Graduate Courses

                                                                                                                             Updated Nov. 14, 2016

How to Enrol

Graduate students in the Department of Ecology and Evolutionary Biology can access the Student Web Service (SWS) to change personal information (addresses and telephone numbers), view their academic record and current courses and to enrol in, request or drop courses. Note: you can only use SWS to enrol in courses if you do so by the deadlines listed below. For complete information on using the SWS please view Instructions for Course Enrolment using ACORN/ROSI. It is your responsibility to ensure that course enrolment is accurate on SWS.

Graduate Student Run Non-Credit Workshops & Courses

The Department recognizes that individual graduate students have developed considerable expertise in many important research tools and concepts and it wishes to encourage such students to share their expertise with other graduate students. Accordingly, as a pilot project the Department will offer some financial support to students or student groups who volunteer to offer not-for-credit workshops or short not-for-credit courses that meet significant demand for skills or knowledge beyond what is commonly generated within study groups. To access departmental support, potential graduate student instructors or organizing groups should submit to the Grad Office a proposal that: 1) describes the need and the project designed to fill it, including giving it a descriptive name; 2) assesses the demand within the department and specifies a measure of success for the project (e.g. the number of students completing the training); 3) optionally describes a small budget (maximum $500) for supplies, course resources, and/or a small honorarium for the chief instructor; 4) provides a list of fewer than 10 questions that would constitute a suitable evaluation of the quality or success of the project in meeting student needs. The Grad Office will respond with a decision about the level of support, which may be contingent on the project meeting its specified index of success. At the end of the project we will also provide a letter of documentation to any student who leads a successful one.  

Graduate Courses Offered in 2016-2017

You may sign up for a course(s) beginning August 15, 2016 (but not before that date) on Student Web Services with ACORN or ROSI (please see the link above to the instructions).  Please also note that, for some courses, you may sign up for a course but you will not be registered in the course until permission has been granted by the course instructor (this is normal procedure for many courses).

Deadlines: Please make sure that you have signed up for your course(s) by the following deadlines: for Fall or full-year courses, the deadline to enrol is *September 26, 2016* and the deadline to enrol in January session courses is *January 23, 2017*.

New students should consult their supervisor(s) and fellow students about the courses
most appropriate to meet their needs. 

The coursework requirements for the M.Sc. and Ph.D. programs are provided in the EEB Graduate Handbook: http://www.eeb.utoronto.ca/grad/current/grad-forms.htm 

Note: Section Code: usually F, S or Y. This indicates whether the course is offered in the fall session (F), the winter session, i.e., second term (S) or over both (Y).

PDF version of Graduate Courses offered by EEB in 2016-2017 (note: see below for courses offered by other departments/groups) (note: all of the information in this document is provided below)

Graduate courses and seminars officially begin in the week of September 12th for September session courses (F) and January 9th for January session courses (S); however, some of the EEB graduate courses will not begin until the second week of classes—check with the course instructor.

EEB Graduate Courses Offered in Fall 2016:

EEB1210H F (1/4 course)  Advanced Statistics [M-J. Fortin] 6 weeks
Day & Time: Tuesdays, 9:30-12:00 (starting September 13th)  Location:  St. George Campus, RW 015A

Biologists need to use statistical methods to test their hypotheses. Given the increasing complexity of experiments carried out by biologists, they need however to understand the limitations of these statistics and how to select the appropriate statistics for their needs and how to interpret them properly both statistically and biologically. The goal of this advanced course in statistics is to teach biologists how to choose and use statistics so that they can address relevant biological questions and test them with the appropriate methods. Specifically, an overview of advanced notions about regression and ANOVA will be presented. To do so, a combination of lectures and computer laboratory sessions will be used.
Course Syllabus

EEB 1310H F Philosophy & Methods [H. Rodd (team leader), Njal Rollinson, and guests] 
Day & Time: Thursdays, 2-5pm    Location: St. George Campus, Room TBA
The first class will be September 22, 2016

