Hocus Pocus Razzle Dazzle–African Origin of Light skin-Again

[djoser-xyyman]

Here is another example of the extent some researchers will go to lie and misrepresent conclusion in the interest of…. what? They have concluded that an area OUTSIDE the actual gene is a better indicator than the gene itself on where that said gene originates. This is a first. . If they go strictly by the gene’s haplotypes then they will have to concluded light skin originated in SSA. Just as Shriver et al concluded. This is analogous to a murder investigator discovering a room soaked in blood with a headless body in Philadelphia and concluding the murder took place in Baltimore because the head was found in Baltimore.

Here they are trying to remove the origin of light skin outside Africa and place it in the Middle East somewhere . They admitted light skin did NOT evolve in Europe irregardless of the fact Europe has the highest frequency and is "fixed". Just as Shriver et al. These researchers saw the same data pattern as Shriver but tried to razzle dazzle and place the origin of light skin outside Africa in the Middle East or near India. They try to do this by focusing on a region FAR away from the gene C11/SLC24A5/ A111T allele ie D4(Baltimore). The data is consistent with Shriver et al on the origin of light skin in Africa. It also supports the SEGREGATING of haplotypes surrounding SLC24A5 in Africans just as was discussed in the La Brana man paper. At least Shriver was honest enough to admit an African origin of light skin. Read on

[djoser-xyyman]

Molecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection

- Victor A. Canfield



ABSTRACT. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin.

[djoser-xyyman]

To learn about the time and location of origin of the A111T mutation, we studied haplotypes in the region around SLC24A5 across world populations.

A111T shows a latitudinal decline toward the Equator, with high frequencies in Northern Africa (.0.80), intermediate (0.420.6) in Ethiopia and Somalia, and lower (,0.35) in sub-Saharan Africa. This pattern is broadly consistent with strong positive selection for decreased skin pigmentation throughout Europe. There is a cline of decreasing frequency of A111T in indigenous populations east of approximately longitude 75_ in Central Asia, with near-absence in East Asia, Oceania(Paupans), and the Americas. The extent to which the spread of A111T to the east has been inhibited by the absence of substantial eastward population migrations postdating its origin or by the presence of other loci responsible for decreased skin pigmentation in East Asia is presently unclear.

Characterization of haplotypes in the genomic region encompassing SLC24A5

Diminished variation in the genomic region around SLC24A5 in the HapMap CEU (European ancestry) sample led us to ask what the haplotypes associated with the A111T allele looked like, and how, when, and where they might have arisen..

TRANSLATION-XYYMAN COMMENT: - Europeans have the highest frequency of the SLC45A2 polymorphism but the areas surrounding this SNP is VER VERY homologous ie NOT DIVERSE. This an indication that the gene did NOT originate in Europe and the researchers set out to discover where the gene originated.

[djoser-xyyman]

Blocks B, C, and D together encompass the region of diminished variation in CEU. Analysis of the core subregion C, which includes SLC24A5, yielded 46 haplotypes in HapMap Phase 3 populations (Table S3 and Table S4). This finding is consistent with a common origin for A111T worldwide.

Interestingly, the greatest diversity of B-region haplotypes associated with C11 is found in GIH (Indians) (89% B6). Taken together, these results establish that the 147-kb founder haplotype containing A111T was B6 + C11 + D4. RAZZLE! DAZZLE! HOCUS! POCUS!!!!!


Phylogeographic analysis of SLC24A5 haplotype distributions:

The world distribution of CORE region haplotypes, together with their phylogenetic relationships, suggests which haplotypes likely originated in Africa and which most likely arose outside of Africa.


As expected from the near fixation of A111T in Europe, the C11 clade predominates there, and all other haplotypes are rare. Of the remaining 10 common core haplotype groups, [/b]all ancestral at rs1426654, eight clearly have their origins in Africa [/b](Figure 3B, Figure 4, and Table S4). Three early diverging haplotypes, C1, C2, and C4, are rare outside of Africa and clearly originated there. In the lineage containing the majority of haplotypes, each of the three branches, containing C5, C6-C7, and C8-C11, give strong evidence of having originated in Africa. C5 reaches its greatest abundance in West Africa and is rare outside of Africa. Within the other two branches, C6 and C9, which are the most common haplotypes in Africa, are also common worldwide, whereas C7 is abundant in East Asia and much less common but widespread in Africa. Consideration of the relationships among haplotype variants (Figure 4) indicates that C6, C7, and C9 (but not C8) dispersed out of Africa and have diverse descendants present and originating in East Asia. Among these descendants is C10, which is abundant in East Asia (and the New World) but extremely rare in Africa (0.5% in LWK). Haplotype C3 represents the final early diverging lineage (Figure 4). Although the lineage containing this haplotype must have originated in Africa, C3 is rare in Africa (1.0% in MKK) but widely distributed in East Asia, the New World, and Oceania. The distributions of C3 and C10 are most consistent with origin outside of Africa and subsequent introduction into Africa by migrations such as those documented by uniparental markers (Richards et al. 2006).

