Teaching

Evolution of animal development

EVE 150

Instructor: Artyom Kopp

Animals show an astonishing variety of body plans, life histories, morphologies and decorations. Yet all of them have evolved from a single common ancestor. How did this happen? What is the molecular basis of animal diversity? How do new structures and organs evolve, and how do old ones acquire new functions? Are there any unifying principles? The answers to these and other questions lie at the interface between developmental biology and evolution.
In this class, we explore the burgeoning field of evolutionary developmental biology, with emphasis on the most recent research and ideas. Topics will include an introduction to animal diversity and phylogeny; principles of comparative analysis; overview of developmental mechanisms in different animal phyla; genetic control of development; conservation and evolution of developmental pathways; evolution of gene regulation and function; the origin of evolutionary novelties; convergent evolution; genetic basis of phenotypic diversification; polyphenism and ecological impact of developmental variation, and many others.

Who is this class for?
This course may give a new perspective to students whose main interests are in either molecular biology or evolution. It is open to graduate students and advanced undergraduates with some background in developmental biology or molecular genetics.

Class format and schedule.
In Winter 2007, we will meet Tuesdays and Thursdays 9:00 – 10:20 am in Wellman Hall, Room 1. There will be no midterm exam; instead, there will be at least two homework assignments. There will be no lecture on March 8 – homework will be assigned instead. Classes will be about 75% lecture : 25% discussion. Original scientific papers will be assigned every week, and will form the basis of our discussions. If you have no desire to read a bunch of papers, you will probably not enjoy this class very much.

Grading.
Your grades will be based on homeworks, the final exam, and discussions. If you do well on the exam and homeworks, you will get a B or B+. To get an A, you’ll need to LEAD a discussion of an original scientific article. I’ll lead the first two papers (Lectures 2 and 4) to illustrate what it looks like. You have until the 4th lecture to decide whether you want to give it a try. In the meantime, take a look at the course outline and see which theme interests you the most. If we get more volunteers than papers, you will do your presentations in teams.

Preparing to lead paper discussion.
Once you choose your theme, I will give you a paper to read. Read it as soon as you can. We will then meet one week before you are due to lead the discussion to go over the paper. I will answer any questions you have, and give you some questions to think about and suggestions for organizing the discussion. Other than that – it’s your show!

Suggested books.
We do not have a textbook for this class – it is based entirely on original literature. But here are some books you might enjoy. The one by Carroll is the most accessible.
Carroll et al., 2001. From DNA to diversity: molecular genetics and the evolution of animal design. Blackwell Science, Oxford ; Malden, Mass.
Wilkins, 2002. The evolution of developmental pathways. Sinauer Associates, Sunderland, Mass.
Raff, 1996. The shape of life. The University of Chicago Press.
Arthur, 1997. The origin of animal body plans. Cambridge University Press.
Davidson, 2001. Genomic regulatory circuits.

Course outline.

Lecture 1. Principles of comparative analysis.
    - How can infer the past from the present?
    - How do we build and interpret phylogenetic trees?
    - How can we use these trees to reconstruct evolution?
Lecture slides

Lecture 2. A brief history of animals.
    - When and how did multicellular animals first appear?
    - How can we combine fossil evidence with analysis of molecular evolution?
    - What ecological signatures did animals leave in the fossil record?
Lecture slides
Papers
    Peterson and Butterfield 2005        (required – discussion paper)

Lecture 3. The toolkit of animal development.
    - How do cells in animal bodies know where they are, and what to do about it?
    - How can you generate many cell types with relatively few genes?
    - What are transcription factors and signaling pathways, and how do they work?
Lecture slides

Lecture 4. Life histories and modes of development.
    - How much does a single cell know, and how does it learn it?
    - Why do some animals have larvae, while others develop straight into adults?
    - What can different developmental mechanisms tell us about animal origin?
Lecture slides
Papers
    Rouse 2000            (required – discussion paper)
    Peterson et al 1997        (optional)

Lecture 5. A case study: HOX genes and animal body plans.
    - How does the HOX cluster make a blueprint for the whole animal?
    - Can different body plans share the same basic blueprint?
- What happens if you need to make a totally different blueprint?
Lecture slides
Papers
    Averof and Patel 1997    (optional)

Lecture 6. Conservation and change at the molecular level.
    - How can the same genes control development in worms, flies, and humans?
    - Are homologous organs controlled by homologous genes?
    - Do homologous genes function in homologous developmental pathways?
Lecture slides
Papers
    Wray and Abouheif 1998    (required)
    Prud’homme et al 2003    (required – discussion paper)

