Difference between revisions of "Phylogenetics: Syllabus"

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== Lecture Topics ==
 
== 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 © 2009 by Paul O. Lewis.
+
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.
  
 
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|-
 
|-
 
| Mon., Jan. 22
 
| Mon., Jan. 22
| '''Tree thinking''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking_6perpage.pdf}}<br/>Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages
+
| '''Tree thinking''' <br/>Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages
| {{EEB349lab|{{SERVER}}/people/plewis/courses/phylogenetics/labs/paupnexus.html}} Nexus data files
+
| Nexus data files
 
|-
 
|-
 
| Wed., Jan. 24  
 
| Wed., Jan. 24  
| '''Consensus trees''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Consensus_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Consensus_6perpage.pdf}} '''Parsimony''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Parsimony_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Parsimony_6perpage.pdf}}<br/>
+
| '''Consensus trees''' <br/>
 
Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix
 
Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw2_Parsimony.pdf}} Parsimony
+
| Parsimony
 
|-
 
|-
 
| Mon., Jan. 29
 
| Mon., Jan. 29
| '''Polyphyly vs. Paraphyly Revisited''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking2_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TreeThinking2_6perpage.pdf}} '''Searching''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Searching_1perpage.pdf}}  {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Searching_6perpage.pdf}}<br/>Exhaustive, branch-and-bound, star decomposition, stepwise addition, heuristic, genetic algorithms
+
| '''Polyphyly vs. Paraphyly Revisited''' <br/>Exhaustive, branch-and-bound, star decomposition, stepwise addition, heuristic, genetic algorithms
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Parsimony_Lab}} Searching
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Parsimony_Lab}} Searching
 
|-
 
|-
 
| Wed., Jan. 31
 
| Wed., Jan. 31
| '''Distances''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Distances_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Distances_6perpage.pdf}}<br/>Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ
+
| '''Distances''' <br/>Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw3_Distances.pdf}} Distances
+
| Distances
 
|-
 
|-
 
| Mon., Feb. 5  
 
| Mon., Feb. 5  
| '''Substitution models''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Models_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Models_6perpage.pdf}}<br/>Transition probability, instantaneous rates, JC69 model, K2P model, F81 model, F84 model, HKY85 model, GTR model
+
| '''Substitution models''' <br/>Transition probability, instantaneous rates, JC69 model, K2P model, F81 model, F84 model, HKY85 model, GTR model
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Distances_Lab}} Distance methods
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Distances_Lab}} Distance methods
 
|-
 
|-
 
| Wed., Feb. 7  
 
| Wed., Feb. 7  
| '''Maximum likelihood''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Likelihood_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Likelihood_6perpage.pdf}}<br/>Likelihood of a DNA sequence, likelihood of a pair of sequences, parameter estimation (MLEs), likelihood of a tree, likelihood ratio test, simulation
+
| '''Maximum likelihood''' <br/>Likelihood of a DNA sequence, likelihood of a pair of sequences, parameter estimation (MLEs), likelihood of a tree, likelihood ratio test, simulation
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw4_Likelihood.pdf}} Likelihood
+
| Likelihood
 
|-
 
|-
 
| Mon., Feb. 12  
 
| Mon., Feb. 12  
| '''Rate heterogeneity''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/RateHeterogeneity_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/RateHeterogeneity_6perpage.pdf}} '''Addendum''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/RateHeterogeneityAddendum.pdf}}<br/>Proportion of invariable sites, discrete gamma, site-specific rates
+
| '''Rate heterogeneity''' <br/>Proportion of invariable sites, discrete gamma, site-specific rates
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Likelihood_Lab}} Likelihood
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Likelihood_Lab}} Likelihood
 
|-
 
|-
 
| Wed., Feb. 14
 
| Wed., Feb. 14
 
| '''*** Snow day: no class today ***''' (but do begin working on homework 5)  
 
| '''*** Snow day: no class today ***''' (but do begin working on homework 5)  
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw5_RateHet.pdf}} Rate Het.
+
| Rate Het.
 
