Difference between revisions of "Phylogenetics: Syllabus"

From EEBedia
Jump to: navigation, search
m (Reverted edits by PaulLewis (Talk); changed back to last version by NicTippery)
Line 5: Line 5:
 
|-
 
|-
 
|rowspan="2" valign="top"|[[Image:Adiantum.png|200px]]
 
|rowspan="2" valign="top"|[[Image:Adiantum.png|200px]]
|<span style="font-size: x-large">EEB 5349: Phylogenetics</span>
+
|<span style="font-size: x-large">EEB 349: Phylogenetics</span>
 
|-
 
|-
| '''Lectures:''' TuTh 11:00-12:15 (TLS 313)<br/>'''Lab:''' Th 2-4 (TLS 313)<br/>'''Lecture Instructor:''' [mailto:paul.lewis@uconn.edu Paul O. Lewis]<br/>'''Lab Instructor:''' [mailto:yu.fan@uconn.edu Daniel Fan]
+
| '''Lectures:''' MW 11-12:15 (CUE 320)<br/>'''Lab:''' M 1-3 (TLS 477)<br/>'''Lecture Instructor:''' [mailto:paul.lewis@uconn.edu Paul O. Lewis]<br/>'''Lab Instructor:''' [mailto:maxi.polihronakis@uconn.edu Maxi Polihronakis]
 
|}
 
|}
  
 
== 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. '''Downloading PDFs from this web site now requires a username and password.''' All content linked to this page is copyright &copy; 2011 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 &copy; 2007 by Paul O. Lewis.
  
 
{| border="1"
 
{| border="1"
 
|-
 
|-
 
| Day || Lecture || Lab/Homework
 
| Day || Lecture || Lab/Homework
|- style="background:#eeee00"
 
| Tue., Jan. 18
 
| '''Introduction'''{{pdf|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/1_Intro.pdf}}<br/>The terminology of phylogenetics, rooted vs. unrooted trees, ultrametric vs. unconstrained, paralogy vs. orthology, lineage sorting, "basal" lineages, crown vs. stem groups
 
| Homework 1: Trees from splits {{pdf|{{SERVER}}/people/plewis/courses/phylogenetics/homeworks/Homework1.pdf}}
 
 
|-
 
|-
| Thu., Jan. 20
+
| Wed., Jan. 17
| '''Introduction to optimality criteria and search strategies''' <br/>Exhaustive enumeration, branch-and-bound search, algorithmic methods (star decomposition, stepwise addition, NJ), heuristic search stragegies (NNI, SPR, TBR), evolutionary algorithms
+
| '''Introduction''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Introduction_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/Introduction_6perpage.pdf}}<br/>Significance, history, terminology
| (1) [[Phylogenetics: NEXUS Format|Nexus data file format]], (2) [[Phylogenetics: Bioinformatics Cluster|using the cluster]], and (3) [[Phylogenetics: Introduction to PAUP*|Introduction to PAUP*]]
+
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw1_TreeFromSplits.pdf}} Tree from splits
 
|-
 
|-
| Tue., Jan. 25
+
| Mon., Jan. 22
| '''Consensus trees''' and '''Parsimony'''  <br/>Strict, semi-strict, and majority-rule consensus trees; maximum agreement subtrees; Camin-Sokal, Wagner, Fitch, Dollo, and transversion parsimony; step matrices and generalized parsimony
+
| '''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
| Homework 2: Parsimony
+
| {{EEB349lab|{{SERVER}}/people/plewis/courses/phylogenetics/labs/paupnexus.html}} Nexus data files
 
|-
 
|-
| Thu., Jan. 27
+
| Wed., Jan. 24
| '''History of Parsimony''' , '''Bootstrapping''' , and '''Distance Methods'''<br/>History of parsimony: Hennig, Edwards, Sokal, Camin, Dayhoff, Kluge, Farris, Fitch, Sankoff, and Wiley; character vs. character state; bootstrapping, least squares criterion, minimum evolution criterion
+
| '''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/>
| [[Phylogenetics:_Searching_Lab|Searching]]
+
Camin-Sokal, Wagner, Fitch, Dollo, transversion, generalized, step-matrix
 +
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw2_Parsimony.pdf}} Parsimony
 
|-
 
|-
| Tue., Feb. 1
+
| Mon., Jan. 29
| '''Distance Methods''' <br/>Split decomposition, quartet puzzling, DCM, NJ
+
| '''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
| Homework 3: Distances
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Parsimony_Lab}} Searching
 
|-
 
|-
| Thu., Feb. 3
+
| Wed., Jan. 31
| '''Substitution models'''<br/>Transition probability, instantaneous rates, JC69 model, K2P model, F81 model, F84 model, HKY85 model, GTR model
+
| '''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
| [[Phylogenetics: Python Primer|Python 101]]
+
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw3_Distances.pdf}} Distances
 
