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Genetic Closeness of the East/West African SNP population clusters (blog source)
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[QUOTE]Originally posted by Amun-Ra The Ultimate: [QB] As we well know on this site, modern East and West Africans populations are united between each others through the E-P2(PN2) Y-DNA haplogroup, and various MtDNA counterpart haplogroups (L3eikx, L2a, etc), from a time period after the main OOA migrations. So at a relatively recent time in relation to human history. In this thread, I'm posting the results from a mere blogger (Dienekes) with a reputation of being biased. But in other threads, I posted "similar" results analysis from real peer-reviewed study: http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=008817 http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009076 What Dienekes did with the dodecad results ([URL=http://dodecad.blogspot.ca/2012/10/globe13-participant-results.html]LINK[/URL]) is a bit what Tishkoff did in her genetic history of African and African-American study discussed in the thread linked posted above. Which is what all the studies based on the admixture software (with the colored bar) should do. That is also include the genetic distance between the various putative population components (aka the various Ks, aka the various colored bars). Here's the version from the Tiskoff study: http://i48.tinypic.com/8ydx.jpg (also available in the threads linked above and in the Tiskoff Supplementary Online Material [URL=http://www.sciencemag.org/content/suppl/2009/04/30/1172257.DC1/Tishkoff.SOM_REVISED.pdf]DOWNLOAD[/URL] ) I won't repost it in here since I've already discussed it in the threads linked above. Basically, it used autosomal STR genetic distance between population components (at K=14) found using the admixture software. We can see that generally African populations are closer to each others than they are to non-African populations. Same for non-African populations within each non-African sub-groups respectively. Notably the Cushitic and Niger-Kordofanian populations are relatively close to each others. This graph also has the advantage of using the Euclidean genetic distance which I prefer to the Fst which measure population differentiation (although Fst is often used in such study). The Tiskoff study also use a much larger number of populations. Since in the Tishkoff study since Cushitic and Niger-Kordofanian speakers are relative close to each others while showing no sign of recent admixtures, we can deduce this genetic closeness if from their common origin. A common origin postdating the OOA migrations (as the Cushitic/Niger-Kordofanian speakers are closer to each others than they are to any non-African populations). I post this globe13 results from the Dienekes analysis because it's informative. It also used SNPs while Tiskoff was using autosomal STRs. So it give us another point of view. Adding to the point of view already provided by uniparental analysis. The results are basically similar: East and West African populations, and African populations in general, are very close to each others. Especially if you remove the more recent Eurasian component from recent post-OOA back migrations by Semitic (ethio-semitic) and Muslim Arabs speakers (See [URL=http://www.pnas.org/content/111/7/2632.full]Pagani (2014)[/URL]) . [b]A neighbor-joining tree of the 13 components based on the Fst divergences:[/b] [IMG]http://2.bp.blogspot.com/-aDcB98_NT8M/UJBgPOHIk2I/AAAAAAAAAzc/wQUT4GkY-K8/s640/nj.png[/IMG] It's similar to the Tiskoff genetic distance tree above but this time using SNP data and the FST divergence formula instead of the D-square Euclidean genetic distance formula. Clearly we can see East and West African clustering close to each others. Here's the TreeMix plot for those interested: [IMG]http://1.bp.blogspot.com/-IS_fRlD7V5k/UJBi-JEMqjI/AAAAAAAAAzs/FWBI9YH6zLU/s1600/treemix.png[/IMG] Palaeo_African are basically modern San people. I don't know why they are called Palaeo since they are not more Palaeo than any other modern populations as they went through about the same number of generations and mutations than other populations since the time of their common origin with them. Again, we can again East and West Africans clustering close to each others. From this blogger analysis we also got the spreadsheet with the FST "distances" between populations as well as the percentage of the K-Populations component(like East African, West African, Artic) for each populations sampled (like Somali, Yoruba, etc). FST divergence between populations: https://docs.google.com/spreadsheet/ccc?key=0ArAJcY18g2GadF9CLUJnTUdSbkVJaDR2UkRtUE9kaUE#gid=3 We can see for example at the last line at the bottom that the West African population cluster (at K=13) is the closest to the the East African population cluster with a value of 0.046. Something we already know since I just posted the neighbor-joining tree above. https://docs.google.com/spreadsheet/ccc?key=0ArAJcY18g2GadF9CLUJnTUdSbkVJaDR2UkRtUE9kaUE#gid=2 This is equivalent to the usual Admixture component analysis with K=13 but in a tabular form instead than graphical form with different colors for each 13 putative population component. What is good for us is we can see what populations were used (where the data were taken). We can see Yoruba populations as well as East Africans from the Pagani study were used for example. So a good diversity of East African populations (Oromo, Somali, Amhara, Afar, Ari, etc). For example, using the spreadsheets above, generated by the blogger running the software, Ethiopian Jews got 51.4% of the East African component. It also has a large recent Southwest Asian component at 39.2%. A very low 0.2% recent West African component. This show that while the East and West African component are very close to each others (from the Fst Distance), Ethiopians Jews have basically no recent admixture with West Africans after their moment of separation from them. That is the separation of the E-P2 lineage into the P2/e1b1a andd P2/e1b2b lineages. A bit similar for Somali. The Somali population sample from the Pagani study (position 271 on the spreadsheet) has 62.3% of the East African component at K=13. They got 33.2% of recent SouthWest Asian component and 0.8% of recent West African component. This show that while the East and West African component are very close to each others (from the Fst Distance), Somali have basically no recent admixture with West Africans after their moment of separation from them. That is the separation of the E-P2 lineage into the P2/e1b1a andd P2/e1b2b lineages. Of course you must always view those as estimate. They are often based on small samples sizes but it gives us a good general idea of the situation. We can see again the genetic closeness of the East African and West African SNP population clusters. This genetic closeness is not the product of recent admixtures between those 2 populations but from their common ancestral origin in Northeast Africa. The E-P2 population. So basically both East and West African populations have their common origin in Northeast Africa at a time period after the OOA migrations but before the foundation of the Ancient Egyptian state. This complement my peer-reviewed study analysis posted in those threads: http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=008817 http://www.egyptsearch.com/forums/ultimatebb.cgi?ubb=get_topic;f=8;t=009076 [/QB][/QUOTE]
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