|-
 
|-
 
| Mon., Feb. 19
 
| Mon., Feb. 19
| '''Secondary structure (stem) models''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/StemModels_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/StemModels_6perpage.pdf}} <span id="codon_models">'''Codon models'''</span> {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CodonModels_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CodonModels_6perpage.pdf}}<br/>RNA stem/loop structure, compensatory substitutions, stem models, nonsynonymous vs. synonymous rates, codon models
+
| '''Secondary structure (stem) models''' <br/>RNA stem/loop structure, compensatory substitutions, stem models, nonsynonymous vs. synonymous rates, codon models
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Bioinformatics_Cluster}} Using the cluster
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Bioinformatics_Cluster}} Using the cluster
 
|-
 
|-
 
| Wed., Feb. 21
 
| Wed., Feb. 21
| '''Bootstrapping''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bootstrapping_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bootstrapping_6perpage.pdf}} '''Bremer support''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bremer_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Bremer_6perpage.pdf}} '''Topology tests''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TopologyTests_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/TopologyTests_6perpage.pdf}}<br/>Bootstrapping, Bremer support, KH test, SH test, SOWH test
+
| '''Bootstrapping''' <br/>Bootstrapping, Bremer support, KH test, SH test, SOWH test
 
| No homework assignment this week
 
| No homework assignment this week
 
|-
 
|-
 
| Mon., Feb. 26  
 
| Mon., Feb. 26  
| '''Simulation''' (updated) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Simulation_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Simulation_6perpage.pdf}} '''Long branch attraction''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LBA_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LBA_6perpage.pdf}} '''Model selection, part I''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LRT_AIC_BIC_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/LRT_AIC_BIC_6perpage.pdf}} <br/>Stochastic simulation, statistical consistency, long branch attraction, long branch repulsion, likelihood ratio tests, Akaike Information criterion (AIC), Bayesian Information Criterion (BIC)
+
| '''Simulation''' (updated) <br/>Stochastic simulation, statistical consistency, long branch attraction, long branch repulsion, likelihood ratio tests, Akaike Information criterion (AIC), Bayesian Information Criterion (BIC)
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_HyPhy_Lab}} Hy-Phy
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_HyPhy_Lab}} Hy-Phy
 
|-
 
|-
 
| Wed., Feb. 28  
 
| Wed., Feb. 28  
| '''Data partitioning''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Partitioning_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Partitioning_6perpage.pdf}} '''Expected substitutions''' (updated) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ExpectedSubstitutions_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ExpectedSubstitutions_6perpage.pdf}} <br/>ILD test for combinability, using different model for each partition
+
| '''Data partitioning''' <br/>ILD test for combinability, using different model for each partition
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw6_Simulation.pdf}} Simulation
+
| Simulation
 
|-
 
|-
 
| Mon., Mar. 5  
 
| Mon., Mar. 5  
Line 80: Line 81:
 
|-
 
|-
 
| Mon., Mar. 12
 
| Mon., Mar. 12
| '''Bayes primer''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianIntro_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianIntro_6perpage.pdf}} <br/>Conditional/joint probabilities, Bayes rule, prior vs. posterior distributions, probability mass vs. probability density, Markov chain Monte Carlo (start)
+
| '''Bayes primer''' <br/>Conditional/joint probabilities, Bayes rule, prior vs. posterior distributions, probability mass vs. probability density, Markov chain Monte Carlo (start)
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Modeltest_Lab}} ModelTest/Gamma dist.
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Modeltest_Lab}} ModelTest/Gamma dist.
 
|-
 
|-
 
| Wed., Mar. 14  
 
| Wed., Mar. 14  
| '''Bayesian phylogenetics''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianPhylogenetics_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianPhylogenetics_6perpage.pdf}} <br/>MCMC (continued), heated chains, choosing prior distributions  
+
| '''Bayesian phylogenetics''' <br/>MCMC (continued), heated chains, choosing prior distributions  
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw7_MCMC.pdf}} MCMC
+
| MCMC
 
|-
 
|-
 
| Mon., Mar. 19  
 
| Mon., Mar. 19  
| '''Prior distributions''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/PriorDistributions_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/PriorDistributions_6perpage.pdf}}<br/>Summarizing posterior distributions, commonly-used prior distributions, problem priors, reversible-jump MCMC, star tree paradox
+
| '''Prior distributions''' <br/>Summarizing posterior distributions, commonly-used prior distributions, problem priors, reversible-jump MCMC, star tree paradox
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_MrBayes_Lab}} MrBayes
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_MrBayes_Lab}} MrBayes
 
|-
 
|-
 
| Wed., Mar. 21  
 
| Wed., Mar. 21  
| '''Confidence intervals''' (follow-up on last lecture) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ConfidenceIntervals_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/ConfidenceIntervals_6perpage.pdf}}&nbsp; '''Model Selection, part II''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelection_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelection_6perpage.pdf}}<br/>Bayes  factors, posterior predictive approaches to model selection  
+
| '''Confidence intervals''' (follow-up on last lecture) <br/>Bayes  factors, posterior predictive approaches to model selection  
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw8_LocalMove.pdf}} LOCAL move
+
|   LOCAL move
 
