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Fall 2018 Graduate courses

BIO 380 Population Genetics

Prof. Kirkpatrick, TTh 3:30-5:00pm. 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.

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.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.

BIO 389D Subject/Skills Graduate Students in Biological Sciences I

Prof. Jha, W 9:00 am-12:00 pm. Designed for first-year graduate students in ecology, evolution, and behavior. Provides training in many of the skills required of research scientists. Introduction to the writing, presentation and appraisal skills needed to excel in all fields of biological research.


spring 2019 courses

BIO 380C/BIO 375 Advanced Conservation Biology 

Prof. Norma Fowler. 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.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 382L Introduction to Biology for Data Science

Prof. Hans Hofmann. 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 384K.38 Recent Advances in Ecological and Evolutionary Genetics: Behavioral Epigenetics

Prof. Phelps. Behavioral Epigenetics surveys the how stable changes in behavior emerge during development and across generations. The course synthesizes evolutionary and ecological work on phenotypic plasticity, behavioral neuroscience, and the molecular biology of transcription, to understand how and why nervous systems respond to environmental variation.

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

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

BIO 384L Issues in Population Biology

Prof. Mueller.

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 387J/BIO 374 Plant Anatomy

Prof. Boucher.

BIO 187L/BIO 174L Plant Anatomy Lab

Prof. Boucher.

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

Profs. Crews and Farrior. 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 390C Fundamentals of Evolution

Prof. Mark Kirkpatrick and Randy Linder. This course introduces the fundamental concepts and facts of evolutionary biology.  Topics include natural and sexual selection, population genetics, molecular evolution and genomics, speciation, and phylogenetics.  Lectures will be complemented with assigned reading and a writing assignment.