Grad Core Phylogenetics 2012

Syllabus Fall 2012:

Day 1

Topics:
Why phylo?
Continuous time Markov Chain finite state space
Doing this in Geiger: get exercise Discrete.R
Slides (PDF)

Day 2

Topics:
In class review quiz
Central limit theorem CLT.R
Brownian motion, Ornstein Uhlenbeck, Independent Contrasts
Slides (PDF)

Day 3

Topics:
In class review quiz
Likelihood vs Bayes redux
Model comparison exercise
Tree stretching
Tree stretching exercise
Slides (PDF)

Day 4

Topics:
In class review quiz
Working through homework. What did you conclude? What does it mean? (relevant R script is here)
Delve deeper into how to do an analysis.
Diversification
Slides (PDF)

Day 5

Topics:
Doing a good analysis
Slides (PDF)

Day 6

Topics
Continuing pair analyses

Final

Concatenation of all slides (PDF)
Study guide (PDF)

Biodiversity 2012

This is Biodiversity 130, Spring 2012. It is a course covering basic evolution and a walk through various taxa. The main site content is set up on Blackboard (behind a log in wall). You may want to check out the Lampyr web/iOS app being developed as part of this course. The syllabus is here.

Lectures

Creative Commons License
You can adopt these for your own work, with attribution. Note that I have attempted to use only images licensed under such terms myself, but you should take care, especially with images from papers or embedded videos. I have attributed all the media used (with some exceptions for public domain items), and I think this is fair use for education, but I am not a lawyer.
All lectures are available, concatenated, as PDF (344 MB) and Apple Keynote (3.6 GB).

Macroevolution 2011

Macroevolution (EEB464, 2011)

Syllabus PDF

Lectures
Creative Commons License
You can adopt these for your own work, with attribution. Note that I have attempted to use only images licensed under such terms myself, but you should take care, especially with images from papers or embedded videos. I have attributed all the media used (with some exceptions for public domain items), and I think this is fair use for education, but I am not a lawyer.

Slides are generally available as PDFs below.

This class is taught with a mixture of lecture, class discussions, readings, white board scribblings, and interactive programs, generally written de novo for the course. The slides alone thus do not contain all the information the students learned (or at least were exposed to).

Office hours
Meeting with a faculty member one on one is something that is not done enough by students. Rather than have a fixed time for office hours, where it might not be convenient for many students, they are by appointment. You can see empty slots in my schedule here. Please email ahead of time for an appointment (and wait for a reply), don’t just show up.

Also, please do not forget the anonymous feedback form. If you see a way to improve the class, let me know while it can still benefit you.

Date Topic Big question Taxon to have learned Assignment
W 08/17 Pre-test, syllabus
F 08/19 History of planet & life  What is the history of life? Crinoid
M 08/22 History of planet & life What is the history of life? Archaea
W 08/24 Evidence What is the history of life? Bdelloid rotifers
F 08/26 Taphonomy What is the history of life? Trilobite
M 08/29 Jargon Acromyrmex
W 08/31 Phylogenetics What is the history of life? Ammonite
F 09/02 What is the history of life? What explains
trait frequencies?
Ichthyornis dispar
M 09/05 Labor day
W 09/07 McClung field trip What is the history of life? What
explains trait frequencies?
McClung foyer
F 09/09 Biogeography What is the history of life? Brachiopod
M 09/12 Speciation Why are some groups more speciose than others? Wolbachia
W 09/14 Speciation Why are some groups more speciose than others? Anomalocaris
F 09/16 Guest lecture 1 HOX Gasterosteus aculeatus
M 09/19 Extinction Why are some groups more speciose than others? Geospizinae
W 09/21 Extinction Why are some groups more speciose than others? Dionaea muscipula
F 09/23 Diversification Why are some groups more speciose than others? Tribolium
M 09/26 BISSE and ML/Bayes Why are some groups more speciose than others? bonobo
W 09/28 Learning synthesis Lichen In class fill out this.
F 09/30 Fall break
M 10/03 Natural selection & drift What explains trait frequencies? What sets the rate of phenotypic evolution? Fig wasp
W 10/05 Discussion of speciation essays Anolis
F 10/07 Sex Tunicates
M 10/10 Trends What explains trait frequencies? What sets the
rate of phenotypic evolution?
Spiny anteater Midterm distributed
W 10/12 Escalation What explains trait frequencies? What sets the
rate of phenotypic evolution?
Eubacteria
F 10/14 Correlated Traits What explains trait frequencies? What sets the
rate of phenotypic evolution?
Maiasaura
M 10/17 Contingency What explains trait frequencies? What sets the
rate of phenotypic evolution?
Isopod Midterm due at 8 pm [postponed to Wed]
W 10/19 Symbiosis All Riftia pachyptila
F 10/21 Systematics What explains trait frequencies? What sets the
rate of phenotypic evolution?
Ground sloth
M 10/24 Origin of life Basic Thermus aquaticus
W 10/26 Evolution of flight What explains trait frequencies? Why are some
groups more speciose than others?
Lycophytes
F 10/28 Heterochrony What explains trait frequencies? Why are some
groups more speciose than others?
Strepsiptera heterochrony.zip
M 10/31 Insects What is the history of life? Diatom Paper due at 8 pm
W 11/02 Animal culture Dimetrodon
F 11/04 Contemporary human evolution Buchnera
M 11/07 Game theory Welwitschia
W 11/09 Animal play Ginkgo
F 11/11 Work on presentations silversword
M 11/14 Evolution in Tennessee orca
W 11/16 Philosophy of science Cordyceps
F 11/18 Presentations Presentation
M 11/21 Presentations Presentation
W 11/23 Presentations Presentation
F 11/25 Thanksgiving break
M 11/28 Review

