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Department of Ecology and Evolution

This is an archived copy of the 2012-13 catalog. To access the most recent version of the catalog, please visit


  • Joy Bergelson


  • Joy Bergelson
  • Jerry Coyne
  • Richard R. Hudson
  • Martin Kreitman
  • Manyuan Long
  • Trevor D. Price
  • Molly Przeworski
  • John Reinitz
  • Kevin White
  • J. Timothy Wootton
  • Chung-I Wu

Associate Professors

  • Gregory Dwyer
  • Stephen Pruett-Jones
  • Catherine Pfister
  • Ilya Ruvinsky

Assistant Professors

  • Stefano Allesina
  • Jack Gilbert
  • Marcus Kronforst

Emeritus Faculty

  • Wen-Hsiung Li
  • Thomas Nagylaki
  • Manfred D.E. Ruddat
  • Janice B. Spofford

Research Associate

  • Michael Z. Ludwig


Department of Ecology and Evolution

The Department of Ecology and Evolution provides training for research and teaching in the ecology, evolution and behavior of whole organisms, at the levels of the organism, the population, and the ecosystem. The research interests of our faculty include molecular evolution, population genetics, quantitative genetics, animal behavior, plant and animal ecology, evolutionary theory, systematics, paleontology, and related subjects. Individual levels of study range from molecules to communities. A common theme is the conduct of studies in a rigorous ecological and conceptual context, and the faculty share an interest in the architecture of populations, species and communities.

The department stresses scientific breadth and the interrelations between various specialized fields. Students are encouraged to approach basic biological problems with the most appropriate techniques: biophysical, biochemical, mathematical, physiological, or organismal. Departmental laboratories are equipped for a wide variety of contemporary research methods. Courses in other departments may be taken for credit in ecology and evolution for example, in the Departments of Organismal Biology and Anatomy, Biochemistry and Molecular Biology, Molecular Genetics and Cell Biology, Statistics, Geophysical Sciences, Anthropology, and Chemistry. Many students in the Department of Ecology and Evolution participate in interdepartmental programs in genetics, cell biology, developmental biology, population biology, theoretical biology, and evolutionary biology, and in these programs dissertation research may be co-sponsored by faculty from different departments. Collaboration is also maintained with the Field Museum and the Shedd Aquarium for students interested in research in systematics, taxonomy, and evolutionary biology, and with the Brookfield Zoo for basic research in conservation and behavior involving zoo animals. Possibilities also exist for field studies in Central America, Africa, and other regions of the earth.

Program of Study

Most students in the Department of Ecology and Evolution complete their Ph.D. program in about five years, though students entering with master’s degrees may finish in slightly less time. A student advisory committee advises all incoming and second year students on academic and research concerns. The first and second years consist largely of course work and individual reading courses, aiming toward successful completion of an oral general knowledge examination by the spring quarter of the first year, supervised by the student advisory committee. The student and faculty advisor in consultation with the Department chair, then choose a five member faculty doctoral committee, scheduling a defense of the dissertation research proposal by the end of the second year of study. Work in subsequent years shifts to dissertation centered research and, finally, preparation and defense of the Ph.D. dissertation. All students are required to register to be a supervised teaching assistant in two approved courses during their tenure in the doctoral program. While there is no master’s program in the department, students may elect to receive the S.M. degree upon successful completion of their dissertation proposal defense.

Entrance Requirements

Entering students are expected to have received a broad undergraduate training in biology, and a good background in related quantitative subjects, such as chemistry, statistics and calculus. Students who are admitted without having fully satisfied these requirements will be required to remedy their deficiencies by taking appropriate courses during their first two years in the graduate program.

General Knowledge Examination

Each first year student will be expected to pass an oral general knowledge examination during the first year of study, generally no later than the 10th week of the spring quarter. This examination session shall be attended by all three members of an examination committee appointed by the student advisory committee. The goal of the examination will be to assess each student’s general knowledge of key concepts, processes and issues in ecology and evolutionary biology, as covered in the courses recommended to the student by the student advisory committee during the student’s first year in the program.

Dissertation Proposal Defense

This examination consists of the submission of a written Ph.D. research proposal and an oral presentation of the proposal in a public or closed/private seminar format, followed by a closed discussion and examination on the proposal presentation with the faculty committee chosen by the student and the chair of the department. Students are expected to schedule the dissertation proposal defense before the end of their second year.

Doctor of Philosophy

Upon successful completion of the dissertation proposal defense and admission into candidacy for the Ph.D., students work closely with the faculty advisor and dissertation committee on the dissertation project. During the period of two to three years in which students do primary original research, they also participate in seminars, discussion groups, and professional meetings and conferences, leading to the completion of the written Ph.D. dissertation. The Ph.D. in Ecology and Evolution is awarded based upon:

  • Submission of a written dissertation based on original research, which must be approved by the faculty adviser and dissertation committee.
  • Presentation of a public seminar based on the dissertation research.
  • Following the public seminar, successful performance during an oral examination by the dissertation committee and other relevant faculty.
  • Acceptance of the approved written dissertation by the University Office of Academic Publications in compliance with that office’s regulations.


