Monday, July 7, 2008

U6: A standalone clade?

It is a lineage that spans west and east Africa, and spilling over to portions of southern Europe and "southwest Asia".

In looking at the following diagram...

 -
For those with inadequate screen size, view the above image in full with: here

...it is apparent that at the least, U5 and U6 diverge into respective branches independent from that of the rest of U macro-haplogroup. Similar observation has been made about U1, which too, seems to have an independent branch from the rest of the U haplogroup. In other words, these three—either U1, U5 or U6—don't appear to have an ancestral clade within the main haplogroup U branch which is defined by the nucleotide transition at 1811 or vice versa. This is how it goes, courtesy of Maca-Meyer et al. 2003:

U6 is defined by two motifs represented by positions in the coding and HVR respectively: 3348 and 16172.

U5 is defined by the transitions at: 3197, 9477, 13617 and 16270.

And the rest of the U haplgroup [sans U1], defined by the mutation designated by position: 1811.

Maca-Meyer et al. add that:

U presents the following mutations with respect to rCRS: 73, 263, 311i, 750, 1438, 2706, 4769, 7028, 8860, 11467, 11719, 12308, 12372, 14766 and 15326.
- Maca-Meyer et al. 2003

N macrohaplogroup is removed from the root of L3 by about 5 mutations, we are told. This is relevant, in that U haplogroup is often posited as having split from R, which derives from Haplogroup N. Speaking of haplogroup U splitting from R, we are told that this is the case via three mutations represented by: 11467, 12308 and 12372

Hence, the family association has been made between U6 [as is for U1 & U5] and the rest of the U haplogroup, primarily thanks to sharing of the above mentioned transition trio; if it weren't for these basic transitions, U6 would have likely just been considered as just another separate sub-branch of haplogroup R. Perhaps, if a clade was located—sharing the same transition trio but devoid of any known downstream coding or HVR mutations in either U6, U1 or U5 and the rest of haplogroup U, it could provide us with a possible candidate as the proto-U ancestor that gave rise to the divergent U branches in question. However, to date, no such lineage has come to light.

In their publication "The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa" - 2006, Anna Olivieri et al.'s argument, like that of Gonzalez et al., depends on the idea that U6 entered Africa in a parallel dispersal with M1, which the present author has demonstrated elsewhere to be a weak hypothesis [see: Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007]. M1 basal coding markers emerge from that of an African background, and the "missing-link" lineage of the M Macrohaplogroup was found in a sub-Saharan sample [specifically in a Senegalese sample].

Furthermore, Olivieri et al. 2006 themselves acknowledge:

An ancient arrival of M1 in Africa (or in its close proximity) is supported by the fact that none of the numerous M haplogroups in Asia (20, 21) harbors any of the distinguishing M1 root mutations, and by the lack of Asian-specific clades within M1 (and U6), as might be expected in the case of a more recent arrival. The arrival of M1 and U6 in Africa 40 to 45 ka would temporally overlap with the event(s) that led to the peopling of Europe by modern humans.

Not to mention...

Indeed, M1 and U6 in Africa are mostly restricted to Afro-Asiatic–speaking areas.

Why is that? Where did the Afrisan super language phylum emerge? Answer: East Africa.

And they say...

The hypothesis of a back-migration from Asia to Africa is also strongly supported by the current phylogeography of the Y chromosome variation, because haplogroup K2 and paragroup R1b*, both belonging to the otherwise Asiatic macrohaplogroup K, have been observed at high frequencies only in Africa (15, 16). However, because of the relatively low molecular resolution of the Y chromosome phylogeny as compared to that of the mtDNA, it was impossible to come to a firm conclusion about the precise timing of this dispersal (15, 16).

To which, elsewhere [see: R1*-M173 bearing chromosomes in Cameroon], I commented:

By the way, previous genetic research work made very enthusiastic attempts to correlate the likes of U6 and possible "Eurasian"-tagged mtDNA with R1*-M173, supposedly as an attempt to buttress a possible back-migration into Africa; all but failed, with results showing considerable African mtDNA gene pool instead, for populations bearing these chromosomes.

