The Department of Ecology
and Evolution
Graduate Course Description
(Revised June 2007)
30600. MOLECULAR
EVOLUTIONARY GENETICS. (=EVOL 30600).
This course deals with advanced topics in evolutionary genetics and
molecular evolution. The main goal is to
survey the frontiers and to develop research projects of the future. C.-I. Wu
30700. COMPUTATIONAL
BIOLOGY. (=EVOL 30700). This course provides mathematical and statistical
backgrounds and computational skills in computational biology. Laboratory
sessions are an integral part of the course, so students can have hands-on
practice of computer skills. Topics will cover theory and methods for
comparative analyses of DNA and protein sequence data; statistical tests of
molecular clocks; methods of phylogenetic reconstruction and statistical tests
of phylogenies; gene identification in DNA sequences; protein homology
detection; and structure prediction methods using protein sequences.
Prerequisite: BIOS 18200; Math 15300; Stat 24400-24500 (or equivalent), or
consent of instructor. W.-H. Li.
30800. CURRENT TOPICS IN EVOLUTIONARY GENOMICS.
(=EVOL 30800). This course will cover current topics in evolutionary genomics
including comparative genomics, evolution of duplicate genes, evolution of
genome structure and organization, evolution of protein-protein interaction
network, and evolution of gene expression. It will also review methods for data
analyses. Some background in molecular evolution is required. W.-H. Li.
30900. EVOLUTION AND MEDICINE. (=EVOL 30900, CHSS
39600, BIOS 29285, GNDR 26600). A seminar-reading-discussion course on medical
implications of different areas in the evolutionary half of biology, with
special attention to brain and sex. L. Van Valen, M. Stoller.
31000. EVOLUTIONARY
PROCESSES. (=EVOL 31000, BIOS 29306, CHSS 34800). Discussion, essays, and much
reading on conceptual and empirical aspects of the evolutionary half of
biology. Also a laboratory in the philosophy of science. Prerequisite: consent of instructor. L. Van Valen.
31200. DATA ANALYSIS IN
ECOLOGY AND EVOLUTION. (=EVOL 31200). This course covers the design and
analysis of experiments, focusing on tests used commonly in evolutionary
biology. Both parametric and nonparametric tests will be considered. J.
Bergelson, T. Price
31300. ECOLOGICAL APPLICATIONS
TO CONSERVATION BIOLOGY. (=EVOL 31300, BIOS 23351). We focus on the
contribution of ecological theory to the understanding of current issues in
conservation biology. The course emphasizes quantitative methods and their use
for applied problems in ecology, such as the design of nature reserves, the
risk of extinction and the impact of harvesting, the dynamics of species
invasions, and the role of species interactions. Course material is drawn
mostly from the current primary literature. Two Saturday field trips and
computer modeling labs are in addition to scheduled class time. J. Bergelson,
C. Pfister.
31400. GEOGRAPHICAL
VARIATION. (=EVOL 31400). Theoretical and empirical aspects of geographical
variation in population genetics will be treated. Theoretical topics will
include protected polymorphism and clines maintained by migration and
selection; random genetic drift in a cline; and spatial patterns under
migration, mutation, and random genetic drift. Estimation from molecular
gene-frequency data of parameters that describe population structure and the
relative contribution of random genetic drift and natural selection will be
covered. Offered in even-numbered years. Prerequisite: basic population
genetics. M. Kreitman, T. Nagylaki
31500. ECOLOGICAL GENETICS.
(=EVOL 31500). A graduate class in ecological
genetics (evolution of the phenotype, without considering molecular
approaches). This will be a weekly
2-hour seminar, emphasizing quantitative genetic approaches. Basic theory will cover such topics as
heritability and breeding value, genetic correlation, Price’s theorem and
sexual selection. Seminars will include
discussions of current topics from the literature. T. Price.
31600. Smallpox, mumps, and beyond: vaccination
strategies in an age of emerging infectious diseases. The looming threats of bioterrorism and
emerging diseases arouse the specters of wide-spread death and suffering. Meanwhile, mistrust of science is leading
many parents to withhold vaccines from their children, leading in turn to
rising levels of childhood diseases. Addressing these risks requires innovative
vaccination strategies. An important
tool for evaluating vaccination strategies comes from mathematical models of
epidemics. But how can a health-care
professional understand the uses of models without a Ph.D in math? In this course, we will learn how to evaluate
models of vaccination strategies, from the perspective of officials charged
with constructing public-health policy.
