Evolutionary Quantitative Genetics 2015

This will be my third year teaching in this course, organized by Steve Arnold and Joe Felsenstein. I am teaching about Brownian motion, Bayesian vs likelihood, and Ornstein-Uhlenbeck processes. Please see the ECQ2015 site for more information. Thanks to NIMBioS and American Society of Naturalists for funding.

Teaching overview

I teach a variety of classes: usually a portion of the Graduate Core course (phylogenetics), a mandatory course for all graduate students; a 400-level (upper level undergrads and beginning grad students) course on macroevolution; introductory biology (Biodiversity: Bio150); and a variety of smaller graduate seminars. My usual teaching load is Macroevolution every fall, Core every fall, Biodiversity every other spring, and usually a graduate seminar or two (often phyloseminar) per semester. In 2015-16, I’ll be stepping back from teaching Core to start a new, intensive graduate class on phylogenetic methods.
You can check the links above for updates to the courses, but an even easier way is to subscribe to an RSS feed. This is a way websites can let readers know when a new post is available; a popular free app for receiving these updates (on the web, iOS, or Android) is feedly, but there are many others, and some web browsers (Explorer, the newest Safari, Firefox, but not Chrome) also support this.

I am always eager to get feedback on teaching: please do that at
http://www.brianomeara.info/teaching/feedback

Macroevolution / Biodiversity videos removed

I typically record videos of all my lectures and post them to YouTube. In my lectures, I may include a video clip or two available on YouTube, often from the BBC or a similar source of high quality videos. I make sure to credit these appropriately, and of course they’re being used as short clips, educationally, with no ads or other commercial benefit to me. However, the BBC has lately been quite vigorous in scrubbing YouTube of any of my lectures with their content. I believe my use of their videos falls under “Fair Use”, but I am not a lawyer, and I don’t want to take the time to go through each of my lectures and scrub them of any video content or contest the BBC’s claims. In any case, it is validly their content. I am thus turning all my videos from Macroevolution and Biodiversity “private”: I can review them later to see what worked or didn’t in class, but they are no longer available for anyone else to see. However, this is not a great loss: I have been surprised that in a class of ~200 students, most videos have 8 or fewer views, even on days where there were many students absent. I am keeping online my other videos, and will be creating more content for the Spring 2016 PhyloMeth class (which will be taught as a flipped class, with content available to everyone).

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.

Feedback

This is an anonymous feedback form (not even IP address is tracked).

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)