[djoser-xyyman]

Where did C11 originate?

The precursors to C11, haplotypes C3 and C10, are common in East Asia and the New World (Figure S5), but the DISTRIBUTION of C11 indicates that these locations are not likely sites for the origin of C11 or its immediate precursor.

Although too few African C11 sequences have been determined to draw strong conclusions, those available from the 1000 Genomes Project show no evidence of greater age in the form of greater SNP diversity than the European examples. It should be noted that the relatively high abundance of A111T in several equatorial East African samples indicates the absence of sustained strong negative selection against this allele at low latitudes. Although a non-African origin for C11 is clear, near fixation of this haplotype over a wide geographical region prevents strong inferences regarding a precise location of origin..!!!! Ha! Ha! Ha!

In fact, the decrease in frequency of A111T to the east of Pakistan suggests that C11 originated farther to the west and after the initial genetic split between western and eastern Eurasians. On this basis, we hold the view that an origin of C11 in the Middle East, broadly defined, is most likely.

I am not sure many of us grasp the significance of the La Brana and Loschbour pigmentation variation. And to a lesser extent Stuttgart woman. It not only shows the white skin “new” to Europe but when it arrived it annihilated the Black Europeans. The replacement of dark skin by light skin was profound, rapid and explosive. It seems like the Black Europeans occupied and dominated Europe between 40,000ya – 7,000ya. Close to 35,000years. Reminds me of Neanderthal replacement. The really intriguing question is HOW, Why and Time frame.

[djoser-xyyman]

[djoser-xyyman]

[djoser-xyyman]

[zarahan]

Excellent work. Help us break down some of this info for easier layman grasp.

diagram:


So you are saying that:
1) The A111T polymorphism in SLC24A5 is prevalent in white Europeans, aka the "white skin" gene variant?
2) That A111T is made up of several haplotypes C1 thru C11?
3) Taken together, Africans have the most variation of said "white skin" A111T polymorphism?
4) C11 may have at least part origin in Africa and not necessarily the "Middle East"?
5) Ques- does the presence of this greater diversity suggest an earlier African origin? or not at all?

^Correct me if I am wrong on the above.
I am just trying to make it clear and break it down for when I
talk to people so they can begin to grasp the outlines...


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At least Shriver was honest enough to admit an African origin of light skin.
^^ Do you have a quote somewhere or diagram where they/Shriver do this
clearly?


On this basis, we hold the view that an origin of C11 in the Middle East, broadly defined, is most likely.
^^Just what is taken in by this "broad definition" of the Middle East?
Parts of Africa that somehow are not mentioned?


"HBD" types are desperate to link light skin with the Gravettian developments
cuz see- it then would be all this "transformation" linked on with "whiteness."
That's the game.
Per DINKs blog- some posters yearn for this openly:
I think Eurologist would argue the date would be a little further back to sync with the Gravettian, but still, can we find another gene which has expanded so fast?

"The (corrected) age estimate, distribution, and likely place of origin all are in agreement with a Gravettian expansion".

^^Only its not. A "whiter shade of pale" occurred much LATER than the Gravettian
would you say XYZ?


I am not sure many of us grasp the significance of the La Brana and Loschbour pigmentation variation. And to a lesser extent Stuttgart woman. It not only shows the white skin “new” to Europe but when it arrived it annihilated the Black Europeans. The replacement of dark skin by light skin was profound, rapid and explosive. It seems like the Black Europeans occupied and dominated Europe between 40,000ya – 7,000ya. Close to 35,000years. Reminds me of Neanderthal replacement. The really intriguing question is HOW, Why and Time frame.


I think "annihilate" might be too strong a word. Based on some of the
things I have read, if you throw in climate change, the lighter types
may have evolved/arrived at at time when colder, more arid conditions
reduced the older dark-skinned Europeans, giving an edge to lighter types
better cold-adapted. With the return of better conditions, the once small
edge grew into a bigger advantage, with the lighter types gradually gaining
ground, absorbing the older, darker types. I would put climate/enviro change
as the main factor. The lighter types arrived/returned to a much more
favorable climate and could expand population, perhaps reinforced by
other similar variants from the Middle East over time. Under such a scenario
the once dark types that dominated even the cold zones would be gradually eased out
and absorbed. Naturally the lighter types could inherit and build on all that
their darker brethren pioneered.- whether in art, tool-making, transport, food
production, etc etc. Hard to say with tight certainty.




















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HapMap populations consist of CEU (CEPH individuals of northern and western European descent, sampled in Utah), TSI (Tuscan, Italy), GIH (Gujarati, sampled in Houston), CHB (Chinese, Beijing), CHD (Chinese descent, sampled in Denver), JPT (Japanese, Tokyo), YRI (Yoruba, Ibadan, Nigeria), LWK (Luhya, Webuye, Kenya), MKK (Maasai, Kinyawa, Kenya), ASW (African-Americans from southwest United States), and MEX (Mexican, sampled in Los Angeles).

