{"id":237,"date":"2014-11-21T14:13:05","date_gmt":"2014-11-21T20:13:05","guid":{"rendered":"http:\/\/agrilife.org\/casolalab\/?page_id=237"},"modified":"2017-11-21T14:50:42","modified_gmt":"2017-11-21T20:50:42","slug":"689-ecological-genomics","status":"publish","type":"page","link":"https:\/\/agrilife.org\/casolalab\/courses-2\/689-ecological-genomics\/","title":{"rendered":"ESSM 689  Special Topics in Ecological Genomics"},"content":{"rendered":"<h3><span style=\"color: #0000ff;\">Syllabus Spring 2015:<\/span><\/h3>\n<ul>\n<li><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/689-EcologicalGenomics_Spring20155.pdf\">689-EcologicalGenomics_Spring2015<\/a><\/li>\n<\/ul>\n<h3>\u00a0<span style=\"color: #0000ff;\">Contact:<\/span><\/h3>\n<ul>\n<li>Dr. Claudio Casola<br \/>\nAssistant Professor in Forest Genomics<br \/>\nESSM Department<br \/>\nPhone:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (979) 845-8803<br \/>\nemail:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 ccasola@tamu.edu<br \/>\nOffice hours:\u00a0\u00a0\u00a0\u00a0 Monday 10-12 or by appointment<br \/>\nOffice:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 HFSB 317<\/li>\n<\/ul>\n<h3>\u00a0<span style=\"color: #0000ff;\">Classroom map (Heep Center 123x):<br \/>\n<\/span><\/h3>\n<ul>\n<li><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/HeepCenter_123x.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-medium wp-image-260\" src=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/HeepCenter_123x-300x225.jpg\" alt=\"HeepCenter_123x\" width=\"300\" height=\"225\" srcset=\"https:\/\/agrilife.org\/casolalab\/files\/2014\/11\/HeepCenter_123x-300x225.jpg 300w, https:\/\/agrilife.org\/casolalab\/files\/2014\/11\/HeepCenter_123x.jpg 720w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h3><span style=\"color: #0000ff;\">Presentations:<\/span><\/h3>\n<p><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/Schedule_Presentations.docx\">Schedule_Presentations<\/a><\/p>\n<h3><\/h3>\n<p>&nbsp;<\/p>\n<h3><\/h3>\n<h3><span style=\"color: #0000ff;\">Readings Questionnaire:<\/span><\/h3>\n<p><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/Reading-assignments-questionnaire.docx\">Reading assignments questionnaire<\/a><\/p>\n<h3><\/h3>\n<p>&nbsp;<\/p>\n<h3><span style=\"color: #0000ff;\">Resources on leading a discussion:<\/span><\/h3>\n<p><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/discussion_leading.pdf\">discussion_leading<\/a><\/p>\n<p><a href=\"http:\/\/arthropodecology.com\/2015\/01\/21\/leading-a-discussion-of-a-scientific-paper\/\">http:\/\/arthropodecology.com\/2015\/01\/21\/leading-a-discussion-of-a-scientific-paper\/<\/a><\/p>\n<p>&nbsp;<\/p>\n<h3><span style=\"color: #0000ff;\">Readings:<\/span><\/h3>\n<p><strong>January 20:<\/strong><\/p>\n<p><span style=\"text-decoration: underline;\">Chapter 1<\/span>: <em>Molecular Ecology<\/em>. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell.\u00a0<a href=\"http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365\">http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365<\/a><\/p>\n<p><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/689_Ecol_Genom_Jan20.pdf\">689_Ecol_Genom_Jan20<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>January 22:<\/strong><\/p>\n<p><span style=\"text-decoration: underline;\">Chapter 2<\/span>: <em>Molecular Ecology<\/em>. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell.\u00a0<a href=\"http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365\">http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365<\/a><\/p>\n<p><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/689_Ecol_Genom_Jan22.pdf\">689_Ecol_Genom_Jan22<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>January 27:<\/strong><\/p>\n<p>Neafsey et al. Highly evolvable malaria vectors- The genomes of 16 Anopheles mosquitoes-Science-2015. <a href=\"http:\/\/www.sciencemag.org\/content\/347\/6217\/1258522.abstract\">http:\/\/www.sciencemag.org\/content\/347\/6217\/1258522.abstract<\/a><\/p>\n<p>De novo genome assembly- what every biologist should know-NatMet-2012. <a href=\"http:\/\/www.nature.com\/nmeth\/journal\/v9\/n4\/full\/nmeth.1935.html\">http:\/\/www.nature.com\/nmeth\/journal\/v9\/n4\/full\/nmeth.1935.html<\/a><\/p>\n<p><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/689_Ecol_Genom_Jan27.pdf\">689_Ecol_Genom_Jan27<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>January 29:<\/strong><\/p>\n<p><span style=\"text-decoration: underline;\">Chapter 3<\/span>: <em>Molecular Ecology<\/em>. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell.\u00a0<a href=\"http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365\">http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365<\/a><\/p>\n<p>Whitney et al. A role for nonadaptive processes in plant genome size evolution? Evolution. 