Haplogroup Assignment; Old Habits that Die Hard

Introduction:

It has become a common theme in DNA research papers dealing with population genetics, particularly those that are either published in the "west" or else rely heavily on references to previous publications by "western" research teams, to dichotomize human phylogeny neatly into two main types: African and non-African. As a result, a good amount of the readership of these papers have also become accustomed to treating human phylogeny accordingly. No doubt that the reactionary segment of that readership have applied such a phylogenetic arrangement synonymously with "races" of humanity.

It's one thing to assign human phylogeny into two main types, but it's another, in terms of how these assignments take form. One would be hard-pressed not to come across a single example, whereby lineage that is given an "L" designation in mictochondrial phylogeny, is automatically treated as "African", while the two main offshoots of the L3 clade are taken for granted as "non-African". Such arrangements tacitly or by design, insinuate non-overlapping phylogeny between the so-named two main groups. The discussion section will deal with this kind of arrangement of human phylogeny further, applying specific examples from published material.

R1*-M173 Chromosomes in Africa - II

On another matter of African haplogroup R chromosomes...

As of Dec 4, 2009, the following was released by Molecular Anthropology in the Genomic Era team which oversaw the 4th International conference of the series on DNA polymorphisms in human populations that took place at University La Sapienza - Rome from December 3 through to 5, 2009: 

Fulvio CRUCIANI (Italy)*

Human Y-chromosome haplogroup R1b1a (R-V88): A paternal genetic record of early-mid Holocene trans-Saharan connections

Human Y chromosomes belonging to haplogroup R-P25 are quite rare in Africa, being found mainly in Asia and Europe. However, a group of P25 Y chromosomes that are not defined by the presence of a downstream derived marker (the paragroup R-P25*) are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25* chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back-migration in prehistoric times. Here we describe six new mutations that define the relationships among the African R-P25* Y chromosomes and between these African chromosomes and previously reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R-P25 haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25*, about half of the few European/west Asian R-P25*, and the R-M18 chromosomes. A world-wide phylogeographic analysis of the R-P25 haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in more than 1,800 males from 69 African populations, revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic speaking groups from North Africa. The R-V88 coalescence time was estimated at 9,200-5,600 kya, in the early-mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin.

* With:

Beniamino Trombetta (1), Daniele Sellitto (2), Andrea Massaia (1), Giovanni Destro-Bisol (3), Elizabeth Watson (4) Eliane Beraud Colomb (5), Jean-Michel Dugoujon (6), Pedro Moral (7), Rosaria Scozzari (1)

(1) Dipartimento di Genetica e Biologia Molecolare, Sapienza Università di Roma, Rome 00185, Italy; (2) Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome 00185, Italy; (3) Dipartimento di Biologia Animale e dell'Uomo, Sapienza Università di Roma, Rome 00185, Italy; (4) The Swedish Museum of Natural History, Stockholm, Sweden; (5) Laboratoire d'Immunologie, Hôpital the Sainte-Marguerite, Marseille, France; (6) Laboratoire d'Anthropobiologie, FRE 2960, Centre National de la Recherche Scientifique (CNRS) Université Paul Sabatier, Toulouse, France; (7) Departament of Biologia Animal, Universitat de Barcelona, Barcelona, Spain.

Cruciani is known for making observations that don't exactly match up with what his actual DNA results show. The present author pointed this out on this site with both R1*-M173 chromosomes, E-M78 clusters and E-M34. So, the present author now reiterates what's wrong with his so-called "Asia-to-Africa back migration", which he seems bent on promoting, since otherwise would implicate European ancestry directly from Africa, which is known to get Eurocentrists' and closet-Eurocentrists' pants in a bunch.

Previously, when Cruciani (2002) thought he had come up with undifferentiated, upstream Hg R1* chromosomes, he considered it a possibility that this could be suggestive of African origin, since the African counterparts were phylogenetically more basal than his non-African sample collection; yet, this didn't phase him to entertain the alternative then, about back-migration to Africa, predicated on a flimsy case about Hg R, in its entirety as a family, not being as diverse in Africa as it appears to be in Asia. At the time, this was essentially Cruciani's sole argument for his preference of a back-migration scenario, which obviously contradicted the fact then, that his African samples were the ONLY ones which tested positive for the most basal R markers.

