Difference between revisions of "Molecular systematics Spring 2019"
Chris Simon (Talk | contribs) (→Schedule) |
Chris Simon (Talk | contribs) (→Schedule) |
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|Tuesday <br/> Apr 2 || Lecture 5. Bull et al. 1993, Tests for combining data; testing whether the same tree underlies each data partition. Partitioning; Choosing among models for pre-assigned partitions. Lecture notes:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20EEB%205350%20Day%205%20Combining%20Data%20%28cont%29%202019.ppt.pdf}} EEB 5350 Day 5 Combining Data (cont) 2019.ppt.pdf || Read and Summarize for Class on Tuesday April 9th Kanier and Landfear 2015. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Kainer_and_Landfear._2015._Effects_of_Partitioning_on_Phylogen.pdf}} || | |Tuesday <br/> Apr 2 || Lecture 5. Bull et al. 1993, Tests for combining data; testing whether the same tree underlies each data partition. Partitioning; Choosing among models for pre-assigned partitions. Lecture notes:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/%20EEB%205350%20Day%205%20Combining%20Data%20%28cont%29%202019.ppt.pdf}} EEB 5350 Day 5 Combining Data (cont) 2019.ppt.pdf || Read and Summarize for Class on Tuesday April 9th Kanier and Landfear 2015. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Kainer_and_Landfear._2015._Effects_of_Partitioning_on_Phylogen.pdf}} || | ||
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− | |Thursday <br> Apr 4 ||Lecture 6. Finish partitioning: Automated partition assignment and partition simplification; Model averaging and mixture models; Long Branches. What is a long branch?; The meaning of “basal”; Node density artifacts; Felsenstein 1978- when will parsimony be positively misleading?; Penny & Hendy 1989- long branch attraction; Huelsenbeck & Hillis simulations to explore tree space. Accuracy of different phylogenetic methods; Swofford et al. 2001. Bias in Phylogeny estimation due to long branches: Parsimony vs. likelihood in tree space; Remaining uncommitted. Lecture notes: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%206.%20Partitions%2C%20Mixtures%2C%20Long%20Branches%204Apr2019.pptx.pdf}}Day 6. Partitions, Mixtures, Long Branches 4Apr2019.pptx.pdf ||Read and Summarize for Class on Thursday, April 11th. Gruenheit, Nicole, Peter J. Lockhart, Mike Steel, and William Martin. 2008. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Gruenheit_et_al._(Lockhart)_2008._Covarion_under_changing_proportions_var_sites.pdf}}|| Covarion, Heterotachy, Nucleotide Bias Readings: : | + | |Thursday <br> Apr 4 ||Lecture 6. Finish partitioning: Automated partition assignment and partition simplification; Model averaging and mixture models; Long Branches. What is a long branch?; The meaning of “basal”; Node density artifacts; Felsenstein 1978- when will parsimony be positively misleading?; Penny & Hendy 1989- long branch attraction; Huelsenbeck & Hillis simulations to explore tree space. Accuracy of different phylogenetic methods; Swofford et al. 2001. Bias in Phylogeny estimation due to long branches: Parsimony vs. likelihood in tree space; Remaining uncommitted. Lecture notes: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%206.%20Partitions%2C%20Mixtures%2C%20Long%20Branches%204Apr2019.pptx.pdf}}Day 6. Partitions, Mixtures, Long Branches 4Apr2019.pptx.pdf ||Read and Summarize for Class on Thursday, April 11th. Gruenheit, Nicole, Peter J. Lockhart, Mike Steel, and William Martin. 2008. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Gruenheit_et_al._(Lockhart)_2008._Covarion_under_changing_proportions_var_sites.pdf}}|| Covarion, Heterotachy, Nucleotide Bias Readings: Dirichlet Process Models |
+ | |||
+ | Antoniak, C. 1974. Mixtures of Dirichlet processes with applications to Bayesian | ||
+ | nonparametric problems. The Annals of Statistics 2:1152–1174. | ||
+ | |||
+ | Ferguson, T. 1973. A Bayesian analysis of some nonparametric problems. The Annals of Statistics 1:209–230. | ||
+ | |||
+ | Lartillot, N. and H. Philippe. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution 21:1095–1109. | ||
+ | |||
+ | Huelsenbeck, J., S. Jain, S. Frost, and S. Pond. 2006. A Dirichlet process model | ||
+ | for detecting positive selection in protein-coding DNA sequences. Proceedings of the | ||
+ | National Academy of Sciences of the United States of America 103:6263–6268. | ||
+ | |||
+ | Huelsenbeck, J. P. and M. A. Suchard. 2007. A nonparametric method for accommodating and testing across-site rate variation. Systematic Biology 56:975–987. | ||
+ | |||
|- | |- | ||
|Tueday <br/> Apr 09 ||Lecture 7. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models. Lecture notes: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%207%29%20Covarion%20evolution%2C%20heterotachy%202019.pptx.pdf}}Day 7) Covarion evolution, heterotachy 2019.pptx.pdf || || | |Tueday <br/> Apr 09 ||Lecture 7. ALRV: heterotachy, covarion models;Among Lineage rate variation: Covarion evolution: codon models. Lecture notes: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Day%207%29%20Covarion%20evolution%2C%20heterotachy%202019.pptx.pdf}}Day 7) Covarion evolution, heterotachy 2019.pptx.pdf || || | ||