Not only is there lack of apparent parallelism between R1* paragroup distribution and those markers, as the authors seem to be so desperately yearning for, but also the paragroup is essentially absent in all Afrasan speaking groups but those in the Northeast African corner. The marker is even rarer in so-called Southwest Asia than it is in Africa.

Thus, the re-examination point:

— U6 with respect to U5 , or U6 with respect to U1, and U6 with respect to the rest of haplogroup U, doesn't share defining motifs, outside of the basic transitions, particularly at the aforementioned position trio.

— In relation to the above, U6 doesn't have a common recent ancestor that is a U5 sub-lineage or vice versa, U6 doesn't have a common recent ancestor that is a U1 sub-lineage or vice versa, nor does U6 have a common recent ancestor that is a U*(xU1, U5) sub-lineage or vice versa.

...brings us to the question of:

Could U6 then be a standalone clade, in that, short of the aforementioned basic mutations by which the U-designated lineages diverge from macro-haplogroup R — particularly at 11467, 12308 and 12372, it is essentially mutually-independent of the other U-designated lineages?

Simply put...

The relationship of U6 with other U haplogroups is only inferred from non-U subclade-specific basal markers.

U6 is a branch on its own, independent from other U groups, and proto-U6 has not been located to date.

Time will tell, as to whether much more improved resolution of mtDNA will bear out the possible candidate of the elusive proto-U6 ancestor, but until then, it would appear that the proto-U6 bearing population was quite small in size, such that proto-U6 itself would eventually be overwhelmed and essentially be erased by expansion of descendant U6 carriers and possibly, incursions from other populations. It is uncertain whether a proto-U6 ancestor would have been the very same ancestor that begot U1, U5 and U*(xU6,U1,U5) respectively elsewhere, or whether it would have been a single step or a few steps genetic-neighbor to those which begot the latter U groups, but it appears that the latter respective ancestors too were modestly represented 'population-wise', such that they too would have been overwhelmed by subsequent demographic expansions that gave rise to descendant populations and incoming groups from elsewhere. Whatever may be said about a proto-U6 ancestor's origin, one thing is clear: U6 itself is an autochthonous African marker, which would eventually spill over to parts of Europe, particularly those hugging the Mediterranean sea, and parts of "southwest Asia". It too, like M1 (clickable), has been implicated in the expansion of proto-Afrasan (aka proto-Afro-Asiatic) and/or Afrasan speakers outside of mainland Africa.
__________________________________________________________
*References:

— Maca-Meyer et al. 2003, Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography.

8 comments:

Proud Canadian said...

How do you see the DNA backlfow theories positing the arrival of Eurasian races into Africa based on what you post about U6? Some argue that after the Out of Africa movement, races evolved, then doubled back to east/north Africa in the form of Caucasoids, Hamites or Mediterraneans, thereby bringing genetic diversity to the natives.

Proud Canadian said...

It seems to me that the Semino study is much more solidly based that Gonzalez's more speculative conclusions, and the highest frequencies even she herself notes occurs among Africans, and little among Asians to support the Asiatic origin hypothesis. As you stated:

A total of 50 Europeans detected for M1.
A total of 154 for Africans.
A total of 28 Asians, barring 8 unknown Arabian haplotypes.
And a total of 29 Jews, who were lumped together from the various continents.
The sum of the above totals, amount to 261 "known" M1 lineages.

QUOTE:

"haplogroup M originated in eastern Africa approximately 60,000 years ago and was carried toward Asia. This agrees with the proposed date of an out-of-Africa expansion approximately 65,000 years ago10. After its arrival in Asia, the haplogroup M founder group went through a demographic and geographic expansion. The remaining M haplogroup in eastern Africa did not spread, but remained localized up to approximately 10,000-20,000 years ago, after which it started to expand." -- Semino et al.

You rightly point out how tenuous these claims are, but too often, in their summaries, they make misleading "sound bite" statements, feeding perceptions along certain racial lines.