Grad Core Phylogenetics 2011

Syllabus Fall 2011:

Day 1

Topics:
Speciation
Hybridization
Slides: PDF.
For homework, due by start of class Monday, do steps 1-15 of this tutorial.

Day 2

Topics:
What trees are used for
history of life + cool discoveries about topology
tree terminology
clades (dinos birds, reptiles, fish)
sister groups, crown/stem, etc.
rank and its importance
homology
heuristic search
treespace
Slides: PDF.

Day 3

Topics:
Distance
Parsimony
Long branch attraction
Models
Model selection
Bayes/Likelihood

Slides: PDF
Homework:
The next assignment should be pretty fun. By next Monday, write a heuristic search algorithm for getting the maximum parsimony tree in R after downloading a set of GenBank sequences, also within R. I’ve sketched out a lot of the code — the main tricky bit should be figuring out how to store the best tree as you go and learning how to use an if() function. Comments in ALL CAPS are the sections you should focus on for changing. You’re encouraged to play with this assignment: maybe you want to plot the scores as you search, maybe you want to try different search strategies, etc. Feel free to email me for help or talk to your cohort-mates (remember you can use the blackboard forum, too). R template here.

Day 4

Slides: PDF

Day 5

Slides: PDF

Day 6

Slides: PDF

Macroevolution 2010

Macroevolution (EEB461, 2010)

This course is offered in Fall 2010. It will be offered in the future as EEB464.

Syllabus PDF

Lectures
Creative Commons License
You can adopt these for your own work, with attribution. Note that I have attempted to use only images licensed under such terms myself, but you should take care, especially with images from papers or embedded videos. I have attributed all the media used (with some exceptions for public domain items), and I think this is fair use for education, but I am not a lawyer.

Files are generally available in Apple Keynote format, as PDFs, and as QuickTime movies. These files can be large: in the case of some of the movie versions, up to 500 MB in size. In the movies, you will need to click to advance from slide to slide.

All the lectures are now available in one PDF file. There are 663 slides and the file is 184 MB. Note that movies used in the actual slides do not run in the PDF. To see the movies, too, look at the original Keynote file (warning: 1.58 GB) or the small (256 x 192 pixel resolution, 105 MB) or medium (512 x 384 pixel resolution, 309 MB) QuickTime movies.

This class was taught with a mixture of lecture, class discussions, readings, white board scribblings, and interactive programs, generally written de novo for the course. The slides alone thus do not contain all the information the students learned (or at least were exposed to).

Also, please do not forget the anonymous feedback form.