Lecture 7. Evolution of developmental pathways.
    - How are developmental pathways re-wired during evolution?
    - Is there more that one way to make the same morphology?
    - Can development diverge without any effect on adult appearance?
Lecture slides
Papers
    Schroeder 2003    (optional)

Lecture 8. Molecular basis of morphological diversity.
    - How can organs be different, yet still essentially the same?
    - How do you tweak adult morphology by tweaking gene expression?
    - Why do we have so many different kinds of teeth?
Lecture slides
Papers
    Jernvall et al 2000        (required – discussion paper)
    Salazar and Jernvall 2002    (recommended – discussion paper)
    Jernvall and Thesleff 2000    (optional)
    Presenter: Joseph Huang

Lecture 9. Modularity, dissociation and co-option.
    - How do animals assemble complex organs from simple parts?
    - Can you teach an old gene new tricks?
    - If you have a working developmental pathway, why not re-use it?
Lecture slides
Papers
    Duboule and Wilkins 1998        (optional)
    Keys et al 1999            (optional)

Lecture 10. Radical events in evolution.
    - How much genetic change do you need to make drastic changes in adult form?
    - What kinds of genes are responsible for these changes?
    - What happens to homologous genes when homologous organs disappear?
Lecture slides
Papers
    Zhurov et al 2004        (required - discussion paper)
    Grbic 2000            (optional)
    Presenters: Jasmin Camacho and Ellen Nordman

Lecture 11. The origin of evolutionary novelties.
    - How can you evolve a new organ?
    - Do you need new genes to get a new morphological structure?
    - Is there anything truly new, anyway???
Lecture slides
Papers
    Averof and Cohen 1997        (required – discussion paper)
    Damen et al 2002            (recommended – discussion paper)
    Shubin et al 1997            (optional)
    Presenter: Daniel Neudorf

Lecture 12. Reconstructing extinct ancestors.
    - What did extinct animals look like, and how did they develop?
    - What features of development do all animal have in common – and why?
    - How can we distinguish homology from chance resemblance?
Lecture slides
Papers
    Lowe et al 2006         (required – discussion paper)
    Gerhart 2000            (optional)
    Dunn et al 2007        (optional)
    Presenters: Sarah Signor and Brian Turner

Lecture 13. Evolution of sex.
    - How does an animal know if it’s male or female?
    - Why does sex determination evolve at all – and why so rapidly?
    - Can you change sex determination mechanism without changing sex?
Lecture slides
Papers
    Haag and Doty 2005            (optional)

Lecture 14. Convergent evolution.
    - Why do you see similar changes in different evolutionary lineages?
    - Are similar traits controlled by the same genes?
    - Is natural selection constrained by fundamental features of development?
Lecture slides
Papers
    Prud’homme et al 2006        (required – discussion paper)
    Gompel et al 2005            (optional)
    Parra-Olea and Wake 2001        (optional)
    Presenters: Stephen Medland, Stephanie Nehasil, and Kirstin Jorgenson

Lecture 15. Evolution of gene regulation.
    - Why do regulatory changes play such an important role in evolution?
    - How does gene regulation evolve?
    - How can different regulatory sequences have the same function?
Lecture slides
Papers
    Ludwig et al 2005            (required – discussion paper)
    Marcellini and Simpson 2006        (optional)
    Presenter: Luca Venturini

Lecture 16. The origin of new genes and gene functions.
    - OK, so proteins do change their functions sometimes – how do they do that?
    - Where do new genes come from?
    - What is the role of gene duplications in evolution?
Lecture slides
Papers
    Tvrdik and Capecchi 2006        (required – discussion paper)
    Greer et al 2000            (optional)
    Presenters: Katherine Szulewski and Jennifer Dang

Lecture 17. Evolution of development among close relatives.
    - Does development evolve on microevolutionary timescales?
    - How can we use recent divergence of species to our advantage?
    - How many genes are involved in differentiating sister species?
Lecture slides
Papers
    Balhoff and Wray 2005        (optional)
    Shapiro et al 2004            (optional)
    Wang and Chamberlin 2004        (optional)
    Need presenter

Lecture 18. Developmental drift, polyphenisms and ecological developmental biology.
    - Why are different species reproductively isolated?
    - Can development vary within species – and even in the same genotype?
    - How does development interact with the outside world?
Lecture slides
Papers
    Skaer and Simpson 2000        (optional)
    Abouheif and Wray 2002        (optional)
Need presenter

Lecture 19 – To be decided.
    - I am leaving an extra lecture in reserve for “overflow”, catching-up, or review.

Homework 1
Homework assignment
Dale and Pourquie 2000
Guidicelli and Lewis 2004
Pourquie 2003
Schoppmeier and Damen 2005
Stollewerk et al 2003