Friday, October 10, 2008

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!
______________________________________________________________________________
*Further reading:

Skin pigmentation gene alleles

Skin pigmentation gene alleles — Part 2

7 comments:

the big valley said...

The link to the original article sez: "..other studies have found that approximately 5.5 percent of members of the U.S. Black community have no detectable African genetic admixture."

How is this possible? Is the definition of "black" in this case, purely a social one or what?

The Big Valley said...

Speaking of genetic variation, I have really learned a lot from your page. Hence comparing your data with that of others, I came across Wikipedia article "Hapogroup E" What do you make of the article or the following intro blurb below?

It claims that 'E" "would appear to have arisen in Northeast Africa" and is "closely linked with Haplogroup "D" which is not found in Africa. Exactly what does this so-called "linkage" mean I wonder? I see no reference to any published academic source, only a link to a website by the so-called "International Society of Genetic Genealogy". Most interesting..

There is a swift glide from 'E" to 'D" that "leaves open the possibility" that "E" originated in the Mideast. Huh? How exactly the "possibility is left open" is unspecified.

Just on the face of it, I don't see how "D" comes into the picture, and the exact "linkage" is left rather vague. Are they trying to "de-Africanize E" with the red herring of "D"?



The blurb on Cruciani is curious too: "However, M34 chromosomes have been found in a large majority of the populations from the Near East. M34 chromosomes from Ethiopia show lower variances than those from the Near East and appear closely related in the M34 network. Thus, it is assumed that M34 chromosomes were introduced into Ethiopia from the Near East.."
What seems weird is that if M34 originated in East Africa as part of "E" how is it "assumed" that it was introduced into Ethiopia from the Mideast? Are they trying to say that well, the origin of E is in East Africa, but then it went out a long time ago, and came back in as a M34 variant, thus making the Ethiopians more like white people?


The main article editors are among those pushing a "East Africans are more related to Eurasians" line across several Wikipedia pages, but based on an objective head to head comparison of data, much of what they are saying does not seem to add up, and it doesnt look like Cruciani is saying what they claim him to be saying, based on my reading of your analyis of that Cruciani article. Scratch head...



Makes me wonder if the editors are forming patties of yet more Wikipedia BS.



Haplogroup E (Y-DNA)
http://en.wikipedia.org/wiki/Haplogroup_E_(Y-DNA)

quote: - blurb 1


"This clade is divided into two sub-clades: E1 (or E-P147), defined by SNP mutation P147, and E2 (or E-M75), defined by M75.

E1a and E2 are found almost exclusively in Africa, and only E1b1b is observed in significant frequencies in Europe and western Asia in addition to Africa. Most Sub-Saharan Africans belong to subclades of E other than E1b1b, while most non-Africans who belong to haplogroup E belong to its E1b1b subclade.[3]

Haplogroup E would appear to have arisen in Northeast Africa based on the concentration and variety of E subclades in that area today. But the fact that Haplogroup E is closely linked with Haplogroup D, which is not found in Africa, leaves open the possibility that E first arose in the Near or Middle East and was subsequently carried into Africa by a back migration[4]. Indeed, geneticist Stephen Oppenheimer theorizes that early humans first (successfully) left Africa across the mouth of the Red Sea, between Ethiopia and Yemen[5]. This further suggests that, if haplogroup DE first crossed over to Yemen, D carried on to southeast Asia, while E stayed back in, or near, Arabia."



quote- Blurb 2 on Cruciani

"E1b1b1b (E-M81) M81, the other major subclade of E1b1b, is heavily concentrated in North Africa among both the Berber and Arab populations of that region. M81 is also found, albeit at low frequencies of 1.6-4%, in Iberia. Cruciani attributes its presence in Iberia to a recent migration of M81 carrying peoples from the Maghreb, perhaps coinciding with the Islamic conquest of Spain.

Scholars such as Hammer et al. and Semino et al. have linked the spread of E1b1b into Europe to an ancient migration from East Africa mediated through North African and Middle Eastern farmers during the Neolithic period. However, given the predominance of α cluster of subclade M78 in Europe, Cruciani concluded that it was spread through Europe via peoples indigenous to Southeastern Europe, perhaps in response to the arrival of Neolithic farming by way of cultural contact with the Near East. In turn, it originally arrived into Europe, perhaps, directly from North or Northeast Africa. Thus, its distribution is not simply due to a process of uniform spread of people from a single Near Eastern origin, but rather a series of distinct migrations.

