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BIOL 443

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Evo-Devo: Evolution of Developmental Mechanisms

 

Spring 2014

BIOL 443 (3 credits)

Monday, Wednesday, Friday 12:20 – 1:10 PM

107 Wartik Lab

Schedule Number 251998

 

Instructor:

Dr. Heather Hines

Department of Biology

517 Mueller Hall

University Park, PA 16801 

Phone: 814-863-8830 

Email: hmh19@psu.edu

 

Office Hours: Wednesday 1:30 – 2:30 PM or by appointment

 

Description 

 

Evolution & Development (Evo-devo) is an interdisciplinary field that combines developmental biology, comparative genetics and genomics, and evolution to understand how organisms have attained diversity in form. While the field of developmental biology aims to understand how a given organism develops, evo-devo focuses on how genetic changes alter developmental mechanisms to impart the phenotypic variation observed across life. Course instruction involves a combination of lectures on major principles in this field and discussion of several case studies from the primary literature. 

 

Course Objectives

 

The goal of this course is to educate on the major underlying principles and themes that have emerged from the study of how developmental mechanisms evolve. Most broadly you will learn how body plans form, how their development varies across life, and the underlying genetic mechanisms in their formation and modification. Major take home points from this course will involve an understanding of the multiple levels of homology (morphological, developmental, genetic); how modularity in body form and gene regulation have enabled developmental evolution; how changing the timing (heterochrony), spatial distribution (heterotopy), extent (heterometry), and kinds (heterotypy) of gene expression results in diversity; how the environment can change developmental trajectories (eco-evo-devo); and how developmental processes have changed across the tree of life with examples from the first multicellular life to plants, vertebrates (including humans) and invertebrates. This course integrates concepts in evolution, development, and genetics providing a good supplemental, introductory, or all-encompassing course for those fields. Compared to development this course will cover less of the detailed aspects of how cells and pathways interact and more about how such processes are modified to create heritable variation. It will cover aspects of evolution pertinent to the modification of form and genetics from the prospective of gene regulation and gene interactions, the primary mechanisms responsible for evolutionary change. In addition to learning these materials, this course will provide experience with synthesizing the primary scientific literature through student presentations of research papers in symposia.

 

Course Outline

 

 

 

 

 

Chpt.

 

 

 

Introduction

 

1

1-13

M

Introduction to the Class

 

2

1-15

W

The History of Evo-Devo

 

3

1-17

F

The Diversity of Life and Key Innovations I

1

 

1-20

M

NO CLASS – Martin Luther King Day

 

4

1-22

W

The Diversity of Life and Key Innovations II

 

 

 

 

The Developmental Toolkit

 

5

1-24

F

Embryogenesis & the General Developmental Toolkit

2,3

6

1-27

M

Establishing Body Axes and Segmentation

 

7

1-29

W

Homeotic Mutants and Hox Genes

 

8

1-31

F

Building Parts: Selector Genes & Signaling Pathways

 

9

2-3

M

Vertebrate Body Plan

 

10

2-5

W

Symposium I

 

 

 

 

Genetic Regulation of Development

 

11

2-7

F

Gene Regulation

4

12

2-10

M

Gene Interactions & Networks

 

13

2-12

W

Cis- vs. Trans and Modular Regulation

8

14

2-14

F

Genome Diversification & The Origin of Complexity

 

15

2-17

M

Symposium II

 

16

2-19

W

Exam I

 

 

 

 

Creating Variation

 

17

2-21

F

Hox and Homeotic Gene Diversification across Life

5,5

18

2-24

M

Segmental Evolution in Arthropods

 

19

2-26

W

Evolution of Arthropod Appendages

 

20

2-28

F

Symposium III

 

21

3-3

M

Vertebrate Skeletal Evolution

 

22

3-5

W

Vertebrate Limb Diversity (& Loss)

 

23

3-7

F

Symposium IV

 

 

3-10

M

NO CLASS – SPRING BREAK

 

