{"id":291,"date":"2018-08-06T13:41:35","date_gmt":"2018-08-06T11:41:35","guid":{"rendered":"http:\/\/wp.unil.ch\/phylo\/?page_id=291"},"modified":"2023-07-03T09:44:27","modified_gmt":"2023-07-03T07:44:27","slug":"phylogeny-and-comparative-methods","status":"publish","type":"page","link":"https:\/\/wp.unil.ch\/phylo\/teaching\/phylogeny-and-comparative-methods\/","title":{"rendered":"Phylogenetics and Comparative Methods"},"content":{"rendered":"<p>Master level course for the master MLS and BEC (10H lectures; 18H exercices).<\/p>\n<p>The objectives of this course are to know and understand methods of phylogenetic reconstructions, and to be able to use tree to test evolution of genes and organisms<\/p>\n<p>Beside discussing what is a phylogenetic tree and how to interpret it, we will introduce the main reconstruction methods available. This will include a thorough description of<\/p>\n<ul>\n<li>optimization critera and models of evolution<\/li>\n<li>finding the optimal tree<\/li>\n<li>Bayesian methods and MCMC<\/li>\n<li>how to be sure you have the right tree?<\/li>\n<\/ul>\n<p>Then we will discuss several aspects that uses phylogenetic trees as tool to understand gene and organisms evolution. This includes<\/p>\n<ul>\n<li>dating phylogenetic trees<\/li>\n<li>gene trees vs species tree inference<\/li>\n<li>detecting positive selection on coding genes<\/li>\n<li>macroevolution: i) models of trait evolution; ii) mode and tempo of evolution; iii) testing key innovations<\/li>\n<\/ul>\n<p>Check the Moodle page and the specific Teams channel for the course for the documents and more information.<\/p>\n<h4>Books important for the course:<\/h4>\n<ul>\n<li>Felsenstein, J. 2003. Inferring phylogenies. Sinauer Associates.<\/li>\n<li>Lemey, P., Salemi, M. and Vandamme, A.-M. 2009. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. Cambridge University Press.<\/li>\n<li>Page, R. 2003. Tangled trees: Phylogeny, cospeciation, and coevolution. University of Chicago Press.<\/li>\n<li>Purvis, A., Gittleman, J.L. and Brooks, T. 2005. Phylogeny and conservation. Cambridge University Press.<\/li>\n<li>Swofford, D.L., Olsen, G.K., Waddell, P.J. and Hillis, D.M. 1996. Phylogeny reconstruction. Pages 407-514 In Molecular Systematics (D.M. Hillis, C. Moritz, B.K. Mable, eds.). Sinauer Associates.<\/li>\n<li>Yang, Z.H. 2014. Molecular Evolution: A Statistical Approach. Oxford University Press.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Master level course for the master MLS and BEC (10H lectures; 18H exercices). The objectives of this course are to know and understand methods of phylogenetic reconstructions, and to be able to use tree to test evolution of genes and<\/p>\n","protected":false},"author":1124,"featured_media":0,"parent":296,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"class_list":["post-291","page","type-page","status-publish"],"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages\/291","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/users\/1124"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/comments?post=291"}],"version-history":[{"count":0,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages\/291\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/pages\/296"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/phylo\/wp-json\/wp\/v2\/media?parent=291"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}