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|Tuesday <br/> Apr 23 ||Lecture 11: Secondary structure & alignment. ||Read and Summarize for class: Hickson et al. 1996 Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12s rRNA. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Hickson_et_al._1996._rRNA_structure_&_alignment._Mol_Biol_Evol.pdf}} ||Secondary structure assignment {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB_5350_secondary_structure_assignment_Sp18.pdf}} and templates for Magicicada {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Magicicada_12S_rRNA.pdf}} and conserved motif template {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/rRNA_12S_3rd_Domain_Template_2018_04_23_09_57_12_OCR.pdf}}. Structure and alignment readings: | |Tuesday <br/> Apr 23 ||Lecture 11: Secondary structure & alignment. ||Read and Summarize for class: Hickson et al. 1996 Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12s rRNA. {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Hickson_et_al._1996._rRNA_structure_&_alignment._Mol_Biol_Evol.pdf}} ||Secondary structure assignment {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB_5350_secondary_structure_assignment_Sp18.pdf}} and templates for Magicicada {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Magicicada_12S_rRNA.pdf}} and conserved motif template {{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/rRNA_12S_3rd_Domain_Template_2018_04_23_09_57_12_OCR.pdf}}. Structure and alignment readings: | ||
|- | |- | ||
− | |Thursday Apr 25 ||Lecture 12: | + | |Thursday Apr 25 ||Lecture 12: Guest lecture by Eric Gordon. Molecular Clocks, Types of dating studies, Fossil calibration of nodes Tip dating; Fossilized birth-death model, Examples. || || Molecular clock readings: |
|- | |- | ||
− | |Tuesday <br> April 30 ||Lecture 13: | + | |Tuesday <br> April 30 ||Lecture 13: Guest lecture by Eric Gordon. Complications to Phylogenetic Inference, Incomplete lineage sorting; Rationale for failure of concatenation in certain situations; Coalescence-based methods (ASTRAL *BEAST, SVDQuartets); Problems (including a little bit about combinability of data--also address in lecture 5)"Concatalescence"; Reticulate evolution- Various causes, Summary of how some methods work, Examples, Problems||Species tree readings: || |
|- | |- | ||
− | |Thursday <br> May 2 ||Lecture 14: Applications of molecular phylogenetic datasets beyond a traditional phylogeny | + | |Thursday <br> May 2 ||Lecture 14: Applications of molecular phylogenetic datasets beyond a traditional phylogeny Macroevolution genomic studies, Investigation of Pseudogenes, Gene family diversification (CAFE, COUNT), Investigating selection (PAML); Examples, Species delimitation methods, Methodology, Tools and Examples, Problems, Brief mention of some other population level methods, Brief mentions of ASR, correlated trait evolution and diversification and biogeographic methods.|| || |
|- | |- | ||
|Sunday <br/> Sunday May 5th || Lab notebook due. Take home final handed out.|| || | |Sunday <br/> Sunday May 5th || Lab notebook due. Take home final handed out.|| || |
Revision as of 22:22, 16 April 2019
Molecular Systematics EEB 5350 Spring 2019
2 Credits- half-semester module
Lectures:
Lectures: Tu & Th 2:00-3:15 Bio-Pharm 3rd floor conference room.
Labs:
Tu 3:30-5:30 (Each lab session starts in 3rd floor conference room then moves to BioPharm 325).
Instructor:
Chris Simon, Biopharm 305D, 6-4640, <chris.simon@uconn.edu>
Graduate Assistant: Diler Haji, TLS 479, Diler.Haji@uconn.edu, 6-3947
Readings: will be posted as PDF’s.
Reference books: 1) Paul Lewis's unpublished text; 2) The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); 4) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 5) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference.
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, among-site 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 and we will pursue a class project.
SEE: Molecular Systematics Google Docs
EEB 5350 Lab Syllabus
https://docs.google.com/document/d/1IbrXonoc63Ihj_vFEdT_le9Jl1IwzQzBwDmRgEPZ-RA/edit
EEB 5350 shared Lab folder
https://drive.google.com/drive/u/1/folders/16IODJWzL_8CZ605j83zl99nADRvoyy2g
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 one-page 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 hand-in 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 10-15 minute Powerpoint presentation relating to techniques used in that day’s lab. Ursula 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 5th: Lab project and notebook due. Take Home FINAL EXAM handed out. Sunday 12th May: Take home final due.
Syllabus:
Schedule