"The only, and I mean only, hg L3 clade that has *both* mentioned restriction and insertion sites [@ np 10394 and @ np 10397], is the African L3a "AF24" haplotype. This haplotype is a downstream clade of L3, but it is upstream vis-a-vis haplogroup M".

I'd like to know where you get that from because it sounds potentially interesting. It'd be interesting if M is not directly a basal subclade of L3 but a second level one. It'd be interesting also to know if this also applies to N, etc.

But as far as I can tell, no updated reference makes any mention to that and I fear you may be confusing moder L3a (unrelated to M) with Salas' L3A which is nothing but L3(xM,N). In other words, in 2002, when the mtDNA phylogeny was still poorly understood, Salas was probably stating that M and N are descendants from L3, something that was found out about those dates, not before.

"Therefore, a proto-clade for hg M1 and the rest of the M family has already been located...in Africa!"

Of course: L3 (I understand). That still says nothing about the direct ancestry of M1, which is M (and M1'51 as intermediate clade). So the matrilineal ancestors of modern M1 carriers in Africa did the following:

1. They lived in Africa (up to the L3 node or maybe a bit later)
2. They migrated to South Asia (M node, probably also the M1'51 node)
3. They migrated back to Africa (M1, either at the origin of this clade or after it formed "in route")

It is not that difficult and I think that you cannot accept something so obvious because of ideological fundamentalism. What is a real pity to be honest.

...

Maju said...

...

"This is represented by the transition 10873C. Haplogroup M is the ONLY non-African mtDNA family that retains this transition along with the African L types".

This is tricky. 10873T is the CRS value. CRS as you probably know is a European lineage in mtDNA H2a. 10873C is the ancestral value and the transition actually happened leading to mtDNA N, however as the CRS is downstream of N (it's within N) a lot of papers will indicate it as "happening" towards the root, i.e. towards non-N lineages but this is nothing but a confusing way of describing things because of where the CRS is located. Geneticists almost invariably refer to the CRS and we have to be a bit alert about that "Eurocentric bias" (yes, for me it's a case of factual eurocentrism in research).

What they discovered with that transition is nothing but haplogroup N.

"But I suspect that all this is too much for your mind"...

No, no. Now you are speaking more clearly. Thanks to that I can spot where you are right and where you are wrong more easily - and why.

Mystery Solver said...

Maju writes:

M is defined by transitions at the following sites (under L3): 489, 10400, 14783, 15043 (per PhyloTree), specifically (per Ian Logan's M1 page):

T489C C10400T T14783C G15043A

Where the first letter refers to the CRS and the last one to the M clade. All people under M have those mutations in their mtDNA (excepting maybe some back-mutation in some specific sublineage).


And...? Other than unnecessary spam-filling and to self-compensation, I fail to see how this follows up on anything specific from my last few posts.

This is somewhat different than your claim of "Hg M is defined by 10400 C->T transition, as well as DdeI site at nucleotide position 10394 and an AluI site of nucleotide position 10397".

It feels different, because you lack basic insight into the M clade, and any other for that matter. I am sure you managed to even overlook the fact that you merely repeated one of mentioned facts -- transition 10400 C->T, while trying to imply that the KEY nucleotide positions I cited are made up. You could easily cure yourself off this ignorance, by minimal research effort, and realize that these are very much real. The key insertion and restriction positions I noted can easily be googled, considering that you are obviously ignorant of them. They are key M motifs, because ONLY the M lineage has these nucleotide positions simultaneously. Simultaneous appearance of these sites denotes unique event polymorphisms that only characterize the M family. It is common knowledge. That you are in the dark about it, speaks volumes. Plus, these other nucleotide information that you speak of, are already mentioned in the blog post, which you didn't bother reading, while pretending to be debating with me.

And oh, denial is not a form of a rebuttal. It is a cop-out.

Nobody seems to be using DdeI or AluI as markers anymore.

That's a lie. I just cited recent journals making use of them. It would be foolish to ignore them, when they denote unique events that characterize a monophyletic unit.

Mystery Solver said...

I did not look up anything. I popped it out from my head knowing it is a correct description.

You must have looked it up, because in prior exchanges you didn't seem to have a clue about what makes an ancestral clade different from a haplogroup. When asked to cite an ancestral clade, you'd instead cite the name of a haplogroup.

It is, for our purposes, the same as a haplogroup (per Wikipedia: "a group consisting of an organism and all its descendants"). So, your request has the following answers: L3 and and R, "respectively".