|-
 
|-
| Tue., Feb. 8
+
| Mon., Feb. 5
| '''Maximum likelihood''' <br/>Poisson processes; Likelihood: the probability of data given a model, maximum likelihood estimates (MLEs) of model parameters, likelihood of a tree, likelihood ratio test
+
| '''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
| Homework 4: Likelihood
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Distances_Lab}} Distance methods
 
|-
 
|-
| Thu., Feb. 10
+
| Wed., Feb. 7
| '''Rate heterogeneity''' <br/>Proportion of invariable sites, discrete gamma, site-specific rates
+
| '''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
| [[Phylogenetics: Likelihood Lab|Likelihood]]
+
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw4_Likelihood.pdf}} Likelihood
 
|-
 
|-
| Tue., Feb. 15
+
| Mon., Feb. 12
| '''Codon and secondary structure models''' <br/>RNA stem/loop structure, compensatory substitutions, stem models, nonsynonymous vs. synonymous rates, codon models
+
| '''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
| Homework 5: Rate heterogeneity
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Likelihood_Lab}} Likelihood
 
|-
 
|-
| Thu., Feb. 17
+
| Wed., Feb. 14
| '''Model selection''' <br/> Likelihood ratio test (LRT), Akaike Information criterion (AIC), Bayesian Information Criterion (BIC)<br/>'''Expected number of substitutions for a model'''  <br/>An example calculation for the F81 model
+
| '''*** Snow day: no class today ***''' (but do begin working on homework 5)  
| [[Phylogenetics: Large Scale Maximum Likelihood Analyses|ML analyses of large datasets]]<br/>The RAxML CAT model
+
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw5_RateHet.pdf}} Rate Het.
 
|-
 
|-
| Tue., Feb. 22
+
| Mon., Feb. 19
| '''Simulation'''<br/>How to simulate nucleotide sequence data, and why it's done<br/>'''Long-branch attraction''' <br/>Statistical consistency, long branch attraction (real), long branch repulsion (real?)<br/>
+
| '''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
| Homework 6: Simulation
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Bioinformatics_Cluster}} Using the cluster
 
|-
 
|-
| Thu., Feb. 24
+
| Wed., Feb. 21
| '''Statistical tests involving phylogenies''' <br/>ILD parsimony test for combinability, KH test, SH test, SOWH test<br/>'''Generating exponential random numbers'''<br/>For Geert
+
| '''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
| [[Phylogenetics: HyPhy Lab|HyPhy]]
+
| No homework assignment this week
 
|-
 
|-
| Tue., Mar. 1
+
| Mon., Feb. 26
| '''Bayes primer''''<br/>Conditional/joint probabilities, Bayes rule, prior vs. posterior distributions, probability mass vs. probability density, Markov chain Monte Carlo
+
| '''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)
| No homework this week
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_HyPhy_Lab}} Hy-Phy
 
|-
 
|-
| Thu., Mar. 3
+
| Wed., Feb. 28
|'''Bayes primer (continued)'''
+
| '''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
| '''Midterm exam'''
+
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw6_Simulation.pdf}} Simulation
 
|-
 
|-
| Tue., Mar. 8
+
| Mon., Mar. 5
| '''Spring break'''  
+
| '''Spring break'''<br/>no class
| no class
+
| no class
 
|-
 
|-
| Thu., Mar. 10
+
| Wed., Mar. 7
 
| '''Spring break'''  
 
| '''Spring break'''  
 
| no class  
 
| no class  
 
|-
 
|-
| Tue., Mar. 15
+
| Mon., Mar. 12
| '''Discussion of midterm'''<br/>'''Bayes primer (continued)'''<br/>Introduction to Markov chain Monte Carlo  
+
| '''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)
no homework this week
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Modeltest_Lab}} ModelTest/Gamma dist.
 +
|-
 +
| 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
 +
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw7_MCMC.pdf}} MCMC
 +
|-
 +
| 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
 +
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_MrBayes_Lab}} MrBayes
 +
|-
 +
| 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
 +
{{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw8_LocalMove.pdf}} LOCAL move
 +
|-
 +
| 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}}
 +
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Mesquite_Lab}} Mesquite
 +
|-
 +
| 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
 +
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw9_AncStates.pdf}} Anc. states
 
|-
 
|-
| Thu., Mar. 17
+
| Mon., Apr. 2
| '''Bayesian phylogenetics'''<br/>Heated chains and MCMCMC, stepping through tree space and parameter space
+
| No lecture today
| [[Phylogenetics: R Primer|Using R to explore probability distributions]]
+
| No lab today
 