Description: This course will involve a combination of (i) student-lead discussions, (ii) lectures/discussions lead by faculty designed to cover general and often controversial scientific issues frequently confronted in both ecological and evolutionary studies, and (iii) short presentations by students introducing the background and context for their proposed research. This course is recommended for students just starting an MSc or PhD. It is intended to be a forum for students to enhance their current skills and understanding of how to do ‘good’ science and to discuss some issues that they will encounter as scientists. The class will read papers on and discuss topics that will include: human subjectivity and biases and their role in science; some semi-philosophical controversies about approaches to science and research tactics; some common and important pitfalls/errors in experimental design and statistical analysis (note: a strong background in statistics is not necessary for the course, but at least one undergraduate course in statistics is recommended); brief overviews of some new statistical approaches; and a variety other issues that are important to researchers (e.g. ethics). Faculty from the department and other guests will give brief, overview lectures to provide a bit of background on some of the topics (e.g. power analysis). The major assignment for the course is an essay that aims to facilitate students’ progress in thinking broadly about their thesis research, before they write their thesis proposal; to this we ask the students to put their research questions in the context of their general field (ecology or evolution)—both historically and with respect to the exciting questions currently being asked.

EEB1451H F: Special Topics in Ecology/Evolution: Parasites in Communities
[B. Gilbert & N. Mideo]
Day & Time: Tuesdays (alternating weeks) 2-5pm       Location: St. George Campus, ESC 1014
(This course will meet in alternate weeks over the entire school year (September – April)). The first class will be Sept. 20, 2016.

Please contact Ben Gilbert (benjamin.gilbert@utoronto.ca) and Nicole Mideo (nicole.mideo@utoronto.ca) by Sept. 7 if you are interested in taking this course. Please include the following information in your email:  Your name; Your supervisor(s); Your degree program (MSc or PhD); Your year of student (e.g., I am in the 2nd year of a PhD); A couple of sentences about why you are interested in taking this course.
Because of limited resources, they may not be able to accommodate all students showing an interest in this course.  

There is a growing appreciation that parasites may not only make up the majority of species in a community but can fundamentally alter population dynamics, community assembly, ecosystem services, and evolution in complex environments. The goal of our course is to simultaneously review, understand, and contribute to this body of literature. Students will review the relevant literature pertaining to parasites in communities focusing both on classic papers and recent developments. Concurrently students (potentially in groups) will be required to develop an exciting and unanswered research question in the field then answer their questions using modelling, meta-analytic, or experimental approaches.
Course Outline

EEB1452H F (1/4 course) Special Topics in Ecology/Evolution: Mutualisms [M. Frederickson]
Date & Time: Wednesdays, 1-4pm           Location: St. George Campus, ESC 3056
(this course will take place from September 21 - October 26).

A short (0.25 FCE) graduate course focused on the ecology and evolution of mutualism. We will pair chapters from the new Mutualism book (2015, edited by JL Bronstein, Oxford University Press) with recent empirical or theoretical papers from the primary literature. Book chapters/potential topics include macroevolution, coevolution, and evolutionary genetics of mutualism, as well as population and community ecology of mutualism, and mutualisms and global change. Students will give presentations and lead/contribute to discussions during the 2-3 hour sessions which will be held on six concurrent Wednesday afternoons, starting Sept. 21. 

EEB1452 will meet for six 2-3 hours sessions starting Sept. 21 (21/09, 28/09, 05/10, 12/10, 19/10, 26/10). 

**Please see more graduate courses (with significant undergraduate content) offered in the Fall 2016 term listed below**

EEB Graduate Courses Offered in Winter 2017:

EEB1315H S (1/4 course) Professional Skills Development  [M. Sokolowski, H. Rodd and others]
Day & Time: Thursdays, 4pm (tentative)        Location: St. George Campus, TBA

This course is only open to PhD students and there are restrictions on whether this course will count towards their degree (a max. two of the three following courses may be taken for credit: EEB1315, R and Python) 
Note: all students will be invited to the panel discussions and some of the workshops.

A short (0.25 FCE) graduate-level course focused on developing the academic and professional skills required to succeed during and beyond graduate education in basic life sciences, with an emphasis on ecology and evolution. 

