

Line 33: 
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 Final Exam: The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.   Final Exam: The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors. 
   
−  Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out. Sunday May 6th: Take home final due.  +  Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th. 
   
 Syllabus Coming soon!   Syllabus Coming soon! 
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− 
 
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−  #:{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Syllabus%20Molecular%20Systematics%20rev%2027%20March%2012%20CLOCS.pdf}}Syllabus Molecular Systematics rev 28 Mar 12.pdf
 
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−  Assignment 1.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/%20Checks%26Data_Molec%20Syst%20Sp%202012%20rev.doc}} Checks&Data_Molec Syst Sp 2012 rev.doc
 
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−  First Reading Assignment:
 
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−  Simon, C., F. Frati, A. Beckenbach, B. Crespi, H. Liu, and P. Flook. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved PCR primers. Annals Entomol. Soc. Am. 87: 651701. PDF will be mailed to you because it is too large to post here.
 
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−  Sample outline (note a summary is also required but is not illustrated).
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/%20%20Molecular%20Systematics%20Sample%20Outline%20%26%20Guide.pdf}} Molecular Systematics Sample Outline & Guide.pdf
 
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−  Readings for Lecure 1. "How Molecules Evolve and Models of Evolution"
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/How%20molecules%20evolve%20Readings%2012.pdf}}How molecules evolve Readings 12.pdf
 
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−  Lecture 1. Notes.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Day%201%20How%20Molecules%20Evolve.%20Parts%20I%20%26%20II%2020Mar12.pdf}}EEB 5350 Day 1 How Molecules Evolve. Parts I & II 20Mar12.pdf
 
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−  Lab 1. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20First%20Lab%20mini%20lecture%202012.pdf}}EEB 5350 First Lab mini lecture 2012.pdf
 
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−  Lecture 2. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Day%202%20Models%2C%20ASRV%20History%202012.pdf}}EEB 5350 Day 2 Models, ASRV History 2012.pdf
 
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−  Lab 2. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Minipresentation.%20Chris%20Owen.%20DNA%20Extraction%2022Mar12.pdf}}EEB 5350 Minipresentation. Chris Owen. DNA Extraction 22Mar12.pdf
 
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−  Readings for Lecture 2. Among Site Rate Variation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/%20EEB%205350%20ASRV%20readings_Sp%2012.pdf}} EEB 5350 ASRV readings_Sp 12.pdf
 
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−  Lecture 3. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Day%203%20ASRV%2C%20Partitions%2C%20Clocks.pdf}}EEB 5350 Day 3 ASRV, Partitions, Clocks.pdf
 
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−  Lab 3. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Lab.%203.%20Minipresentation%20DNA%20extractions%20museums%202012%20Chris%20Owen%20sm.pdf}}EEB 5350 Lab. 3. Minipresentation DNA extractions museums 2012 Chris Owen.pdf
 
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−  Molecular Clock Readings
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Molecular%20Clock%20Readings%202012.pdf}}EEB 5350 Molecular Clock Readings 2012.pdf
 
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−  Lecture 4. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Day%204%20Molecular%20Clocks%20Systematic%20Error%20Biases%202012.pdf}}EEB 5350 Day 4 Molecular Clocks Systematic Error Biases 2012.pdf
 
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−  Lab 4. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205305.%20Minipresentation.%20PCR.%20Ursula%20King.pdf}}EEB 5305. Lab 4 Minipresentation. PCR. Ursula King.pdf
 
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−  Lecture 5. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Day%205%20EEB%205350%20nucleotide%20bias%2C%20covarion%20evolution%20part%20I%202012.pdf}}EEB 5350 Day 5 EEB 5350 nucleotide bias, covarion evolution part I 2012.pdf
 
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−  Lab 5. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/PatGero%20MolecSyst%20Minipresentation%2043.pdf}}EEB 5305 Lab 5. PatGero MolecSyst Minipresentation 43.pdf
 
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−  Nucleotide Bias, Covarion Readings:
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Covarion%2C%20Heterotachy%2C%20bias%20readings%202012%20rev.doc}}Covarion, Heterotachy, bias readings 2012 rev.doc
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Pages%20from%20Daniel%20Fan%20dissertation%20Chp%203%20Heterotachy.pdf}}Pages from Daniel Fan dissertation Chp 3 Heterotachy.pdf
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Whelan%20et%20al.%202011.%20%20Heterotachy%20Mol%20Biol%20Evol.pdf}}Whelan et al. 2011. Heterotachy Mol Biol Evol.pdf
 
