Course Syllabus

BIO 342 Evolutionary Biology (Winter 2014)

Course Description
The course will offer a focused introduction to the major concepts in evolutionary biology and how evolution has
shaped biodiversity, agriculture, and impacted human biology and culture. Students will first learn about the
origin and importance of genetic variation for evolutionary change, and how five specific mechanisms shape this
variation to drive evolutionary change within populations. Students will then learn how these mechanisms
influence evolutionary processes and patterns, including adaptation, sexual selection, speciation, coevolution, and
how evidence for evolution is gained from fossils, experiments, genetics and molecular systematics. Students will
finally learn about the importance of evolutionary biology to humans, including the preservation of biodiversity,
sustainable agricultural practices, and the origin of humans and their parasites. Throughout the course instruction
will emphasize how evolution impacts the world around us, and emphasis will be placed on the scientific process
and critical thinking through lecture, reading and assignments, as well as term-test and final exams.

Learning Goals and Outcomes

The goal of BIO342 is to provide students with a focused introduction to evolutionary biology, including the key
concepts, history of the field, and its importance to modern science and society.
Students will achieve the following outcomes by the conclusion of the course:
1) Understand the fundamental concepts in evolutionary biology and the impact of evolution on the natural world.
2) A working understanding of how heritability, natural selection and evolutionary response are estimated using
data collected from natural populations and common garden field experiments.
3) An ability to critically read and evaluate scientific papers.

Instructor
Prof. Marc Johnson, Ph.D.
Email: [email protected]
Web Page: www.evoeco.org
Office Location: 3040 W.G. Davis Building
Office Hours: Wed: 4-5pm or by appointment.

E-Mail Policy

The University's official method of correspondence with students is through their University of Toronto e-mail
accounts. It is the student's responsibility to keep his/her @utoronto.ca account active and check it on a regular
basis. All e-mails from students must include their full name and student number as well as have the course code
in the subject line. Please allow for at least three business days for a response before making further inquiry.
Please speak directly with Professor Johnson in person regarding urgent matters (e.g. illness, bereavement). If
Prof. Johnson is unavailable you can contact the TA or Ms. Yen Du (Biology undergraduate coordinator).

Teaching Assistant
Connor Fitzpatrick, Ph.D. student
Email: [email protected]
Office hours: None. Please direct all questions to Prof. Johnson, unless he is unavailable.

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Course Meetings
Lecture
Days: Monday & Wednesday
Time: 2:00pm 4:00pm
Location: 1140 CCT

Course Materials
Textbooks
Evolutionary Analysis - Scott Freeman and Jon C. Herron
Edition: Fifth
ISBN: 0-13-227584-8
Purchasing the book: Hard Copies are available in the Bookstore for $150. You can purchase a digital copy of

the book for $56.99 from http://www.coursesmart.com/032170696X

The library has also added a copy of this book to their reserve materials.
Required readings are available in the book.
Articles will also be assigned for reading in class.

Calculator
All students are required to obtain a calculator capable of simple calculations (addition, subtraction,
multiplication, division), taking the natural logarithm loge (same as Ln) of a number and exponentiating
functions (e.g. yx). Devices that can store text (e.g. smart phones, graphing calculators, etc.) are not permitted.

Requisites and Restrictions

Prerequisites
BIO207 - Introductory Genetics

Grading
Grade Components

Component Weight Details

Quizzes

10

Five quizzes (2% each) related to assigned readings of peer-reviewed articles marked by !! on
either side of the citation to the paper.

Assignment 10

Collect samples from the field (Feb 24), record data and enter data in the lab (2-5pm, Feb 26) and
complete assignment in class on estimating and interpreting heritability, selection and
evolutionary responses (March 3).

Exam 1

20%

Students will be responsible for all lecture material in classes 1-7 and required readings from the
textbook (marked with **). Required readings from articles will not be covered on the exam.

Exam 2

20%

Students will be responsible for all lecture material in classes 9-17 and required readings (marked
with **). Required readings from articles will not be covered on the exam.

