Wednesday, December 9, 2009

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 groupsthough in small frequencies [pooled] — tested positive for the paraphyletic R1b*, lacking the established downstream R1b markers. Henceforth, R*-M207, lacking downstream mutations have been identified in African groups via this study; and yes, the basic nodes of all presently known Hg R's downstream clades had been accounted for, which means that R*, as predicted above, is NOT relegated to the Indian sub-continent. All in all, this suggests that African Hg R pool is actually more diverse than many seem to think.

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!

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.

Monday, December 7, 2009

More Analysis on Body Proportions; A review of:

Body proportions of circumpolar peoples as evidenced from skeletal data: Ipiutak and Tigara (Point Hope) versus Kodiak Island Inuit.

Holliday TW, Hilton CE.

Am J Phys Anthropol. 2009 Nov 19.

Given the well-documented fact that human body proportions covary with climate (presumably due to the action of selection), one would expect that the Ipiutak and Tigara Inuit samples from Point Hope, Alaska, would be characterized by an extremely cold adapted body shape. Comparison of the Point Hope Inuit samples to a large (n > 900) sample of European and European- derived, African and African-derived, and Native American skeletons (including Koniag Inuit from Kodiak Island, Alaska) confirms that the Point Hope Inuit evince a cold-adapted body form, but analyses also reveal some unexpected results. For example, one might suspect that the Point Hope samples would show a more cold-adapted body form than the Koniag, given their more extreme environment, but this is not the case. Additionally, univariate analyses seldom show the Inuit samples to be more cold-adapted in body shape than Europeans, and multivariate analyses that include a myriad of body shape variables such as femoral head diameter, biiliac breadth, and limb segment lengths fail to effectively separate the Inuit samples from Europeans. In fact, in terms of body shape, the European and the Inuit samples tend to be cold-adapted and tend to be separated in multivariate space from the more tropically adapted Africans, especially those groups from south of the Sahara. - abstract ends

One excerpt from the study states:
There is strong evidence for such selection operating in the millennia following the initial appearance of modern humans in Europe, i.e., among Late Upper Paleolithic and Mesolithic Europeans (Holliday, 1999).

Specifically, the earliest modern humans in Europe for whom we have body proportion data tend to show more African-like body proportions (Holliday, 1997a), while later European modern humans show foreshortened limbs in spite of archeological data indicative of improved cultural buffering. This suggests selection for shorter limbs in Late Pleistocene Europe, although we also cannot as of yet rule out the possibility that late Pleistocene gene flow from Neandertals to early modern Europeans played some role in establishing more ‘‘cold-adapted’’ limb proportions for this latter population (Holliday, 1997a, 2006b).
Several issues stand out here: Fair enough, the earliest modern human evidence in Europe show "tropical African-like" body stature; however, here, we are told that evidence of "cold adaptation" starts to appear in the late Upper Paleolithic. Is it then safe to say, that while "tropical limb-proportions" has more than likely always been coexistent with considerable skin pigmentation, short index limb-proportions—as seen in Europe—are not as good as indicators of change in soft body phenotype, such as skin tone? If one goes by published journals from several skin tone analysts, it is hypothesized that the change in skin tone appeared to be marked by an episode of a selective sweep, likely some time close to the middle of the Neolithic (or early Neolithic in Europe) era [and the present author takes it that the suggested dates mainly correspond to contemporaneous European archeological status quo, as the dates may vary from region to region according to state of then existing economy type]. Now remember, it is hard to determine the ages of skin tone alleles under selective pressure with any degree of certainty. One has to therefore infer that skin tone analysts turn to secondary disciplines, outside of genetics, to come up with their age estimations; such disciplinary candidate is archaeology [like those associated with Neolithic farming traditions] and possibly, its paleontology sub-discipline. Only here, human paleontology appears to be disconcordant with examples of such age estimations that come to attention.