EEB1315 will meet for approx. eight 2-3 hour sessions in alternate weeks (tentatively on Thursdays for 2017).  The sessions will run from 3-6 or 4-7 depending on the availability of the guest participants.  The class sessions will be comprised of A (see below) in some weeks and A+B in other weeks:
(A) Lecture and/or student led discussion and/or working group activities: 1-3 hours (depending on the schedule for that week).   Topics will include converting CVs to resumes, informational interviews, speaking and writing for non-specialists, time and project management.
(B) Guest Panel Discussions: 1.5 hours.  There will be 2-3 panel discussions over the duration of the course.  Guest panelists will be chosen largely from the department's graduate alumni, and they will speak about their career pathways and the skills that they developed during their graduate education that they find valuable in their careers.  They will be selected from a range of careers including government, industry, higher education.

EEB1230H S Multivariate Statistics [D. Jackson] (not offered in Winter 2017)

EEB1350H S Core Course in Evolution [A. Agrawal]
Day & Time: Fridays, 10-12     Location:  St. George Campus, ESC 3088

This is a half course.
Aneil has provided this syllabus from a previous year to provide some information about the course. The material and organization of the course in Winter 2017 will be similar, but not identical, to the description in this old version of the syllabus. 
Course Syllabus - Pre-2016

Graduate Courses with Significant Undergraduate Content:

(These courses will normally constitute only a minor component of the required credits for a graduate degree)

Fall courses with some undergraduate content:

EEB 1328H F Physiological Ecology [R. Sage]
Day & Time: Fridays, 10-12; Fridays, 1-3     Location:  St. George Campus, ESC 3087

An advanced treatment of the physiological mechanisms controlling plant and animal distribution and ecological success. Topics of focus include photosynthesis and resource balance, water and nutrient relations, temperature effects, and adaptations to abiotic stress.

EEB 1421H F Special Topics in Ecology: Plant-animal Interactions [M. Frederickson]
Day & Time: Tuesdays & Thursdays, 1:00-2:00; Fridays 1:00-3:00    Location: St. George Campus, RW 142

Major concepts in ecology and evolution from the perspective of plant-animal interactions. The richness of interactions between plants and animals is explored including antagonistic interactions (herbivory), mutualistic interactions (pollination, seed dispersal, ant-plant associations), and interactions involving multiple species across trophic levels. There may be a field trip held on a Saturday or a Sunday; a small fee may be charged for field trip transportation.

EEB 1443H F  Phylogenetic Principles  [S. Stefanovic] (up to 5 grads)
Day & Time: Tuesdays and Thursdays, 10 am -12 pm      Location: UTM; Room: IB 210

Lectures will provide an in-depth coverage of modern methods of phylogenetic reconstruction including molecular systematics based on DNA sequences. The principles and philosophy of classification will be taught with an emphasis on ’tree-thinking’, one of the most important conceptual advances in evolutionary biology. Tutorials will focus on recent developments in the study of evolutionary patterns while gaining proficiency in reading, presenting, and critiquing scientific papers.

*Shuttle Bus (Hart House to/from UTM) stop is right in front of this building (IB).

EEB 1460H F  Molecular Evolution  [D. Irwin & B. Chang] (up to 5 grads)
Day & Time: Wednesdays, 10 am – 11 am; Fridays, 10 am – 12 pm     Location: St. George Campus, TBA

Processes of evolution at the molecular level, and the analysis of molecular data. Gene structure, neutrality, nucleotide sequence evolution, sequence evolution, sequence alignment, phylogeny construction, gene families, transposition.

Spring courses with undergraduate content:

EEB 1330H S Systematic Botany [J. Eckenwalder] (up to 3 grads)
Day & Time: Tuesdays and Thursdays, 1 pm – 2 pm; Thursday, 2 pm – 5 pm    
Location: St. George Campus, ESC 3087/3088

The theoretical foundations of taxonomy and the types of evidence used in constructing plant classifications. Labs emphasize taxonomic characters and their uses. Includes an independent taxonomic project.

EEB 1340H S  Comparative Plant Morphology   [T. Sage] (no limit on grads)
Day & Time: Mondays and Wednesdays, 1 pm – 2 pm; Thursdays, 9 am – 12 pm         
Location: St. G., ESC 3087/3088

This course focuses on land plant origins and subsequent diversification of land plant vegetative and reproductive form and function.  Discussions synthesize morphological and anatomical knowledge from living organisms and fossil records with cellular, physiological, and molecular information on the developmental tool kit of land plants and their ancestors throughout geological time. Topics address the evolution of vegetative and reproductive meristems; stem, leaf, and root architecture; vascular tissue; the ovule habit; fertilization processes; and pollination biology.

