Evolutionary Biology Spring 2013

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EEB 2245
Evolutionary Biology
Meeting Time: Tuesdays and Thursdays, 9:30-10:45 in TLS154
Textbook: Futuyma, D.J. 2009. Evolution. 2nd ed. Sinauer Associates, Inc. (ISBN 978-0-87893-223-8)


Contents

Instructors

First half of the course, 22 January - 7 March
Dr. Charles Henry
Office: TLS 479/481
Phone: 486-4450
E-mail: charles.henry@uconn.edu
Office hours: By arrangement

Second half of the course, 12 March - 2 May
Dr. Chris Simon
Office: BioPharm 305D
Phone: 486-4640
Email: chris.simon@uconn.edu
Office hours: By arrangement

Teaching Assistants

Geert Goemans
Office: BioPharm 323
Phone: 486-3947
Email: geert.goemans@uconn.edu
Students A-K
Office hours: By arrangement

Brigette Zacharczenko
Office: TLS 471
Phone: 486-5503
Email: brigette.zacharczenko@uconn.edu
Students L-Z
Office hours: By arrangement

Grading

EEB 2245: Your grade will be based on your performance in 4 lecture exams and a 1-hour final exam (cumulative). Your lowest score on the 4 lecture exams will be dropped. Your 3 remaining scores and your score on the final exam will each constitute one quarter of your final grade. University regulations require that students who miss the final exam without an excuse from the Dean of Students receive an F for that exam. Thus, you are required to take the final exam.

Note: because you are allowed to drop your lowest score, we will not give make-up exams.

EEB 2245W: Your final grade in the lecture portion of the course will be calculated as above. If you are taking the W version of the course, that grade will constitute 75% of your final course grade. Your grade in the W part of the course, as determined by your “W” instructor, will constitute the remaining 25% of your final course grade, except that an F in the W part of the course will result in an F for the entire course. An F in the lecture part of the course will also result in an F for the entire course. Refer to the 2245W website for further information. Dr. Kristiina Hurme (TLS 379A; tel: 486-5434; kristiina.hurme@uconn.edu) is the coordinator of the W part of the course.

Announcements

31 January 2013: Note that we will continue to post revised hardcopy versions of the course syllabus on the web site, reflecting changes that have already been recorded in the web version of the syllabus (below). The link to it is under "Course Resources," below.

4 February 2013: A study guide for the first lecture exam has been posted. The link to the guide can be found under "Course Resources," below, and within the on-line syllabus. If we modify this study guide between now and February 14th, I will post an announcement here and the new version will automatically replace the old one.

6 February 2013: Under "Course Resources," below, we have posted a few sample exam questions to help you study for the first lecture exam. Because of various changes in the course format, we have no complete lecture exams from previous years to post.

7 February 2013: In preparation for the review sessions coming up on Monday and Tuesday, you can e-mail specific questions to your TA that can then be answered and discussed at the review sessions.

10 February 2013: Cancellation of all UConn classes on Monday, 11 February, means that we also must cancel the Monday review session (see below). Instead, all students interested in attending a review session should show up at the Tuesday review session. Both TAs will be present at that session (Biophysics Building 131).

18 February 2013: Answer keys for Exam 1 (both versions) have been posted below, under "Course Resources." If one thing has emerged from your overall performance on this exam, it is the importance of attending lecture. Simply studying from the lecture slides and book is usually not enough; I add explanatory material when I lecture, and I suggest which points are important and which ones are not. It's a relatively easy, painless way to improve your performance in the exams.

27 February 2013: A study guide for the second lecture exam has been posted. The link to the guide can be found under "Course Resources," below, and within the on-line syllabus. If we modify this study guide between now and March 7th, I will post an announcement here and the new version will automatically replace the old one.

28 February 2013: In preparation for the review sessions coming up on Monday and Tuesday, you can e-mail specific questions to your TA that can then be answered and discussed at the review sessions.

6 March 2013: Brigette has prepared her own study guide for the second lecture exam, which I have posted below under "Course Resources." There are two versions, one with answers and the other without.

12 March 2013: Answer keys for Exam 2 (both versions) have been posted below, under "Course Resources." The first (top) key is to version 1; the second (bottom) key is to version 2.

14 March 2013: Systematics study guide posted (covers first three systematics lectures)

Course Resources

Pdficon small.gif EEB2245 syllabus (printable)
Pdficon small.gif Study Guide for Exam 1 (latest version)
Pdficon small.gif Sample exam questions to help you study for Exam 1.
Pdficon small.gif Key to Exam 1. Version 1 (blue exam) and Version 2 (pink exam) are shown, in that order, followed by answers to the written questions.
Pdficon small.gif Study Guide for Exam 2 (latest version)
Pdficon small.gif Sample exam questions to help you study for Exam 2.
Pdficon small.gif Brigette's Study Guide for Exam 2
Pdficon small.gif Brigette's Study Guide for Exam 2, with answers
Pdficon small.gif Key to Exam 2. Version 1 (yellow exam) and Version 2 (green exam) are shown, in that order, followed by answers to the written questions.