We strongly advise students considering application to the department to begin preparation of their application early in the autumn quarter, so that all materials will arrive by the December 1 deadline. The department requires GRE General Test scores from all applicants, and recommends submission of GRE subject test scores in biology. Foreign applicants whose first language is not English also must submit TOEFL test scores with their application materials.

Further information also may be obtained from the department’s home page at

Ecology and Evolution Courses

ECEV 31100. Evolution of Biological Molecules. 100 Units.

This introductory graduate-level course connects evolutionary changes in genes and genomes with the structure, function and behavior of the protein and RNA molecules they encode.  Our central themes will be the mechanisms and dynamics by which molecular structure and function evolve, how protein/RNA architecture shapes evolutionary trajectories, and how patterns in present-day sequences can be interpreted to reveal the interplay data of evolutionary history and molecular properties.  We will teach core concepts in both macromolecular biochemistry (folding and stability of proteins and RNA, structure-function relationships, kinetics, catalysis) and molecular evolution (selection, mutation, drift, epistasis, effective population size, phylogenetics) and specifically explore the interplay between them. Students will derive and simulate evolution using molecular-level models; analyze empirical structure, function and sequence data in an evolutionary framework; and, through discussion and reading of classic and recent literature, trace the development of key ideas in molecular evolution up to the present day.

Instructor(s): D. Allan Drummond, Joseph Thornton     Terms Offered: Winter
Prerequisite(s): Comfort with basic computer programming (course will use Python and R); undergraduate biology, chemistry, calculus, and introductory statistics.
Equivalent Course(s): HGEN 31100,BCMB 31100

ECEV 31500. Ecological Genetics. 100 Units.

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.

Instructor(s): T. Price     Terms Offered: Autumn
Equivalent Course(s): EVOL 31500

ECEV 31800. Cancer Genomics and Systems Biology. 100 Units.

Cancer is a genetic disease characterized by the complex actions and interactions of environmental factors, multiple inherited and acquired genetic factors, networks, and cells.  Together, they predispose some individuals to develop cancer, protect others against it despite lifelong exposures to carcinogens, and determine the likelihood of response to therapy.  This inherent complexity presents constant challenges for diagnosing and treating patients with cancer.  Until recently, it has not been possible to explore the myriad genetic and biological factors varying among individuals that may account for the differences in susceptibility to cancer, the response to treatment, and the trajectory of disease.  With the advent of new genome-wide and high-throughput technologies, we are now beginning to unravel the genetic underpinnings of cancer.  A systems biology approach towards cancer examines the many components of the disease simultaneously.  It is hoped that findings resulting from systems biology studies will form the foundation for “personalized medicine.” The goal of this course is to teach students to manipulate and analyze the enormous datasets generated by genome-wide platforms.  The course is divided into four modules, each of which is dedicated to an in depth exploration of a single platform: 1) genome-wide association studies (GWAS); 2) next-generation sequencing 3) systems analysis of proteins; and 4) integrated data analysis.  Modules are comprised of both lectures and labs, and for each module, there is a student-led presentation of seminal papers demonstrating the translational potential of each technology to the investigation of human disease.   Although the focus of the course is cancer, the course has relevance to students interested in using systems biology strategies to investigate a variety of complex diseases. The course is complementary and non-overlapping with material covered by other Cancer Biology courses. 

Instructor(s): K. Onel, A. Skol, R. Jones     Terms Offered: Autumn
Equivalent Course(s): CABI 31800

ECEV 32000. Introduction to Scientific Computing for Biologists. 100 Units.

The course will cover basic concepts in computing for an audience of biology graduate students. The students will receive basic training in the use of version control systems, databases and regular expressions. They will learn how to program in python and R and how to use R to produce publication-grade figures for their manuscripts, and how to typeset scientific manuscripts and theses using LaTeX. All the examples and exercises will be biologically motivated and will make use of real data. The approach will be hands-on, with lecturing followed by exercises in class.

Instructor(s): S. Allesina     Terms Offered: Autumn

ECEV 32900. Plant Development and Molecular Genetics. 100 Units.

Genetic approaches to central problems in plant development will be discussed.  Emphasis will be placed on embryonic pattern formation, meristem structure and function, reproduction, and the role of hormones and environmental signals in development.  Lectures will be drawn from the current literature; experimental approaches (genetic, cell biological, biochemical) used to discern developmental mechanisms will be emphasized. Graduate students will present a research proposal in oral and written form; undergraduate students will present and analyze data from the primary literature, and will be responsible for a final paper. 