 

3-12

W

NO CLASS – SPRING BREAK

 

 

3-14

F

NO CLASS – SPRING BREAK

 

24

3-17

M

Evo-Devo of Plants

 

25

3-19

W

Evo-Devo of Plants

 

26

3-21

F

Symposium V

 

27

3-24

M

Mechanisms of Macroevolutionary Change I

 

28

3-26

W

Mechanisms of Macroevolutionary Change II

 

29

3-28

F

Mechanisms of Microevolutionary Change

 

30

3-31

M

Sexual Dimorphism

 

31

4-2

W

Symposium VI

 

32

4-4

F

Eco-Evo-Devo: Phenotypic Plasticity

 

33

4-7

M

Eco-Evo-Devo: Epigenetics

 

34

4-9

W

Symposium VII

 

35

4-11

F

Exam II

 

 

 

 

Evolution of Novelties & Case Studies

6,7

36

4-14

M

Wings

 

37

4-16

W

Color Pattern

 

38

4-18

F

Feathers, Hair, and other Projections

 

39

4-21

M

Symposium VIII

 

40

4-23

W

Eyes

 

41

4-25

F

Evo-Devo of Humans

 

42

4-28

M

Evo-Devo of Humans

 

43

4-30

W

Symposium IX

 

44

5-2

F

Final Review and Synthesis

 

 

 

Final Exam – Date and Location TBD

 


Textbook & Required Readings

 

From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design 2nd Ed., Sean Carroll, Jennifer Grenier, Scott Weatherbee, 2005

This textbook provides supplemental reading to the materials covered in class. However, lectures will not adhere that closely to the text. You are strongly encouraged to read the chapters that pertain to the lecture materials to ensure a grasp of the materials. Reading assignments that accompany the lectures are listed in the course outline above, are available on ANGEL (https://cms.psu.edu/default.asp), and will be mentioned in class.  Additional required readings beyond this textbook, either from the recommended texts below or the primary literature, will be provided in ANGEL and mentioned in class.

 

Recommended Textbooks 

Evolution: A Developmental Approach, Wallace Arthur, 2010

Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution, Scott Gilbert, David Epel, 2009

Developmental Biology, Scott Gilbert, 2013

Quirks of Human Anatomy: An Evo-Devo Look at the Human Body, Lewis Held Jr., 2009

Keywords and Concepts in Evolutionary Developmental Biology, Brian Hall, Wendy Olson, 2003 

These will provide supplemental and required readings for topics not covered in the Carroll book. 

 

 

Exams, Assignments and Grading

 

Percentage Breakdown by Activity:

Exam I: 25%

Exam II: 25%

Final Exam: 30%

Symposium Presentation: 10%

Participation: 10%

 

Grading Scale:

Final grades will be assigned based upon the following percentages:

A 94-100% A- 90-93

B+ 87-89 B 83-86 B- 80-82

C+ 76-79 C 70-75

D 60-69

F < 60

 

Exams – You will be tested on course material in three exams. Exams will include multiple choice, short answer, and critical thinking components and will include topics presented in lecture and papers covered in the symposia. The final exam will cover all course materials. Exam grades may be adjusted upwards if particularly challenging. 

 

Symposia – In 9 class periods throughout the semester we will hold symposia on recently covered lecture topics. In each symposium, 4-5 students will each give a presentation on a scientific research article. Each student will select a topic at the beginning of the course, identify a scientific paper of interest on that subject, and give a presentation on the contents of that paper (7 minutes long with 3 minutes for questions). The presentation should provide a general overview of the background, methods, results, and conclusions of the paper synthesized in the presenters own words. The goal is to excite the audience about the paper, emphasizing the take home points and what is particularly innovative about the work. The goal of this exercise is to expose students directly to research being done in evo-devo, to gain experience with reading and interpreting the scientific literature, and to gain experience presenting scientific work. All students in class will be required to provide feedback on the presentations, which will make up part of the participation grade.