Some questions:

1) What do you think for example of the sound bite in "High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males," Juan J Sanchez- 2005, that "WEast Africans are more related to more related to Eurasians than sub-Saharan Africans" referencing a Cavalli-Sforza study whch in turn cites a 1964 Britannica Article. The Sanchez study was on Somalians, and shows that East Africans (Somalians, Oromos of Ethiopia and North Kenya, etc) are more related to each other than anyone else, including Eurasians, but that is buried deep in the text and only the misleading and distorted "sound bite" remains that suggests East Africans are Caucasians. The "sound bite" technique also appears in other studies by Cavalli-Sforza et al. usually drawng a contrast with distant "sub-Saharan" Africans. A 1997 Hammer studty drawing samples from the far north (Cairo) to "represent" all Egyptians uses the same "sound bite" method, to once again draw contrasts with "sub-Saharan" peoples.

1a) Doesn;t "sub-Saharan" include the Horn of Africa, (Somalians and EWthiopians) and the Sudan as well? I am thinking of what Keita quotes here:

"However, the Horn is at the same latitude as Nigeria, and its languages are African. The latitude of 15 degree passes through Timbuktu, surely in "sub-Saharan Africa," as well as Khartoum in Sudan; both are north of the Horn. Another false idea is that supra-Saharan and Saharan Africa were peopled after the emergence of "Europeans" or Near Easterners by populations coming from outside Africa. Hence, the ancient Egyptians in some writings have been de-Africanized. These ideas, which limit the definition of Africa and Africans, are rooted in racism and earlier, erroneous "scientific" approaches." (S. Keita, "The Diversity of Indigenous Africans," in Egypt in Africa, Theodore Clenko, Editor (1996), pp. 104-105. [10])



2) How would you answer the argument some might make that the shaky "Asiatic origin" supports an influx of Caucasoids into the Nile Valley to bring advancement to the natives?

3) And on the flip side, if the lineage (which seems very shaky now given the data of Semino), did have a Northwest African origin, would this make them "non-African" and translate into Caucasoids flitting back and forth over the continent?

4) How do you see the Gurna study below? It mentions M1 - "a more specific 2004 mtDNA study of upper Egyptians from Gurna performed found a genetic ancestral heritage to modern East Africans, characterized by a high M1 haplotype frequency." (Stevanovitch A, Gilles A, Bouzaid E, et al, "Mitochondrial DNA sequence diversity in a sedentary population from Egypt," (Ann. Hum. Genet., 2004), vol 68, pp 23-29);

5) also by Lucotte: "a 2003 Y chromosome study was performed by Lucotte on modern Egyptians, with haplotypes V, XI, and IV being most common. Haplotype V is common in Berbers and Ethiopian Falashas (black Jews) has a low frequency outside Africa. Haplotypes V, XI, and IV are all supra/sub-Saharan horn of Africa haplotypes, and they are far more dominant in Egyptians than in Near Eastern or European groups.
(Klintschar, M., N.B. al-Hammadi, and B. Reichenpfader. 1999. "Population genetic studies on the tetrameric short tandem repeat loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 in Egypt." Forensic Sci. Int. 104:23-31.)

Mystery Solver said...

proud canadian writes:

You rightly point out how tenuous these claims are, but too often, in their summaries, they make misleading "sound bite" statements, feeding perceptions along certain racial lines.

A. Gonzalez's claims go beyond just "misleading sound bite statements"; they make arguments throughout their study, which do not hold up to scrutiny, as I have amply demonstrated by stacking their claims against other research findings, as well as those whom they purport to be referencing.

proud canadian writes:

What do you think for example of the sound bite in "High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males," Juan J Sanchez- 2005, that "WEast Africans are more related to more related to Eurasians than sub-Saharan Africans" referencing a Cavalli-Sforza study whch in turn cites a 1964 Britannica Article. The Sanchez study was on Somalians, and shows that East Africans (Somalians, Oromos of Ethiopia and North Kenya, etc) are more related to each other than anyone else, including Eurasians, but that is buried deep in the text and only the misleading and distorted "sound bite" remains that suggests East Africans are Caucasians. The "sound bite" technique also appears in other studies by Cavalli-Sforza et al. usually drawng a contrast with distant "sub-Saharan" Africans.