[anansi]

Yeah reminds me of when they tried to locate E in the so-called Middle of the East some yrs back good job on calling Bs on this guyz.

[anastasiaescrava]

I agree with Zarahan, laymen terms, please.

[djoser-xyyman]

Let me try to explain further…..

In summary: Shriver et al concluded that AMH left Africa with the ability to evolve light skin. This is clearly observed by the smooth transition of skin shade phenotype from central Africa to Northern Europe. East Asia warrants a different explanation( to be discussed some other time). Based upon the work on La Brana Man, Loschbour Man and Stuttgart woman the researchers saw segregation of SNPs(Haplotypes) around the “white gene” (SLC24A5/ A111T/C11/ rs1426654 – these are many of the names used). This segregation pattern implies ORIGIN of the mutation. Europeans do NOT have the segregation around the mutation. South Asian/Indians show slightly more variation than Europeans but far less than Africans in that region. Africans have segregation (derived/underived) near the gene IN ADDITION to the derived of the ACTUAL genetic marker.

What the researchers of this paper, Victor A. Canfield et al, tries to do is “explain away” the observed data. ie remove the origin from Africa and put it someplace else ie in the “Middle East”. They agreed with Shriver et al that light skin did NOT originate in Europe. But unlike Shriver they tried to place the origin outside Africa. .

[djoser-xyyman]

Their ruse …..using unproven recombination hypothesis(meiosis from high school biology) and genetic markers FAR outside the SLC24A5 region. No other genetic researchers do that. This is what they call the “D” region. They place less emphasis the C or Core region.

But here is what they initially observe.

====

Quote:

As expected from the near fixation of A111T in Europe, the C11 clade predominates there, and all other haplotypes are rare. Of the remaining 10 common core haplotype groups, all ancestral at rs1426654, eight clearly have their origins in Africa (Figure 3B, Figure 4, and Table S4). Three early diverging(SEGREGATING) haplotypes, C1, C2, and C4, are rare outside of Africa and clearly originated there. In the LINEAGE containing the majority of haplotypes, each of the three branches, containing C5, C6-C7, and C8-C11(Light Skin), give strong evidence of having originated in Africa.

====

C11(their nomenclature) is the genetic region that contains the marker for light skin. After admitting that they then used a hypothetical model using the D region as a better indicator of the light skin gene. As I said no other researchers do that.
This is their hypothesis- Quote:

===

Taken together, these results establish that the 147-kb FOUNDER haplotype containing A111T was B6 + C11 + D4

And

subsequent introduction into Africa by migrations such as those documented by uniparental markers (Richards et al. 2006).

===

In other words D4/B6 should be used to determine origin of C11. They combined C11 with B6 and D4 claiming this is the ‘founder” haplotype. From there they showed D4/B6 originated OUTSIDE Africa therefore concluding C11 ALSO originated outside Africa. They then used “hokey” method to explain its presence in Africa. But to Brada point, it is not through back-migration. Their explanation…..? – Richards et al 2006 is cited..

[djoser-xyyman]

But here is what Rees et al says

Quote:

Understanding the Evolution of Human Pigmentation: Recent Contributions from Population Genetics

Jonathan L. Rees1 and Rosalind M. Harding2

****For technical reasons relating to the diversity and representation present in many genome-wide studies, there may be a bias toward genes important in European populations rather than African populations (Pritchard et al., 2010; Casto and Feldman, 2011). African populations remain under strong selective forces, and although the majority of pigment diversity is between continents, there remains substantial pigmentary variation within Africa (Relethford, 2002), which is as yet largely unexplained in genetic terms.****

XYYMAN: Now, Relethford 2002 question has been answered in 2013!!!

[djoser-xyyman]

Following up on their source Richards et al 2006


****Richards, M 2006 A model for the dispersal of modern humans out of Africa, pp. 223–263 in Human Mitochondrial DNA and the Evolution of Homo sapiens: Nucleic Acids and Molecular Biology

Quote: The observation that the ancestral state of a HindI site (at nucleotide positions 12406-12411) is frequent in sOllie Asian populations likewise suggested a similar conclusion (Denaro et al. 1981; Blanc et al. 1983). The 'Oriental' origins of human mtDNA variation were further deduced from a study of Tharus from Nepal (Brega et al. 1986), and high mtDNA diversity was found also to be present among Japanese populations (Horai et al. 1984; Horai and Matsunaga 1986). Besides Asian populations and Africans, Cann (1984) reported……*****


XYYMAN: In other words they are using uniparental markers on origin of AMH in Asia based upon genetic work from the 1980’s to explain the SLC24A5 mutation in the Middle East to Africa. The old Orientalist multi-regional theory. AMH originated in Asia and entered Africa as data from the 1980’s show!!! Wow! Talk about wacky!