Students will not need any more math than the vague memory that they
might once have known what a derivative is. G. Dwyer
32500. EVOLUTIONARY ASPECTS OF GENE REGULATION
(=EVOL 32600, BIOS 23281, GENE 32500, DVBI 32500) Ruvinsky. Using primary research literature, this course will examine recent
advances in understanding of evolution of gene regulation. Among others it will
cover the following topics: patterns and forces of evolutionary change in
regulatory DNA and transcription factors, genetic changes that are responsible
for phenotypic evolution, and discovery and evolutionary of implications of
gene control by microRNAs.
32900. PLANT
DEVELOPMENT AND MOLECULAR GENETICS (=BIOS 23299, DVBI 36100, MGCB 36100). This course describes the growth
differentiation and development of plants at the organismal, cellular, and
molecular levels. Emphasis is placed on the regulatory function of plant
hormones, particularly in response to environmental stimuli and in control of
gene expression. Recent advances in using molecular genetic approaches in Aribidopsis and maize are a central
feature of this course. M. Ruddat, J Greenberg.
34600. CURRENT ISSUES IN
EVOLUTION. (=EVOL 34600). A seminar on unresolved problems in the evolutionary
half of biology. Prerequisite: consent
of instructor. L. Van Valen.
34700. EVOLUTION OF
DEVELOPMENT. (=EVOL 34700). A seminar on developmental aspects of evolution and
evolutionary aspects of development. Prerequisite: consent of instructor. N.
Shubin, L. Van Valen
35000. EVOLUTIONARY ECOLOGY.
(=EVOL 35000). An evolutionary approach to the study of ecological interactions. Topics include plant-animal interactions,
life history evolution, host-parasite and host-mutualist interactions,
competition, and predation. Appropriate
for graduate students who have had little background in ecology. J.T. Wootton.
35200. PALEOBIOLOGY OF
MAMMALS. (=EVOL 35200). Detailed treatment of mammalian evolution, including
all recognized families, and its various evolutionary implications.
Prerequisite: chordate biology or equivalent or consent of instructor. (Offered alternate years.) L. Van Valen.
35600. PRINCIPLES OF
35700. PRINCIPLES OF
POPULATION GENETICS II. (=EVOL 35700). Continuation of EVOL 35600. R. Hudson, T. Nagylaki.
35800.
Classics of Evolutionary Genetics. (=EVOL 35800). Major Classic papers in evolutionary
genetics that had great impact on the development of the field are reviewed.
W-H Li, M. Long.
35901. EvolutioNARY GENOMICS. (=EVOL 35901,
GENE 35901). We focus on the newly proposed and solved problems related to
evolution of genomes. Instructors will give a series of lectures, dealing with
basic concepts and techniques used in the research of topics. Students will
present and evaluate literatures. M. Long, M. Kreitman.
36200. CURRENT TOPICS IN
EVOLUTIONARY BIOLOGY. (=EVOL 36200). Critical analysis of recent literature on
empirical research in evolutionary biology. Prerequisite: some knowledge of
population genetics, evolutionary biology or consent of instructor. J. Coyne
36300. SPECIATION. (=EVOL
36300). A review of the literature on the origin of species beginning with
37500. SEXUAL SELECTION.
(=EVOL 37500). A discussion and critical analysis of sexual selection. The
course will consist of lectures, reading and discussion. Prerequisite: Common
Core Biology, BIOS 248, or consent of instructor. (odd-numbered years.) S.
Pruett-Jones.
40100. GRANTS, PUBLICATIONS,
AND PROFESSIONAL ISSUES. (=EVOL 40100). Covers professional topics in
evolutionary biology, such as strategies in grant and article writing,
construction and submission of professional articles for journals in the field,
career alternatives and strategies, ethical issues, etc. Topics are decided
upon by enrolled students and faculty leading the seminar. J. Bergelson, .