Graduate Courses offered by other departments/groups at the University of Toronto that will be of interest to some EEB graduate students:

EEB graduate students may take a graduate course offered by other departments for credit as long as they have discussed the course with and have permission from the course instructor, their supervisor, the other members of their supervisory committee, and the EEB graduate office (see below for more details).

EES3000H S Applied Conservation Biology will be offered this winter semester at
University of Toronto Scarborough, Tuesdays 1-4.  It will be taught by Prof. Nick Mandrak.
Canada has a complex conservation landscape. Through lectures and interactive discussions
with leading Canadian conservation practitioners, this course will examine how
conservation theory is put into practice in Canada from our international obligations to
federal and provincial legislation and policies, and the role of environmental
non-government organizations.

EES3113H Topics in Population and Community Ecology
The field of ecology is rapidly changing and this course will cover recent advances, concepts or controversies in ecology. This course will focus on specific scientific issues using current literature and the learning experience will be augmented by student presentations and discussions. The course will help ensure that students become familiar with current understanding and basic ecological concepts.  This will be an elective course, and will be especially attractive to those students who did not take advanced ecology courses during their undergraduate studies. This ‘Topics’ course is meant to be a flexible offering that focuses on recent advances, concepts or controversies in ecology.
Lecture: Tue, 4-6PM, AA204
Instructor: TBA

SciNet quarter (6 week) courses (information about specific timing, how to register, etc. for these courses will be emailed when we receive it):
-R (offered in Oct.)
-Python
MSc students may take the R/Python courses, but you will not receive credit towards your degree for taking it/them.
For PhD students, you will only receive a half course credit for a max. of 2 of the following ¼ course (6 week) modules: R, Python, EEB1315 (Professional Development).

Statistics Department: 
STA4515H--Multiple Hypothesis Testing and its Applications Course
Description:
A central issue in many current big-data scientific studies is how to assess statistical significance while taking into account the inherent large-scale multiple hypothesis testing. This 6-week graduate course will first go over the fundamental elements of single and multiple hypothesis testing, then it will move on to more advanced topics such as incorporating prior information to improve power, specific applications to whole genome genetic association studies, as well as discussions of the fallacy of p-value and alternative measures of statistical evidence and significance. Both analytical and empirical arguments will be presented, and participating students are expected to write a research report on suggested or self-selected topics related to multiple hypothesis testing.

STA2080H – Fundamentals of Statistical Genetics Course 
Description: Statistical analysis of genetic data is an important emerging research area with direct impact on population health. This course provides an introduction to the concepts and fundamentals of statistical genetics, including current research directions. The course includes lectures and hands-on experience with R programming and state-of-the-art statistical genetics software packages.

Public Health: Bayesian Statistics

Cell and Systems Biology offers some courses that EEB grad students have taken in previous years. For example, see this CSB webpage:http://csb.utoronto.ca/graduate-studies/current-students/courses/

If you wish to take a course offered by another department, please discuss it with your
supervisor and your supervisory committee.  If they agree that it would be useful to
take the course, contact the graduate office in the department offering the course. You
will need to fill out the 'Request to add/drop course(s)
form:http://www.sgs.utoronto.ca/Documents/Add+Drop+Courses.pdf

Some courses require the instructor's approval in addition to that of the
coordinator/academic advisor of the host department.  Once it is approved by the host
department and your supervisor, please bring or scan and email the form to the EEB
Graduate Office (ESC 3046) so that the course enrollment form must be approved by EEB's
Associate Chair of graduate students.

Graduate Courses and seminars may begin as early as the week of September 12th, 2016 for September session (F) and as early as January 9th, 2017 for January session courses (S). Faculty running the course will provide information on the start date for their course.

TENTATIVE LIST OF EEB GRADUATE COURSES THAT MAY BE OFFERED IN 2017-18:

Special Topics in Ecology and Evolution - Classics and Cutting Edge of Ecology and Evolution: Marc   Johnson
Landscape Genetics: Helene Wagner and Marie-Josee Fortin
Core course in Ecology
EEB1250 Spatial Statistics (1/4 course): Marie-Josee Fortin
EEB 1210 Advanced Statistics(1/4 course): Marie-Josee Fortin
Other courses: TBA