Date Topic Big question Taxon to have learned Assignment Lecture Other materials
W 08/18 Pre-test, syllabus        
F 08/20 History of planet & life What is the history of life? Crinoid   .key
.pdf
.mov
.R script for making timelines
Timing.txt input for script (with student names anonymized)
M 08/23 History of planet & life What is the history of life? Archaea   .key
.pdf
.mov
 
W 08/25 Evidence What is the history of life? Bdelloid rotifers   .key
.pdf
.mov
Made inferences about animals and interactions using “fossils” [leaves from around my house]
F 08/27 Taphonomy What is the history of life? Trilobite   .key
.pdf
.mov
 
M 08/30 Jargon   Acromyrmex   .key
.pdf
.mov
 
W 09/01 Phylogenetics What is the history of life? Ammonite   .key
.pdf
.mov
 
F 09/03 Empirical distributions What is the history of life? What explains trait
frequencies?
Ichthyornis dispar   .key
.pdf
.mov
 
M 09/06 Labor day          
W 09/08 McClung field trip What is the history of life? What explains trait
frequencies?
  McClung foyer    
F 09/10 Biogeography What is the history of life? Brachiopod   .key
.pdf
.mov
 
M 09/13 Speciation Why are some groups more speciose than others? Wolbachia   .key
.pdf
.mov
In class derivation of Dobzhansky-Muller incompatibility idea
W 09/15 Speciation Why are some groups more speciose than others? Anomalocaris   .key
.pdf
.mov
 
F 09/17 Speciation Why are some groups more speciose than others? Gasterosteus aculeatus   .key
.pdf
.mov
 
M 09/20 Extinction Why are some groups more speciose than others? Geospizinae   .key
.pdf
.mov
 
W 09/22 Extinction Why are some groups more speciose than others? Dionaea muscipula      
F 09/24 Extinction Why are some groups more speciose than others? Tribolium   .key
.pdf
.mov
 
M 09/27 Diversification Why are some groups more speciose than others? bonobo   .key
.pdf
.mov
 
W 09/29 Diversification Why are some groups more speciose than others? Lichen   .key
.pdf
.mov
 
F 10/01 Diversification Why are some groups more speciose than others? Fig wasp      
M 10/04 BISSE Why are some groups more speciose than others? What
explains trait frequencies?
Anolis   .key
.pdf
.mov
 
W 10/06 Natural selection & drift What explains trait frequencies? What sets the rate
of phenotypic evolution?
Tunicates   .key
.pdf
.mov
 
F 10/08 Fall break          
M 10/11 Sex What explains trait frequencies? What sets the rate
of phenotypic evolution?
Spiny anteater Midterm distributed .key
.pdf
.mov
 
W 10/13 Trends What explains trait frequencies? What sets the rate
of phenotypic evolution?
Eubacteria   .key
.pdf
.mov
 
F 10/15 Trends What explains trait frequencies? What sets the rate
of phenotypic evolution?
Maiasaura      
M 10/18 Trends What explains trait frequencies? What sets the rate
of phenotypic evolution?
Isopod Midterm due at 8 pm    
W 10/20 Escalation What explains trait frequencies? What sets the rate
of phenotypic evolution?
Riftia pachyptila      
F 10/22 Correlated traits What explains trait frequencies? What sets the rate
of phenotypic evolution?
       
M 10/25 Correlated traits What explains trait frequencies? What sets the rate
of phenotypic evolution?
Thermus aquaticus      
W 10/27 Many to one mapping What explains trait frequencies? What sets the rate
of phenotypic evolution?
Lycophytes      
F 10/29 Contingency All Strepsiptera      
M 11/01 EvoDevo What explains trait frequencies? What sets the rate
of phenotypic evolution?
Diatom Paper due at 8 pm    
W 11/03 Systematics Basic Dimetrodon      
F 11/05 Coevolution What explains trait frequencies? Why are some groups
more speciose than others?
Buchnera      
M 11/08 Symbiosis What explains trait frequencies? Why are some groups
more speciose than others?
Welwitschia      
W 11/10 Origin of life & astrobiology What is the history of life? Ginkgo      
F 11/12 Free topic 1   silversword      
M 11/15 Free topic 2   orca      
W 11/17 Free topic 3   Cordyceps      
F 11/19 Presentations     Presentation    
M 11/22 Presentations     Presentation    
W 11/24 Presentations     Presentation    
F 11/26 Thanksgiving break          
M 11/29 Review          

Grad Core Phylogenetics 2010

Syllabus Fall 2010:

Day 1

Topics:
What trees are used for
history of life + cool discoveries about topology
Tree terminology
clades (dinos birds, reptiles, fish)
sister groups, crown/stem, etc.
rank and its importance
homology

Slides: pdf, keynote, mov (QuickTime movie)
R assignment:
By the start of class Wednesday, please:
1) Install R on a computer you can access (you don’t need to bring it in, so a desktop at home is fine). You can get an installer from http://cran.r-project.org/ .
2) Read this web page: http://bodegaphylo.wikispot.org/Phylogenetics_and_Comparative_Methods_in_R
3) Read and do the exercises (aka “type ~8 lines”) from this web page: http://bodegaphylo.wikispot.org/I._Getting_Started_with_R . Do the task view route (it’s easier).
4) Write me an email with the info you get from the See Also section when you run ?read.tree after doing the tutorial (should be one line).

