{"id":39318,"date":"2011-04-02T00:32:00","date_gmt":"2011-04-02T08:32:00","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=10712"},"modified":"2011-04-02T00:32:00","modified_gmt":"2011-04-02T08:32:00","slug":"you-learn-from-failure","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2011\/04\/02\/you-learn-from-failure\/","title":{"rendered":"You learn from failure"},"content":{"rendered":"<p>In yesterday&#8217;s <a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/2011\/03\/the-bantu-volkerwanderung\/\">post<\/a> on African genetics I tried to work with a large set of populations, but narrowed SNPs down to ~40,000. Today I thought I&#8217;d go another route, focus on having a thicker market set, but with fewer populations. So I did a bunch of runs with 400,000 SNPs. Here&#8217;s K = 8. Please note, <strong>I did some &#8220;trial&#8221; runs and pulled out people with obvious admixture which was recent or an outlier within their population.<\/strong> (e.g., Mozabites  with a lot of Sub-Saharan African or San which obviously had European ancestry).<br \/>\n<a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/04\/thickrunaf.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-10713\" title=\"thickrunaf\" src=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/04\/thickrunaf.png\" alt=\"\" width=\"600\" height=\"352\" \/><\/a><\/p>\n<p>Notice that there are three non-Sub-Saharan modal components. South of the Sahara the European one is absent. But here&#8217;s the weird thing. Below are MDS representations of genetic distance between the ancestral groups inferred above:<\/p>\n<\/p>\n<p><a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/04\/MDSAll.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-10714\" title=\"MDSAll\" src=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/04\/MDSAll.png\" alt=\"\" width=\"564\" height=\"506\" \/><\/a><\/p>\n<p>Now without Eurasians + North Africans:<\/p>\n<p><a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/04\/MDSAf.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-10715\" title=\"MDSAf\" src=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2011\/04\/MDSAf.png\" alt=\"\" width=\"563\" height=\"500\" \/><\/a><\/p>\n<p>All of these &#8220;ancestral&#8221; groups are abstractions. More plainly, they&#8217;re fake but useful (physicists would say &#8220;toy models,&#8221; economists &#8220;stylized facts&#8221;). But the Nilotic one seems kind of crazy here. It told the program to go look &#8230;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In yesterday&#8217;s post on African genetics I tried to work with a large set of populations, but narrowed SNPs down to ~40,000. Today I thought I&#8217;d go another route, focus on having a thicker market set, but with fewer populations. So I did a b&#8230;<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[290,4,82],"tags":[],"class_list":["post-39318","post","type-post","status-publish","format-standard","hentry","category-admixture","category-genetics","category-genomics"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/39318","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=39318"}],"version-history":[{"count":8,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/39318\/revisions"}],"predecessor-version":[{"id":39474,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/39318\/revisions\/39474"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=39318"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=39318"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=39318"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}