School of Graduate Studies

School of Graduate Studies
School of Graduate Studies

Biology

BIOL-860 to BIOL-865 inclusive are modules worth 1.5 credit units each.  All other  courses are half-courses (3.0 credit units) which are offered either in the fall or winter term if there is sufficient student interest. Detailed outlines of course content are available during the summer of each year. Most courses are offered in alternate years.

BIOM-800*     Introduction to Mathematical Modeling in Ecology and Evolution       
Modeling will be presented in the context of biological examples drawn from ecology and evolution, including life history evolution, sexual selection, evolutionary epidemiology and medicine, and ecological interactions.  Techniques will be drawn from dynamical systems, probability, optimization, and game theory with emphasis put on how to formulate and analyze models. Three term hours.

BIOL-801*     Evolutionary Medicine     
A survey of the ways in which concepts from evolutionary biology can be used to better address and understand issues related to human health. Topics might include the evolutionary biology of infectious diseases, the utility of phylogenetics in infectious diseases, the evolution of drug (e.g., vaccines) and antibiotic resistance, the evolutionary biology of human genetic disorders, aging and senescence.   Three term hours; fall.

BIOL-806*     Plant Molecular Biology     
Model systems for plant molecular genetics; gene identification and cloning; gene transfer techniques including vector construction; transposons; genetic regulation and expression.

BIOL-811*     Plant Metabolism     
This course explores contemporary research ideas and techniques used to elucidate plant metabolism and its control. Topics include plant signal transduction, plant metabolic adaptations to abiotic and biotic stress, as well as the application of proteomics, genomics, and molecular biology for comprehending plant metabolism and the production of 'improved' transgenic crops via metabolic engineering.

BIOL-812*     Introduction to computational analysis in biology     
This course will be a hands-on introduction to essential bioinformatics skills. The goal is to build a foundation of computational skills that enable analysis of large biological data. We will learn command-line Unix/Linux, shell scripting, and installation/testing/usage of popular public bioinformatics packages. We will spend significant time learning Perl and/or Python and Matlab. The course will rely heavily on problem-based learning and in-class discussion. Assignments will involve analyses that use primary literature data, particularly next-gen sequencing data. 50% of the final grade is based on a research project conceived and carried out independently. No prior programming experience is necessary.

BIOL-817*     Contemporary Issues In Biology     
The focus will be on biological issues of current importance to provide a broad exposure within a range of specific disciplines. Topics will include critical analysis of biological issues that have been featured as news items either in the popular press or in science news journals within the previous 12 months. Three term-hours; winter.

BIOL-818*     Stress Biology     
Environmental stress is addressed with respect to water, nutrition, temperature, toxins, and competition between organisms. Topics include adaptations to cope with stress; biological responses at the organismal, cellular, biochemical, physiological and molecular genetic levels. No specialized molecular biology background is required. Three term hours; fall.

BIOL-819*     Selected Topics in Molecular Genetics     
Topics will range from population genetics to transcriptional regulation in both plants and animals. Application of the tools of molecular genetics to biological problems will be emphasized. No previous specialization in molecular biology is required, although some background in this area is highly recommended. Three term hours; Fall. P. Young.

BIOL-820*     Commercialization of Biological Research     
Current issues relating to the biotechnology industry will be dealt with in detail. Topics covered include: grant writing; patenting; circumventing patents; funding sources; business plans; venture capital investments; public awareness; public perspective; and layperson presentations. Three term hours. PREREQUISITE: At least one of the following: BIOL-201*, BIOL-205*, MBIO-318*, BIOL-441*, BIOL-330*/430* or equivalent.
EXCLUSION: PHGY-801.

BIOL-821*     Communication Skills     
Scientific writing and methods for the presentation of research in seminars, posters, and the popular media. Three term hours.

BIOL-822*     Long-Term Environmental Change     
The main focus of this course will be to review and assess the many techniques currently available to track long-term environmental change. An emphasis will be placed on biological approaches dealing with sedimentary analyses, but other proxy methods (e.g. ice cores, bore holes, etc.) will also be covered. General topics to be covered will include climatic change, acidification, eutrophication, lake and reservoir management, UV penetration, etc.

BIOL-824*     Gateway to graduate studies     
This course will introduce intellectual and professional skills important for success in graduate school and in careers in Biology. Course structure and content is applicable to all fields of biology, from ecology and evolution to cell biology, biochemistry, and molecular biology. Sessions will span topics from study design and hypothesis testing, to communication skills, to career paths and mentoring. The final assignment will be a written research proposal, following the departmental guidelines for the PhD proposal. The goals of the course include 1) introducing graduate students to an array of skills and topics important to their success, 2) helping to develop a community among new graduate students, 3) improving students' communication skills, and 4) introducing graduate students to several Biology faculty who will lead some of the sessions. Students are required to attend a mandatory weekend at the Queen's University Biological Station, with a cost-recovery fee for accommodation and meals.

