{"id":39471,"date":"2011-04-06T14:21:41","date_gmt":"2011-04-06T22:21:41","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=10739"},"modified":"2011-04-06T14:21:41","modified_gmt":"2011-04-06T22:21:41","slug":"africa-in-12-admixture-chunks","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2011\/04\/06\/africa-in-12-admixture-chunks\/","title":{"rendered":"Africa in 12  ADMIXTURE chunks"},"content":{"rendered":"<p>Some have asked what the point is in poking around African population structure when <a href=\"http:\/\/www.sciencemag.org\/content\/324\/5930\/1035.abstract\">Tishkoff et al.<\/a> and <a href=\"http:\/\/www.pnas.org\/content\/early\/2011\/03\/01\/1017511108\">Henn et al.<\/a> have done such a good job in terms of coverage. First, <strong>it is nice to run your own analyses so you can slice &amp; dice to your preference, and not rely on the constrained menu provided by others.<\/strong> There&#8217;s value in home cooking; you can flavor to your taste. Second, you never know what data people might leave on your doorstep. I&#8217;ve received the genotypes of three Somalis. Nothing too surprising, a touch more Cushitic than the Ethiopians in <a href=\"http:\/\/www.harappadna.org\/2011\/01\/behar-et-al-data\/\">Behar et al.<\/a>, but interesting nonetheless.<\/p>\n<p>Also, you can see how ADMIXTURE tends to come to weird conclusions in certain circumstances. Below is a K = 12 run ~50,000 SNPs. I&#8217;ve included in a few Behar et al. and HGDP populations to the Henn et al. set, as well as pruned a lot of the African groups which seem redundant in terms of information. I&#8217;ve added a few geographically informative labels as well.<\/p>\n<p>Observe below that there is a Fulani cluster. <strong>I think this is pretty much an artifact.<\/strong> At K = 7 the Fulani have a majority component &#8230;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Some have asked what the point is in poking around African population structure when Tishkoff et al. and Henn et al. have done such a good job in terms of coverage. First, it is nice to run your own analyses so you can slice &amp; dice to your preferen&#8230;<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1233,611,4,82,30,294,209,1234],"tags":[],"class_list":["post-39471","post","type-post","status-publish","format-standard","hentry","category-african-population-structure","category-bantu-expansion","category-genetics","category-genomics","category-human-evolution","category-population-structure","category-population-substructure","category-sandawe"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/39471","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/users\/12"}],"replies":[{"embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/comments?post=39471"}],"version-history":[{"count":9,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/39471\/revisions"}],"predecessor-version":[{"id":39656,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/39471\/revisions\/39656"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=39471"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=39471"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=39471"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}