Well, it would be misleading to those who are not adequately read in genetics; it is designed to mislead such people. Sanchez et al. say "East Africans are more related to more related to Eurasians than sub-Saharan Africans" supposedly on the basis that the share certain markers like Hg K and Hg J with their neighbors across the Red Sea, which might imply gene flow, as well as autochthonous E1b1b (E3b) chromosomes. The idea here, is that the said shared lineages which are generally lower in other sub-Saharan regions with some exceptions, tend to make sub-Saharan East Africa appear relatively closer to their neighbors to east. On the flip side, if one were to consider the internal makeup of autochthonous clades, such as the PN2 derived clades and deep-root African clades, sub-Saharan east Africans will cluster more closely with much of sub-Saharan Africa elsewhere before they do with their neighbors across the Red Sea. So, it is all about context, which is why I say that there wording is meant to dupe only those with fairly limited insight into molecular genetics. It is for the same reason that populations in the African Horn appear "intermediate" in cluster maps between other Africans and non-African groups; it has nothing to do with them being "hybridized populations". On the contrary, it is primarily because this region contains a gene pool, a subset of which would form the basis of the non-African gene pool; Although not particularly significant or decisive in the aforementioned phenomenon, what little historic gene flow that has occurred with between populations in the African Horn and their neighbor across the Red Sea, has a role to play in the commonality of select shared lineages. As far as "East Africans are more related to more related to Eurasians than sub-Saharan Africans" go, that statement itself is bankrupt, because those East Africans ARE sub-Saharan Africans themselves...which would answer the following:

proud canadian writes:

1a) Doesn;t "sub-Saharan" include the Horn of Africa, (Somalians and EWthiopians) and the Sudan as well?

proud canadian writes:

"However, the Horn is at the same latitude as Nigeria, and its languages are African. The latitude of 15 degree passes through Timbuktu, surely in "sub-Saharan Africa," as well as Khartoum in Sudan; both are north of the Horn. Another false idea is that supra-Saharan and Saharan Africa were peopled after the emergence of "Europeans" or Near Easterners by populations coming from outside Africa. Hence, the ancient Egyptians in some writings have been de-Africanized. These ideas, which limit the definition of Africa and Africans, are rooted in racism and earlier, erroneous "scientific" approaches." (S. Keita, "The Diversity of Indigenous Africans," in Egypt in Africa, Theodore Clenko, Editor (1996), pp. 104-105. [10])

Yes; I've raised several topics on Egyptsearch on this issue a few years go, relaying the very same point. That this is ignored, is testament to the obvious fact that pseudo-science relies on absurdity as its lifeline.

proud canadian writes:

2) How would you answer the argument some might make that the shaky "Asiatic origin" supports an influx of Caucasoids into the Nile Valley to bring advancement to the natives?

I'd tell them to prove it; the odds are against them, in the face of all known facts.

pround canadian writes:

3) And on the flip side, if the lineage (which seems very shaky now given the data of Semino), did have a Northwest African origin, would this make them "non-African" and translate into Caucasoids flitting back and forth over the continent?

Even it that were the case, which as I have demonstrated -- is unlikely, then the answer would still be "no", as "Northwest Africans" are still predominantly native Africans. And even then, its presence in non-Africans would mark African ancestry.

proud canadian writes:

4) How do you see the Gurna study below? It mentions M1 - [b]"a more specific 2004 mtDNA study of upper Egyptians from Gurna performed found a genetic ancestral heritage to modern East Africans, characterized by a high M1 haplotype frequency."[/b] (Stevanovitch A, Gilles A, Bouzaid E, et al, "Mitochondrial DNA sequence diversity in a sedentary population from Egypt," (Ann. Hum. Genet., 2004), vol 68, pp 23-29)

I see no fault with the highlighted, except to emphasize that it isn't the only authochthonous African maternal marker to be ancestral to modern East Africans!

Mystery Solver said...

