Macroevolution 2014

Macroevolution (EEB464, 2014)

Syllabus PDF

Slides

  • Lecture 1: History of Life, part 1: PDF
  • Lecture 2: History of Life, part 2: PDF
  • Lecture 3: Evidence: PDF
  • Lecture 4: Taphonomy: PDF
  • Lecture 5: Jargon: PDF
  • Lecture 6: Phylogenetics: PDF
  • Lecture 7: Empirical distributions: PDF
  • Lecture 8: Biogeography: PDF
  • Lecture 9: Speciation1: PDF
  • Lecture 10: Speciation2: PDF
  • Lecture 11: Extinction1: PDF
  • Lecture 12: Extinction2: PDF
  • Lecture 13: Diversification: PDF
  • Lecture 14: Diversification2: PDF
  • Lecture 15: Natural Selection: PDF. mutationSelection.R. Do this on your local installation of R (download here) or use the online implementations of R at http://pbil.univ-lyon1.fr/Rweb/ or http://www.unt.edu/rss/Rinterface.htm
  • Lecture 16: Sex: PDF
  • Lecture 17: Trends: PDF
  • Lecture 18: Symbiosis: PDF
  • Lecture 19: Game theory: PDF
  • Lecture 20: Inclusive fitness: PDF
  • Lecture 21: Systematics: PDF
  • Lecture 22: Darwin: PDF
  • Lecture 23 & 24: Escalation: PDF
  • Lecture 25: Flight: PDF
  • Lecture 26: Dominance: PDF
  • Lecture 27: Invasive humans: PDF
  • Lecture 28: Disease evolution: PDF
  • Lecture 29: Origin of life: PDF
  • Lecture 30: Contemporary evolution: PDF
  • Lecture 31: Insects: PDF
  • Lecture 32: Stephen Jay Gould: PDF
  • Lecture 33: Language evolution: PDF
  • Lecture 34: Evolution of intelligence: PDF
  • Lecture 35: Marsupials: PDF

Study guide for final
Some sample questions for the essay portion of the final:

Study guide/possible exam questions for EEB464 Macroevolution. This focuses on the essay type questions for the exam.

Why may life have been single celled for a long time?

Describe a major event (such as a mass extinction, colonization of land, etc.) and its subsequent effects.

How do we learn about organisms with no living descendants, such as trilobites? How would living descendants affect how we can learn about them?

Can behavior be fossilized? If so, give two examples.

How can something become a fossil?

How has continental drift affected the location of organisms?

Why don’t barracuda eat cleaner wrasse?

Why bother making phylogenies?

What is a phylogeny?

Can species be treated as independent data points in a statistical analysis? Why or why not?

How can movement of land lead to speciation?

What was the Great Faunal Interchange?

Describe island biogeography. Why is it relevant to this class?

Contrast pre and postzygotic mating barriers

What are Dobzhansky-Muller Incompatibilities?

Compare allopatric and sympatric speciation.

How might hybrids have greater fitness than their parents?

Explain the importance of Wolbachia.

Describe the cause of a contemporary group of extinctions.

Give an example of a biological trait that may increase extinction risk. Why might it?

How could phylogenetic diversity be useful for conservation?

Describe a simple model for species diversification.

Compare and contrast speciation rate and diversification rate.

How may trait transitions and diversification rates together affect evolution of a group?

Which requirement for natural selection is most important? Why?

What, in the context of this class, is an advantage of sexual reproduction?

Describe Muller’s ratchet

Describe one mechanism of sexual selection.

What is Cope’s rule? Why might it be true?

Contrast what a passive and an active trend mean.

How would you detect evidence of a trend?

Contrast mutualism with parasitism. How can one change into the other?

Give an example of a commensalism.

Define what is an evolutionarily stable strategy?

Why is “the good of the species” a problematic concept?

Why might a prey item call out to a predator?

What is inclusive fitness?

What is Hamilton’s rule?

Give a behavior the idea of inclusive fitness could explain.

Why can it be empirically difficult to know if two populations are the same or different species?

Relate Darwin’s work on reefs to his work on evolution.

What are some potential reasons that gliding evolves much more often than flight?

What evidence links humans to some megafaunal extinctions?

Pasteur showed life does not spontaneously appear. Biologists believe life originally spontaneously appeared. Reconcile these views.

Use insects as an example of a macroevolutionary process.

What may explain evolution of intelligence?

What factors affect evolution of virulence in diseases?

How would you test the idea of punctuated equilibrium?

Have marsupials converged on placental mammals more than you’d expect under a null model? Why or why not?

Has development of agriculture and modern medicine stopped human evolution via natural selection? Provide evidence.


Don’t forget the anonymous feedback form

Grad Core Phylogenetics 2014

UTK EEB requires new graduate students to take an intensive team-taught course covering ecology and evolution. I present the phylogenetics portion (tree creation and tree use).

Note the anonymous feedback form: Suggest changes while it can still help you in class.

Fall 2014:

This year I am teaching the entire phylogenetics portion. Here is the syllabus (PDF) and lectures are below; the recorded videos are here.

  1. Intro to phylo (PDF), R exercise
  2. Likelihood, Bayes, model selection, bootstrap. (PDF), R exercise, R exercise answers Background reading: Lewis 2001
  3. Ingredients for phylogenetic methods. PDF. Background reading: O’Meara 2012
  4. DNA models, heterogeneity, alignment (PDF). Mesquite, Tracy Heath’s Beast Tutorial
  5. Continuous traits and tree stretching (PDF). R script
  6. Gene tree incongruence. Background reading: Maddison 1997 PDFQuiz
  7. Species, speciation, taxonomy PDF
  8. Diversification PDF

Study Guide
I had three main goals in this section: making sure you know what sort of questions you can address using phylogenies, having some idea of what methods are available (or close to being available, with a little work) to answer these questions, and having the basic understanding to read and know how to build a tree.

Things you won’t have to know: the difference between gamma and kappa, the equation for multivariate normal, authors behind methods, or similar specifics that you’ll forget again in a month. What I do want you to know:

  • How are trees made?
  • Why are trees made?
  • Compare and contrast a phylogram and a chronogram.
  • Given a tree, answer questions about its topology or other features (i.e., what’s the closest relative to X on the tree?).
  • Compare and contrast bootstrapping and Bayesian approaches for understanding uncertainty.
  • What is a continuous time Markov chain with a finite state space?
  • Why do we care about the above?
  • How are models for DNA related to models for a binary morphological trait?
  • Connect the central limit theorem to the multivariate normal. Why does this make sense for an evolutionary model?
  • What is independent contrasts? When would you use this?
  • What are ways to deal with heterogeneity of processes on a tree? Why is this important?
  • What is tree stretching? What questions does this let you ask?
  • What are sister group comparisons used for?
  • What is the difference between Bayesian and likelihood approaches?
  • Compare and contrast hypothesis testing, model selection, and parameter estimation.
  • What are some approaches to understanding diversification?
  • Why are there methods for jointly looking at diversification and trait evolution?
  • Given a certain biological question, I may ask you what sort of approach you would take to it. The various empirical examples should help with this.

Note that this is the content I want you to know, but not necessarily the questions. There would not be time for these to be essay questions, so I will ask for some of this information in short answer questions and just a few essays.

Macroevolution 2012

Macroevolution (EEB464, 2012)

Syllabus PDF

Lecture slides (PDF)

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.

Here are some scripts for teaching:

genetreesim.R
NidWar

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