|-
 
|-
| Tue., Mar. 22
+
| Wed., Apr. 4
| '''Confidence intervals'''<br/>Frequentist confidence intervals differ from Bayesian credible intervals<br/>'''Prior distributions'''<br/>Commonly-used prior distributions
+
| '''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
| Homework 7: MCMC
+
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw10_CondVar.pdf}} Mk model
 
|-
 
|-
| Thu., Mar. 24
+
| Mon., Apr. 9
| '''Priors (cont.)'''<br/>Pros and cons, hierarchical models and hyperpriors
+
| '''Discrete Character Correlation''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CorrelatedEvolution_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/CorrelatedEvolution_6perpage.pdf}}   
| [[Phylogenetics: MrBayes Lab|MrBayes lab]]
+
'''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
 +
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Morphology_and_Partitioning_in_MrBayes}} Partitioning/Morphology
 
|-
 
|-
| Tue., Mar. 29
+
| Wed., Apr. 11
| '''Star tree paradox'''<br/>When posteriors and bootstraps conflict (slightly modified since last week)<br/>'''Bayesian model selection'''<br/>Bayes  factors, posterior predictive approaches to model selection
+
| '''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
| Homework 8: Larget-Simon move
+
| {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw11_MorphMap.pdf}} Mapping
 
|-
 
|-
| Thu., Mar. 31
+
| Mon., Apr. 16
| '''Models for discrete morphological data'''<br/>DNA sequences vs. morphological characters, Symmetric vs. asymmetric 2-state models, Mk model, Tuffley-Steel no-common-mechanism model
+
| '''Stochastic Character Mapping''' (finish)
| [[Phylogenetics: Morphology and Partitioning in MrBayes|Morphology and partitioning in MrBayes]]
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_BayesTraits_Lab}} BayesTraits
|-
+
| Tue., Apr. 5
+
| '''Discrete character correlation'''<br/>Pagel's likelihood ratio test<br/>'''Continuous character correlation'''<br/>Felsenstein's independent contrasts
+
| Homework 9: Independent contrasts
+
 
|-
 
|-
| Thu., Apr. 7
+
| Wed., Apr. 18
| '''Estimating Bayes factors'''<br/>Harmonic mean method, more accurate approaches<br/>'''Ancestral states'''<br/>Likelihood, (empirical) Bayesian and parsimony reconstruction of ancestral states
+
| '''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
| [[Phylogenetics: Phycas Lab|Phycas]]
+
| Read chapter and paper for Apr. 25
|-
+
| Tue., Apr. 12
+
| '''Stochastic Character Mapping'''<br/>Concentrated changes test, stochastic mapping for estimating ancestral states and character correlation, SIMMAP demo
+
| Homework 10: Stochastic Mapping
+
 
|-
 
|-
| Thu., Apr. 14
+
| Mon., Apr. 23
| '''Mixture models'''<br/>rjMCMC, heterotachy models, Dirichlet process prior models
+
| '''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)
| [[Phylogenetics: BayesTraits Lab|BayesTraits lab]]
+
| {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_r8s_Lab}} r8s
|-
+
| Tue., Apr. 19
+
| '''Divergence time estimation (part 1)'''<br/>Non-parametric rate smoothing, penalized likelihood, cross-validation
+
| no homework assigned
+
|-
+
| Thu., Apr. 21
+
| '''Divergence time estimation (part 2)''' <br/>Bayesian approaches: Thorne/Kishino autocorrelated log-normal model; BEAST uncorrelated log-normal model; coalescent, exponential growth coalescent, and Yule tree priors
+
| [[Phylogenetics: BEAST Lab|BEAST lab]]
+
|-
+
| Tue., Apr. 26
+
| '''Lineages through time analyses'''
+
| '''Final exam now available'''  
+
|-
+
| Thu., Apr. 28
+
| '''Estimating species trees''' <br/>'''Evaluations''' (last part of lecture)
+
| [[Phylogenetics: APE Lab|APE Lab]]
+
 
|-
 
|-
| Wed., May 5
+
| Wed., Apr. 25
| Final exam and project reports due by 5:30pm (but if you need an extension, write to me)
+
| '''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}}
|  
+
| No homework today
 
|}
 
|}
  
Line 146: Line 140:
 
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.
 
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.
  
Compared to many graduate courses, you will spend less time reading papers and more time using state-of-the-art software tools and doing homework assignments designed to ensure that you understand the output of the programs.
+
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 [http://evolution.genetics.washington.edu/phylip/software.html 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.
 