Note that the authors indirectly insinuate that a scenario of descendance into poor dietary and life style, relative to the preceding epochs—which is lacking here, does not seem to be a factor in such change in body stature; see:
Specifically, the earliest modern humans in Europe for whom we have body proportion data tend to show more African-like body proportion (Holliday, 1997a), while later European modern humans show foreshortened limbs in spite of archeological data indicative of improved cultural buffering.
Could it then be inferred that change in skin tone very likely accommodated change in body stature, but that such change was gradual in its spread and not in the extreme states that we now see in European populations? And as follows, that the spread of Neolithic farming subsistence factored into a subsequent selective sweep, given Europe's latitudinal positioning? If so, then only here, without extraordinary visible distinctions between "would-be intermediary Europeans" [in terms of skin tone developments] and the more extreme cases of contemporary Europeans, in terms of human remains record, one is hard-pressed to discern between such changes in soft body parts like skin tone.

A look back at older publication from the same author implicated above—Holliday (1999)—suggests that very possibility, the transitory scenario mentioned in the winding comment of the last paragraph (above); here is a copy of the abstract:
Among recent humans brachial and crural indices are positively correlated with mean annual temperature, such that high indices are found in tropical groups. However, despite inhabiting glacial Europe, the Upper Paleolithic Europeans possessed high indices, prompting Trinkaus (1981) to argue for gene flow from warmer regions associated with modern human emergence in Europe. In contrast, Frayer et al. (1993) point out that Late Upper Paleolithic and Mesolithic Europeans should not exhibit tropically-adapted limb proportions, since, even assuming replacement, their ancestors had experienced cold stress in glacial Europe for at least 12 millennia. This study investigates three questions tied to the brachial and crural indices among Late Pleistocene and recent humans. First, which limb segments (either proximal or distal) are primarily responsible for variation in brachial and crural indices? Second, are these indices reflective of overall limb elongation? And finally, do the Late Upper Paleolithic and Mesolithic Europeans retain relatively and/or absolutely long limbs?

Results indicate that in the lower limb, the distal limb segment contributes most of the variability to intra-limb proportions, while in the upper limb the proximal and distal limb segments appear to be equally variable. Additionally, brachial and crural indices do not appear to be a good measure of overall limb length, and thus, while the Late Upper Paleolithic and Mesolithic humans have significantly higher (i.e., tropically-adapted) brachial and crural indices than do recent Europeans, they also have shorter (i.e., cold-adapted) limbs. The somewhat paradoxical retention of "tropical" indices in the context of more "cold-adapted" limb length is best explained as evidence for Replacement in the European Late Pleistocene, followed by gradual cold adaptation in glacial Europe. - TW Holliday, Brachial and crural indices of European late Upper Paleolithic and Mesolithic humans, 1999.
In other words, the concluding portion of that abstract suggests that while the brachial and crural indices of the limb components reported relatively high scores—generally characteristic of those seen in populations inhabiting the tropics, the overall actual lengths of the limbs of the Late Upper Paleolithic and Mesolithic European specimens tend to be shorter in comparison to contemporary European examples. This means that recent Europeans would generally be considered taller in comparison to their said earlier European counterparts, notwithstanding the higher limb proportion indices characterizing the latter; in simple terms, one may interpret this seeming contrasting manifestations of limb proportions vis-a-vis overall limb length as suggestive of being part of a transitory phase towards gradual cold adaptation, as noted above. As to the question of the most probable state of soft tissue phenotype such as that of skin tone, one which would have been contemporaneous with the said Late Upper Paleolithic and Mesolithic physical states, one can only surmise some form of relaxation in epidermal melanin, without knowing the precise level; for instance, one might guess that it could have been along the lines of the Inuit, but then again, the Inuit are considered fully cold-adapted. So the question of skin tone is not clear here, and not nearly as neat as the correlation that can be made between tropically adapted body plan and the intense UV radiation levels of tropical latitudes.

And from the remaining segment of the first excerpt,...
This suggests selection for shorter limbs in Late Pleistocene Europe, although we also cannot as of yet rule out the possibility that late Pleistocene gene flow from Neandertals to early modern Europeans played some role in establishing more ‘‘cold-adapted’’ limb proportions for this latter population (Holliday, 1997a, 2006b).
If such event took place, i.e. gene flow between Neanderthals and early modern Europeans, then it appears that genetic drift had effectively sifted it out of modern human gene pool, almost akin to saying that the offspring emanating from such activity died out. On the other hand, molecular genetics presently rules out such undertaking, on the account of which, the analysts/authors here seem to be kept in the dark of.

