{"id":74102,"date":"2012-09-25T23:39:06","date_gmt":"2012-09-26T07:39:06","guid":{"rendered":"http:\/\/blogs.discovermagazine.com\/gnxp\/?p=18476"},"modified":"2012-09-25T23:39:06","modified_gmt":"2012-09-26T07:39:06","slug":"re-imagining-genetic-variation","status":"publish","type":"post","link":"https:\/\/www.razib.com\/wordpress\/2012\/09\/25\/re-imagining-genetic-variation\/","title":{"rendered":"Re-imagining genetic variation"},"content":{"rendered":"<p><a href=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2012\/09\/genetic00.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"alignleft size-medium wp-image-18478\" title=\"genetic00\" src=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2012\/09\/genetic00-300x241.jpg\" alt=\"\" width=\"300\" height=\"241\" \/><\/a>To the left is a PCA from <a href=\"http:\/\/www.amazon.com\/exec\/obidos\/ASIN\/0691029059\/geneexpressio-20\">The History and Geography of Human Genes<\/a>. If you click it you will see a two dimensional plot with population labels. How were these plots generated? In short what these really are are visual representations of a matrix of genetic distances (those distances being general FST), which L. L. Cavalli-Sforza and colleagues computed from classical autosomal markers. Basically what the distances measure are the differences across populations in regards to their genetics. The unwieldy matrix tables can be visualized as a neighbor-joining tree, or a two dimensional plot as you see here. But that&#8217;s not the end of the story.<\/p>\n<p>In the past ten years with high density SNP-chip arrays instead of just representing the relationship of populations, these plots often can now illustrate the position of an individual (the methods differ, from components analysis or coordinate analysis, to multi-dimensional scaling, but the outcomes are the same).<\/p>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-18481 alignleft\" title=\"genmap1\" src=\"http:\/\/blogs.discovermagazine.com\/gnxp\/files\/2012\/09\/genmap1-300x234.jpg\" alt=\"\" width=\"300\" height=\"234\" \/>\u00a0For example, the famous <a href=\"http:\/\/www.nature.com\/nature\/journal\/v456\/n7218\/abs\/nature07331.html\">genetic map of Europe<\/a>. Here you see the colors representing nationalities, and centroid positions of the populations as well as individuals. In this &#8230;<img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/feeds.feedburner.com\/~r\/GeneExpressionBlog\/~4\/lcRnTxTXWcw\" height=\"1\" width=\"1\"\/><\/p>\n","protected":false},"excerpt":{"rendered":"<p>To the left is a PCA from The History and Geography of Human Genes. If you click it you will see a two dimensional plot with population labels. How were these plots generated? In short what these really are are visual representations of a matrix of gen&#8230;<\/p>\n","protected":false},"author":12,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,82,585],"tags":[],"class_list":["post-74102","post","type-post","status-publish","format-standard","hentry","category-genetics","category-genomics","category-pca"],"_links":{"self":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/74102","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=74102"}],"version-history":[{"count":6,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/74102\/revisions"}],"predecessor-version":[{"id":74160,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/posts\/74102\/revisions\/74160"}],"wp:attachment":[{"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/media?parent=74102"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/categories?post=74102"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.razib.com\/wordpress\/wp-json\/wp\/v2\/tags?post=74102"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}