2010. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1558-5646.2010.00967.x\/abstract\">http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1558-5646.2010.00967.x\/abstract<\/a><\/p>\n<p><span style=\"text-decoration: underline;\">Optional additional readings:<\/span><\/p>\n<p>Lynch and Conery.\u00a0The origins of genome complexity. Science. 2003. <a href=\"http:\/\/www.sciencemag.org\/content\/302\/5649\/1401.abstract?sid=d3e177ae-238e-468c-9bbc-ce953f6c06dd\">http:\/\/www.sciencemag.org\/content\/302\/5649\/1401.abstract?sid=d3e177ae-238e-468c-9bbc-ce953f6c06dd<\/a><\/p>\n<p>Ai et al. Genome size is not correlated with effective population size in the Oryza species. Evolution. 2012. <a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1558-5646.2012.01674.x\/abstract\">http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1558-5646.2012.01674.x\/abstract<\/a><\/p>\n<p><a href=\"http:\/\/agrilife.org\/casolalab\/files\/2014\/11\/689_Ecol_Genom_Jan29.pdf\">689_Ecol_Genom_Jan29<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>February 3, MICHAEL:<\/strong><\/p>\n<p><span style=\"text-decoration: underline;\">Chapter 4<\/span>: <em>Molecular Ecology<\/em>. Joanna R. Freeland, Heather Kirk and Stephen Petersen. Second edition. 2011. Wiley-Blackwell.\u00a0<a href=\"http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365\">http:\/\/onlinelibrary.wiley.com\/book\/10.1002\/9780470979365<\/a><\/p>\n<p>Ellegren et al. The genomic landscape of species divergence in Ficedula flycatchers-Nature. 2012. <a href=\"http:\/\/www.nature.com\/nature\/journal\/v491\/n7426\/full\/nature11584.html\">http:\/\/www.nature.com\/nature\/journal\/v491\/n7426\/full\/nature11584.html<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>February 5, CARLOS:<\/strong><\/p>\n<p>Stick Insect Genomes Reveal Natural Selection\u2019s Role in Parallel Speciation-Science-2014.<br \/>\n<a href=\"http:\/\/www.sciencemag.org\/content\/344\/6185\/738\">http:\/\/www.sciencemag.org\/content\/344\/6185\/738<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>February 12, DANIEL:<\/strong><\/p>\n<p>Genetic and Neural Modularity Underlie the Evolution of Schooling Behavior in Threespine Sticklebacks-Current Biology 2013<\/p>\n<p><a title=\"Genetic and Neural Modularity Underlie the Evolution of Schooling Behavior in Threespine Sticklebacks-Current Biology 2013\" href=\"%20http:\/\/www.cell.com\/current-biology\/abstract\/S0960-9822%2813%2900919-6\">\u00a0http:\/\/www.cell.com\/current-biology\/abstract\/S0960-9822%2813%2900919-6<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>February 17, RYAN:<\/strong><\/p>\n<p>Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping-PLoS Genetics 2013<\/p>\n<p><a title=\"Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping-PLoS Genetics 2013\" href=\"http:\/\/journals.plos.org\/plosgenetics\/article?id=10.1371\/journal.pgen.1003246\">http:\/\/journals.plos.org\/plosgenetics\/article?id=10.1371\/journal.pgen.1003246<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>February 19, MICHAEL\/KYLE:<\/strong><\/p>\n<p>Ten years of next-generation sequencing technology-Trends in Genetics 2014<\/p>\n<p><a href=\"http:\/\/www.cell.com\/trends\/genetics\/abstract\/S0168-9525%2814%2900112-7\">http:\/\/www.cell.com\/trends\/genetics\/abstract\/S0168-9525%2814%2900112-7<\/a><\/p>\n<p>Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis-Cell 2013<\/p>\n<p><a href=\"http:\/\/www.cell.com\/abstract\/S0092-8674%2813%2900646-6\">http:\/\/www.cell.com\/abstract\/S0092-8674%2813%2900646-6<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>February 24, GRANT:<\/strong><\/p>\n<p>Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing-Molecular Ecology 2013<\/p>\n<p><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mec.12239\/abstract;jsessionid=0B27265233B3431EB90C9A01C5E359A1.f02t04\">http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mec.12239\/abstract;jsessionid=0B27265233B3431EB90C9A01C5E359A1.f02t04<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>March 3 , KYLE:<\/strong><\/p>\n<p>Genes Involved in the Evolution of Herbivory by a Leaf-Mining, Drosophilid Fly-Genome Biol Evol 2012<\/p>\n<p><a href=\"http:\/\/gbe.oxfordjournals.org\/content\/4\/9\/900.full\">http:\/\/gbe.oxfordjournals.org\/content\/4\/9\/900.full<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>March 5:<\/strong><\/p>\n<p>Computer demonstration<\/p>\n<p>&nbsp;<\/p>\n<p><strong>March 10, GRANT:<\/strong><\/p>\n<p>Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions-eLIFE 2014<\/p>\n<p>&nbsp;<\/p>\n<p><strong>March 24, DANIEL:<\/strong><\/p>\n<p>Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus-Science 2014<\/p>\n<p><a href=\"http:\/\/www.sciencemag.org\/content\/344\/6182\/416\">http:\/\/www.sciencemag.org\/content\/344\/6182\/416<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>March 