Moving onto a second extract...
It has two main branches—a long and linear body build branch that includes the Egyptians, Sub-Saharan Africans (except for the Pygmies), and African-Americans and a second, less linear body form branch that includes the Inuit, Europeans, Euro-Americans, Puebloans, Nubians, and Pygmies. Note that the Nubians used in this study are thought by some to represent an immigrant population from Europe or Western Asia [see Holliday (1995)].
Well, it is not surprising to see ancient Egyptian specimens consistently group with sub-Saharan Africans, and not with Europeans, notwithstanding whatever supposed "caucasoid" archetype tendencies are said to be implicated in cranio-morphometric estimations according to some publications of the past, which are prone to inconsistency across different authors, because of variations in sampling selections to the discretion of the samplers. Several published journals have made note of this post-cranial feature of Nile Valley specimens, and they have been covered elsewhere on this blog.

However, the pygmies notably standout here in terms of body "linearity", given their traditional habitat in the African tropics of "sub-Saharan" Africa. Could it have anything to do with discordance between crural-brachial indices and "body build" brought about by their characteristic short height (in correlation to short limbs)? It certainly warrants further examination into the authors' findings and the premise thereof. Likewise the "Nubians", but explanation is offered here for the seeming anomaly. Funny thing about the latter, is the less likely inclination of fringe Eurocentric sects to seize on such isolated finding and use it to suggest that "Nubians" were primarily drawn from the "Nordic" or "caucasoid" stock.

On a winding note, there appears to be disconcordance between the post-cranial report from Holliday & co. (2009) and cranial report from Katerina Harvati (2009). As seen above, Holliday and co. deduced selection for shorter limbs in their late Upper Paleolithic European sample [as opposed to the earlier Upper Paleolithic European specimens], which is interpreted as a sign of "cold adaptation" to the temperate environment of Europe; whereas, Harvati's report shows closer positioning of both early Upper Paleolithic and late Paleolithic European specimens to modern examples from sub-Saharan Africa [Kenyan and South African, Zulu in particular] than they are to modern west European and north Levantine [Syria] counterparts. Now of course, we are looking at post-cranial analysis on the one hand, and a cranial one on the other; hence, precisely what sort of body proportions Harvati's late Paleolithic European specimens exhibited, is anyone's guess, unless data for such is made available. This disconcordance noted here though, as Holliday's 1999 study shows, is not total; after all, retention of "tropically-adapted" phenotype in the limb proportion indices is observed in the Late Upper Paleolithic to Mesolithic European specimens. That said, as a preliminary consideration, could the said contrast in reports from two different sections of human skeleton have something to do with that "gradual change" mentioned in the question put forth above? Perhaps the same question may be asked of the Zhoukoudian Upper Cave [in China] specimens, who are claimed to have close cranial affinities with the late Paleolithic European counterparts.

Naturally, this question makes sense, only if the said Harvati's late Paleolithic European specimens [the Zhoukoudian Upper Cave specimens as well] showed up body proportions consistent with observations made by Holliday et co. in their post-cranial analysis. However, it should be noted that the precise nature of the interplay of several different underlying factors behind cranial morphology is less clear than that underlying post-cranial skeleton, and while cranial morphology exhibits perhaps the most visibly diverse manifestations of hard human physical form, it is also more prone to overlapping [through happenstance in some cases, and gene flow in others] between a wide range of populations from across different latitudinal environments than the case is for post-cranial phenotype; for instance, specimens bearing tropical body-proportions in an unquestionably sub-tropical refugium serves as a fairly good indicator of  a peopling event, shortly after emigration from a tropical environment. If Europeans' earliest ancestors came from a sub-tropical refuge center of a generally cool geographical clime of say, central Asia, then one would expect less inclination towards the display of tropical body proportions, having undergone some level of adaptation or another to the sub-tropical environment. On the other hand, certain crania from populations in the tropics have been inflicted with pseudo-scientific labels such as "caucasoid", even as the body proportions prevalent in those populations turned out to be markedly distinct from so-called "caucasoids" of temperate latitudes.

*Keep an eye on possible future updates.

—as already cited.
— the rest is based on personal notes posted elsewhere.