 

Deadlines for Symposium – Your paper citation must be sent to me 1 week in advance of your symposium for approval and your presentation must be uploaded to ANGEL by 8AM the day of your presentation. If you miss either of these deadlines without an official excuse, your grade will be deducted by 10%. You will not be allowed to present if the presentation is not uploaded prior to class. 

 

Participation - Participation grades are based on participation in class discussions and activities. 5% of the grade will be based on the completion of peer evaluations for the symposium.

 

Missed Exams – If you miss an exam you must notify the instructor within 24 hours of the missed exam. The exam must be rescheduled and taken within one week of the original exam date. You must provide a legitimate and preferably documented excuse; please see  University policies on legitimate excuses for missed exams. (http://studentaffairs.psu.edu/familyservices/academics_support.shtml) If you miss an exam and do not have a legitimate excuse (for example, sleeping in or a social event), you will be allowed to take it within one week with a 30% automatic deduction. 

 

Additional Course Policies

To gain the most benefit from this course, you are asked to attend all of the lecture sessions and participate in group activities and discussion. Please plan to arrive a few minutes early and to remain until class is dismissed to avoid disrupting your classmates’ concentration. Please see the instructors if you’re struggling in this class, feel you could be doing better, or you’re not having fun.

 

Academic Integrity/Academic Dishonesty

Academic dishonesty is not limited to simply cheating on an exam or assignment.  The following is quoted from the "PSU Faculty Senate Policies for Students" regarding academic integrity and academic dishonesty (http://www.psu.edu/ufs/policies/47-00.html#49-20): “Academic integrity is the pursuit of scholarly activity in an open, honest and responsible manner. Academic integrity is a basic guiding principle for all academic activity at The Pennsylvania State University, and all members of the University community are expected to act in accordance with this principle. Consistent with this expectation, the University's Code of Conduct states that all students should act with personal integrity, respect other students' dignity, rights and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts. Academic integrity includes a commitment by all members of the University community not to engage in or tolerate acts of falsification, misrepresentation or deception. Such acts of dishonesty violate the fundamental ethical principles of the University community and compromise the worth of work completed by others.” All University and Departmental policies regarding academic integrity/academic dishonesty apply to this course and the students enrolled in this course.  Refer to further details on the academic integrity policies of the Eberly College of Science (http://www.science.psu.edu/academic/Integrity/Policy.htm .) You are responsible for ensuring that their work is consistent with Penn State's expectations about academic integrity.

 

Disability statement

Penn State welcomes students with disabilities into the University's educational programs. In order to receive consideration for reasonable accommodations, you must contact the appropriate disability services office at the campus where you are officially enrolled (http://equity.psu.edu/ods/dcl), participate in an intake interview, and provide documentation (http://equity.psu.edu/ods/guidelines.)  If the documentation supports your request for reasonable accommodations, your campus’s disability services office will provide you with an accommodation letter. Please share this letter with your instructors and discuss the accommodations with them as early in your courses as possible. 

 

Symposium Presentation Guidelines

 

Paper Selection – Scientific research papers should be chosen by the student from the primary literature and should be an empirical study (papers that involve experiments). Papers chosen should be on a topic from one of the lectures preceding the symposium but since the last symposium. Students should peruse the scientific literature to find papers of particular interest to them on these topics that are relevant and impactful to the field of evo-devo. One of the easiest ways to find papers is by typing keywords into Google Scholar. Papers from leading scientific journals (e.g., Nature, Science, Proceedings of the National Academy of Sciences, PLoS Biology) have been preselected for their broad public interest and impact and are written in more general scientific language, so often (but not always) make better papers for presentation. Another way to find papers is to look for papers referenced in the textbook on the subject or, partly because the textbook is somewhat outdated, by looking at articles that cite these referenced articles on Google Scholar. If you are having difficultly finding articles or understanding what the lecture topic entails, please contact me and I can help direct your search. You must email me the citation for your chosen research article one week before your presentation for approval (see section on deadlines in the syllabus) – this is to ensure that each paper is represented only once and that you have targeted a relevant research article to the subject. Article choice is first come first serve so the earlier you send these the better. If your paper involves a lot of experiments and components that are not relevant, you may focus on a specific aspect of your paper. A list of potential topics for each symposium is provided below. 