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−  Lecture 6. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Day%206.%202010%20Heterotachy%2C%20Covarion%20evolution%20Taxon%20Sampling%2C%20Long%20Branches%202012.pdf}}EEB 5350 Day 6. 2010 Heterotachy, Covarion evolution Taxon Sampling, Long Branches 2012.pdf
 
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−  Lab 6. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Lab%206Minipresentation%20Big%20Dye%20Russ%20Meister.pdf}}EEB 5350 Lab 6Minipresentation Big Dye Russ Meister.pdf
 
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−  Long Branches Big Trees Readings
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/LBA%2C%20taxon%20sampling%2C%20big%20trees%20readings%202012.pdf}}LBA, taxon sampling, big trees readings 2012.pdf
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Philippe%20et%20al.%202011.%20%20More%20sequences%20not%20enough.pdf}}Philippe et al. 2011. More sequences not enough.pdf
 
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−  Lecture 7. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Day%207.%20%20Long%20Branches%20and%20Big%20Trees%20%202012.pdf}}EEB 5350 Day 7. Long Branches and Big Trees 2012.pdf
 
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−  Lab 7. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Lab%207.%20RNA%20isolation%20minipresentation%20Hamid%20Razifard%209Apr12.pdf}}EEB 5350 Lab 7. RNA isolation minipresentation Hamid Razifard 9Apr12.pdf
 
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−  Lecture 8. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Day%208%20Long%20Branches%20cont.%20Combining%20data%202012.pdf}}EEB 5350 Day 8 Long Branches cont. Combining data 2012.pdf
 
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−  Lab 8. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf
 
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−  Lecture 9. Notes
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Day%209%20Combining%20Data%2C%20Species%20Trees%202012.pdf}}EEB 5350 Day 9 Combining Data, Species Trees 2012.pdf
 
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−  Lab 9. Minipresentation.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RTPCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RTPCR Brigette.pdf
 
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−  Lecture 10. Notes.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Day%2010.%20Choosing%20Partitions%2C%20Comparing%20Trees.pdf}}EEB 5350 Day 10. Choosing Partitions, Comparing Trees.pdf
 
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−  Lab 10. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Lab%2010.%20Minipresentation%20Cloning%2C%20Emily%20Ellis.pdf}}EEB 5350 Lab 10. Minipresentation Cloning, Emily Ellis.pdf
 
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−  Combining Data, Species trees, Comparing Trees Readings
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Comparing%20Trees%20Combining%20Data%20Readings%202012.pdf}}Comparing Trees Combining Data Readings 2012.pdf
 
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−  Reading for Tuesday: Summarizes most material covered in the class. Write a summary of each major section using one to two pages. Outline not necessary.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Simon%2C%20Buckley%2C%20Frati%2C%20Stewart%2C%20Beckenbach%202006%20AREES%20%26%20supplement.pdf}}Simon, Buckley, Frati, Stewart, Beckenbach 2006 AREES & supplement.pdf
 
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−  Lecture 11. notes.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Day%2011%20Nodal%20Support%202012.pdf}}EEB 5350 Day 11 Nodal Support 2012.pdf
 
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−  Nodal/Branch Support Readings
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/%20%20Nodal%20support%20readings%20Sp%202012.doc}} Nodal support readings Sp 2012.doc
 
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−  Lab 11. Minipresentation
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350.%20Lab%2011%20Minipresentation%20Blast%20Veronica%20Bueno.pdf}}EEB 5350. Lab 11 Minipresentation Blast Veronica Bueno.pdf
 
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−  Lecture 12. Notes.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Day%2012.%20%20Alignment%20%26%20Secondary%20Structure%202012.pdf}}EEB 5350 Day 12. Alignment & Secondary Structure 2012.pdf
 
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−  Hickson et al. Structure paper:
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Hickson%20et%20al.%201996.%20Secondary%20structure%20evolution%20MBE.pdf}}Hickson et al. 1996. Secondary structure evolution MBE.pdf
 
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−  Robin Gutell structure paper:
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Gutell%20et%20al.%202002.%20rRNA%20structures.%20curr.%20opin.struct.%20Biol.}}Gutell et al. 2002. rRNA structures. curr. opin.struct. Biol.
 