So now, he comes up with new markers, and tries to see if he can solidify his earlier rather debatable, if not flimsy, position. But even here, having sampled a number of Chadic-speaking populations in the central Sahel as a gesture of applying fine-tooth combing to the DNA sequencing of the Hg R chromosomes, particularly the perplexingly-unique African examples, he points out that the Hg R chromosomes bearing the "new mutations" he tested for are still more prevalent in Africa, and rarer in non-African areas. Yet, Cruciani wants to convince us that this is some sort of unequivocal proof that Africans must have attained it from back-migration, and he tries to reinforce this effort, by invoking early Holocene estimation dates. Also, contrary to Cruciani's mindset, it is not necessary for *all* the sub-clades of K to emerge in Africa, in order for the origin of K-M9 on the continent to be probable. Hg K's most immediate descendants like Hgs T, K1, K2...etc do not form monophyletic branching with respect to one another, but each of them form their own distinctive branch from the ancestral K-M9 node. Nor is it even necessary for the M9 mutation to have emerged in Africa, in order for R to emerge in Africa; humans are not static creatures. All that is needed, is for the P clade to have been present in Africa at some point in time. To the present author's knowledge, P has not been uncovered as a standalone clade [lacking downstream markers] anywhere. However, it is interesting to note that African R1*-M173 chromosomes were previously tested for the P25 mutation, and came up negative. What does this then mean? It means that while Africans carried rare Hg R1 chromosomes bearing the P25 marker, they also carried examples without the P25 marker [see Hassan et al. 2008, for example]. In other words, African R1-bearing chromosomes aren't homogeneous as Cruciani would perhaps like us to believe.

Furthermore, as the present author has noted here and elsewhere before,...

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

So once again, African R-bearing chromosomes lacking the P25 marker have been identified, whereas Cruciani's Hg R chromosomes all appeared to have tested positive for P25; his samples bearing the R-positive chromosomes only differed from subsequent downstream markers - presumably aside from one or more of those "new mutations" that Cruciani claims he had used in his DNA sequencing. African chromosomes transcend even the ancestral Hg R1* marker; the paraphyletic R* is also implicated, which is ancestral to R1* marker!

...but the present author has a hunch that Cruciani isn't done fine-combing Hg R chromosomes just yet, if he is to unequivocally prove that back-migration scenario he seems to so desire. So, watch this space, and please go over the cited R1*-M173 link(s) again, as it is constantly updated!
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References*

—As already cited.

—Personal notes retrieved from elsewhere.

Additional reading:

R1*-M173 Chromosomes in Africa

More on R1*-M173 bearers 

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

 *Last edited on 10/22/2010.

An Interesting Encounter...

Several months back, in a forum discussion, the present author came across something quite interesting on the website of the owner of the said forum—going by the name of F. W. Sweet, and this is what it says/said:

"It seems that Dr. Shriver’s maternal grandfather moved from Pennsylvania to Iowa, then to California, leaving behind in the process most of his ties with his relatives.23 Dr. Shriver, it turns out, (see photograph above) is one of the 74 million White Americans with significant recent African genetic admixture.

In a coincidentally similar fashion, Dr. Rick Kittles, Shriver’s collaborator from Howard University in Washington, discovered that he carries the FY-null genetic marker at genome position 16q24.3. This marker is found in 998 out of every thousand Europeans but found in only one out of thousand Africans. Many of Dr. Kittles’s other ancestry-informative markers tell the same unexpected story. Dr. Kittles (see photograph above) is one of the many Black Americans with strong European genetic admixture. And yet, and there is no other way to say this, Dr. Shriver “looks White” and Dr. Kittles definitely “looks Black.” Why is there such a discrepancy between measured genetic admixture and physical appearance?" - by F. W. Sweet

At the time, this is what the present author posted in response to the extract:

Yes, I’ve seen both Dr. Shriver’s and Dr. Kittle's appearance, and I must say, it is hard to believe that either have low European or African recent ancestry respectively. If indeed the labeled sample belonged to either party, assuming that the said alternative coincidences did not arise from any probable technicality in the labeling, then I can only come to the conclusion that, the DNA sites examined as such, were made possible because those sites were kept intact in either one of their immediate parents, and if Shriver’s mum’s reaction is any indicator to go by, upon hearing the news, these markers would have been kept intact in her “white-appearing” father. Speaking of father, according to Mr. Shriver, how did he reach the conclusion that it had to be from his mother’s dad’s side, and not necessarily from his mother’s maternal side? Also, could it not have come from his father's side, and if not, why? Were many of the said ‘markers’ deemed to have been sex-biased in their genetic transmission?

