Difference between revisions of "Phylogenetics: Syllabus"
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|- | |- | ||
| Wed., Jan. 17 | | Wed., Jan. 17 | ||
− | | Introduction [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Introduction_1perpage.pdf 1 slide/page] [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Introduction_6perpage.pdf 6 slides/page]<br/>Significance, history, terminology | + | | '''Introduction''' ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Introduction_1perpage.pdf 1 slide/page]) ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Introduction_6perpage.pdf 6 slides/page])<br/>Significance, history, terminology |
| [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/hw1_TreeFromSplits.pdf Homework #1] | | [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/hw1_TreeFromSplits.pdf Homework #1] | ||
|- | |- | ||
| Mon., Jan. 22 | | Mon., Jan. 22 | ||
− | | Tree thinking [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking_1perpage.pdf 1 slide/page] [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking_6perpage.pdf 6 slides/page]<br/>Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages | + | | '''Tree thinking''' ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking_1perpage.pdf 1 slide/page]) ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking_6perpage.pdf 6 slides/page])<br/>Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages |
| [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/labs/paupnexus.html PAUP* and NEXUS] | | [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/labs/paupnexus.html PAUP* and NEXUS] | ||
|- | |- | ||
| Wed., Jan. 24 | | Wed., Jan. 24 | ||
− | | Consensus trees [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Consensus_1perpage.pdf 1 slide/page] [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Consensus_6perpage.pdf 6 slides/page]<br/>Parsimony [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Parsimony_1perpage.pdf 1 slide/page] [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Parsimony_6perpage.pdf 6 slides/page]<br/> | + | | '''Consensus trees''' ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Consensus_1perpage.pdf 1 slide/page]) ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Consensus_6perpage.pdf 6 slides/page])<br/>'''Parsimony''' ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Parsimony_1perpage.pdf 1 slide/page]) ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Parsimony_6perpage.pdf 6 slides/page])<br/> |
Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix | Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix | ||
| [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/hw2_Parsimony.pdf Homework #2] | | [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/hw2_Parsimony.pdf Homework #2] | ||
|- | |- | ||
| Mon., Jan. 29 | | Mon., Jan. 29 | ||
− | | Polyphyly vs. Paraphyly Revisited [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking2_1perpage.pdf 1 slide/page] [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking2_6perpage.pdf 6 slides/page]<br/>Searching [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Searching_1perpage.pdf 1 slide/page] [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Searching_6perpage.pdf 6 slides/page]<br/>Exhaustive, branch-and-bound, star decomposition, stepwise addition, heuristic, genetic algorithms | + | | '''Polyphyly vs. Paraphyly Revisited''' ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking2_1perpage.pdf 1 slide/page]) ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/TreeThinking2_6perpage.pdf 6 slides/page])<br/>'''Searching''' ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Searching_1perpage.pdf 1 slide/page]) ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Searching_6perpage.pdf 6 slides/page])<br/>Exhaustive, branch-and-bound, star decomposition, stepwise addition, heuristic, genetic algorithms |