Instructor(s): J. Greenberg     Terms Offered: Spring
Prerequisite(s): Completion of the general education requirement in the biological sciences
Equivalent Course(s): BIOS 23299,DVBI 36100,MGCB 36100

ECEV 35400. Gene Regulation. 100 Units.

This course covers the fundamental theory of gene expression in prokaryotes and eukaryotes through lectures and readings in the primary literature. Natural and synthetic genetic systems arising in the context of E. coli physiology and Drosophila development will be used to illustrate fundamental biological problems together with the computational and theoretical tools required for their solution. These tools include large-scale optimization, image processing, ordinary and partial differential equations, the chemical Langevin and Fokker-Planck equations, and the chemical master equation. A central theme of the class is the art of identifying biological problems which require theoretical analysis and choosing the correct mathematical framework with which to solve the problem.

Terms Offered: Winter
Prerequisite(s): Consent of instructor
Note(s): Not offered in 2012-13
Equivalent Course(s): STAT 35400,MGCB 35401

ECEV 35600. Principles of Population Genetics-1. 100 Units.

Examines the basic theoretical principles of population genetics, and their application to the study of variation and evolution in natural populations. Topics include selection, mutation, random genetic drift, quantitative genetics, molecular evolution and variation, the evolution of selfish genetic systems, and human evolution.

Instructor(s): R. Hudson     Terms Offered: Winter
Equivalent Course(s): EVOL 35600,GENE 35600

ECEV 36300. Speciation. 100 Units.

A review of the literature on the origin of species beginning with Darwin and continuing through contemporary work. Both theoretical and empirical studies will be covered, with special emphasis on the genetics of speciation.

Instructor(s): J. Coyne     Terms Offered: Spring
Prerequisite(s): Coursework in genetics and evolution.
Equivalent Course(s): ECOL 36300

ECEV 37500. Sexual Selection. 100 Units.

A discussion and critical analysis of sexual selection. The course will consist of lectures, reading and discussion.

Instructor(s): S. Pruett-Jones     Terms Offered: Winter
Prerequisite(s): Common Core Biology, BIOS 248, or consent of instructor.
Note(s): odd-numbered years
Equivalent Course(s): EVOL 37500

ECEV 40100. Grants, Publications and Professional Issues. 100 Units.

Covers professional topics in evolutionary biology, primarily strategies in grant writing and review. Each student will work towards the submission of an application of their choice. The course meets weekly and involves extensive writing and discussion.

Instructor(s): Bergelson, Ho, Coates     Terms Offered: Autumn
Note(s): Only open to first year graduate students in the Darwinian Sciences Cluster
Equivalent Course(s): EVOL 40100,ORGB 40100

ECEV 42600. Community Ecology. 100 Units.

Lectures and readings cover advanced topics in multi-species systems, and include an introduction to basic theoretical approaches.

Instructor(s): Wootton     Terms Offered: Autumn
Equivalent Course(s): EVOL 42600

ECEV 42800. Population Ecology. 100 Units.

A lecture course on the empirical and theoretical approaches to the study of natural populations, including field methodologies and quantitative approaches. Includes computer assignments.

Instructor(s): C. Pfister     Terms Offered: Winter
Equivalent Course(s): EVOL 42800

ECEV 42900. Theoretical Ecology. 100 Units.

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.

Instructor(s): G. Dwyer     Terms Offered: Winter
Equivalent Course(s): EVOL 42900

ECEV 44001. Molecular Evolution I: Fundamentals and Principles. 100 Units.

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 that govern molecular variation, divergence, and genome organization. Particular attention is given to selectively neutral models of variation and evolution, and to alternative models of natural selection. The course 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.

Instructor(s): M. Kreitman L.     Terms Offered: Winter
Prerequisite(s): Two quarters of biology and calculus, or consent of instructor
Equivalent Course(s): BIOS 23258,EVOL 44001

ECEV 44002. Molecular Evolution II: Genes and Genomes. 100 Units.

This course covers the knowledge and well-established evolutionary analyses of genes and genomes, as well as related areas (e.g., origination and evolution of new genes, exon-intron structure, sex-related genes, sex-determination genetic systems, transposable elements, gene regulation systems, duplication of genes and genomes, evolution of genome sizes). These topics are discussed under the processes driven by various evolutionary forces and genetic mechanisms. The analysis of these problems is conducted with the genomic context. Lectures, discussions, and experiments are combined.

Instructor(s): M. Long     Terms Offered: Spring. This course is offered in alternate (odd) years.
Prerequisite(s): BIOS 23258 or consent of instructor
Equivalent Course(s): BIOS 23259,EVOL 44002