Ecology and Evolutionary Biology

Osborn Memorial Laboratories, 432.3837, www.eeb.yale.edu
M.S., Ph.D.

Chair
TBA

Director of Graduate Studies
Margaret Riley (101 OML, 432.3837)

Professors
Leo Buss, Michael Donoghue, Jacques Gauthier (Geology & Geophysics), Willard Hartman (Emeritus), Vivian Irish (Molecular, Cellular, & Developmental Biology), Gene Likens (Cary Arboretum), Alvin Novick, Jeffrey Powell, Charles Remington (Emeritus), Oswald Schmitz (Forestry & Environmental Studies), Stephen Stearns, J. Rimas Vaisnys (Electrical Engineering), Günter Wagner

Associate Professors
Junhyong Kim, Sean Rice, Margaret Riley, Anne Yoder

Assistant Professors
David Skelly (Forestry & Environmental Studies), Paul Turner

Lecturers
Adalgisa Caccone, Theodora Pinou, Nancy Rosenbaum, Marta Martinez Wells

Fields of Study
The Department of Ecology and Evolutionary Biology (EEB) offers training programs in organismal biology, ecology, and evolutionary biology including molecular evolution, phylogeny, molecular population genetics, developmental evolution, and evolutionary theory.

Special Admissions Requirements
Applicants should have had training in one of the following fields: biology, mathematics, chemistry, physics, statistics, and/or geology. Candidates are selected, regardless of their major, based on overall preparation for a career in research in ecology and evolutionary biology. Some, planning for careers in applied fields, may have prepared with courses in public policy, economics, and agriculture.

Special Requirements for the Ph.D. Degree
Each entering student, in consultation with the director of graduate studies, develops a specific program of courses, seminars, laboratory research, and independent reading tailored to the student's interests, background, and goals. There are normally no foreign language requirements. Each student is required to undertake laboratory research in the form of two research rotations in the first year. Students must also attend a survey course in methods and research design and participate in (1) a program of ethics of research and authorship; (2) weekly EEB seminars; and (3) symposia of faculty and graduate student research. In addition, graduate students must enroll in a minimum of three additional graduate-level courses (numbered 500 and above) during their first two years of study. All students are required to teach two courses during their first two years of study.

In the third term of study each student takes a comprehensive examination in ecology and evolutionary biology. By the end of the third term, each student organizes a formal preprospectus consultative meeting with his/her advisory committee to discuss the planned dissertation research. By the end of the fourth term, students present and defend their planned dissertation research at a prospectus meeting, where the department determines the viability and appropriateness of the student's Ph.D. proposal. A successful prospectus meeting and completion of course requirements result in candidacy for the Ph.D. The remaining requirements include completion, presentation, and successful defense of the dissertation, and submission of copies of the dissertation to the Graduate School and to the Kline Science Library.

Teaching experience is regarded as an integral part of the graduate training program. All students are required to serve as teaching fellows for two terms, normally at the Teaching Fellow 2 level. This teaching is typically done during the first two years of study.

Honors Requirement
Students must meet the Graduate School's requirement of Honors in two courses by the end of the fourth term of study. The EEB department also requires an average grade of at least High Pass in course work during the first two years of study.

Master's Degrees
M.S. (en route to the Ph.D.). Satisfactory completion of the first two years of study leading to the Ph.D. up to, but not necessarily including, the prospectus.

Additional material providing information on the department, faculty, courses, and facilities is available from Maureen Cunningham, Office of the Director of Graduate Studies, Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven CT 06520-8106 (maureen.cunningham@yale.edu).

Courses
E&EB 501a, Methods and Research Design. Staff.
This course provides an introduction to the methods and approaches generic to most research in the biological sciences. Topics include quantification and measurement, data analysis, sequence analysis, phylogenetic reconstruction and the comparative method, morphometrics, experimental design, presentation of results, and grant writing. This course is required for all first-year EEB students.

E&EB 510au, Introduction to Statistics: Life Sciences. Joseph Chang, Junhyong Kim.
Statistical and probabilistic analysis of biological problems is presented with a unified foundation in basic statistical theory. A general lecture covering statistical theory and a discipline-based lecture covering statistical modeling of biological problems drawn from genetics, ecology, epidemiology, and bioinformatics. Graduate students are expected to finish a course project in addition to regular homework and exams.

E&EB 515au, Conservation Biology and the Environment. Jeffrey Powell, Oswald Schmitz, Stephen Stearns, Adalgisa Caccone. Mon/Wed 9.30-10.20, 1 htba
An introduction to the basic ecological and evolutionary principles underpinning efforts to conserve the earth's biodiversity. These principles are then examined in the context of efforts to halt the rapidly increasing disappearance of both plants and animals. Case studies are examined in detail. While some sociological and economic issues are discussed, the emphasis is on the biological aspects of these crucial problems.

E&EB 520au, Population Ecology. Staff. Mon/Wed/Fri 10.30-11.20
An introduction to the theoretical context and empirical grounding of the science of population ecology. Emphasis is placed on the determinants of patterns of distribution and abundance from demographic and population perspectives. Animal behavior is treated in an ecological context, as exemplars of life history consequences of demography, and as modulators of competitive and predatory responses.

E&EB 525bu, Evolutionary Biology. Margaret Riley, Sean Rice. Tues/Thurs 11.30-12.45
An introduction to the study of evolution from both a macro- and microevolutionary perspective. Principles of population genetics, systematics, paleontology, and molecular evolution are addressed as well as application of evolutionary thinking to issues in animal behavior, ecology, and molecular biology.