Day 2

Topics:

Treespace/NP-nasty

History

Distance

Parsimony

Long branch attraction

Slides: pdf, keynote, mov (QuickTime movie)
R assignment: Plot the number of trees vs the number of taxa.
Here is the second assignment. Note that http://cran.r-project.org/doc/contrib/Paradis-rdebuts_en.pdf is a very readable tutorial you may want to download (written by the same guy who wrote the phylogenetic package ape). The homework is due by start of class on Friday.

1. Fire up R. Input library(phangorn) to load the Phangorn package (who gets the geeky reference? Why the F->Ph transition? Get used to this sort of thing). If this gives you an error, try installing it — install.packages(“phangorn”)
2. Create a plain text file (no formatting: .txt rather than .rdf) called treespace.R. We’re going to be typing our commands in this.
3. Go to http://cran.r-project.org/doc/manuals/R-intro.html
4. Read and understand sections 1.5, 1.7, 1.10, 2.1, 2.3, 2.8, 3.2, 12.1, 12.1.4, and 13 [the other bits are handy, too, but I want to minimize your workload].
5. Read the documentation for allTrees (just type ?allTrees ), plot (same way), and length .
6. Treespace is big, as we’ll learn on Friday. Let’s see how big. In your treespace.R file, include the following commands (don’t copy in “7. Don’t paste this…” or the lines after that into the file). Remember that anything after a # sign is ignored by R (it’s a comment). I’m also attaching this as a file in case the formatting is affected by emailing it.


library(phangorn) #to load the phangorn package
x<-c() #creates an empty x vector y<-c() #creates an empty y vector for (number_of_taxa in 3:8) { #this starts a loop: the first time through, variable number_of_taxa=3, the next time, it equals 4, then 5, etc. up to and including 8. print("now doing this number of taxa:") print(number_of_taxa) x[number_of_taxa-2]<-number_of_taxa #here we are sticking the number of taxa into vector x. x[1] is the first slot in that vector, x[2] is the second slot in that vector… (it expands if it is not that size already -- not all languages do that). Think about why we do number_of_taxa - 2 rather than number_of_taxa. #WAY TO STORE THE LENGTH OF THE OUTPUT FROM allTrees, WHICH IS THE NUMBER OF POSSIBLE TREES, FOR PLOTTING ON THE Y-AXIS } #PLOT THE NUMBER OF POSSIBLE TREES VERSUS THE NUMBER OF TAXA (DO A LOG SCALE FOR NUMBER OF TREES)

7. Don’t paste this or following lines into your file
8. Replace the #WAY… and #PLOT… comments with functioning R code. I’ve given you hints (why did I have you look at what the allTrees command does? what’s that y<-c() in the code for?). 9. Try running your code -- copy and paste into R, or on a Mac you can select all and then command+return to have it run (if you're editing the text within an R window), or you can use source("treespace.R") if you have set the working directory to the folder containing the file (?setwd or use an option in the menu). 10. Fix the errors, repeat 9 (see the joys of loops? -- "while (working==FALSE) { debug some more }"). 11. Send me your final figure (screenshot, pdf, etc.) and your treespace.R file. 12. Is the number of trees growing exponentially with the number of taxa? 13. Are you sure? BONUS (optional): How can you tell? 14. If you're still up for it (this part is optional, too), modify your code to look at all trees from 3 to 9 taxa rather than from 3 to 8. You'll need to be very patient. Why? Bang your head against this for awhile, then talk to your cohort-mates for help, and/or email me. A lot of programming issues, especially early on, are frustrating in the way these problems are (i.e., what function lets me count the number of trees? how do I stick things in a vector?), and it's salutary to try to work through them. There are generally several ways to solve each problem -- go for the one that works first. Later you can tweak with speed, memory usage, code beauty (yes, really), etc. There are a few mailing lists for help with R, and help with R for phylogenetics, but [most of you] are too new to R to start posting there.