| [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_Parsimony_Lab Parsimony and searching] | | [http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_Parsimony_Lab Parsimony and searching] | ||
|- | |- | ||
| Wed., Jan. 31 | | Wed., Jan. 31 | ||
− | | Distances [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Distances_1perpage.pdf 1 slide/page] [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Distances_6perpage.pdf 6 slides/page]<br/>Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ | + | | '''Distances''' ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Distances_1perpage.pdf 1 slide/page]) ([http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/Distances_6perpage.pdf 6 slides/page])<br/>Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ |
| [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/hw3_Distances.pdf Homework #3] (ok to proceed) | | [http://hydrodictyon.eeb.uconn.edu/people/plewis/courses/phylogenetics/lectures/hw3_Distances.pdf Homework #3] (ok to proceed) | ||
|- | |- | ||
| Mon., Feb. 5 | | Mon., Feb. 5 | ||
− | | Measuring support<br/>Consensus trees, Bootstrapping, Bremer support, ILD test, KH test, SH test, SOWH test | + | | '''Measuring support'''<br/>Consensus trees, Bootstrapping, Bremer support, ILD test, KH test, SH test, SOWH test |
| Distance methods | | Distance methods | ||
|- | |- | ||
| Wed., Feb. 7 | | Wed., Feb. 7 | ||
− | | Likelihood models<br/>Likelihood of a DNA sequence, likelihood of a pair of sequences, Jukes-Cantor model, Felsenstein 1981 model, likelihood ratio test, simulation | + | | '''Likelihood models'''<br/>Likelihood of a DNA sequence, likelihood of a pair of sequences, Jukes-Cantor model, Felsenstein 1981 model, likelihood ratio test, simulation |
| | | | ||
|- | |- | ||
| Mon., Feb. 12 | | Mon., Feb. 12 | ||
− | | Maximum likelihood<br/>Parameter estimation (MLEs), likelihood of a tree, marginalization | + | | '''Maximum likelihood'''<br/>Parameter estimation (MLEs), likelihood of a tree, marginalization |
| PAUP* | | PAUP* | ||
|- | |- | ||
| Wed., Feb. 14 | | Wed., Feb. 14 | ||
− | | Rate heterogeneity<br/>Proportion of invariable sites, discrete gamma, site-specific rates | + | | '''Rate heterogeneity'''<br/>Proportion of invariable sites, discrete gamma, site-specific rates |
| | | | ||
|- | |- | ||
| Mon., Feb. 19 | | Mon., Feb. 19 | ||
− | | Long branch attraction<br/>Statistical consistency, long branch repulsion | + | | '''Long branch attraction'''<br/>Statistical consistency, long branch repulsion |
| PAUP*, Garli | | PAUP*, Garli | ||
|- | |- | ||
| Wed., Feb. 21 | | Wed., Feb. 21 | ||
− | | Codon models<br/>Nonsynonymous vs. synonymous rates, codons as states | + | | '''Codon models'''<br/>Nonsynonymous vs. synonymous rates, codons as states |
| | | | ||
|- | |- | ||
| Mon., Feb. 26 | | Mon., Feb. 26 | ||
− | | Other models<br/>Stems/loops, GC bias, covariatide | + | | '''Other models'''<br/>Stems/loops, GC bias, covariatide |
| Hy-Phy | | Hy-Phy | ||
|- | |- | ||
| Wed., Feb. 28 | | Wed., Feb. 28 | ||
− | | Likelihood ratio tests<br/>Molecular clock, branch-specific rate shifts | + | | '''Likelihood ratio tests'''<br/>Molecular clock, branch-specific rate shifts |
| | | | ||
|- | |- | ||
| Mon., Mar. 5 | | Mon., Mar. 5 | ||
− | | Spring break<br/>no class | + | | '''Spring break'''<br/>no class |
| no class | | no class | ||
|- | |- | ||
| Wed., Mar. 7 | | Wed., Mar. 7 | ||
