Macroevolution 2015 syllabus

Here’s the syllabus for EEB464 Macroevolution this year. I have it here in HTML as well as .docx and .pdf. Course announcements will come through the official BlackBoard site but materials will appear here, where they are available to all.


 

EEB 464 Macroevolution Fall 2015

Instructor: Dr. Brian C. O’Meara

Office hrs: 1:30-2:30 M and by appointment; 446 Hesler

Meeting time: 10:10-11:00 MWF, 488 Dabney

Description:

The course is a lecture format course with classroom discussion and participation. Students are introduced to fundamental concepts in macroevolution including current areas of debate (drivers of evolutionary rates, modes of speciation, etc.) and taught to think critically. Computer-based exercises, especially simulations, will allow students to learn how processes acting on short to medium time scales affect long term patterns. 3 credits

 

To understand macroevolution, it is important to learn about who, what, where, when, how, and why.

 

Who: Organisms

What: Non-living context (rocks from space, environmental conditions)

Where: Biogeography (on Pangaea or Bermuda?)

When: Geological time scale

How: Pattern of evolution

Why: Process of evolution

 

The course will cover all these areas. The ones that are most interesting, of course, are the how and especially the why. These are also the best to cover in class, where there can be discussion and other interaction. Rote learning (word meanings and the like) is something that you should be able to do on your own at this point in your education, with occasional guidance. We’re not going to use much class time on this, but you will have to learn this info. I will clearly describe what you do have to learn (and if it’s not clear, ASK), and quizzes and tests will be ways to evaluate your progress and provide further incentive to learn.

 

Biology program learning objectives:

I include how this course addresses these in italics.

Explain and provide examples of each the five big ideas in Biology, using their knowledge of biological concepts gained from their course of study:

  • Evolution: Populations of organisms and their cellular components have changed over time through both selective and non-selective evolutionary processes. This is the main point of the course, and will be covered in every lecture and activity.
  • Structure and Function: All living systems (organisms, ecosystems, etc.) are made of structural components whose arrangement determines the function of the systems. This will be highlighted especially in the discussions of morphological evolution (flight, insects, etc.)
  • Information Flow and Storage: Information (DNA, for example) and signals are used and exchanged within and among organisms to direct their functioning. Origin of life will cover this extensively.
  • Transformations of Energy and Matter: All living things acquire, use, and release and cycle matter and energy for cellular / organismal functioning. The discussion of escalation focuses on this, and it comes up in background on the focal organisms.
  • Systems: Living systems are interconnected, and they interact and influence each other on multiple levels. Speciation, extinction, discussion, and history of life all cover this.

Demonstrate the ability to perform the following scientific practices:

  • Formulate empirically-testable hypotheses. This is the point of the final presentation.
  • Interpret visual representations (figures and diagrams). These will come up throughout the class, especially in the context of phylogenetic trees.
  • Evaluate data and come to a conclusion (with evidence) (formulate an argument). Much of class discussion emphasizes this skill: I’ll present information and have you elaborate on this and provide potential explanations.

 

Course learning objectives:

By the end of this course, students will be able to:

  • Formulate, defend, and critically evaluate hypotheses about evolutionary mechanisms
  • Understand the context and reason for evolutionary patterns
  • Interpret information from fossils, phylogenies, and other data sources
  • Generate ideas for feasible, compelling scientific projects

 

To really understand evolution and converse with other scientists, you have to know the names of some groups (imagine trying to talk about the history of some musical genre without knowing the names of any musicians or songs in that genre). Thus, most days, you will be responsible for learning about a particular taxon (on the syllabus, below). This could be a single species or a clade of many species. You should learn very basic info: what is it, what is it related to (i.e., where it attaches to the tree of life we will grow over the class), why it is important to know. For example: “Angiosperms: all flowering plants, lots of species, became common in the Cretaceous but may have originated earlier, sister to Gnetales.” Working together on the website forum to get this info is encouraged (you can decide to rotate the job, let whoever gets the info first post it, etc.). What I really care about is that you learn it. Note that some of the taxa may be subsets of the other taxa (elephants are a kind of vertebrate).

Writing and presentations will be graded on a variety of levels, such as grammar, structure, and substance. The purpose of grading and comments is to improve your writing. Remember that your writing is being graded, not you.