Study guides for Second Half of Course can be found below alongside the lecture notes

More Course Resources: A sample of current evolution-themed Massive Open Online Courses (check them out!)

Stephen Stearns, EEB, Yale, at Academic Earth http://www.academicearth.org/courses/evolution-ecology-and-behavior

and also on Udemy http://www.udemy.com/evolution-ecology-and-behavior-122-with-stephen-c-stearns/

A set of tutorials, more for secondary school http://virtualurchin.stanford.edu/index.html

Introduction to Genetics and Evolution with Mohamed Noor by Duke on Coursera https://www.coursera.org/course/geneticsevolution

This Michigan State University MOOC focuses on Foundations of Science, but also includes components on evolution and creationism http://foundations-of-science.zoology.msu.edu/

Stanford Human Behavioral Biology http://www.youtube.com/watch?v=NNnIGh9g6fA&feature=results_video&playnext=1&list=PL848F2368C90DDC3D

Khan Academy has material on Hardy-Weinberg principle https://www.khanacademy.org/


Review Sessions

Updated 29 January 2013 -- There will be two review sessions for the first exam on Thursday, February 14th. They will be:

** CANCELLED ** Monday, February 11th, 6-8PM in BioPhysics Building Rm 130 (students L-Z, Brigette Z.), and

Tuesday, Feburary 12th, 6-8PM in BioPhysics Building Rm 131 (NOW OPEN TO ALL STUDENTS).

Review sessions are structured to answer any questions you might have encountered while studying or going over the example exam. Please come to the review session with specific questions -- or, you can e-mail questions to your TA ahead of time. If you can not attend either review session but have questions pertaining to the course material prior to the exam please contact your assigned TA to set up a time to meet.

Updated 28 February 2013 -- There will be two review sessions for the second exam on Thursday, March 7th. They will be:

Monday, March 4th, 6-8PM in BioPhysics Building Rm 130 (students L-Z, Brigette Z., primary), and

Tuesday, March 5th, 6-8PM in BioPhysics Building Rm 131 (students A-K, Geert G., primary).

Evolution in the News

5 February 2013, New York Times online: Darwin and pigeon breeding

19 February 2013, New York Time online: East Asian Physical Traits Linked to 35,000-Year-Old Mutation

20 February 2013, Nature online Superstars of Botany: Rare Specimens

20 February 2013, Imgur.com Nothing is stranger than reality -- This entertaining sequence of panels about courtship and mating in an angler fish is actually very accurate. It's good to bear in mind that sexual selection does not always produce large, powerful males!

12 March 2013, New York Times online: Solving the puzzles of mimicry in nature

11 April 2013, YouTube: Convergent evolution of crushing jaws in hyenas and dogs


Lecture Syllabus

Pdficon small.gifEEB2245 Syllabus Sp 2013 2 Apr 13.pdf

Please read assigned chapters, as indicated below, prior to class


Class Day Date Topic Text Readings
Part I Jan 22 - Mar 7 Processes of Evolution Dr. Charles Henry
1 T Jan 22 Populations, variation, & the Hardy-Weinberg principle
Pdficon small.gif Populations, Variation, and H-W Lecture
Ch. 1 (pgs 7-11), 9, & 13
2 Th Jan 24 Agents of evolutionary change: Mutation and gene flow (migration)
Pdficon small.gif Mutation and Gene Flow Lecture
Ch. 9
3 T Jan 29 Sampling error: genetic drift and the bottleneck/founder effects
Pdficon small.gif Genetic Drift Lecture
Ch. 10
4 Th Jan 31 Charles Darwin and natural selection, part 1
Pdficon small.gif Natural Selection Lecture, Part 1
Ch. 1 & 11
5 T Feb 5 Natural selection, part 2
Pdficon small.gif Natural Selection Lecture, Part 2
Ch. 11, 12, & 13
6 Th Feb 7 Adaptation and life-history evolution, part 1
Pdficon small.gif Adaptation and Life History 1 Lecture
Ch. 13 & 14
M Feb 11 Review Session for Exam 1
6-8 PM
BioPhysics Building Rm 130
7 T Feb 12 Life history evolution, part 2
Pdficon small.gif Life History Evolution Lecture, Part 2
Ch. 14
T Feb 12 Review Session for Exam 1
6-8 PM
BioPhysics Building Rm 131
8 Th Feb 14 EXAM #1
You may bring a calculator (NO iphone/smartphone)
Pdficon small.gif Study Guide for Exam 1
Covers Lectures 1-6
9 T Feb 19 Sexual selection
Pdficon small.gif Sexual Selection Lecture
Ch. 15
10 Th Feb 21 Levels of selection
Pdficon small.gif Levels of Selection Lecture
Ch. 16
11 T Feb 26 Species and species concepts
Pdficon small.gif Species and Species Concepts Lecture
Ch. 17 & 18
12 Th Feb 28 Geographic variation, clines, and allopatric speciation
Pdficon small.gif Speciation 1 Lecture
Ch. 17 & 18
M Mar 4 Review Session for Exam 2
6-8 PM
BioPhysics Building Rm 130
13 T Mar 5 Non-allopatric speciation; class evaluations
Pdficon small.gif Speciation 2 Lecture
Ch. 18 & 22
T Mar 5 Review Session for Exam 2
6-8 PM
BioPhysics Building Rm 131
14 Th Mar 7 EXAM #2
You may bring a calculator (NO iphone/smartphone)
Pdficon small.gif Study Guide for Exam 2