BIOL-830*     Ecological and Evolutionary Genetics     
Each year brings new molecular tools and significant advances in analytical techniques for using molecular data to address evolutionary and ecological questions. This course is an exploration of these with emphases varying from year to year depending on the expertise of the instructor. Topics may span natural selection and phenotypic plasticity, parentage and mating systems, speciation, hybridization, macroevolution, and phylogenetics.Students gain a thorough theoretical grounding of pertinent topics via lectures, student seminars, and readings from the current primary literature. Hands-on analytical experience will be provided through student exercises using the latest software applications.Three term hours.

BIOL-831*      Bioremediation     
Bioremediation is the use of organisms to alleviate environmental problems.  Topics will include the biology of the organisms involved and their bioremediation processes.  Plants act to absorb and concentrate heavy metals from soils whereas micro-organisms, invertebrates and plants degrade organic toxins and remove excess nutrients from soils, substrates and water.  The processes include extraction, absorption, concentration, and degradation of contaminants.

BIOL-839*     Plant Ecology and Evolution     
Mechanisms of natural selection involving adaptive strategies for growth, survival and reproduction in plants and the consequences of this selection on the characteristics of plant populations and communities. Recent research topics and theoretical developments are stressed. Three term hours; fall.

BIOL-843*     Advanced Data Management and Experimental Design     
This course provides an introduction to advanced statistical methods (multivate analysis, randomization methods, phylogenetic analysis) and experimental design for biologists. The emphasis is on problem solving and the use of microcomputers for data acquisition, management, analysis and publication. Three term hours; fall.  PREREQUISITE OR COREQUISITE: BIOL-343* or equivalent.

BIOL-847*     Data Analysis in Community and Paleoecology     
A variety of quantitative techniques are now being used increasingly in the fields of community ecology, paleoecology and paleolimnology (e. g. linear and unimodal regression and calibration, direct and indirect multivariate ordination, quantitative reconstruction models, rate of change analysis and analysis of spatial and temporal data). This course will investigate these computational techniques and explore their applications in the above mentioned fields. This course assumes a working knowledge of classical statistics. Three term hours; Winter. B.F. Cumming.
PREREQUISITE: BIOL-343* or permission by instructor.

BIOL-848*     Field Course in Population Biology     
This is a two-week field course designed to introduce graduate students to field research problems and methods in behavioural ecology, ethology, population and community ecology, and ecological genetics. The course consists of lectures, field research projects and data analysis. Fall/Winter/Summer.  C.G. Eckert, S. Lougheed, and Y. Wang.

BIOL-849*     Environmental Issues     
Consideration will be given to environmental, legal, economic, political, sociological and biological aspects of current issues in the management of the Great Lakes. Models for managing nutrients, toxics and fisheries will be compared from a multidisciplinary viewpoint. Three term hours.

BIOL-850*     Darwinism and cultural evolution     
Contributions of Darwinian evolutionary theory to the understanding of contemporary culture. Through seminars, essays, and group discussions, students explore ideas, research objectives, and recent discoveries in applying Darwinism to the interpretation of cultural products like art and literature, social-cultural institutions like religion and marketing, societal problems like war and environmental conservation, and emerging designs for new models of sustainable civilization in the 21st century. EXCLUSION: BIOL-535

BIOL-855*     Conservation Biology     
Key issues in conservation biology will be explored in seminars and discussions. Topics will include: minimum viable populations, habitat configuration and sustainable populations, biodiversity, habitat fragmentation, edge effects, keystone species, meta-populations, restoration ecology, endangered species, inbreeding, heterozygosity and fitness, genetics of captive breeding, population genetics and conservation. Three term hours; winter.

BIOL-860     Introduction to Management and Statistical Analysis of Biological Data     
This course is for new graduate students who are at early stages of planning their research projects and collecting data. Topics will include experimental design, matching hypotheses with appropriate statistical analyses, parameter estimation, and graphing. Statistical analyses will be based on a foundation using normal error distribution. Students will be introduced to R, a Language and Environment for Statistical Computing. 1.5 credit units. Lectures (1.5 hrs) tutorials (1.5 hrs); Fall. S. Arnott. Enrolment is limited to 12 students.EXCLUSION: BIOL-843

BIOL-861     Introduction to Linear Models for Biological Data     
This course is designed for Biology graduate students with a basic introductory statistics/experimental design course and a working knowledge of R, a Language and Environment for Statistical Computing. In-depth exploration of all aspects of fitting linear models to continuous and categorical data, using mainly the lm function in R. Topics include residual analysis, maximum-likelihood methods, graphical presentations, ordinary least squares, model II regression, transformations, model selection with focus on information-theoretic approaches and outlier detection. 1.5 credit units. Lectures (1 hr); Seminars (0.5 hrs); Tutorials (1.5 hrs); Fall. W. Nelson. Enrolment:10 MSc students; 5 PhD students, postdocs and/or faculty.

