{"id":10,"date":"2016-12-27T16:50:56","date_gmt":"2016-12-27T16:50:56","guid":{"rendered":"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/?page_id=10"},"modified":"2023-08-24T13:24:50","modified_gmt":"2023-08-24T13:24:50","slug":"notes","status":"publish","type":"page","link":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/notes\/","title":{"rendered":"Notes"},"content":{"rendered":"\n<p class=\"has-drop-cap\">The links below correspond, roughly, to the material covered in different lectures in the course. You can also download a single PDF that contains all of them. Just click the &#8220;Lecture notes in population genetics&#8221; link. <span class=\"footnote_referrer\"><a role=\"button\" tabindex=\"0\" onclick=\"footnote_moveToReference_10_1('footnote_plugin_reference_10_1_1');\" onkeypress=\"footnote_moveToReference_10_1('footnote_plugin_reference_10_1_1');\" ><sup id=\"footnote_plugin_tooltip_10_1_1\" class=\"footnote_plugin_tooltip_text\">[1]<\/sup><\/a><span id=\"footnote_plugin_tooltip_text_10_1_1\" class=\"footnote_tooltip\">Note: The single PDF doesn&#8217;t have revisions I&#8217;m making this fall. The differences aren&#8217;t big, but if you want the most up-to-date version of the single PDF, you&#8217;ll want to&nbsp;&#x2026; <span class=\"footnote_tooltip_continue\"  onclick=\"footnote_moveToReference_10_1('footnote_plugin_reference_10_1_1');\">Continue reading<\/span><\/span><\/span><script type=\"text\/javascript\"> jQuery('#footnote_plugin_tooltip_10_1_1').tooltip({ tip: '#footnote_plugin_tooltip_text_10_1_1', tipClass: 'footnote_tooltip', effect: 'fade', predelay: 0, fadeInSpeed: 200, delay: 400, fadeOutSpeed: 200, position: 'top center', relative: true, offset: [-7, 0], });<\/script> If you&#8217;re a real masochist, the LaTeX source and all of the associated files are available in a public <a href=\"https:\/\/github.com\/kholsinger\/Lecture-Notes-in-Population-Genetics\">Github repository<\/a>. If that last sentence is incomprehensible, don&#8217;t worry about it. Just click on the Lecture notes in population genetics link below and download the PDF, or download the individual topic notes that you find interesting.<\/p>\n\n\n\n<p><a href=\"http:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/notes\/\">Graham Coop<\/a> (UC Davis) also teaches a graduate course in population genetics, and he&#8217;s also put his lecture notes online: <a href=\"https:\/\/github.com\/cooplab\/popgen-notes\/blob\/master\/popgen_notes.pdf\">PDF<\/a>, <a href=\"http:\/\/cooplab.github.io\/popgen-notes\/\">HTML<\/a>. (If you want to download a copy of the PDF, click on &#8220;Raw&#8221;). Again, if you&#8217;re a masochist, Graham has made all of the associated files available in a <a href=\"https:\/\/github.com\/cooplab\/popgen-notes\">Github repository<\/a>.<\/p>\n\n\n\n<p><a href=\"https:\/\/figshare.com\/articles\/journal_contribution\/Lecture_notes_in_population_genetics\/100687\" data-type=\"URL\" data-id=\"https:\/\/figshare.com\/articles\/journal_contribution\/Lecture_notes_in_population_genetics\/100687\">Lecture notes in population genetics<\/a><\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>The genetic structure of populations <ul><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/genetic-transmission.pdf\" target=\"_blank\">Genetic transmission in populations<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/hardy-weinberg.pdf\" target=\"_blank\">The Hardy-Weinberg principle and estimating allele frequencies in populations<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/inbreeding.pdf\">Inbreeding and self-fertilization<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/genetic-structure.pdf\" target=\"_blank\">Analyzing the genetic structure of populations<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/genetic-structure-assignment.pdf\" target=\"_blank\">The genetic structure of populations: individual assignment<\/a> <\/li><\/ul><\/li><li>The genetics of natural selection <ul><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/selection.pdf\" target=\"_blank\">The genetics of natural selection<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/selection-estimate.pdf\" target=\"_blank\">Estimating viability<\/a> <\/li><\/ul><\/li><li>Genetic drift <ul><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/drift.pdf\" target=\"_blank\">Genetic drift<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/mutation-drift.pdf\" target=\"_blank\">Mutation, migration, and genetic drift<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/selection-drift.pdf\" target=\"_blank\">Selection and genetic drift<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/coalescent.pdf\" target=\"_blank\">The coalescent<\/a> <\/li><\/ul><\/li><li>Molecular evolution <ul><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/molevol-intro.pdf\" target=\"_blank\">Introduction to molecular population genetics<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/molevol-patterns.pdf\" target=\"_blank\">Patterns of nucleotide and amino acid substitution<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/molevol-selection.pdf\">Detecting selection on nucleotide polymorphisms<\/a> <\/li><\/ul><\/li><li>Phylogeography <ul><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/molevol-amova.pdf\" target=\"_blank\">AMOVA<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/statistical-phylogeography.pdf\">Statisical phylogeography<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/statistical-phylogeography-admixture.pdf\" data-type=\"URL\" data-id=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/statistical-phylogeography-admixture.pdf\">Admixture