Final exam

40%

Students will be responsible for all material presented during the course

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Letter Grades
This Course uses the standard University of Toronto Letter Grading:
90
85
80
77
73
70
67
63
60
57
53
50
0

A+
A
AB+
B
BC+
C
CD+
D
DF

<
<
<
<
<
<
<
<
<
<
<
<

100
90
85
80
77
73
70
67
63
60
57
53
50

Late Assignments, Missed Tests, and Missed Exams

In the event of illness please follow these procedures:
1. Declare your absence on ROSI within 48 hours.
2. Contact Prof. Johnson via email within 48 hours of the missed quiz/test/assignment
3. Submit your official Student Verification of Illness/Injury Form (see below) AND an explanation in
writing within one week, detailing the University-approved circumstances, beyond your control, that
caused you to miss the quiz/test/assignment. Hardcopies of the form, official documentation and
explanation must be submitted to Yen Du ([email protected]) in the Department of Biology. Include
your name, your student number, your @utoronto email address, your phone number, the course
designator/code, and a description of the item you missed (e.g., term-test 1). Please note, the official
Student Verification of Illness/Injury Form is the only documentation that will be accepted.
You can obtain the form from the following website: http://www.illnessverification.utoronto.ca and
from the course Blackboard site.
Note: It is insufficient simply to visit a doctors office; the documentation must show that you were incapable
of writing the test or completing the assignment, for medical reasons. You must use the official form cited
above and the documentation must be obtained from a physician within 24h of the test/assignment/quiz. A
statement merely confirming the report of an illness made by a student is not acceptable.
Note that holidays and pre-purchased plant tickets, family plans (unless related to death of an immediate family
member), conflicting class schedules/tests and lack of preparation are not acceptable excuses.
If an appeal is accepted the grades for missed tests/exams will be redistributed to the final exam.
Students who miss more than one exam/test due to medical reasons should see Prof. Johnson as soon as
possible because the grades from only one missed exam/test can be redistributed.
Procedures for missed final exams are subject to policies set out by the Registrar. In brief, an online petition
and original supporting documentation must be submitted to the Office of the Registrar within 72 hours of the
missed examination.

Attendance and Classroom Management

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Attendance
Students are expected to attend all classes.
Electronic devices
Students are asked to turn off cell phones during lecture. If students must use these devices they are asked to first leave the
lecture hall quietly.
Laptops are permitted for note-taking only. Students who use laptops for anything other than note-taking will lose the
privilege of using their laptop in class.

Academic Integrity
The Universitys code of Behaviour on Academic Matters states that:
The University and its members have a responsibility to ensure that a climate that might encourage, or conditions that
might enable, cheating, misrepresentation or unfairness not be tolerated. To this end all must acknowledge that seeking
credit or other advantages by fraud or misrepresentation, or seeking to disadvantage others by disruptive behaviour is
unacceptable, as is any dishonesty or unfairness in dealing with the work or record of a student.
- University of Toronto Mississauga Academic Calendar
It is your responsibility as a student at the University of Toronto, to familiarize yourself with, and adhere to, both the
Code of Student Conduct and the Code of Behaviour on Academic Matters.
This means, first and foremost, that you should read them carefully.

The Code of Student Conduct is available from the U of T Mississauga website (Registrar > Academic Calendar >
Codes and Policies) or in your print version of the Academic Calendar.
The Code of Behaviour on Academic Matters is available from the U of T Mississauga website (Registrar >
Academic Calendar > Codes and Policies) or in your print version of the Academic Calendar.

Electronically-Hosted Course Components

Electronically-hosted Components: All lectures will be made available on Blackboard.
You are expected to monitor Blackboard for course announcements and upcoming assignments/quizzes/exams.

Accommodations for Disabilities

The University accommodates students with disabilities who registered with the AccessAbility Resource Centre.
Please let Prof. Johnson know in advance, preferable in the first week of class, if you will require any
accommodation on these grounds. To schedule a registration appointment with a disability advisor, please call
the centre at 905-569-4699 or e-mail at: [email protected].
http://www.utm.utoronto.ca/access/

Policy on Discrimination
The University of Toronto and Professor Johnson believe in equality of opportunity in education and employment for all
students and employees. Accordingly, University of Toronto affirms its commitment to maintain a work environment for
all employees and an academic environment for all students that is free from all forms of discrimination. Discrimination
or harassment of any person based on race, color, religion, creed, sex, national origin, age, disability, veteran status, or
sexual orientation is in violation of Provincial and Federal laws and University policy and will not be tolerated.
Retaliation against any person who complains about discrimination is also prohibited. University of Torontos policies
and regulations covering discrimination, harassment and retaliation may be accessed at
http://www.governingcouncil.utoronto.ca/policies/harass.htm. Any person who feels that he or she has been the subject of
prohibited discrimination, harassment, or retaliation should contact Prof. Johnson, the Registrar or Campus Police.