I had the result for two or three years before I even looked up the ID number of the person whom we tested. I looked at who it was and it was me! I checked myself and the rest of my relatives and tracked it through my family. I never considered that there were any African people in my family. There’s no real variation in my family. The admixture must have been pretty far back. It just so happens that we can detect it with the markers we have. My mom especially stood out as being surprised, maybe because I told her it was coming through her father. She still doesn’t believe it about her family! The part of Pennsylvania where my mother’s father came from is where the Underground Railroad ended. There are several towns right here in Southern Pennsylvania where there are very light-skinned African-American communities that are the remnants of the Underground Railroad. - by Shriver

So, not only would those markers have to be deemed “invisible” in terms of their impression on phenotype, but they would have had to remain intact to account for their genetic integrity throughout the parent-to-offspring transmissions for at least a few generations. For Dr. Kittles to retain that level of melanin, it occurs to me that he’d had to have been a product of a union between parents from families that had maintained endogamy for at least a few recent generations, likely of families that have had long enough tradition of socially identifying with the “black“ or “colored” community. I suspect, since I cannot say for certain without independent corroboration, that either of these two researchers would likely indirectly clue us in on this possibility through either paternal and/or maternal DNA markers, which by normal account, correspond to Y-chromosome markers and mtDNA respectively. Either that, or else more “AIM” would have been needed to be identified to account, if not *indirectly*, for the genetic component counterparts of their ancestors who were responsible for transmission of their phenotypic appearance - as is the case with skin color and hair texture for example. I realize these traits have their own markers, but I'm referring to the broader hereditary component of the parties who were primarily responsible for transmitting those traits. It is hard to imagine that only those 'visible' markers of those ancestors withstood the test of time, while every other component of their genetic transmission was swamped through the generations, particularly for 'immediate' family households who would swear that the maternal and paternal lines of the said family come predominantly from one ethnic endogamous group [be it "white" or "black"].

With regards to piece about Kittle’s ancestry, this was said:

In a coincidentally similar fashion, Dr. Rick Kittles, Shriver’s collaborator from Howard University in Washington, discovered that he carries the FY-null genetic marker at genome position 16q24.3. This marker is found in 998 out of every thousand Europeans but found in only one out of thousand Africans. - by F.W. Sweet

But in the tables provided, this location should have been associated with MC1R-314*, and not the FY-null marker, which is supposed to have been located at 1q23.2. Was this a typo, or something else is at work here?

And indeed, that was a typo, as the author himself admitted, upon my issuing of the notification above. If indeed the typo was in wrongly naming the loci, which it appears it is/was, then MC1R-314*'s — an allele known to prevalent in folks of recent African ancestry — location in Mr. Kittles' sample should come as no surprise.

Short of some extraordinarily rare situation of these two geneticists — aka Shriver and Kittles — being products of union between a) a parent heterozygous at certain loci linked to outward phenotype traits like skin color, eye color, hair thickness et al., which are generally observed predominantly in one geography than another or in one ethnic group than another, and a parent largely homozygous across said loci, b)OR else, between parents who happen to both be heterozygous at some or the other section of said loci, wherein the offspring [in this case, either Shriver or Kittles] somehow wound up being largely homozygous across said loci, from the look of things, there are very strong indications here that what Shriver was actually looking at as his own, might well have been Rick Kittles' DNA sample, and likewise, Shriver's DNA sample was mistaken for Kittles'. There might have been a technicality at the lab [could be labeling mishap for example, though some other yet-to-be-determined factor(s) could have been the cause] , which somehow escaped both Shriver's and Kittles' attention, and so, they took it for granted, no matter how awkward the results turned out to be, as their own, respectively. This would explain the seemingly reverse results for each candidate, who coincidentally, were partners on research work. Short of specific independent corroboration, obviously this amounts to conjecture on my end; let's just say that I'm throwing out there, a possible scenario for what could have accounted for the results we are told about, aside from considering one of those rare genealogical situations. One thing most of us would agree on, is that those results are certainly interesting!
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*Further reading:

— Skin pigmentation gene alleles

— Skin pigmentation gene alleles — Part 2

"Ethno-specific" markers?

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

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

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

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

Originally posted by MyRedCow:

Al Takruri and Supercar,

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

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

My response was thus:

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

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

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

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

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

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

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

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

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

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

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

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