Biology 3444 F Molecular Ecology (Western University, Canada) 2016/2017 Professor: Dr. Nusha Keyghobadi Office: BGS 2076 Email: nkeyghob@uwo.ca Phone: ext. 80471 Teaching assistant: Benoit Talbot (btalbot4@uwo.ca) Brief Course Description: An introduction to the use of molecular tools, particularly genetic tools, in addressing both basic and applied questions in ecological research. We will consider the use of molecular tools for addressing questions in population, behavioural, community and ecosystem ecology. We will also consider various areas of practical application such as species conservation, studies of the origin and spread of invasive species, wildlife forensics, and agriculture and fisheries. Lectures and student-led seminars will develop basic knowledge and theory underlying molecular ecology, and will present many recent case studies from the primary literature. Prerequisites: Biology 2483 (Ecology) and Biology 2581 (Genetics). Biology 3466 (Evolutionary Genetics) would be helpful and is recommended as a pre- or co-requisite, but is not required. It is your responsibility to ensure that you have the prerequisites for this course. Unless you have either the requisites for this course, or written special permission from your Dean to enroll in it, you may be removed from this course and it will be deleted from your record. This decision may not be appealed. You will receive no adjustment to your fees in the event that you are dropped from a course for failing to have the necessary prerequisites. Lectures: Tutorials: Office Hours: Tuesdays, 10:30am 12:30pm in P&AB-34 Thursdays, 11:30am 12:30pm in BGS-0153 By appointment. Please send me an email and we can arrange a meeting. OWL: Materials for the course will be available on OWL. Please do not send me messages or emails through OWL; contact me using my.uwo email instead. Textbooks: Required: Freeland, J. R., S. D. Petersen, & H. Kirk. 2011. Molecular Ecology (2 nd ed n.). John Wiley & Sons. Available in the UCC Bookstore. Used copies should also be available. Note: The first edition has some important differences from the second edition, so buying used first edition texts is not recommended. Additional readings will be provided by the instructor and fellow students (as pdfs on OWL). If you want further background in basic population genetics, the following books may be helpful: v Halliburton, R. Introduction to Population Genetics. Pearson Education. Biology 3444f Syllabus 1 of 5
Evaluation: v Hartl, D. L. A Primer of Population Genetics, 3 rd Ed n. Sinauer & Associates. v Frankham, R., J. D. Ballou, & D. A. Briscoe. Introduction to Conservation Genetics. Cambridge University Press. Research Proposal Outline and Bibliography due Oct. 13 15% Molecular Ecology Snippet various dates in Oct. and Nov. 10% Midterm Exam essay format, open book Nov. 15 (during class time) 30% Updated Research Proposal Outline due Nov. 17 5% Group Evaluation of Research Proposal Outlines Nov. 22 (in class assignment) 5% Research Proposal (2500 words) due Dec. 6 th 30% Class and Tutorial Participation 5% Total 100% At the end of term you will be handing in a Research Proposal, which will be a formal description of a proposed research project in the field of Molecular Ecology. Students are free to work on any question or study system of their choice, as long as the topic fits within the scope of Molecular Ecology (check with the instructor or TAs if you aren t sure about a particular topic). The Research Proposal proposes a question and a clearly stated scientific hypothesis to be tested. It provides background information on the question and hypothesis, including some justification for why the topic is interesting or important. It also provides detailed description, and justification, of the methods that will be used to answer the question and test the hypothesis. As many students are not familiar with writing a research proposal, the Research Proposal Outline and Bibliography is designed to help you prepare for the larger Research Proposal assignment. This Outline and Bibliography assignment involves formulating your question and hypothesis, providing a brief amount of background information that explains why the topic is interesting or important, and a point-form outline of the methods you would propose to use. A bibliography of at least 20 relevant research papers is also required. You will be graded on the Outline and Bibliography, and the TA will provide detailed feedback that is intended to help you write the full Research Proposal. The mid-term examination will be written during class time. It will cover all material presented during lectures (up to, and including, Nov. 8 th ), and in the assigned readings. It will be in essay format and you will be allowed to use your class notes and textbook in writing your answers. No internet access (wifi or cellular) will be allowed during the exam, including phones. The Molecular Ecology Snippet is a short group presentation that involves presenting, in a fun and engaging way, the results of an interesting recent paper in the field of Molecular Ecology. Students will work in pairs and prepare a five-minute presentation suitable for a general audience (i.e., not scientists). Sign-up for presentation dates will take place in the first week of lecture. Students will be graded on their participation during classes and tutorials. Note that participation involves active and positive involvement in discussions and activities, asking questions, etc. Attendance alone is not sufficient to obtain a good participation grade. Biology 3444f Syllabus 2 of 5