|-
 
|-
 
| Mon., Mar. 26  
 
| Mon., Mar. 26  
| '''Model Selection, part II (4 extra slides)''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelExtra_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelExtra_6perpage.pdf}}
+
| '''Model Selection, part II (4 extra slides)'''
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Mesquite_Lab}} Mesquite
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Mesquite_Lab}} Mesquite
 
|-
 
|-
 
| Wed., Mar. 28  
 
| Wed., Mar. 28  
| '''Ancestral Character States''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/AncStates_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/AncStates_6perpage.pdf}} <br/>Parsimony approach, ML approach, empirical Bayes approach
+
| '''Ancestral Character States''' <br/>Parsimony approach, ML approach, empirical Bayes approach
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw9_AncStates.pdf}} Anc. states
+
| Anc. states
 
|-
 
|-
 
| Mon., Apr. 2  
 
| Mon., Apr. 2  
Line 108: Line 109:
 
|-
 
|-
 
| Wed., Apr. 4  
 
| Wed., Apr. 4  
| '''Models for discrete morphological data''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphModels_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphModels_6perpage.pdf}} <br/>DNA sequences vs. morphological characters, Symmetric vs. asymmetric 2-state models, Mk model, estimating morphological branch lengths
+
| '''Models for discrete morphological data''' <br/>DNA sequences vs. morphological characters, Symmetric vs. asymmetric 2-state models, Mk model, estimating morphological branch lengths
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw10_CondVar.pdf}} Mk model
+
| Mk model
 
|-
 
|-
 
| Mon., Apr. 9  
 
| Mon., Apr. 9  
| '''Discrete Character Correlation''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CorrelatedEvolution_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CorrelatedEvolution_6perpage.pdf}}   
+
| '''Discrete Character Correlation'''    
'''Continuous Character Correlation''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/IndependentContrasts_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/IndependentContrasts_6perpage.pdf}} <br/>Pagel's likelihood ratio test, Felsenstein's threshhold model, Felsenstein's independent contrasts
+
'''Continuous Character Correlation''' <br/>Pagel's likelihood ratio test, Felsenstein's threshhold model, Felsenstein's independent contrasts
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Morphology_and_Partitioning_in_MrBayes}} Partitioning/Morphology
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Morphology_and_Partitioning_in_MrBayes}} Partitioning/Morphology
 
|-
 
|-
 
| Wed., Apr. 11
 
| Wed., Apr. 11
| '''Stochastic Character Mapping''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphMappingSIMMAP_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/MorphMappingSIMMAP_6perpage.pdf}} <br/>Concentrated changes test, stochastic mapping for estimating ancestral states and character correlation, SIMMAP demo
+
| '''Stochastic Character Mapping''' <br/>Concentrated changes test, stochastic mapping for estimating ancestral states and character correlation, SIMMAP demo
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw11_MorphMap.pdf}} Mapping
+
| Mapping
 
|-
 
|-
 
| Mon., Apr. 16
 
| Mon., Apr. 16
Line 125: Line 126:
 
|-
 
|-
 
| Wed., Apr. 18  
 
| Wed., Apr. 18  
| '''Divergence Time Estimation''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/DivergenceTimes_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/DivergenceTimes_6perpage.pdf}} <br/>Non-parametric rate smoothing, penalized likelihood, cross-validation, Bayesian approaches
+
| '''Divergence Time Estimation''' <br/>Non-parametric rate smoothing, penalized likelihood, cross-validation, Bayesian approaches
 
| Read chapter and paper for Apr. 25
 
| Read chapter and paper for Apr. 25
 
|-
 
|-
 
| Mon., Apr. 23
 
| Mon., Apr. 23
| '''Inferring key innovations''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/KeyInnovations_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/KeyInnovations_6perpage.pdf}} '''The Remainder''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Conclusion2007_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Conclusion2007_6perpage.pdf}}<br>Key innovations, clade contrast approach, stochastic mapping method, what ''was'' and ''was not'' covered in this course (also course evaluations)
+
| '''Inferring key innovations''' <br>Key innovations, clade contrast approach, stochastic mapping method, what ''was'' and ''was not'' covered in this course (also course evaluations)
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_r8s_Lab}} r8s  
 