 

Presentation – Each student will have 10 minutes: 7 minutes to present their research article in a Microsoft Powerpoint presentation and 3 minutes for questions. The goal of the presentation is to summarize the research article in a slightly more technical way than a scientific blogger would. You should make the presentation maximally interesting: try to convince the audience that this paper is worth a read. The components of the talk should include:

 

1) Introduction: State your name, the lecture topic covered, and the title and authors of the paper. Describe the specific topic of the paper and its importance to science and evo-devo. Clearly state the major aims of the scientific research. 

2) Methods: Briefly state the experimental methods used to address the question. Provide general techniques rather than a lot of detailed methods. This should be a slide or 2.

3) Results: Show the major results using figures from the manuscript. Make sure to guide the audience through the graphics.

4) Discussion/Conclusions: Highlight the general conclusions and the major insights in evo-devo that it provides.

 

Tips: Slides are typically more interesting if they have minimal amount of text and good visuals. Generally you can cover a slide every minute. Use language that your audience will understand. Practice to ensure you are within your time limit. 

 

Feedback – Your peers will provide feedback on the presentation. The goal of this is not only to provide feedback for the speaker but also to allow students to think more critically about what makes for an effective presentation. Audience evaluations will also be used towards the participation grade, comprising 50% of their participation points. Evaluation sheets will be handed out prior to class. Evaluations and your grade will be available in the next class period to pick up after class.

 

Symposium Topics

 

Feb. 5 - Symposium I. Homeotic Mutants; discovery of the homeobox; Reconstructing ancestral developmental plans (e.g., Urbilateria); phylogeny of early life as it relates to development; radial Symmetry vs. bilaterial symmetry; larval evolution; evolution of multicellularity; the hourglass model; the universal function of homeotic genes. Avoid papers on Hox or limb evolution.  

 

Feb. 17 - Symposium II. Cis- vs. trans- regulated phenotypes; genome size evolution; role of gene duplication in diversification; role of pleiotropy in gene mutation; redundancy in gene networks; constructing gene networks; ways cis- regulatory regions operate; evolving gene networks; genomic hotspots for evolution. Avoid the diversification of hox genes.

 

Feb. 28 - Symposium III. Hox genes in early Metazoan lineages; segmentation in arthropods; genetics of differentiation of leg, wing, and mouthpart structures in arthropods. Avoid coverage of wing patterning and wing origins and of novel appendages (e.g. beetle horns).

 

Mar. 7 - Symposium IV. Vertebrate skeletal and limb evo-devo.

 

Mar. 21 - Symposium V. Plant evo-Devo (e.g. meristem diversification, modularity, floral evolution).

 

Apr. 2 - Symposium VI. Examples of heterochrony (e.g., paedogenesis, shifts in life history stages, shifts in timing of gene expression), heterotopy (shifts in location of gene expression), heterometry (allometric shifts and whole body effects on growth); how adaptive alleles flow and become fixed; evolutionary genetics of adaptive radiations; genetics of sex determination and sexual dimorphism; endocrine control of developmental variation.

 

Apr. 9 - Symposium VII. Eco-Evo-Devo: Phenotypic plasticity – how conditions like temperature, social interactions, nutrition, and available diet impact development to impart phenotypic variation; heritable epigenetics.

 

Apr. 21 - Symposium VIII. Origin of insect wings; color pattern; evolutionary novelties that are projections (horns, scales, hair, feathers).

 

Apr. 30 - Symposium IX.  Evo-devo of eyes; evo-devo of humans.