Covers Lectures 7-12
Part II Mar 12 - May 2 Patterns of Evolution Dr. Chris Simon
15 T Mar 12 Systematics: Tree-thinking, phylogeny, polymorphism, & homoplasy :Pdficon small.gifEEB 2245 (4 per page) Lect. 15. Systematics EEB 2245 S 2013.pdf Ch. 2 & 3
16 Th Mar 14 Parallelism and reversals; molecular & morphological methods
Pdficon small.gifLect 16. S13 Building Trees 13 Mar 13.pdf
Pdficon small.gifLect 16. Handout Constructing Evolutionary Trees 2013.pdf
Ch. 2 & 3
T Mar 19 SPRING BREAK - no class
Th Mar 21 SPRING BREAK - no class
17 T Mar 26 Reconstructing trees from morphology; how molecules evolve
Pdficon small.gifLect. 17 Building Trees Morph. Molec. Evolution 26 Mar 13.pdf
Pdficon small.gifEEB 2245 Systematics studyguide. Sp 13.pdf Systematics Study Guide for the first three lectures.
Pdficon small.gifSystematics Study Guide. with answers Sp 13.rtf


Ch. 2 & 3
18 Th Mar 28 Molecular evolution and molecular clocks
Pdficon small.gifLect. 18 EEB2245 Molecular trees molecular clocks 28 Mar 13.pdf
Ch. 2 & 3
19 T Apr 2 Overview of the Tree of Life; animal evolutionary innovations
Pdficon small.gifLect. 19. Overview of Life & Animal Phylogenies 2 Apr 13 part 1.pdf
Pdficon small.gifLect. 19. Overview of Life & Animal Phylogenies 2 Apr 13 part 2.pdf
Pdficon small.gifStudy Guide 2 Clocks, Life Sp 13.docx
Pdficon small.gifEutrochozoa vs Articulata Hypothesis.pdf


IntroBio textbook or lecture notes
20 Th Apr 4 Evolutionary novelties: Body plans, constraints, gene regulation
Pdficon small.gifLect 20. Evolutionary Novelties S 13.pdf
Pdficon small.gifStudy Guide 3. Evol. Novelties Part 1 Sp 13.docx
Ch. 21 & 22
21 T Apr 9 Homeobox genes, ontogeny & phylogeny, allometry, & fossils
Pdficon small.gifLect. 21. Origin of Evol. Novelties 9 Apr 13.pdf
Ch. 4; 21 & 22


T Apr 9 Review Session for Exam 3
6-8 PM
Brigette (L-Z)
BioPhysics Building Rm 131
W Apr 10 Review Session for Exam 3
6-8 PM
Geert (A-K)
BioPhysics Building Rm 131
22 Th Apr 11 EXAM #3
Covers Lectures 15-20
23 T Apr 16 The Paleozoic: Origin of invertebrates, vertebrates, & land plants
Pdficon small.gifLect. 22. Overview of Fossil Record & Paleozoic 16 Apr 13 Part 1.pdf
Pdficon small.gifLect. 22. Paleozoic part 2. 18 Apr 13.pdf
Ch. 4 & 5; p 168-71
24 Th Apr 18 Mesozoic I: Pangea, Laurasia, Gondwanaland; reptiles & birds
Pdficon small.gifLect. 23. Mesozoic Part 1 18 Apr 13.pdf
Ch. 4, 5, & 6
25 T Apr 23 Mesozoic II: Insects & angiosperms, K-T extinction; Cenozoic I Ch. 17
26 Th Apr 25 Cenozoic II: Continental drift & dispersal; primates and humans Ch. 17
27 T Apr 30 Human Evolution; Biogeography Ch. 17
T Apr 30 Review Session for Exam 4 & Final
6-8 PM
BioPhysics Building Rm 131
W May 1 Review Session for Exam 4 & Final
6-8 PM
BioPhysics Building Rm 131
28 Th May 2 Biogeography and Biodiversity; class evaluations Ch. 17
Th May 9 Exam #4 covers lectures 23-28 (first hour) & FINAL EXAM (second hour)cumulative for entire semester TLS 154. 8-10 am
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