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I was told that the reason is that DNA companies use alot of SNPs that are fixed ancestral in both Africans and Eurasians or that have high allele frequencies in both. If they captured positions that were variable in Africans then Neanderthals would not score like 90% African because in fact Neanderthals are more related to Eurasians than Africans.
As far as I know Eurasian DNA's SAPDA software is the only one that doesn't show Neanderthal as 90% African. Unlike Admixture calculators SAPDA actually correctly shows Neanderthal more related to Eurasians than Africans ( fig 1 and 2 https://eurasiandna.com/sapda-admixt...tes-revisions/
This diagram shows S African pygmies split from Eurasian and other African ancestors around 270,000 years ago compared to only around 40,000 years ago for W. Eurasian-E. Eurasian split. So Europeans are much much more related to E. Asians than African pygmies
[IMG][/IMG]
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