Fall 2016 Graduate courses

BIO 389D Subjects and Skills for Graduate Students in the Biological Sciences I

Prof. Ulrich Mueller, M 1:00-4:00pm. The class will serve as a general introduction to the writing, presentation and appraisal skills needed to excel in all fields of biological research, and to help prepare graduate students for their qualifying exams. Over the course of the semester, we will focus on four interrelated topics and skills: 1) How to select a research project; 2) How to review a manuscript; 3) How to write a grant proposal; 4) How to give a seminar. The course will include lectures and presentations; but note that these skills are gained primarily through practice and perseverance, so you will need to complete (and evaluate and edit and revise) many assignments in order to develop expertise in each area.

BIO 390C Fundamentals of Evolution

Prof Mark Kirkpatrick, TTH 12:30-2:00pm. The course covers key concepts in evolutionary biology at a graduate level. Topics include: adaptation, population genetics, quantitative genetics, molecular evolution, adaptation, speciation, and phylogenetics. The course combines rigorous mathematical descriptions of evolutionary processes, illustrated with empirical case studies. Lectures cover both classic topics and major open questions in these fields, with an emphasis on interpreting data and reading the primary literature. This is a lecture course with both homework and appreciable reading from the primary scientific literature.

BIO 382K.05 Informatics and Data Analysis in Life Sciences

Prof. Timothy Keitt, TTH 11am-12:30pm. This course will focus on synoptic analysis of large datasets with a particular emphasis on biodiversity and climate, but student activities may focus on any area of life sciences including molecular and organismal data. The objectives hinge on three main questions: 1) How can we inform our research fields through analysis of large datasets?; 2) What are current best practices in “big data” informatics and analytics?; 3) What tools are techniques are available to facilitate learning from big data? We will address these through reading, discussion and hands-on data wrangling. The two major tools of the course will be R, a data-programing platform, and PostgreSQL, a relational database system. The major student products will be documented workflows generating synoptic reports. The course will also survey major topics in data analysis and model fitting as implemented in R. The goal is a basic toolbox for data-driven science.

BIO 384K.29 Recent Advances in Population Ecology

Prof. Norma Fowler, W 2:00-5:00pm. This course is designed to give graduate students an introduction to population ecology. Lectures will stress (a) the fundamental concepts and questions of this field; (b) current research foci and directions in this field; (c) the uses and applications of population models. Labs will train students in constructing and analyzing population dynamic models. Models to be covered include simple geometric and exponential growth; population project models (the current "industry-standard"); and integral population models (IPMs, a recent development that look like they will become the new standard). We will also briefly visit mark-recapture and time series.

BIO 384K Recent Advances in Ecological and Evolutionary Genetics

Prof. Mark Kirkpatrick, TTH 12:30-2:00pm. The course introduces students to population genetics.  The emphasis is on a quantitative understanding of evolutionary change caused by selection, drift, mutation, and migration.  Both phenotypic and molecular evolution will be covered.  Most class meeting will be lectures.  The lectures will be complimented by discussions of assigned readings from recent primary literature.

BIO 384K.39 Phylogenetic Perspectives in Ecology, Evolution, and Behavior

Prof. David Hillis, W 10:00am-1:00pm. The first half of this graduate course consists of lectures on the theory, methods, and applications of phylogenetics in ecology, evolution, and behavior. I will lecture on the development of phylogenetics; the various optimality criteria and their advantages and disadvantages (include non-parametric, semi-parametric, and parametric methods); models of evolution for molecular and morphological data; algorithms and heuristics for searching solution space, including discussion of Bayesian Markov chain Monte Carlo approaches; phylogenetic simulation; statistical assessment of phylogenetic results; molecular clocks; and major applications of phylogenetics. In the second half of the course, enrolled students will select current papers that apply phylogenetic methods in ecology, evolution, and behavior for discussion and critique. My lectures in the second half of the course will be tailored to the individual papers (as selected by enrolled students) to provide sufficient background on the methods used in those papers, to enhance and promote discussion of the papers. These lectures are dependent on the papers selected.

BIO 384K.45 Seminars in Brain, Behavior, and Evolution

Prof. Mike Ryan, F 12:00-1:00pm. This course addresses the general question: Why do animals behave the way they do? Answering this question involves a consideration of both the proximate and ultimate issues of animal behavior, how behavior is acquired and regulated, and how behavior evolved.  The emphasis is on integration of proximate and ultimate analyses.


spring 2017 courses

BIO 389E Subjects and Skills for Graduate Students in the Biological Sciences II

Profs. Hillis and Meyers. The goal of this course is to provide training in the general topics and skills required of research scientists.  The class will focus on the research, teaching, and service skills needed by professional biologists, as well as on the major research themes and questions in ecology, evolution, and behavior.  It builds on the writing skills developed in BIO 384C to include issues of ethical behavior in research, effective presentation of results, oral presentation skills, interacting with the media, work-life balance, and public outreach.

BIO 390E Fundamentals of Ecology

Prof. Mathew Leibold, TTh 3:30-5:00pm. This class will cover basic principles of ecology at a level suitable for graduate students in related fields.  It assumes some background in basics as may have been covered in typical undergraduate curricula in Biology.  The class will have about 2/3 of the effort devoted to lectures and 1/3 to discussion of readings and selected topics.  It will cover basic concepts and explore emerging fields in ecology.

BIO 386K.03 Advances in Plant Systematics

Prof. Bob Jansen. This course is intended to provide graduate students with an in depth understanding of current issues in plant systematics and evolution.  The theme of the course changes each year to provide a broader perspective on current research trends in plant systematics, genome evolution, biogeography and other related topics in plant biology.  This semester’s theme is Plant Phylogenomics.

