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Ancient west Eurasian ancestry in southern and eastern Africa 2013
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[QUOTE]Originally posted by The Explorer: [QB] [QUOTE]Originally posted by zarahan- aka Enrique Cardova: [QUOTE]Originally posted by The Explorer: Synopsis of what transpired, starting with this partial recap from page 1: [b]The easing up of skin eumelanin in San hunter-gatherers has generally been attributed to local evolution in lower UV radiation environments they frequent, as opposed to the result of gene flow[/b]. In the Ethiopian samples, on the other hand, the presence of the "derived" variant of the SLC24A5 gene was peculiar in that it was not found in tandem with other "skin-pigmentation" affiliated genes whose distribution generally paralleled that of the "derived" SLC24A5 variant, particularly in Europeans. Hence, "frequency" in itself is not a sufficient enough indicator for ascribing a single-source origin in the form of a "non-African" origin. - Extract ends From blog entry, "[i]What Ethiopian Genetic Diversity—Really—Reveals![/i]", May 15, 2013: This [SLC24A5] gene, in its derived form, which is said to be under positive selection in "lightly" pigmented populations, was [b]implicated in the San[/b], who as noted above, [b]tend to generally be isolated[/b], and [b]culturally-conservative hunter-gatherers[/b]. [b]"Derived" variants[/b] of [b]other[/b] pigmentation-associated genes were also cited, [b]with respect to the San[/b]([5]). It is [b]questionable that this gene is serving as a "non-African" marker in the San[/b]. The [b]same issue actually surfaces with regards to its presence in Ethiopian[/b] groups: Secondly: [i][b]Given that SLC24A5 is one of the most highly differentiated genes between African and European[/b] populations, we then [b]looked for other highly differentiated genes[/b] among the outlier windows, [b]but found none[/b]... To [b]further investigate the effect of admixture on the genetic landscape of skin pigmentation in Ethiopia[/b], we also [b]looked at other genes associated with pigmentation in Europe[/b]; however, [b]none were found in our outlier regions[/b].[/i] If this gene, in its "derived" form, was essentially serving as a "non-African" marker in the Ethiopians, then [b]one would expect that other "derived" skin-pigmentation markers would have been introduced along with the SLC24A5 allele[/b], by the foreign "non-African" group(s) that is supposed to have been the source. [b]Skin pigmentation is the byproduct of the consortial work of a number of distinct genes[/b], and [b]so, it's highly unlikely that a "derived" SLC24A5 allele would be introduced without other accompanying skin-pigmentation genes[/b]. No less, it's [b]highly unlikely that only the derived "SLC24A5" allele would survive[/b] from a foreign "non-African" source, [b]in a population for which the allele's presence is "potentially disadvantageous"[/b], as the authors note, on grounds of the kind of UV-radiation intensive environment they generally reside. Likewise, [b]if as the authors note[/b], the [b]presence of the derived SLC24A5 allele in Ethiopians may be attributable to "socially"-promoted selection[/b], then one would think that [b]other skin-pigmentation genes, which would have accompanied the SLC24A5 allele[/b] in an introduction by a foreign "non-African" source, [b]would have likely also survived in some capacity or another[/b], so as [b]to serve the same role that the SLC24A5 may be serving[/b]. --Extract ends .. a marker serving as "gene flow" would be introduced "as is", and as such, one that is under selective pressure, will continue to have that selective attribute. From there, it boils down to whether the selective trait is advantageous or deleterious--and to what degree--to the "receiving" population, which will subsequently decide the fate of an allele. The "receiving" population doesn't get to cherry pick which trait to pick and which to discard at a conference table; that's not how nature works to swenet's dismay. .. [i][b]Skin pigmentation is the byproduct of the consortial work of a number of distinct genes[/b][/i] - from the blog So, it is not unheard of for a population to have a skin pigmentation allele that resembles that of populations which are usually identified with said allele, and yet, have other skin pigmentation alleles that are different from said populations. The derived variant of SLC24A5 similar to the type present in Europe and "southwest Asia" can be present in Ethiopians, yet other alleles that typically accompany the variant in the said regions can be absent in Ethiopians. As such, even if SLC24A5 has a phenotypic trait that is generally disadvantageous in the tropics, by its lonesome, it is not going to have as profound an impact on skin pigmentation as it allegedly does in say, Europeans... which brings us to the question of why then, there seems to be indication (as shown in the Z-scores) that a derived variant is "selected for" in Ethiopians. Pagani et al., apparently working with their "gene flow" theory, posit that it could be the byproduct of "socially" channeled "selection", like say, "sexual selection". I've already laid out the coherency difficulties which inflict that [b]composite[/b] theorizing. While the "social factor" is a plausible scenario, unlike Pagani et al., I posit that the allele could have been selected initially for a different environment, on the African continent itself (the sub-tropical Sahara), in the ancestral populations of Ethiopians in question. My theory takes into account the plausibility that the "derived" SLC24A5 variant may have been initially selected for in a different African environment, but because it merely contributed to the skin tone continuum seen in said Ethiopians, as opposed to having a decisive role, SLC24A5 variant managed to survive the UV environment of the tropics. This is how my theory takes into account, the "social factor" that Pagani et al were speaking of, in an entirely different context. You see, the ancestors of said Ethiopians living in sub-tropical African environment north of the equator may have undergone some skin pigmentation relaxation, initially as a response to the said sub-tropical environment, but not enough to have gone to the extreme relaxations seen in Europe, for instance. As such, their skin pigmentation relaxation was perhaps not extreme enough to make their survival in the tropical African environment unbearable. This will adequately account for why SlC24A5 derived variant happens to appear in Ethiopians at substantial frequencies, while other skin pigmentation alleles generally associated with Europeans do not. [/QUOTE]Just to clarify here: ^^(1) Under what scenario could the derived SLC24A5 variant have been selected for? Climate zone variations over log time spans? Differing micro-clime zones spread over a broad Saharan/NE African geographic space? [/QUOTE]This has already been addressed in the very paragraph you cited. See above: initial selection in the sub-tropical region of the Sahara. Unless the spinning orientation of the Earth has dramatically shifted (as opposed to minor wobbles) time and again, such things should not change much over time. Skin pigmentation content correlates with UV radiation intensity, not heat, or general weather. [QUOTE] 2) Does your approach absolutely reject any outside gene flow or do you still leave the door open for such, while holding that the primary pattern of variation or diversity could well be indigenous, from within the African continent or the NE African region?[/QUOTE]In scientific theory, there generally are no absolutes. If you are referring to SLC24A5, then I'm saying the evidence put before me does not point to "gene flow from outside"; that's what I'm saying. Rather, it points to an autochthonous origin scenario. [QUOTE] 3) On your blog you take issue with Pagani's definitions of a so-called "African" versus "non-African" component. [b]Does the use of Yoruba samples as the primary "African" Exhibit represent a variation of the old "true negro" game, as you see it? [/b][/QUOTE]It's analogous to it. ;) [/QB][/QUOTE]
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