It is funny that you have to turn to something like wikipedia just to get an idea of what a clade is. In molecular genetic terms, it simply means a lineage. A lineage is a basic node or UEP(s) that can characterize a single haplotype and/or a haplogroup.

I'd like to know where you get that from because it sounds potentially interesting.

It is in the blog post that you were supposed to have read before commenting. The question is, why do you comment without bothering to read or pay attention to the blog post you are supposed to be commenting about?

I would not be sitting here, trying to teach you everything that could have been learned from the blog post, had you bothered to do the minimum task expected of you as a reader: i.e. to read the blog post at hand.

Even the nucleotide information I gave you surprises you, while you jump the gun about my saying something different from the genetic research literature, when in fact everything that needs to be said is in the blog post, and that they come from actual genetic literature. The only logical explanation for this bizarre behavior is that you must be agenda/dogma-driven, instead of a pursuit of material truth.

Mystery Solver said...

Maju writes:
It'd be interesting if M is not directly a basal subclade of L3 but a second level one. It'd be interesting also to know if this also applies to N, etc.

This absolutely makes no sense. The marker in question IS L3, just not an ordinary L3 clade. It is a derivative clade, quite simply, because it has additional substitutions in otherwise ancestral loci on other L3 clades. This is 101 stuff, my friend. You should not be perplexed by stuff as basic as this.

But as far as I can tell, no updated reference makes any mention to that and I fear you may be confusing moder L3a (unrelated to M) with Salas' L3A which is nothing but L3(xM,N).

You fear is meritless, because it is based on a pointless a priori personal supposition, born out of personal ignorance and not availability of information. Again, this information I gave you was posted in the blog post you did not bother to carefully read.

Of course: L3 (I understand).

As a matter of fact, you don't understand what you were told just moments ago. I'm not speaking of any old L3 clade, rather I'm speaking of a particular L3 clade.

You argue by way of personal ignorance -- to put it rather politely; that is to say, if you personally are not aware of something, then it must not be so. This is like saying that you are supposed to be the almighty all-knowing omniscient being, who is everywhere. This is not a form of rebuttal by any stretch; it is just a red-herring and argumentative-by-ignorance.

That still says nothing about the direct ancestry of M1, which is M (and M1'51 as intermediate clade).

Of course it does; you are just too slow to realize and understand what you were just told.

It is not that difficult and I think that you cannot accept something so obvious because of ideological fundamentalism. What is a real pity to be honest.

The real pity here, is your inability to recognize just how slow you truly are. The lopsidedness of the exchange, in my favor naturally, speaks enough to this. Don't take my word for it; just review what has transpired here, and it might just sink in...maybe not right away, but when you are calm, collected and in your right mind, it just might eventually.

Mystery Solver said...

Maju writes:
This is tricky. 10873T is the CRS value.

It is only tricky to those who are not acquainted with genetic literature.

CRS as you probably know is a European lineage in mtDNA H2a.

I know what the CRS, I mention it all the time on this site. It sequenced by Caramelli et al., who re-sequenced yet again, along with mtDNA from Upper Paleolithic human remains found in southern Europe, upon critiques about their findings on possible lineages of the latter.

10873C is the ancestral value

Exactly, and the M haplogroup is the only major non-African gene-pool that retains this, outside of African L-type clades. Haplogroup N clades carry nucleotide transition of 10873T.

and the transition actually happened leading to mtDNA N

Absolutely absurd. No haplgroup N clade carries the ancestral locus of the nucleotide position 10873, which in this case is in the form of the transition designated by 10873C.

however as the CRS is downstream of N (it's within N) a lot of papers will indicate it as "happening" towards the root, i.e. towards non-N lineages

Your thinking is very simplistic. The CRS sequences has not only been cross-referenced against not only other N clades, but against M and African L-types. It is from such cross-references, ancestral loci vs. substitution sites have been discerned...and it has been determined that N clades generally have a substitution at the np 10873 in the form of a C->T transition.

but this is nothing but a confusing way of describing things because of where the CRS is located.

The one doing the confusing here, is you, because you don't know how sequencing works.

Geneticists almost invariably refer to the CRS and we have to be a bit alert about that "Eurocentric bias" (yes, for me it's a case of factual eurocentrism in research).

I'm well aware of Eurocentric bias. Using the CRS as a centerpiece in mtDNA sequencing in the first place and building the mtDNA phylogenetic network thereof may be one example of this bias, but empirical data on real distinctions in certain loci, after cross-referencing said loci across a multitude of divergent super-clades, is not one of them.