In Northeast Africa, the subclade M34 appears to be restricted to Ethiopia. However, M34 chromosomes have been found in a large majority of the populations from the Near East. M34 chromosomes from Ethiopia show lower variances than those from the Near East and appear closely related in the M34 network. Thus, it is assumed that M34 chromosomes were introduced into Ethiopia from the Near East.[12]Cruciani 2004

Mystery Solver said...

the big valley writes:

It claims that 'E" "would appear to have arisen in Northeast Africa" and is "closely linked with Haplogroup "D" which is not found in Africa. Exactly what does this so-called "linkage" mean I wonder? I see no reference to any published academic source, only a link to a website by the so-called "International Society of Genetic Genealogy". Most interesting..

Haplogroup E is far more diverse in sub-Saharan east Africa than it is in northeast Africa. Other than to say, the Wiki author(s) are engaged in wishful thinking, there's little else to say about it.

Undifferentiated PN2* chromosomes, the ancestral clade needed to give rise to downstream E clades like E1a1a (E3a) and E1a1b (E3b) are rare to non-existent in northeast Africa.

Undifferentiated YAP+ clade [haplotype DE] devoid of any downstream mutations affiliated with Hg E is also found in sub-Saharan Africa [mainly in West African samples], and essentially non-existent outside of Africa. The fact that haplogroup D is mainly found outside of Africa, simply means that haplogroup D's ancestor was African, but upon population expansion, gave rise to subclades in south Asia, which are distinct from YAP+ descendants in Africa.

the big valley writes:'

There is a swift glide from 'E" to 'D" that "leaves open the possibility" that "E" originated in the Mideast. Huh? How exactly the "possibility is left open" is unspecified.

Again, that rationale is indicative of wishful thinking. The ancestral M168 clades, lacking known downstream mutations, which was located in Africa and would be essential to giving rise to either haplogroup E or D, is virtually non-existent outside of Africa. And to reiterate, the ancestral YAP+ clades which would be essential to giving rise to not only haplogroups E and D, too is virtually non-existent outside of Africa, but found in African samples. It doesn't take a genius to add 2 and 2 and figure out the obvious answer; haplogroup E cannot be deemed non-African in origin.

In fact, virtually all haplogroup E clades are rare to non-existent outside of Africa, not including few areas that received direct gene flow from Africa, save largely for downstream macro-clades of E3a [E1b1a] and E1b1b [E3b]. It is ridiculous to understand these facts, and yet, still maintain that haplogroup E's origin is open; there is only one obvious answer: It is African in origin!

the big valley writes:


The blurb on Cruciani is curious too: "However, M34 chromosomes have been found in a large majority of the populations from the Near East. M34 chromosomes from Ethiopia show lower variances than those from the Near East and appear closely related in the M34 network. Thus, it is assumed that M34 chromosomes were introduced into Ethiopia from the Near East.."

What seems weird is that if M34 originated in East Africa as part of "E" how is it "assumed" that it was introduced into Ethiopia from the Mideast? Are they trying to say that well, the origin of E is in East Africa, but then it went out a long time ago, and came back in as a M34 variant, thus making the Ethiopians more like white people?


I suppose that is one possibility that the authors were referring to; that E-M35 chromosomes left Africa, expanded and gave rise to E-M34 outside mainland Africa, and then returned. However, as your citation makes clear, the authors had actually little to offer in way of substance, other than to note that it supposedly has a somewhat wider intra-clade variation in the so-called Near East. To anyone who is adequately read on population genetics, what this essentially means, is that E-M34 underwent major expansions in the so-called Near East relatively more rapidly in that region upon its situation there, than it may have been allowed to undergo in Eastern Africa. It doesn't really prove beyond a doubt, that E-M34 mutation itself arose in situ the so-called Near East. On the other hand, they acknowledge that the highest frequencies of E-M34 are found in Eastern Africa than anywhere else. All this is really trivial to the issue that E-M34 chromosomes, regardless of whether they arose in East Africa or the so-called Near East, are indicative of recent African ancestry. The only way E-M34 could have come into being, would be through the availability of undifferentiated E-M35 chromosomes, which is essentially confined to sub-Saharan Africa. No E-M35*, means no E-M34; so, either way, E-M34 is still reflective of recent African ancestry, rather than so-called Near Eastern ancestry.

As for the remainder about Wiki "editors", I just have to say that it is one reason not to take Wiki literally as an authoritative or an unquestionably objective source. People with all sort of agenda are allowed to edit, and so, if at some point there was some objective posting, it doesn't mean that it wasn't edited out soon after. I know this personally, because I tried to correct that very page you were referring to, giving more objective accounts about haplogroup E and its major sub-clades, backed with citations from up-to-dated researches, only to find out later, that some clown re-edited the page with largely the sort of dogma-driven, highly-assumptive and essentially little-substantiated material that you've recited herein. My advice is to always refer to Wiki postings with a critical eye, and make sure that a diverse pool of sources are at disposal; I myself, have corrected Wiki postings on even mis-quoting genealogical journals on too many occasions already, so as to be foolish enough not to view postings there with an uncritical eye.