BIO 380C/BIO 375 Advanced Conservation Biology

Prof. Norma Fowler, TTh 9:30-11am. One definition of conservation biology is the application of biological concepts, facts, methods, and questions to the preservation of biological diversity. In this course we will focus upon the applications of ecology (in the academic sense), and more specifically upon applications of population and community ecology. Goals of the course include (a) providing a survey of current concepts, questions, and topics in conservation biology; (b) increasing student skills in identifying, locating, interpreting, and synthesizing both standard scientific publications and the extensive “gray literature” (government documents, for example) so important in conservation biology; and (c) identifying conflicts among values and other non-science factors that impact the application of science to biodiversity conservation. In addition to written exams, graduate students will complete an annotated bibliography, term paper, and short oral presentation, all on a single topic that is relevant to the course and, if desired, to their own research interests.

BIO 380E/BIO 364 Advanced Microbial Ecology

Prof. Christine Hawkes. A graduate-level lecture and discussion course concerning the ecological role of microbes in species interactions, population dynamics and ecosystem processes.

BIO 380G Methods in Ecological Genomics

Prof. Mikhail Matz. The class aims to teach state-of-the-art methodologies for:  (i) genomics-based demographic and population structure analysis; (ii) detection of genomic signatures of natural selection; (iii) analyzing gene expression in EEB context; (iv) quantification of complex communities using metabarcoding.  Half of the class consists of lectures and discussions of current literature, the other half being bioinformatics exercises and problem solving tasks to develop bioinformatics skills.

BIO 380S/BIO 359R Animal Sexuality

Prof. David Crews. This is a survey course and designed to teach both the fundamentals and the principles of modern research in sexuality. At the same time you will learn how to analyze and synthesize diverse scientific information. The course is roughly divided equally into two sections.The first half of the course will emphasize fundamentals and principles of modern research in sexuality. This will include the environmental regulation of reproduction, different mechanisms of sex determination, where and how protein and sex steroid hormones are produced and released and where and how they exert their action, the development of eggs and sperm (the gametes), how the brain, pituitary, and gonads interact to control and coordinate gamete production, how hormones exert their action at a genetic level, the effects of hormones early in life compared to later in life, and the structure and function of various brain areas that are important in the regulation of reproductive behaviors. The second half of the course will build on this information. It is essential that you know the principles from the first half as in the second half we learn about how hormones organize and modify female and male sexual and parental behaviors, the effects of stress on sexuality, the adverse effects of synthetic chemicals such as pesticides and fertilizers on wildlife and humans due to their mimicking the action of steroid hormones, how chemicals produced by one animal influence other individuals (pheromones) and how the production of these pheromones are controlled by hormones and sexual behaviors, how social organization can control of sexuality, and how hormones can influence how animals perceive the world around them.

BIO 382K Introduction to Biology for Data Science

Prof. Hans Hofmann, W 9:00am-12:00pm. This course covers fundamental concepts and experimental methods in genomics, systems biology, neuroscience, and bioinformatics. The course is designed to introduce graduate students with little biological training to the modern life sciences, with a focus on “Big Data in Biology.”

BIO 382K.04 Advances in Biological Statistics

Prof. Dan Bolnick. This course provides an overview of applied data analysis, geared toward research questions in ecology, evolution, and physical anthropology. The course is designed to give students hands-on training in the conventional scientific workflow that follows data collection, including database management, exploratory data analysis and visualization, statistical analysis and interpretation. Statistical topics will focus on advanced techniques that are rarely covered in introductory statistics courses, but frequently used by biologists. Topics will include univariate and multivariate hypothesis testing, general linear models, likelihood and Bayesian estimation, structural equation modeling, as well as more specific tools suited to student interests. The course focuses on the practical side of implementing these techniques, using the statistical programming language R, while also introducing students to other useful software tools (e.g., python, MySQL, Unix shell, SYSTAT). Throughout, emphasis will be placed on when and how to use these methods in practice, and students are encouraged to use their own datasets in the course.

BIO 382K.06 Programming for Biology

Prof. Craig Linder. A lecture and computer-lab based course that teaches students programming skills that are relevant to research in the biological sciences, including but not limited to programming in Python, R, Perl, C++. The exact focus of the course may vary from semester to semester. The course may be taken for credit multiple times when the course content varies.

BIO 384K.33 Ecosystem Services

Prof. Shalene Jha, W 3:00-6:00pm. This course uses an interactive graduate seminar format to cover advanced topics in conservation with a special emphasis on Ecosystem Services.  Ecosystem services include a broad array of ecological functions that benefit humans, including food provision, climate regulation, pest-control, and recreation, amongst many others.  In this course, we will discuss a mixture of foundational as well as recent papers that cover a wide range of topics related to quantifying ecological function and ecosystem services.  Topics include the exploration of abiotic and biotic drivers of ecosystem services, optimization and trade-offs in ecological function and ecosystem services, and valuation of ecosystem services for conservation.

BIO 384K.40 Recent Advances in Biogeography and Phylogeography

Prof. David Cannatella, TTh 9:30-10:45am. This course will examine new trends in phylogeographic and biogeographic research, with an emphasis on formulating general questions/hypotheses. My general lectures will include the history and theory of historical biogeography and phylogeography, emphasizing questions that focus on both ecology and evolution. I will also give lectures about current topics from papers selected by students, to facilitate discussion and critique of these. Students will get hands-on experience with computational methods (using Unix software, python, and R) for analyses such as species distribution modeling, isolation by resistance, vicariance and dispersal, etc.

BIO 384K.45 Seminars in Brain, Behavior, and Evolution

Prof. David Crews. This course is largely focused onreading and discussing a new book relevant to Physiology and Behavior, with chapters presented by registered students.