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Early Back-to-Africa Migration into the Horn of Africa, Hodgson, 2014
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[QUOTE]Originally posted by Amun-Ra The Ultimate: [QB] This is a very bad way to use the Admixture software (I wont enumerate all the reasons here in this post, they are multiple) and does make a lot of baseless hypothesis and unproven conjecture. I won't discuss every conjecture but consider this part of the text: [QUOTE]This Ethio-Somali IAC is found at its highest frequencies in Cushitic speaking Somali populations and at high frequencies in neighboring Cushitic and Semitic speaking Afar, Amhara, Oromo, and Tygray populations. This IAC was not identified in the source study for the HOA SNP data [16], but Tishkoff and colleagues [59], in an analysis of an independent autosomal microsatellite dataset, did recover an equivalent IAC (calling it ‘‘Cushitic’’). While this Ethio-Somali IAC is found primarily in Africa, it has clear non-African affinities (Text S1). [/QUOTE]Basically, [b]he admits his non-African Ethio-Somali IAC was not discovered in the source study he used for the HOA SNP data, but then he lie to us[/b] ! He says "but Tishkoff and colleagues" "did revover an equivalent IAC (calling it "Cushitic"). Then proceed to tell us that this IAC has clear non-African affinities. This is a lie because in the Tishkoff study the Cushitic IAC had clear African affinities: From the Tiskhoff study in question supp.Mat (The genetic structure and history of Africans and African Americans.): [IMG]http://i1274.photobucket.com/albums/y421/amunratheultimate2/CushiticAACinTishkoffgeneticdistance_zps89d8fca2.png~original[/IMG] Clearly the Cushitic AAC/IAC identified in the Tishkoff study had a clear African affinity. In another line of analysis, "the source study for the HOA SNP data [16]" is the Pagani study called [i]"Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool"[/i] beside not showing this non African IAC as he admits, it suffers from a high level of SNP Ascertainment Bias in favor of non-African affiliations. As admitted in the Pagani study: [QUOTE]The Semitic-Cushitic and North African populations showed the highest values of heterozygosity worldwide, which may reflect a combination of [b]SNP ascertainment bias[/b] and the mixture of African and non-African components in these populations. [/QUOTE]Usually African populations have a much higher level of heterozygosity than European or North African population. The effect of SNP ascertainment bias is a consequence of the SNP discovery process where a sub-set of European population are used. This translate in bias PCA analysis and Admixture software proportion of admixture (in favor of Eurasian SNPs/clusters). This SNP ascertainment bias [URL=http://mbe.oxfordjournals.org/content/27/11/2534.abstract]is common[/URL] in many SNP microarray. In general, all such analysis based on a pre-selected group of SNPs/microarray must always take this SNP ascertainment bias in consideration when analyzing population admixture and affiliation. Hopefully, in the future full genome analysis could end this bias toward non-African and Eurasian SNPs. Still those "admixture" and PCAs analysis have their use, but everything must be put in perspective and any bias taken into consideration. So when you see such admixture software analysis with all the K colors always consider this. In my opinion, there always is some ancient and more recent admixture between populations (in both directions) but here the ancient non-African contribution to HOA is greatly over-estimated (you can even see the blue part of the Nilo-Saharan component being engulfed by this so-called non-African component). It simply reflect structuring among African population in Horn Africa on one part and mostly "recent" bi-directional relationship between HOA and Eurasian populations (often confused in admixture software analysis when any K is taken as valid). The Tishkoff Cushitic IAC confusion(lie) by the author points to that direction as does other previous studies. [/QB][/QUOTE]
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