There is a [http://evolution.genetics.washington.edu/phylip/software.html 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.
Line 156: Line 150:
 
== Labs ==
 
== Labs ==
  
The laboratory section of this course consist of tutorials that you work through at your own pace using your own laptop computer. In some cases, you will use the UConn [http://www.biotech.uconn.edu/bf/ Bioinformatics Facility]'s computing cluster to perform analyses. Please contact [mailto:jeffrey.lary@uconn.edu Jeff Lary] (486-5036) to get an account on the cluster at your earliest convenience.
+
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 ==
 
== Homeworks ==
  
Your grade will be based on a midterm exam, a final exam and a number of '''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.
+
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 ==
 
== 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. Please get my approval of your chosen topic before doing extensive work on your paper.
+
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 [http://en.wikipedia.org/wiki/Main_Page 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.
  
 
== Links ==
 
== Links ==
Line 174: Line 168:
 
* [http://www.hyphy.org/ HyPhy]
 
* [http://www.hyphy.org/ HyPhy]
 
* [http://mesquiteproject.org/mesquite/mesquite.html Mesquite]
 
* [http://mesquiteproject.org/mesquite/mesquite.html Mesquite]
* [http://beast.bio.ed.ac.uk/ Beast]
+
* [http://evolve.zoo.ox.ac.uk/beast/ Beast]
 
* [http://evolve.zoo.ox.ac.uk/software.html?id=tracer Tracer]
 
* [http://evolve.zoo.ox.ac.uk/software.html?id=tracer Tracer]
 
* [http://taxonomy.zoology.gla.ac.uk/rod/treeview.html TreeView]
 
* [http://taxonomy.zoology.gla.ac.uk/rod/treeview.html TreeView]

Revision as of 21:14, 12 January 2011

Adiantum.png 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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Significance, history, terminology
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Tree from splits
Mon., Jan. 22 Tree thinking http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Rooted/unrooted, ultrametric/free, paralogy/orthology, lineage sorting, "basal" lineages
http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Nexus data files
Wed., Jan. 24 Consensus trees http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Parsimony http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png

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

http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Parsimony
Mon., Jan. 29 Polyphyly vs. Paraphyly Revisited http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Searching http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Least squares criterion, minimum evolution criterion, split decomposition, quartet puzzling, DCM, NJ
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Distances
Mon., Feb. 5 Substitution models http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Likelihood of a DNA sequence, likelihood of a pair of sequences, parameter estimation (MLEs), likelihood of a tree, likelihood ratio test, simulation
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Likelihood
Mon., Feb. 12 Rate heterogeneity http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Addendum http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png
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) http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Rate Het.
Mon., Feb. 19 Secondary structure (stem) models http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Codon models http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Bremer support http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Topology tests http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Bootstrapping, Bremer support, KH test, SH test, SOWH test
No homework assignment this week
Mon., Feb. 26 Simulation (updated) http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Long branch attraction http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Model selection, part I http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Expected substitutions (updated) http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
ILD test for combinability, using different model for each partition
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Simulation
Mon., Mar. 5 Spring break
no class
no class
Wed., Mar. 7 Spring break no class
Mon., Mar. 12 Bayes primer http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
MCMC (continued), heated chains, choosing prior distributions
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png MCMC
Mon., Mar. 19 Prior distributions http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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) http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png  Model Selection, part II http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Bayes factors, posterior predictive approaches to model selection
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png LOCAL move
Mon., Mar. 26 Model Selection, part II (4 extra slides) http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/0/0d/Flask.png Mesquite
Wed., Mar. 28 Ancestral Character States http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Parsimony approach, ML approach, empirical Bayes approach
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Anc. states
Mon., Apr. 2 No lecture today No lab today
Wed., Apr. 4 Models for discrete morphological data http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
DNA sequences vs. morphological characters, Symmetric vs. asymmetric 2-state models, Mk model, estimating morphological branch lengths
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png Mk model
Mon., Apr. 9 Discrete Character Correlation http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png

Continuous Character Correlation http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Concentrated changes test, stochastic mapping for estimating ancestral states and character correlation, SIMMAP demo
http://hydrodictyon.eeb.uconn.edu/eebedia/images/e/ea/Pencil.png 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 http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
Non-parametric rate smoothing, penalized likelihood, cross-validation, Bayesian approaches
Read chapter and paper for Apr. 25
Mon., Apr. 23 Inferring key innovations http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png The Remainder http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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) http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png Reading: Chapter Pdficon small.gif Paper Pdficon small.gif
Toner-saver version of lecture (note: some details may be obscured by conversion to pure black and white): http://hydrodictyon.eeb.uconn.edu/eebedia/images/f/fa/1perpage.png http://hydrodictyon.eeb.uconn.edu/eebedia/images/1/1b/6perpage.png
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.

Links