− | | Spring break | + | | '''Spring break''' |
| no class | | no class | ||
|- | |- | ||
| Mon., Mar. 12 | | Mon., Mar. 12 | ||
− | | Bayes primer<br/>Conditional/joint probabilities, Bayes rule, posterior distribution, probability densities | + | | '''Bayes primer'''<br/>Conditional/joint probabilities, Bayes rule, posterior distribution, probability densities |
| Hy-Phy | | Hy-Phy | ||
|- | |- | ||
| Wed., Mar. 14 | | Wed., Mar. 14 | ||
− | | Bayesian phylogenetics<br/>MCMC, slice sampling, heated chains | + | | '''Bayesian phylogenetics'''<br/>MCMC, slice sampling, heated chains |
| | | | ||
|- | |- | ||
| Mon., Mar. 19 | | Mon., Mar. 19 | ||
− | | Bayesian phylogenetics<br/>Summarizing posterior distributions, partitioned data | + | | '''Bayesian phylogenetics'''<br/>Summarizing posterior distributions, partitioned data |
| Phycas | | Phycas | ||
|- | |- | ||
| Wed., Mar. 21 | | Wed., Mar. 21 | ||
− | | Bayesian phylogenetics<br/>Reversible-jump MCMC, mixture models, star tree paradox | + | | '''Bayesian phylogenetics'''<br/>Reversible-jump MCMC, mixture models, star tree paradox |
| | | | ||
|- | |- | ||
| Mon., Mar. 26 | | Mon., Mar. 26 | ||
− | | Model Selection<br/>LRT, AIC, BIC, Bayes factors, posterior predictive approaches | + | | '''Model Selection'''<br/>LRT, AIC, BIC, Bayes factors, posterior predictive approaches |
| MrBayes | | MrBayes | ||
|- | |- | ||
| Wed., Mar. 28 | | Wed., Mar. 28 | ||
− | | Ancestral Character States<br/>Parsimony approach, ML approach, empirical Bayes approach | + | | '''Ancestral Character States'''<br/>Parsimony approach, ML approach, empirical Bayes approach |
| | | | ||
|- | |- | ||
| Mon., Apr. 2 | | Mon., Apr. 2 | ||
− | | Continuous Character Correlation<br/>Independent Contrasts | + | | '''Continuous Character Correlation'''<br/>Independent Contrasts |
| PAUP* | | PAUP* | ||
|- | |- | ||
| Wed., Apr. 4 | | Wed., Apr. 4 | ||
− | | Discrete Character Correlation<br/>Pagel's likelihood ratio test | + | | '''Discrete Character Correlation'''<br/>Pagel's likelihood ratio test |
| | | | ||
|- | |- | ||
| Mon., Apr. 9 | | Mon., Apr. 9 | ||
− | | Stochastic Character Mapping<br/>Ancestral states, character correlation, simmap demo | + | | '''Stochastic Character Mapping'''<br/>Ancestral states, character correlation, simmap demo |
| Mesquite | | Mesquite | ||
|- | |- | ||
| Wed., Apr. 11 | | Wed., Apr. 11 | ||
− | | Divergence Time Estimation<br/>Penalized likelihood, Bayesian approaches | + | | '''Divergence Time Estimation'''<br/>Penalized likelihood, Bayesian approaches |
| | | | ||
|- | |- | ||
| Mon., Apr. 16 | | Mon., Apr. 16 | ||
− | | | + | | '''To be announced''' |
| r8s | | r8s | ||
|- | |- | ||
| Wed., Apr. 18 | | Wed., Apr. 18 | ||
− | | To be announced | + | | '''To be announced''' |
− | + | ||
|- | |- | ||
| Mon., Apr. 23 | | Mon., Apr. 23 | ||
− | | To be announced | + | | '''To be announced''' |
| Beast | | Beast | ||
|- | |- | ||
| Wed., Apr. 25 | | Wed., Apr. 25 | ||
− | | To be announced | + | | '''To be announced''' |
| | | | ||
|} | |} |
Revision as of 13:38, 2 February 2007
EEB 349: Phylogenetics | |
Lectures: MW 11-12:15 (CUE 320) Lab: M 1-3 (TLS 477) Lecture Instructor: Paul O. Lewis Lab Instructor: Maxi Polihronakis |
Lecture Topics
The following syllabus is tentative and probably will change without notice numerous times during the semester. Also, the content of linked presentations may change as well (so if you intend to print out lectures before class, do so as late as possible). Changes made after lectures are given will primarily reflect correction of typographical errors. All content linked to this page is copyright © 2007 by Paul O. Lewis.