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_r8s_Lab}} r8s  
 
|-
 
|-
 
| Wed., Apr. 25
 
| Wed., Apr. 25
| '''Alignment''' (guest lecture by Karl Kjer) {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_6perpage.pdf}}&nbsp;Reading: Chapter {{pdf|{{SERVER}}/people/plewis/courses/phylogenetics/restricted/Alignmentchapter_near_final.pdf}}&nbsp;Paper {{pdf|{{SERVER}}/people/plewis/courses/phylogenetics/restricted/Kjer_Gillespie_Ober_2007_SystBiol_56_133-146.pdf}}<br/>Toner-saver version of lecture (note: some details may be obscured by conversion to pure black and white): {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_1perpage_bw.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Alignment_6perpage_bw.pdf}}
+
| '''Alignment''' (guest lecture by Karl Kjer)  
 
| No homework today
 
| No homework today
 
|}
 
|}

Revision as of 14:13, 15 January 2009

Adiantum.png EEB 349: Phylogenetics
Lectures: TTh 12:30-1:45 (TLS 313)
Lab: Th 2-4 (TLS 313)
Lecture Instructor: Paul O. Lewis
Lab Instructor: Jessica Budke

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
Significance, history, terminology
Tree from splits
Mon., Jan. 22 Tree thinking
Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages
Nexus data files
Wed., Jan. 24 Consensus trees

Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix

Parsimony
Mon., Jan. 29 Polyphyly vs. Paraphyly Revisited
Exhaustive, branch-and-bound, star decomposition, stepwise addition, heuristic, genetic algorithms
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Searching
Wed., Jan. 31 Distances
Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ
Distances
Mon., Feb. 5 Substitution models
Transition probability, instantaneous rates, JC69 model, K2P model, F81 model, F84 model, HKY85 model, GTR model
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Distance methods
Wed., Feb. 7 Maximum likelihood
Likelihood of a DNA sequence, likelihood of a pair of sequences, parameter estimation (MLEs), likelihood of a tree, likelihood ratio test, simulation
Likelihood
Mon., Feb. 12 Rate heterogeneity
Proportion of invariable sites, discrete gamma, site-specific rates
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Likelihood
Wed., Feb. 14 *** Snow day: no class today *** (but do begin working on homework 5) Rate Het.
Mon., Feb. 19 Secondary structure (stem) models
RNA stem/loop structure, compensatory substitutions, stem models, nonsynonymous vs. synonymous rates, codon models
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Using the cluster
Wed., Feb. 21 Bootstrapping
Bootstrapping, Bremer support, KH test, SH test, SOWH test
No homework assignment this week
Mon., Feb. 26 Simulation (updated)
Stochastic simulation, statistical consistency, long branch attraction, long branch repulsion, likelihood ratio tests, Akaike Information criterion (AIC), Bayesian Information Criterion (BIC)
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Hy-Phy
Wed., Feb. 28 Data partitioning
ILD test for combinability, using different model for each partition
Simulation
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, prior vs. posterior distributions, probability mass vs. probability density, Markov chain Monte Carlo (start)
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png ModelTest/Gamma dist.
Wed., Mar. 14 Bayesian phylogenetics
MCMC (continued), heated chains, choosing prior distributions
MCMC
Mon., Mar. 19 Prior distributions
Summarizing posterior distributions, commonly-used prior distributions, problem priors, reversible-jump MCMC, star tree paradox
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png MrBayes
Wed., Mar. 21 Confidence intervals (follow-up on last lecture)
Bayes factors, posterior predictive approaches to model selection
LOCAL move
Mon., Mar. 26 Model Selection, part II (4 extra slides) http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Mesquite
Wed., Mar. 28 Ancestral Character States
Parsimony approach, ML approach, empirical Bayes approach
Anc. states
Mon., Apr. 2 No lecture today No lab today
Wed., Apr. 4 Models for discrete morphological data
DNA sequences vs. morphological characters, Symmetric vs. asymmetric 2-state models, Mk model, estimating morphological branch lengths
Mk model
Mon., Apr. 9 Discrete Character Correlation

Continuous Character Correlation
Pagel's likelihood ratio test, Felsenstein's threshhold model, Felsenstein's independent contrasts

http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Partitioning/Morphology
Wed., Apr. 11 Stochastic Character Mapping
Concentrated changes test, stochastic mapping for estimating ancestral states and character correlation, SIMMAP demo
Mapping
Mon., Apr. 16 Stochastic Character Mapping (finish) http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png BayesTraits
Wed., Apr. 18 Divergence Time Estimation
Non-parametric rate smoothing, penalized likelihood, cross-validation, Bayesian approaches
Read chapter and paper for Apr. 25
Mon., Apr. 23 Inferring key innovations
Key innovations, clade contrast approach, stochastic mapping method, what was and was not covered in this course (also course evaluations)
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png r8s
Wed., Apr. 25 Alignment (guest lecture by Karl Kjer) No homework today

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. 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.

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