Word count sets a minimum length (and references are not counted) but you may go a bit longer if needed (try to keep below 125% of required length). Since length is judged by words, not page length, please don’t do any odd formatting of your paper (huge or tiny margins, font sizes of 8 or 18, etc.) to try to meet some page limits.

Papers/midterms will be turned in via Online@UT. This eliminates issues with printers, odd file formats, and the like. The site will automatically check your work for possible plagiarism. I do this in all my classes with written work. Except where noted, assignments are to be done individually. You must cite and reference work properly. When in doubt about citation, plagiarism, or collaboration, ASK. Please turn in work as plain text or RDF. This makes it easier for me to put them in one document so I can give you back grades with comments.

For help with submitting documents online, see http://online.utk.edu/students/assignment.shtml. There is a practice uploading assignment that will allow you to test to make sure you can upload files correctly before the pressure of a deadline. If there is a problem at the moment of a deadline, email me your work instead to verify it is done on time (but normally you should be using BlackBoard).

 

We will be using laptops for some work in class. If you see the laptop cart in the classroom, take a laptop. When class is done, please return them to the cart and plug them in. Take care of them when you are using them. Some of our work will use the statistical analysis package R (http://www.r-project.org/). It is free and work on Mac, Linux, and Windows. For some class activities (announced beforehand) it will be convenient to bring a laptop. If you do not have one, groups can pair up. If you wish to prepare your laptop beforehand, install R on your computer. Then, within R:

 

install.packages(“ctv”)

library(ctv)

install.views(“Phylogenetics”)

 

(you can do this with the graphical user interface as well).

 

Communication is very important. I have set up a forum on the BlackBoard site (Online@UT) for our course. If you post a question there, I will immediately be emailed about it and will respond on the forum (though perhaps not immediately). Emailing me directly will not be any faster (though do email me if the issue is better addressed one-on-one). The benefit of using the forum is that everyone can see the answers and there’s a chance that one of the other students will answer the question first. Feel free to use the forum for other class-related discussions.

 

Though we have the main BlackBoard site, and notices will come through there, I will also be posting things (like slides) to http://brianomeara.info/category/macroevolution/ . Why a second site? The BlackBoard site is only active during the course and only to students enrolled in the course. You might want to look at the materials in other semesters, show your friends/family what you were learning, etc., so I have the public site that will persist.

 

Attendance is expected at all classes, though missing a class or two due to illness, family problem, etc. might happen (and is strongly suggested in the case of flu: http://studenthealth.utk.edu/common_avoidflu.php )

 

We will have discussions in nearly all classes. You should participate in them. Sometimes, discussions in a class such as this consist of students trying to return the right answer to the instructor’s question. To avoid this, sometimes I pursue a policy of not talking during a discussion for several minutes or longer so you have to talk to each other. This can result in complete silence. If you find this annoying, talk! Even if there is not a formal discussion, please ask questions at any point during class.

 

We will be using Turning Point clickers in this class. Many of you will already have them from UT. They cost about $50 at the bookstore and can be used throughout your remaining career here. Note that you while you cannot use someone else’s from this class, you should be able to borrow a friend’s who is not in this class (as long as you use that same one consistently). See the Blackboard site for more on how to use clickers. Our class is now large enough that keeping track of participation manually is infeasible. I would like everyone to have a clicker by Aug 31.

 

Late work is penalized at 10%/day (so something turned in 49 hours late is given a score 70% of what it would have received on the due date). Extensions are not normally granted, except under extraordinary circumstances (having too much work to do does not qualify, for example). Remember that even if you turn something in seven days late, it is still worth more points than not turning it in at all (and the grading for the class is just #points received / #points available, so something getting 20/100 points is still worth twice something getting 10/100 points, even though they are both an “F” individually).

 

My goal is to have you learn. If you are having trouble with something in the course, or if there is a topic you just have to learn more about, let me know (email, office hours, online forum, etc.). Faculty often use evaluations at the end of the semester to get info from students so we can improve before the next class, but this does not help you directly. To allow the class to improve while you are taking it, I have created a site for anonymous feedback at http://brianomeara.info/teaching/feedback/ (and yes, it is really anonymous). Let me know things that are going well or poorly — both are important. I might not implement all your suggestions, but they will all be read and considered, generally the same day you submit them.