42500. CONCEPTS IN ECOLOGY.
(=EVOL 42500). Using a combination of lecture and student-led discussion, this
course will introduce students to the classical ecological literature as well
as the latest work in each of several topics. The goal is to provide students
with a solid framework upon which to build their own research program. J.
Bergelson, C. Pfister, J. T. Wootton.
42600. COMMUNITY ECOLOGY.
(=EVOL 42600). Lectures cover advanced topics in multi-species systems, and
include an introduction to basic theoretical approaches. J. T. Wootton.
42700. TOPICS IN AQUATIC
ECOLOGY. (=EVOL 42700). Theoretical and empirical topics especially relevant to
the ecology of aquatic systems will be presented. Emphasis will be placed on
features of aquatic systems that pose theoretical and empirical challenges such
as the prevalence of complex life histories, the potential for long-distance
dispersal, and the diverse controls of trophic structure. C. Pfister.
42800. Population Ecology. (=EVOL 42800.) A
lecture course on the empirical and theoretical approaches to the study of
natural populations, including field methodologies and quantitative approaches.
Includes computer assignments. C. Pfister
42900. THEORETICAL ECOLOGY.
(=EVOL 42900). An introduction to mathematical modeling in ecology. The course
will begin with linear growth and Lotka-Volterra models, and proceed to partial
differential equations. The course's perspective will emphasize numerical
computations and fitting models to data. P. Amarasekare, G. Dwyer
43000. ECOLOGICAL GENETICS
OF PLANT-ENEMY INTERACTIONS. (=EVOL
43000). This seminar covers current empirical and theoretical issues in the
study of coevolutionary interactions. J. Bergelson, G. Dwyer
43100. APPLICATIONS OF
ECOLOGICAL THEORY. This course focuses on applying ecological theory to
empirical investigations. The emphasis is on reading the most recent
articles on a topic of intense current interest, with an eye towards
identifying areas in which crucial new contributions could be made. The
themes discussed in the past include spatial dynamics, diversity-stability
relationships, and biodiversity and ecosystem functioning.
44000. FUNDAMENTALS OF
MOLECULAR EVOLUTION. (=EVOL 44000, BIOS 23256). The comparative analysis of DNA
sequence variation has become an important tool in molecular biology, genetics,
and evolutionary biology. This course covers major theories that form the
foundation for understanding evolutionary forces governing molecular variation
and divergence and genome organization. It explores the evolutionary assembly
of genes, the origin of novel gene function, the population genetics of
repetitive DNA variation, and the evolution of multi-gene families. The course
also provides practical information on accessing genome databases, searching
for homologous sequences, aligning DNA and protein sequences, calculating
sequence divergence, producing sequence phylogenies, and estimating
evolutionary parameters. The course consists of lectures and computer
laboratories. M. Kreitman, T. Nagylaki.
44100. MOLECULAR METHODS IN
ECOLOGY AND EVOLUTION. (=EVOL 44100). This is a laboratory course intended as
an intense introduction to molecular methods applicable to research in
organismal biology. The topics covered by the course will change from year to
year. Students will learn techniques for manipulating DNA, for identifying
single base substitutions and tandem repeat length variation, and for carrying
out large-scale mapping experiments of a quantitative trait. Class enrollment
will be limited to approximately 6-8 students. J. Bergelson, M. Kreitman.
45300. MODELS OF ANIMAL
BEHAVIOR. (=EVOL 45300). Introduction to mathematical models of naturalistic
behavior. Lectures, discussions and
individual projects. (even-numbered years.) S. Pruett-Jones.
49500. TEACHING IN ECOLOGY
AND EVOLUTION. Under the supervision of University faculty, graduate students
in Ecology and Evolution may serve as teaching assistants for courses in the
College and relevant Graduate Divisions. Students will be evaluated and
mentored throughout the quarter by their faculty supervisor, and at the end of
the quarter by enrolled students. Prerequisite:
successful fulfillment of the BSD teaching requirement and consent of
instructor. Staff.
49700. GRADUATE
49800. GRADUATE RESEARCH -
Off Campus. Advanced research under the direction of the faculty of the
Department of Ecology and Evolution, undertaken away from the
49900. GRADUATE RESEARCH -
On Campus. Advanced research under the direction of the faculty of the
Department of Ecology and Evolution. Staff.