31, RYAN\/CARLOS:<\/strong><\/p>\n<p>Structure, fluctuation and magnitude of a natural grassland soil metagenome-ISME J 2012<\/p>\n<p><a href=\"http:\/\/www.nature.com\/ismej\/journal\/v6\/n9\/full\/ismej2011197a.html\">http:\/\/www.nature.com\/ismej\/journal\/v6\/n9\/full\/ismej2011197a.html<\/a><\/p>\n<p>Functional diversity within the simple gut microbiota of the honey bee-PNAS-2012<\/p>\n<p><a href=\"http:\/\/www.pnas.org\/content\/109\/27\/11002.abstract\">http:\/\/www.pnas.org\/content\/109\/27\/11002.abstract<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 2, Computer Demonstration and paper, GRANT:<\/strong><\/p>\n<p>Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar-PNAS 2012<\/p>\n<p><a href=\"http:\/\/www.pnas.org\/content\/110\/15\/5823.abstract\">http:\/\/www.pnas.org\/content\/110\/15\/5823.abstract<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 7: CLASS CANCELLED TODAY!!<br \/>\n<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 9, DAN:<\/strong><\/p>\n<p>Comparative population genomics in animals uncovers the determinants of genetic diversity-Nature 2014<\/p>\n<p><a href=\"http:\/\/www.nature.com\/nature\/journal\/v515\/n7526\/full\/nature13685.html\">http:\/\/www.nature.com\/nature\/journal\/v515\/n7526\/full\/nature13685.html<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 14, CARLOS:<\/strong><\/p>\n<p>Genomic basis for coral resilience to climate change-PNAS-2013<\/p>\n<p><a href=\"http:\/\/www.pnas.org\/content\/110\/4\/1387.abstract\">http:\/\/www.pnas.org\/content\/110\/4\/1387.abstract<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 16, MICHAEL:<\/strong><\/p>\n<p>Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium-PNAS-2011<\/p>\n<p><a href=\"http:\/\/www.pnas.org\/content\/108\/1\/244.abstract\">http:\/\/www.pnas.org\/content\/108\/1\/244.abstract<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 21, KYLE:<\/strong><\/p>\n<p>Adaptation to Climate Across the Arabidopsis thaliana Genome-Science-2011<\/p>\n<p><a href=\"http:\/\/www.sciencemag.org\/content\/334\/6052\/83.full.html\">http:\/\/www.sciencemag.org\/content\/334\/6052\/83.full.html<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 23, RYAN:<\/strong><\/p>\n<p>Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak-Science-2014<\/p>\n<p><a href=\"http:\/\/www.sciencemag.org\/content\/345\/6202\/1369.full\">http:\/\/www.sciencemag.org\/content\/345\/6202\/1369.full<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 28, homework discussion<br \/>\n<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>April 30, MICHAEL:<\/strong><\/p>\n<p>Convergent evolution of the genomes of marine mammals-Nature Genetics 2015<\/p>\n<p><a href=\"http:\/\/www.nature.com\/ng\/journal\/v47\/n3\/full\/ng.3198.html\">http:\/\/www.nature.com\/ng\/journal\/v47\/n3\/full\/ng.3198.html<\/a><\/p>\n<p><strong>RYAN, PROJECT PRESENTATION<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>MAY 5:\u00a0 FIVE PROJECT PRESENTATIONS<br \/>\n<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>MAY 11: PROJECTS DUE<br \/>\n<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Syllabus Spring 2015: 689-EcologicalGenomics_Spring2015 \u00a0Contact: Dr. Claudio Casola Assistant Professor in Forest Genomics ESSM Department Phone:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (979) 845-8803 email:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 ccasola@tamu.edu Office hours:\u00a0\u00a0\u00a0\u00a0 Monday 10-12 or by appointment Office:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 HFSB 317&#8230; <span class=\"read-more\"><a href=\"https:\/\/agrilife.org\/casolalab\/courses-2\/689-ecological-genomics\/\">Read More &rarr;<\/a><\/span><\/p>\n","protected":false},"author":997,"featured_media":0,"parent":233,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","footnotes":""},"class_list":["post-237","page","type-page","status-publish","entry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>ESSM 689 Special Topics in Ecological Genomics - Casola Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/agrilife.org\/casolalab\/courses-2\/689-ecological-genomics\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"ESSM 689 Special Topics in Ecological Genomics - Casola Lab\" \/>\n<meta property=\"og:description\" content=\"Syllabus Spring 2015: 689-EcologicalGenomics_Spring2015 \u00a0Contact: Dr. Claudio Casola Assistant Professor in Forest Genomics ESSM Department Phone:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (979) 845-8803 email:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 ccasola@tamu.edu Office hours:\u00a0\u00a0\u00a0\u00a0 Monday 10-12 or by appointment Office:\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 HFSB 317... 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