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−  Secondary Structure Assignment:
 
− 
 
−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20secondary%20structure%20%20assignment%20Sp12.pdf%20.pdf}}EEB 5350 secondary structure assignment Sp12.pdf .pdf
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/EEB%205350%20Hickson%20et%20al.%201996.%20rRNA%20template.pdf}}EEB 5350 Hickson et al. 1996. rRNA template.pdf
 
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−  Lab 12. Minipresentation. Genomics.
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/CLOwen_Genomics%20Minpresentation_FINAL.pdf}}Lab 12. CLOwen_Genomics Minpresentation.pdf
 
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−  Secondary structure readings:
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/%20Structure_Alignmnt_readings_Sp%2012.pdf}} Structure_Alignmnt_readings_Sp 12.pdf
 
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−  Final Exam Instructions, Shull et al. paper to review, figures for Shull et al.:
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/%20Final%20Exam%20EEB350%20Reviewer%27s_instructns_S12.pdf}} Final Exam EEB350 Reviewer's_instructns_S12.pdf
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/%20Shull_et_al._28Oct%20MS.pdf}} Shull_et_al._28Oct Manuscript.pdf
 
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−  :{{pdfhttp://hydrodictyon.eeb.uconn.edu/courses/molsysteeb5350/Shull%20et%20al.%20figures17%2C%20Tabs%2015.pdf}}Shull et al. figures17, Tabs 15.pdf
 
   
   
 [[Category:EEB Courses]]   [[Category:EEB Courses]] 
Revision as of 19:35, 23 March 2014
2 Credits halfsemester module, 24 March30 April 2014
Lectures:
Mon & Wed 12:301:45 BioPharm 3rd floor conference room
Labs:
Mon & Wed 2:004:00 (first halfhour in conference room, remainder in BioPharm 325).
Instructor:
Chris Simon, Biopharm 305D, 64640, <chris.simon@uconn.edu>
Graduate Assistant: Russ Meister, Biopharm 325A, <Russell.Meister@uconn.edu>; 63947
Readings: will be posted as PDF’s.
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and AnneMieke Vandamme, 2010).
Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, amongsite rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts.
Laboratory Goals: Labs will cover basic techniques in molecular systematics from DNA extraction to sequencing, alignment and cloning. This lab will be of interest to both experienced and novice molecular systematists because we will try newly developed kits/techniques and compare them to older ones.
Short Assignments:
1) For each topic a bibliography will be provided including one focal paper for which the PDF will be posted. Each student will need to turn in a onepage summary of the importance of each focal paper (1 or occasionally 2 papers per week).
2) The week prior to the start of classes you will be given a checklist discussing practical considerations, organization and data checks for molecular systematics. In certain sections you are asked to answer questions and explain how these procedures are modified in your lab.
3) There will be a short "secondary structure alignment assignment" during the semester.
4) Each student will keep a laboratory notebook and handin data collected during the course in the form of an alignment and a nexus data file. Various exercises will be performed in laboratory and some will be finished outside of class. These are detailed in the laboratory syllabus.
5) For each Lab, one student will present a 1015 minute Powerpoint presentation relating to techniques used in that day’s lab. Russ will be available to advise you, but use web searches and try to do as much as possible on your own. These Powerpoint presentations will be posted on the class website so that in the future when you teach a molecular systematics class, they can be used as a starting point to revise and develop lectures of your own.
Final Exam: The final exam will be a take home test in which each student critiques the first draft of a paper submitted to Systematic Biology (submitted in the past but making comments as if it were submitted today). Each student will also compare the submitted version to the published version. The answer key will be the actual review containing reviewers, associate editors, and editor’s comments (with permission of authors, reviewers and editors) and a list of critical points that need to be considered by the authors.
Final Due Dates: Sunday May 4th: Lab project and notebook due. Take Home FINAL EXAM handed out Sunday May 6th. Take home final due Sunday May 11th.
Syllabus Coming soon!
Schedule
Day

Topics

Reading/Assignment

Lab

Mar 24 
An introduction to looking at your data: How molecules evolve.


Lecture instead of lab this week

Aug 28 
The many roles of biological systematics Species Definitions Species Level Terminology 
Hubbell Reading

Aug 30 
Species definitions & species intermediacy & collections tour 
Templeton 1989 De Queiroz 2007

Sept 2 
Labor Day, No class 

Babbidge Library resources; taxonomic literature Meet in Babbidge library electronic classroom 1 (EC1) on level 1, to the left and behind Info Cafe 1 (http://classguides.lib.uconn.edu/content.php?pid=238531&sid=1968055)