graphs<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/population-genomics.pdf\">Population genomics<\/a> <\/li><\/ul><\/li><li>Quantitative genetics <ul><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/quant-intro.pdf\" target=\"_blank\">Introduction to quantitative genetics<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/quant-resemblance.pdf\">Resemblance among relatives<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/quant-evolution.pdf\" target=\"_blank\">Evolution of quantitative traits<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/quant-multiple.pdf\" target=\"_blank\">Simultaneous evolution of several quantitative traits<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/association-intro.pdf\">Association mapping: the background from two-locus genetics<\/a> <\/li><\/ul><\/li><li>Old notes, no longer updated <ul><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/testing-hardy-weinberg.pdf\">Testing for departures from Hardy-Weinberg<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/two-locus.pdf\" target=\"_blank\">Two-locus population genetics<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/genetic-structure-bayes\/genetic-structure-bayes.pdf\" target=\"_blank\">The genetic structure of populations: Bayesian F-statistics<\/a><\/li><li><a rel=\"noopener\" href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/selection-multiallele.pdf\" target=\"_blank\">Selection at one locus with many alleles, fertility selection, and sexual selection<\/a><\/li><li><a href=\"http:\/\/darwin.eeb.uconn.edu\/eeb348-notes\/population-genomics-britain.pdf\">Genetic structure of human populations in Britain<\/a> <\/li><\/ul><\/li><\/ul>\n<div class=\"speaker-mute footnotes_reference_container\"> <div class=\"footnote_container_prepare\"><p><span role=\"button\" tabindex=\"0\" class=\"footnote_reference_container_label pointer\" onclick=\"footnote_expand_collapse_reference_container_10_1();\">References<\/span><span role=\"button\" tabindex=\"0\" class=\"footnote_reference_container_collapse_button\" style=\"display: none;\" onclick=\"footnote_expand_collapse_reference_container_10_1();\">[<a id=\"footnote_reference_container_collapse_button_10_1\">+<\/a>]<\/span><\/p><\/div> <div id=\"footnote_references_container_10_1\" style=\"\"><table class=\"footnotes_table footnote-reference-container\"><caption class=\"accessibility\">References<\/caption> <tbody> \r\n\r\n<tr class=\"footnotes_plugin_reference_row\"> <th scope=\"row\" class=\"footnote_plugin_index_combi pointer\"  onclick=\"footnote_moveToAnchor_10_1('footnote_plugin_tooltip_10_1_1');\"><a id=\"footnote_plugin_reference_10_1_1\" class=\"footnote_backlink\"><span class=\"footnote_index_arrow\">&#8593;<\/span>1<\/a><\/th> <td class=\"footnote_plugin_text\">Note: The single PDF doesn&#8217;t have revisions I&#8217;m making this fall. The differences aren&#8217;t big, but if you want the most up-to-date version of the single PDF, you&#8217;ll want to download it again in December or January when I&#8217;ve compiled it.<\/td><\/tr>\r\n\r\n <\/tbody> <\/table> <\/div><\/div><script type=\"text\/javascript\"> function footnote_expand_reference_container_10_1() { jQuery('#footnote_references_container_10_1').show(); jQuery('#footnote_reference_container_collapse_button_10_1').text('\u2212'); } function footnote_collapse_reference_container_10_1() { jQuery('#footnote_references_container_10_1').hide(); jQuery('#footnote_reference_container_collapse_button_10_1').text('+'); } function footnote_expand_collapse_reference_container_10_1() { if (jQuery('#footnote_references_container_10_1').is(':hidden')) { footnote_expand_reference_container_10_1(); } else { footnote_collapse_reference_container_10_1(); } } function footnote_moveToReference_10_1(p_str_TargetID) { footnote_expand_reference_container_10_1(); var l_obj_Target = jQuery('#' + p_str_TargetID); if (l_obj_Target.length) { jQuery( 'html, body' ).delay( 0 ); jQuery('html, body').animate({ scrollTop: l_obj_Target.offset().top - window.innerHeight * 0.2 }, 380); } } function footnote_moveToAnchor_10_1(p_str_TargetID) { footnote_expand_reference_container_10_1(); var l_obj_Target = jQuery('#' + p_str_TargetID); if (l_obj_Target.length) { jQuery( 'html, body' ).delay( 0 ); jQuery('html, body').animate({ scrollTop: l_obj_Target.offset().top - window.innerHeight * 0.2 }, 380); } }<\/script>","protected":false},"excerpt":{"rendered":"<p>The links below correspond, roughly, to the material covered in different lectures in the course. You can also download a single PDF that contains all of them. Just click the &#8220;Lecture notes in population genetics&#8221; link. [1]Note: The single PDF doesn&#8217;t have revisions I&#8217;m making this fall. The differences aren&#8217;t big, but if you want &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/notes\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Notes&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-10","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/pages\/10","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/comments?post=10"}],"version-history":[{"count":11,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/pages\/10\/revisions"}],"predecessor-version":[{"id":616,"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/pages\/10\/revisions\/616"}],"wp:attachment":[{"href":"https:\/\/darwin.eeb.uconn.edu\/uncommon-ground\/eeb348\/wp-json\/wp\/v2\/media?parent=10"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}