Missing assignments and exams: If you miss any assignment, deadline, or exam, or require an extension, then you must apply for accommodation directly through your Faculty Dean s office. Supporting documentation will be required. This applies to both medical and non-medical excuses. With respect to medical excuses, a link to the University s policy regarding accommodation for medical illness is provided at: www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_illness.pdf. Please read over this carefully. It outlines, and contains a link to, the specific documentation that you must provide in case of illness. A link to the University s policy on accommodation for religious holidays is here: www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_religious.pdf Students who are experiencing emotional or mental distress should refer to MentalHealth@Western (http://www.uwo.ca/uwocom/mentalhealth/) for a complete list of options about how to obtain help. Late submission of work: All work that is handed in late, without an approved extension as outlined above, will be penalized 10% of the value of the assignment for each day (or part of a day) that it is late, including weekend days. Scholastic Offences: All students are expected to know, understand, and follow the codes of conduct regarding scholastic offences. Scholastic offences are taken seriously and students are directed to read the appropriate policy, specifically, the definition of what constitutes a Scholastic Offence, at the following Web site: http://www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf. Please review this information and ask your professor if you have any questions about how it applies to this course. All required papers may be subject to submission for textual similarity review to the commercial plagiarism detection software under license to the University for the detection of plagiarism. All papers submitted for such checking will be included as source documents in the reference database for the purpose of detecting plagiarism of papers subsequently submitted to the system. Use of the service is subject to the licensing agreement, currently between The University of Western Ontario and Turnitin.com ( http://www.turnitin.com ). Accessibility: Please feel free to contact me if you require material in an alternate format or if you require any other arrangements to make this course more accessible to you. You may also wish to contact Services for Students with Disabilities (SSD) at 661-2111 x 82147 for any specific question regarding course accessibility or related accommodation. The University policy on accommodation for students with special needs is here: www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_disabilities.pdf. Biology 3444f Syllabus 3 of 5
BIO 3444 F: Tentative Lecture Schedule Date Topic Chapters from text Sept. 13 Sept. 20 Overview of course. What is Molecular Ecology? History of Molecular Ecology. Overview of techniques. Molecular markers: Characteristics and how to choose the right one. 1 2 Sept. 27 Primer of Population Genetics 3 & 4 Oct. 4 Identifying species, individuals, and sex. Readings will be provided Oct. 11 Molecular tools in behavioural ecology 7 Oct. 18 Conservation Genetics 8 Oct. 25 Molecular tools in community and ecosystem ecology 5 & Additional readings that will be provided Nov. 1 Molecular basis of ecologically important traits 5 & Additional readings that will be provided Nov. 8 Phylogeography and landscape genetics 6 & pgs. 148-154 Nov. 15 Midterm Examination Nov. 22 Nov. 29 Dec. 6 Group Evaluations of Updated Research Proposal Outlines Group Presentations of Research Proposal Evaluations Research Proposal due *** Research Proposal due on Dec. 6th. Biology 3444f Syllabus 4 of 5
Date Sept. 15 Sept. 22 BIO 3444 F: Tentative Tutorial Schedule Topic / Activity What is a Research Proposal? Coming up with Research Proposal ideas. Writing a Research Proposal Sept. 29 Oct. 6 Research Proposal Topic due. Collaborative feedback on Research Proposal topics (group brainstorming) NO TUTORIAL work on your outlines Oct. 13 Oct. 20 Research Proposal Outline & Bibliography due Oct. 27 STUDY BREAK Nov. 3 Nov. 10 Nov. 17 Updated Research Proposal Outline due Nov. 24 Dec. 1 NO TUTORIAL work on your proposals *** Research Proposal due on Dec. 6th. Biology 3444f Syllabus 5 of 5