Recap:

proud canadian writes:

4) How do you see the Gurna study below? It mentions M1 - "a more specific 2004 mtDNA study of upper Egyptians from Gurna performed found a genetic ancestral heritage to modern East Africans, characterized by a high M1 haplotype frequency." (Stevanovitch A, Gilles A, Bouzaid E, et al, "Mitochondrial DNA sequence diversity in a sedentary population from Egypt," (Ann. Hum. Genet., 2004), vol 68, pp 23-29)

I see no fault with the highlighted, except to emphasize that it isn't the only authochthonous African maternal marker to be ancestral to modern East Africans!

Mystery Solver said...

proud canadian writes:

How do you see the DNA backlfow theories positing the arrival of Eurasian races into Africa based on what you post about U6? Some argue that after the Out of Africa movement, races evolved, then doubled back to east/north Africa in the form of Caucasoids, Hamites or Mediterraneans, thereby bringing genetic diversity to the natives.

U6 itself doesn't reflect any black flow event. And even if one were to assume that the "proto" U6 ancestor -- a hypothetical undetermined U6 ancestor -- originated outside of mainland Africa, that would still not imply modification of Africans by outsiders, from a physiological standpoint. Given that this marker is at least some 60 years old or so, U6 predates anything remotely called "Caucasoid" or "Hamite".

Proud Canadian said...

THIS QUOTE IS WORTH REPEATING:


"Well, it would be misleading to those who are not adequately read in genetics; it is designed to mislead such people. Sanchez et al. say "East Africans are more related to more related to Eurasians than sub-Saharan Africans" supposedly on the basis that they share certain markers like Hg K and Hg J with their neighbors across the Red Sea, which might imply gene flow, as well as autochthonous E1b1b (E3b) chromosomes.

The idea here, is that the said shared lineages which are generally lower in other sub-Saharan regions with some exceptions, tend to make sub-Saharan East Africa appear relatively closer to their neighbors to east. On the flip side, if one were to consider the internal makeup of autochthonous clades, such as the PN2 derived clades and deep-root African clades, sub-Saharan east Africans will cluster more closely with much of sub-Saharan Africa elsewhere before they do with their neighbors across the Red Sea.

So, it is all about context, which is why I say that their wording is meant to dupe only those with fairly limited insight into molecular genetics. It is for the same reason that populations in the African Horn appear "intermediate" in cluster maps between other Africans and non-African groups; it has nothing to do with them being "hybridized populations". On the contrary, it is primarily because this region contains a gene pool, a subset of which would form the basis of the non-African gene pool;

Although not particularly significant or decisive in the aforementioned phenomenon, what little historic gene flow that has occurred with between populations in the African Horn and their neighbor across the Red Sea, has a role to play in the commonality of select shared lineages. As far as "East Africans are more related to more related to Eurasians than sub-Saharan Africans" go, that statement itself is bankrupt, because those East Africans ARE sub-Saharan Africans themselves.."


Thanks. This is a clear and balanced statement of the facts, backed with solid data.

Maju said...

I strongly recommend you to get familiar with PhyloTree, which is nowadays "the ISOGG of mtDNA", so to say.

Before 2009, when this site was created, there was a lot of confusion and lack of good reference sites on mtDNA phylogeny, fortunately now this site helps a lot in getting things straight (regardless of whatever updates, which are done regularly).

U6 shares with all other U lineages the mutations at sites 11467, 12308 and 12372. What Maca-Meyer means when she says that U1, U5 and U6 are standalone clades is that they do not belong to the fourth basal sublineage of U, U2'3'4'7'8'9, defined by the shared mutation at site 1811, and not that they directly derive from R.

Cheers.

Mystery Solver said...

Maju writes:

I strongly recommend you to get familiar with PhyloTree, which is nowadays "the ISOGG of mtDNA", so to say.

I strongly urge you to very carefully read what is posted before parceling out gratuitous advises that don't follow the topic.

U6 shares with all other U lineages the mutations at sites 11467, 12308 and 12372. What Maca-Meyer means when she says that U1, U5 and U6 are standalone clades is that they do not belong to the fourth basal sublineage of U, U2'3'4'7'8'9, defined by the shared mutation at site 1811, and not that they directly derive from R.

This is already pointed out in the blog post. And...?