|
|
Line 92: |
Line 92: |
| |- | | |- |
| | 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}} '''Model Selection, part II''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelection_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelection_6perpage.pdf}} | + | | '''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}} '''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 |
− | '''4 extra slides''' {{1perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelExtra_1perpage.pdf}} {{6perpage|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/BayesianModelSelExtra_6perpage.pdf}} <br/>Bayes factors, posterior predictive approaches to model selection
| + | |
| | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw8_LocalMove.pdf}} LOCAL move | | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw8_LocalMove.pdf}} LOCAL move |
| |- | | |- |
| | Mon., Mar. 26 | | | Mon., Mar. 26 |
− | | finish '''Model Selection, part II''', start '''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 | + | | '''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 | | | {{EEB349lab|{{SERVER}}/eebedia/index.php/Phylogenetics:_Mesquite_Lab}} Mesquite |
| |- | | |- |
| | Wed., Mar. 28 | | | Wed., Mar. 28 |
− | | '''Discrete Character Correlation'''<br/>Pagel's likelihood ratio test | + | | '''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 | | | {{EEB349hw|{{SERVER}}/people/plewis/courses/phylogenetics/lectures/hw9_AncStates.pdf}} Anc. states |
| |- | | |- |
| | Mon., Apr. 2 | | | Mon., Apr. 2 |
− | | '''Continuous Character Correlation'''<br/>Independent Contrasts | + | | '''Discrete Character Correlation'''<br/>Pagel's likelihood ratio test |
| | PAUP* | | | PAUP* |
| |- | | |- |
| | Wed., Apr. 4 | | | Wed., Apr. 4 |
− | | '''Models for discrete morphological data'''<br/>Differences between nucleotide sequences and morphological character data, Mk model, Felsenstein's threshhold model | + | | '''Continuous Character Correlation'''<br/>Independent Contrasts |
| | TBA | | | TBA |
| |- | | |- |
| | Mon., Apr. 9 | | | Mon., Apr. 9 |
− | | '''Stochastic Character Mapping'''<br/>Ancestral states, character correlation, simmap demo | + | | '''Models for discrete morphological data'''<br/>Differences between nucleotide sequences and morphological character data, Mk model, Felsenstein's threshhold model |
| | TBA | | | TBA |
| |- | | |- |
| | Wed., Apr. 11 | | | Wed., Apr. 11 |
− | | '''Divergence Time Estimation'''<br/>Penalized likelihood, Bayesian approaches | + | | '''Stochastic Character Mapping'''<br/>Ancestral states, character correlation, simmap demo |
| | TBA | | | TBA |
| |- | | |- |
| | Mon., Apr. 16 | | | Mon., Apr. 16 |
− | | TBA | + | | '''Divergence Time Estimation'''<br/>Penalized likelihood, Bayesian approaches |
| | r8s | | | r8s |
| |- | | |- |
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
|
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
|
Discrete Character Correlation Pagel's likelihood ratio test
|
PAUP*
|
Wed., Apr. 4
|
Continuous Character Correlation Independent Contrasts
|
TBA
|
Mon., Apr. 9
|
Models for discrete morphological data Differences between nucleotide sequences and morphological character data, Mk model, Felsenstein's threshhold model
|
TBA
|
Wed., Apr. 11
|
Stochastic Character Mapping Ancestral states, character correlation, simmap demo
|
TBA
|
Mon., Apr. 16
|
Divergence Time Estimation Penalized likelihood, Bayesian approaches
|
r8s
|
Wed., Apr. 18
|
TBA
|
Mon., Apr. 23
|
TBA
|
Beast
|
Wed., Apr. 25
|
TBA
|
TBA
|
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.
No textbook is required for this course, although you might find Joe Felsenstein's 2004 book "Inferring Phylogenies" (published by Sinauer) useful.
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