Day 3

Topics:

Models

Model selection

Bayes/Likelihood

R code for animation to make image

Slides: pdf, keynote, mov (QuickTime movie)

R assignment: Do your own tree search

The next assignment should be pretty fun. You are going to write a heuristic search algorithm for getting the maximum parsimony tree in R after downloading a set of GenBank sequences, also within R. I’ve sketched out a lot of the code — the main tricky bit should be figuring out how to store the best tree as you go and learning how to use an if() function. Comments in ALL CAPS are the sections you should focus on for changing. You’re encouraged to play with this assignment: maybe you want to plot the scores as you search, maybe you want to try different search strategies, etc. Feel free to email me for help or talk to your cohort-mates (remember you can use the blackboard forum, too). R code below and attached.

And just think: on Monday, many of you had never coded before. Now, you’re able to create a phylogenetic search program and pull things from an online database!

Brian

library(phangorn)

accessionNumbers <- c("U15717", "U15718", "U15719", "U15720", "U15721", "U15722", "U15723", "U15724") #These come from a paper by Paradis (1997) on Tanagers #USE THE read.GenBank command TO DOWNLOAD THESE SEQUENCES FROM GENBANK AND PUT THEM IN AN OBJECT CALLED sequences. #Note that it's read.GenBank, not read.Genbank, read.genbank, readGenBank, etc. Programming is usually very case-sensitive distanceMatrix<-dist.dna(sequences) #get a distance matrix print(distanceMatrix) convertedSeqs<-phyDat(sequences) #convert to a format useful for phangorn treeBad<-upgma(distanceMatrix) #the UPGMA starting tree actually is not that bad (and a NJ tree is the same as the maximum parsimony tree). So let's make it challenging by giving you a bad starting tree (for larger data sets, you would not have this "problem" of a starting tree that is too good) #note how to get the parsimony score of a tree (use convertedSeqs, not sequences) while(parsimony(treeBad,convertedSeqs)<220) { treeBad<-rNNI(treeBad) } maximumTries<-50 #GET SCORE OF STARTING TREE, treeBad #STORE THE CURRENT BEST TREE, WHICH IS treeBad #PRINT THE STARTING SCORE for (tryNumber in 1:maximumTries) { #GET A NEW TREE BY DOING newTree<-rNNI( __SOMETHING__ ) #COMPARE THE SCORE OF THE NEW TREE TO THE OLD TREE #USE AN IF BLOCK (if (new #INFO ON IF() IS AT http://cran.r-project.org/doc/manuals/R-intro.html#Conditional-execution #HERE IS AN EXAMPLE BLOCK if (1<2) { print("one is less than 2") } #PERHAPS MORE THINGS AFTER THE IF BLOCK } #PRINT THE FINAL SCORE #PLOT THE FINAL TREE #BONUS: THINK OF A WAY TO DO AN EXHAUSTIVE SEARCH USING THE allTrees COMMAND. WILL THIS WORK FOR MANY MORE TAXA?

Day 4

Topics:

Bootstrap

Consensus

Clocking

Slides: pdf, keynote, mov (QuickTime movie)

Day 5

Topics:

Supertrees & Supermatrices

Gene tree species tree

Where to find trees

Slides: pdf, keynote, mov (QuickTime movie)

Grad Core Phylogenetics 2009

Syllabus Fall 2009:

Day 1 (W. Sept. 30, 50 minutes)

Lecture1.pdf

Readings: Gregory 2008, Crisp and Cook 2005

Topics:

What trees are used for

history of life + cool discoveries about topology

Tree terminology

clades (dinos birds, reptiles, fish)

sister groups, crown/stem, etc.

rank and its importance

homology

Day 2 (F. Oct. 2, 50 minutes)

Lecture2.pdf

Readings: Felsenstein 1978.

Topics:

Treespace/NP-nasty

History

Distance

Parsimony

Long branch attraction

Day 3 (M. Oct. 5, 2 hr)

Lecture3.pdf

Readings: Huelsenbeck et al. 2002

Topics:

Models

Model selection

Bayes/Likelihood

Sample analysis walkthrough (genbank, alignment, tree search, sketch of posttree analysis)

Day 4 (W. Oct. 7, 50 minutes)

Lecture4.pdf

Readings: none.

Topics:

Bootstrap

Clocking

Day 5 (F. Oct. 9, 50 minutes)

Lecture5.pdf

Readings: Edwards 2009, Hugall et al. 2007

Topics:

Supertrees

Supermatrices

Gene tree species tree