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Religious Observance
Information about the University's Policy on Scheduling of Classes and Examinations and Other Accommodations for
Religious Observances is at
http://www.viceprovoststudents.utoronto.ca/publicationsandpolicies/guidelines/religiousobservances.htm
Students who must miss an exam/test/assignment for religious reasons should make a written request to Prof. Johnson by
email at least two weeks before the affected date and preferably sooner. Absences will not be considered legitimate if a
request is made within two weeks or after the missed test/assignment/exam.

Other Resources
Robert Gillespie Academic Skills Centre
Students can visit the Academic Skills Centre to consult with one of its strategists about understanding learning style,
developing study plans for upcoming tests/exams, or discussing papers. Special Diagnostic Assessments are also offered
and are designed to help you learn exactly where you stand with respect to critical academic skills.
http://www.utm.utoronto.ca/asc
UTM Library (Hazel McCallion Academic Learning Centre)
The University of Toronto boasts the biggest academic library in Canada and the second biggest in North America.
Various services are available to students at the UTM Library and across the UofT library system. Services including
borrowing, interlibrary loans, online references, laptop loans and the RBC Learning Commons. For more information,
visit http://library.utm.utoronto.ca.

Course Schedule

Important Dates
January 19 Course waiting list closes
January 29 (Class 8) Term-test Exam 1
February 17 Family Day Holiday
February 18-21 Reading Week
February 24 Field assignment: data collection
February 26 Field assignment: submit data
March 3 Field assignment quiz in class
March 12 (Class 18) Term-test 2
April 2 Last day of class

See next page for detailed schedule

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Class

Date

Topic
i) Course overview
06-Jan ii) Origins and evolution of life
08-Jan History of evolutionary biology
i) Reading scientific articles
13-Jan ii) Genetic and phenotypic variation I

15-Jan Genetic and phenotypic variation II

20-Jan Natural Selection and adaptation

1
2

i) Mutation
22-Jan ii) Dispersal
i) Non-random mating
27-Jan ii) Genetic drift
29-Jan Term-test 1

6
7
8
9
10
11
12

03-Feb Maintenance of genetic variation

i) Evolution of sex
ii) Inbreeding
05-Feb iii) Plant sex
10-Feb Sexual selection

13
14

12-Feb
17-Feb
18-21-
Feb
24-Feb
26-Feb

15
16
17
18
19

03-Mar
05-Mar
10-Mar
12-Mar
17-Mar

20

Phylogenetics, fossils and

19-Mar macroevolution

21
22
23
24

24-Mar
26-Mar
31-Mar
02-Apr

Speciation
Holiday (no class)
Reading week (no class)
Collect samples in the field
Collect and enter data in the lab
i) Quiz for field assg
ii) Hybridization and polyploidy
Coevolution
Evolution of plant defenses
Term-test 2
Evolutionary ecology

Molecular evolution
Evolutionary origins of humans
Evolution of modern humans
iEvolution. The meaning of Life

!! Quiz paper !!, ** Required reading **, Suggested Reading

**pp 62-66, Computing Consequences 2.1**;
Chapter 2
Section 3.6
**Computing consequences: 3.1, 5.2, 6.1, 6.2, 6.4**
Chapter 5, Sections: 6.1, 9.1, 9.3
!!Simmons and Firman 2013 Evolution!!
**Computing consequences: 3.1, 5.1, 5.2, 6.1, 6.2, 6.4**
Chapter 5, Sections: 6.1, 9.1, 9.3
**Section 6.3 (pp 201-206); Computing Consequences: 6.3, 6.6, 9.3**
Sections: 3.1-3.5, 9.4, 9.5
!!Grant and Grant 1995 Evolution!!
**Section 6.4 (pp 216-221), Computing Consequences: 6.8, 7.1, 7.2**
Sections: 5.5, 7.1
**Computing consequences: 7.3, 7.4**
Sections: 7.2-7.4
**Computing consequence: 6.7, 6.9**
pp 206-214, 219-222; Sections 9.6-9.7
Sections: 7.4, 8.3, 11.5
Chapter 11
!!Hughes et al 2013 Nature!!
Chapter 16



pp 168-169, p 621, Section 16.4
Turcotte et al. 2012 PLoS Biology (including movies)

Johnson and Stinchcombe 2007 Trends Ecol Evol
!! Johnson et al. 2010 Science !!
**Sections: 4.3, 18.1**
Chapter 4, Section 18.4
**Sect. 7.3**
Chapter 15
Chapter 20
Chapter 20
!!TBD!!