Mystery Solver said...

^Little correction to the closing note above:

I meant to say...

"I myself, have corrected Wiki postings on even mis-quoting genealogical journals on too many occasions already, so as to be foolish enough not to view postings there with an critical eye."

Mystery Solver said...

the big valley writes:

The link to the original article sez: "..other studies have found that approximately 5.5 percent of members of the U.S. Black community have no detectable African genetic admixture."

How is this possible? Is the definition of "black" in this case, purely a social one or what?


I take it by "link", you're referring to Mr. Sweet's site? But getting back to your concern, it would obviously be a social designation. That piece is obviously misleading, because I can't imagine one self-proclaiming to be "black", and yet not have any "detectable African genetic admixture".

It is more the question of what markers the author(s) searched for to begin with, and under what intentions.

I've come across a few studies proclaiming to report higher incidences of "admixture" in Black American samples than their White counterparts; you see, what some fail to realize, is that more often than not, offspring between Black and White self-proclaimed parents, generally identify with the Black social designation. So as a result, it gives the appearance that Black/African Americans are more "admixed" than their White counterparts.

It is also funny that some tend to overlook the ridiculousness of the basic premise of this whole rationale in an ethno-socially stratified multi-ethnic society, given that if the offspring was said to be "admixed" for starters, then it follows that if there is a "Black component", there must be a "non-Black" component in the offspring's ancestry. This would mean that the so-called "admixture" should really cut both ways, Lol. However, geneticists often respect the sampling candidates' rights to self-determination, and so, it is on this basis that they generally build their conclusions around intra-societal demographic stratifications.

the big valley said...

Great analysis. So in a nutshell, if I had to summmarize, you are saying this: (correct me if I'm wrong about some of the terminology)


Some theories speculate that Y-genetic elements associated with the Haplogroup "E" originally beginning in Africa, flowed out from that source and mutated into other sub-clades such as E-M34 chromosomes. These mutations in turn flowed back into Africa. (Cruciani 2004). While gene flow of varying proportions is nothing unusual in the history North and Northeastern Africa, attempts to assign Near Eastern or Mediterranean "racial" categories to the peoples of the region on this basis are problematic.

The original Y-chromone marker "root stock" is of African origin, reflecting its beginning base of vast African genetic diversity. Any backflow mutations may simply reflect the built-in diversity inherent in the original root stock which is based in sub-Saharan Africa, not north or Northeast Africa. Haplogroup E is far more diverse in sub-Saharan east Africa than it is in northeast Africa. The ancestors to outside mutations from the Near East and elsewhere, the ancestral YAP+ clades, gave rise to such mutations as haplogroup "D". Other mutations such as E-M34 are dependent on another African ancestor, the undifferentiated E-M35 chromosomes, which are essentially confined to sub-Saharan Africa.

Undifferentiated PN2* chromosomes, the ancestral clade needed to give rise to downstream E clades like E1a1a (E3a) and E1a1b (E3b) are rare to non-existent in northeast Africa, and the ancestral YAP+ clades which would be essential to giving rise to haplogroups E and D, are virtually non-existent outside of Africa.

In short, backflow mutations are themselves another subset of original sub-Saharan baseline variability, the engine that gave rise to all these variants.

Mystery Solver said...

To big valley:

In a nutshell, what I'm essentially saying, is that the notion that the origins of haplogroup E is open to interpretation, is bogus; preponderance of evidence allows for only one interpretation: It is African in Origin.

I'm also saying that the prospect of haplogroup E's origin in northeast Africa is unlikely or has little merit, given evidence: its YAP+ ancestral clade, not to mention its overall diversity, has thus far been confined to sub-Saharan Africa.

As for the E-M34 subclade of E3b, I'm saying that although *some* theorists prefer to entertain its origin from a so-called Near Eastern angle, even as they don't rule out its African origins [just like Cruciani et al. 2004], it is equally probable that it is East African in origin. Flores et al.'s assessment for instance, seems to be looking at it from the latter angle, i.e. an East African origin, when they relate the co-existence of Jordanian Dead Sea E-M34 chromosomes with other African-specific markers therein. On top of that, regardless of where E-M34 UEP occurred, it is still a marker of recent African ancestry in the so-called Near East, because it is a sub-clade of E3b chromosomes from Africa. E-M34 would have required an upstream E-M35* ancestor, lacking downstream mutations associated with other E3b subclades, and thus far, E-M35* is quite rare to essentially non-existent outside sub-Saharan East Africa.