Day | Lecture | Lab/Homework |
Wed., Jan. 17 | Introduction (1 slide/page) (6 slides/page) Significance, history, terminology |
Homework #1 |
Mon., Jan. 22 | Tree thinking (1 slide/page) (6 slides/page) Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages |
PAUP* and NEXUS |
Wed., Jan. 24 | Consensus trees (1 slide/page) (6 slides/page) Parsimony (1 slide/page) (6 slides/page) Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix |
Homework #2 |
Mon., Jan. 29 | Polyphyly vs. Paraphyly Revisited (1 slide/page) (6 slides/page) Searching (1 slide/page) (6 slides/page) Exhaustive, branch-and-bound, star decomposition, stepwise addition, heuristic, genetic algorithms |
Parsimony and searching |
Wed., Jan. 31 | Distances (1 slide/page) (6 slides/page) Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ |
Homework #3 (ok to proceed) |
Mon., Feb. 5 | Measuring support Consensus trees, Bootstrapping, Bremer support, ILD test, KH test, SH test, SOWH test |
Distance methods |
Wed., Feb. 7 | Likelihood models Likelihood of a DNA sequence, likelihood of a pair of sequences, Jukes-Cantor model, Felsenstein 1981 model, likelihood ratio test, simulation |
|
Mon., Feb. 12 | Maximum likelihood Parameter estimation (MLEs), likelihood of a tree, marginalization |
PAUP* |
Wed., Feb. 14 | Rate heterogeneity Proportion of invariable sites, discrete gamma, site-specific rates |
|
Mon., Feb. 19 | Long branch attraction Statistical consistency, long branch repulsion |
PAUP*, Garli |
Wed., Feb. 21 | Codon models Nonsynonymous vs. synonymous rates, codons as states |
|
Mon., Feb. 26 | Other models Stems/loops, GC bias, covariatide |
Hy-Phy |
Wed., Feb. 28 | Likelihood ratio tests Molecular clock, branch-specific rate shifts |
|
Mon., Mar. 5 | Spring break no class |
no class |
Wed., Mar. 7 | Spring break | no class |
Mon., Mar. 12 | Bayes primer Conditional/joint probabilities, Bayes rule, posterior distribution, probability densities |
Hy-Phy |
Wed., Mar. 14 | Bayesian phylogenetics MCMC, slice sampling, heated chains |
|
Mon., Mar. 19 | Bayesian phylogenetics Summarizing posterior distributions, partitioned data |
Phycas |
Wed., Mar. 21 | Bayesian phylogenetics Reversible-jump MCMC, mixture models, star tree paradox |
|
Mon., Mar. 26 | Model Selection LRT, AIC, BIC, Bayes factors, posterior predictive approaches |
MrBayes |
Wed., Mar. 28 | Ancestral Character States Parsimony approach, ML approach, empirical Bayes approach |
|
Mon., Apr. 2 | Continuous Character Correlation Independent Contrasts |
PAUP* |
Wed., Apr. 4 | Discrete Character Correlation Pagel's likelihood ratio test |
|
Mon., Apr. 9 | Stochastic Character Mapping Ancestral states, character correlation, simmap demo |
Mesquite |
Wed., Apr. 11 | Divergence Time Estimation Penalized likelihood, Bayesian approaches |
|
Mon., Apr. 16 | To be announced | r8s |
Wed., Apr. 18 | To be announced | |
Mon., Apr. 23 | To be announced | Beast |
Wed., Apr. 25 | To be announced |
Goals of this course
This course is designed to give you the background you need to understand and critically evaluate phylogenetic analyses described in current primary literature, and to design appropriate phylogenetic analyses to address your own research questions.
Unlike many graduate courses, you will not spend a lot of time reading papers in this course. Instead, you will spend time using state-of-the-art software tools and doing homework assignments designed to ensure that you understand the output of the programs.
There is a confusing diversity of programs these days for performing phylogenetic analyses. We will concentrate on only a few so that you will know how to use these well by the end of the course.
Textbook
No textbook is required for this course, although you might find Joe Felsenstein's 2004 book "Inferring Phylogenies" (published by Sinauer) useful.
Labs
The laboratory section of this course is held in the MacCarthy computer lab on the fourth floor of Torrey Life Science (TLS 477). The labs will consist of tutorials that you work through at your own pace
Homeworks
Your grade will be largely based on homework assignments, one of which will be assigned (nearly) every week. You are expected to turn in an assignment one week after it is assigned. These homework assignments should be treated as if they were take-home, open-book exams. You may therefore consult with either me or the TA for the course, but not with fellow students when working on the homeworks.
Projects
In addition to homeworks, you will prepare a term paper to be due the last week of the course. There is a lot of flexibility in the nature of the term paper. If you have data of your own, you may decide to write a paper describing a phylogenetic analysis of these data, using appropriate methods learned during the course. If you are not yet at the stage of your graduate career where you have data of your own, you can do a thorough re-analysis of an existing data set. Finally, it is ok to simply write a review paper describing a particular topic in phylogenetics in depth. If you choose this route, I will encourage you to write a paper suitable for contribution to Wikipedia (this way, your efforts will survive the course and benefit the broader community). Please get my approval of your chosen topic before doing extensive work on your paper.