 

Any student who feels s/he may need an accommodation based on the impact of a disability should contact me privately to discuss specific needs. Please contact the Office of Disability Services at 865-974-6087 in Dunford Hall to coordinate reasonable accommodations for students with documented disabilities.

 

All relevant University policies (including, but not limited to, policies on academic integrity, attendance, etc.) apply to this course. In the case of any conflict between the policies in this syllabus and University policy, University policy applies. The instructor reserves the right to revise, alter, and/or amend this syllabus as necessary. Students will be notified by email of any such revisions, alterations, and/or amendments.

 

 

 

# Date Topic Taxon to have learned Assignment
19-Aug Pre-test, syllabus
1 21-Aug History of planet & life Crinoid
2 24-Aug History of planet & life Archaea
3 26-Aug Evidence Bdelloid rotifers
4 28-Aug Taphonomy Trilobite
5 31-Aug Jargon Acromyrmex
6 2-Sep Phylogenetics Ammonite
7 4-Sep Empirical distributions Ichthyornis dispar
7-Sep Labor Day
8 9-Sep Biogeography HIV
9 11-Sep Speciation Wolbachia
10 14-Sep Speciation Anomalocaris
11 16-Sep Extinction Gasterosteus aculeatus
12 18-Sep Extinction Geospizinae Paper due at 8 pm
13 21-Sep Diversification Dionaea muscipula
14 23-Sep Diversification Tribolium
15 25-Sep Natural selection & drift bonobo
16 28-Sep Sex Lichen
17 30-Sep Trends Fig wasp
18 2-Oct Symbiosis Anolis Midterm distributed
19 5-Oct Game theory Tunicates
20 7-Oct Inclusive fitness Brachiopod
21 9-Oct Systematics Spiny anteater
22 12-Oct Darwin Eubacteria Midterm due at 8 pm
23 14-Oct Escalation Maiasaura
16-Oct Fall break
24 19-Oct Flight Isopod
25 21-Oct Dominance Riftia pachyptila
26 23-Oct Invasive humans Ground sloth
27 26-Oct Disease evolution Thermus aquaticus
28 28-Oct Origin of life Lycophytes
29 30-Oct Contemporary evolution Strepsiptera
30 2-Nov Insects Diatom
31 4-Nov Stephen Jay Gould Dimetrodon
32 6-Nov Language evolution Buchnera
33 9-Nov Discoveries from past month Welwitschia
34 11-Nov Evolution of intelligence Ginkgo
35 13-Nov Free topic 1 silversword
36 16-Nov Free topic 2 orca
37 18-Nov Free topic 3 Cordyceps
38 20-Nov Presentations Presentation
39 23-Nov Presentations Presentation
40 25-Nov Presentations Presentation
27-Nov Thanksgiving break
41 30-Nov Review
4-Dec Final exam 8 – 10 am Sorry.

UTK_2015_Fall_EEB464_SyllabusV01.pdfGrading:

100 points: Topic review. 1000 words, including references. Cover a macroevolutionary question: what is known about it, what is the state of work on it, what work might be done in the future? Work should be individual.

100 points: Pair presentation. Imagine you are trying to get money to study a macroevolutionary question. You have to make a compelling case to a potential funder (i.e., the NSF will give you $15K to study it, or a professor might offer you a place in her lab to work on this). You should include 1) why that question is interesting (this should include what is known about it), 2) how you plan to address it, 3) what potential outcomes of your work may be, and 4) the implications of these. 10 minute talk (PowerPoint, Keynote, PDF, etc.). Be sure to include references in your slides.

150 points: Class work. This includes clicker questions (many of which have points regardless of the answer), quizzes, and other in class assignments. In general, these will not be announced in advance. Note that 180 points will actually be assigned but the maximum score possible will be 150 points. The goal of this is to allow you to miss some classes (due to illness, death in the family, or other such reasons) without needing to bring a note justifying your absence.

100 points: Take home midterm. You may NOT work with classmates or other humans, but you can use notes, books, papers, etc. (though do not plagiarize them, not that the questions will be ones you can typically plagiarize).

200 points: Final exam. Similar to the midterm, but with a bit more evaluation of rote knowledge.

In addition to these assignments, students will periodically be given articles to read for later discussion. Clicker questions or quizzes will assess whether the articles have been read.

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.

  • Macroevolution feed-icon-14x14
  • Phyloseminar feed-icon-14x14
  • Biodiversity feed-icon-14x14

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.

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