BIOL-862     Application of Generalized Linear Models to Biological Data     
Biological systems often involve data that are enumerated as counts, densities, or proportions that require non-Normal analysis tools. This course introduces biologists to the framework of Generalized Linear Models (GLMs) and includes topics such as logistic regression, overdispersion and Poisson, Quasi-likelihood, Negative Binomial and Gamma models. Emphasis will be on both the foundation of GLMs and the practical application using R. 1.5 credit units. Lectures (1.5 hrs); Tutorials (1.5 hrs). Winter; W. Nelson. Enrolment:15 students (MSc/PhD).

BIOL-863     Multivariate statistics for Biological Data     
Biologists often measure multiple characteristics of biological systems. The analysis of these data (for example, measures of habitat characteristics, morphological measures plants/animals) require multivariate statistical techniques. This course will cover multiple regression, MANOVA, indirect and direct gradient analyses. Students will use R, a Language and Environment for Statistical Computing as practical platform for these tools. 1.5 credit units. Lectures (1.5 hrs); Tutorials (1.5);  Winter; S. Arnott. Enrolment:15 MSc/PhD students.

BIOL-864     Introduction to Mixed Effects Models for Biological Data     
The course will focus on the use of mixed models that include random effects for biological data. Topics will include partitioning of random variance, nested, partially-nested and repeated-measures experimental designs, and modern aproaches to evaluating competing models. Students will gain in-depth experience using R, a Language and Environment for Statistical Computing. 1.5 credit units. Lectures (1.5 hrs); Tutorials (1.5 hrs); Enrolment:12 MSc/PhD students.

BIOL-865     Advanced Statistical Analysis of Biological Data     
A course in advanced statistical techniques for biological data. Possible topics include comparative methods, phylogenetic analysis, general additive models, nonlinear regression, network analysis, time series analysis, resampling, path analysis. Topics covered will depend upon student and faculty interests. 1.5 credit units. Lectures (1.5hrs); Tutorials (1.5 hrs). Enrolment:Course enrolment will be limited to 12 MSc/PhD students.

BIOL-893 Mentoring Experience in Biology
Students will advise and train other students in biological investigations, normally over a two term period. Open to full-time students having completed two terms of study in Biology M.Sc. or Ph.D. programs. Activities include guidance on research proposals, research procedures, student presentations, and drafts of student work. This is a non-credit course, graded on a Pass/Fail basis.  PREREQUISITE: Permission of Coordinator of Graduate Studies

BIOL-897*     Seminar Course     
Attending a diverse array of seminars is an essential component in the development of a student, especially in a department as diverse as biology.  The aim of this course is to develop skills in listening, synthesizing and critical thinking, as well as fostering the development of important oral and written communication skills.  Students will be required to attend at least 30 department or specialized research seminars, as well as present a seminar based upon their graduate thesis research.  Enrolment is extended over six terms and is limited to new graduate students in Biology. Fall/Winter/Summer. K. Ko and L. Seroude.

BIOL-899     Master's Thesis Research     

BIOL-951*     Advanced Studies in Ecology, Evolution and Behaviour I     
Selected topics in ecology, evolution and behaviour. An advanced course on current research in ecology, evolution and behaviour, based on recent research literature. For detailed information, consult the course coordinator. Three term hours; Fall. F. Bonier.

BIOL-952*     Advanced Studies in Ecology, Evolution and Behaviour II     
Selected topics in ecology, evolution and behaviour. An advanced course on current research in ecology, evolution and behaviour, based on recent research literature. For detailed information, consult the course coordinator.

BIOL-953*     Advanced Studies in Plant Sciences I     
Selected topics in plant sciences. An advanced course on current research in plant science, based on recent research literature. For detailed information, consult the course coordinator.

BIOL-954*     Advanced Studies in Plant Sciences II      
Selected topics in plant sciences. An advanced course on current research in plant science, based on recent research literature. For detailed information, consult the course coordinator.

BIOL-955*     Advanced Studies in Molecular and Cellular Biology I     
Selected topics in molecular biology. An advanced course on current research in molecular biology, based on recent research literature. For detailed information, consult the course coordinator. Three term hours; Winter. T. Babak.

BIOL-956*     Advanced Studies in Molecular and Cellular Biology II     
Selected topics in molecular biology. An advanced course on current research in molecular biology, based on recent research literature. For detailed information, consult the course coordinator. Fall. W. Snedden.

BIOL-957*     Advanced Studies in Animal Physiology I     
Selected topics in animal physiology. An advanced course on current research in animal physiology, based on recent research literature. For detailed information, consult the course coordinator.

BIOL-958*     Advanced Studies in Animal Physiology II      
Selected topics in animal physiology. An advanced course on current research in animal physiology, based on recent research literature. For detailed information, consult the course coordinator.

BIOL-959*     Advanced Studies in Environmental Sciences I     
Selected topics in environmental sciences. An advanced course on current research in environmental sciences. For detailed information, consult the course coordinator.

BIOL-960*     Advanced Studies in Environmental Sciences II     
Selected topics in environmental sciences. An advanced course on current research in environmental sciences. For detailed information, consult the course coordinator.

BIOL-999     Ph.D. Thesis Research