[E&EB 526Lbu, Laboratory for Evolutionary Biology.]

[E&EB 530au, Field Ecology.]

E&EB 540au, AIDS and Society. Alvin Novick. Mon/Wed/Fri 10.30-11.20
The natural history, biology, and epidemiology of AIDS; social, ethical, public policy, and political aspects of AIDS and of the ways societies address a medical crisis.

E&EB 540bu, Animal Behavior. Marta Martinez Wells. Mon/Wed 11.30-12.45
An introduction to animal behavior, including proximate causes, development, and control of behavior; communication; mating systems and sexual selection; and the evolution of social systems.

E&EB 545bu, Problems in Bioethics. Tues/Thurs 9-10.15
A consideration of social and ethical problems raised by advances in biological and medical research. Several timely topics examined in depth, with frequent student oral reports.

E&EB 550au, Biology of Terrestrial Arthropods. Marta Martinez Wells. Tues/Thurs 11.30-12.45
Evolutionary history and diversity of terrestrial arthropods (body plan, phylogenetic relations, fossil record); physiology and functional morphology (water relations, thermoregulation, energetics of flying and singing); reproduction (biology of reproduction, life cycles, metamorphosis, parental care); behavior (migration, communication, mating systems, evolution of sociality); ecology (parasitism, mutualism, predator-prey interactions, competition, plant-insect interactions).

E&EB 551Lau, Laboratory for Biology of Terrestrial Arthropods. Marta Martinez Wells.

[E&EB 555bu, The Invertebrates.]

[E&EB 556Lbu, Laboratory for the Invertebrates.]

[E&EB 560bu, The Vertebrates.]

[E&EB 561Lbu, Laboratory for the Vertebrates.]

[E&EB 565au, The Biology of Birds.]

[E&EB 566Lau, Laboratory for the Biology of Birds.]

E&EB 570bu, Herpetology. Theodora Pinou. Tues/Thurs 1-2.15
A comparative approach to the evolution, anatomy, physiology, ecology, behavior, geographic distribution, and classification of amphibians; venoms and toxins also discussed.

E&EB 571Lbu, Laboratory for Herpetology. Theodora Pinou. Tuesday 2.30
Laboratory and field studies of amphibians and reptiles. Examination of the morphology and systematics of amphibians and reptiles; various phylogenetic methods of sampling and species identification.

E&EB 610bu, Evolutionary Genetics. Jeffrey Powell.
Introduction to population genetics and phylogenetics. Theoretical fundamentals and empirical data, with an emphasis on molecular aspects.

E&EB 615Lau, Laboratory in Molecular Systematics. Adalgisa Caccone. Wednesday 1.30-5.30
A practical introduction to molecular techniques used in systematics (DNA extraction, PCR, sequencing) and their application to field studies in natural history, population genetics, mating systems, paternity, and the historical analysis of lineages. Research projects apply the methodologies.

[E&EB 620a, Biology and Conservation of Endangered Species and Biodiversity.]

[E&EB 621b, World Population and Environmental Issues.]

E&EB 628au, Comparative Physiology. Theodora Pinou. Tues/Thurs 11.30-12.45
A comparative approach to the diversity of physiological processes employed by different animal species, and how these adaptations are related to the physical environment.

E&EB 629Lau, Laboratory for Comparative Physiology. Theodora Pinou. Thursday 1.30
An opportunity to examine various physiological principles of animals under varying environmental conditions. Use of live animals is limited. Some principles are examined using computer simulation.

[E&EB 640bu, Community Ecology.]

[E&EB 641Lbu, Laboratory for Community Ecology.]

[E&EB 650bu, Plant Ecology.]

[E&EB 651Lbu, Laboratory for Plant Ecology.]

E&EB 660bu, Wildlife Conservation Ecology. Oswald Schmitz.
The course explores the evolutionary ecological basis for animal behavior and life history, how behavior evolves, and what factors ultimately shape animal decision making and life histories. Links animal behavior with population dynamics using demographic models that translate behavior into life history strategies. Finally the course examines how environmental perturbations influence animal life histories to alter population structure and dynamics. Also F&ES 560b.

E&EB 665bu, Landscape Ecology. Ofer Ovadia.
An introduction to the study of large-scale ecological patterns and processes. Through lectures and the completion of a project, students learn how to integrate a spatial perspective into consideration of major ecological questions. Also F&ES 760b.

[E&EB 670au, Aquatic Ecology.]

[E&EB 671Lau, Laboratory for Aquatic Ecology.]

E&EB 675bu, Molecular Approaches to Systematics, Conservation Genetics, and Behavioral Ecology. Adalgisa Caccone. Tuesday 3.30-5.20
The goals of this seminar are to understand the potential and limits of a wide range of molecular approaches to the study of ecological and systematic oriented questions with particular emphasis on conservation biology questions. It includes student presentations together with lectures and a discussion of primary literature. Also F&ES 578b.

E&EB 680au, Population Biology. Stephen Stearns. Tues/Thurs 9-10.15
Advanced discussion of life history evolution, sex allocation theory, the evolution of sex, the evolution of phenotypic plasticity, and evolutionary conflict theory. Instructors give introductory lectures, students pick topics and present lectures themselves.

[E&EB 800b, Computational Analysis of Biological Information.]
Several recently developed statistical methods have either already played an important role in the analysis of genomic and post-genomic data or appear to be promising candidates to do so. We study hidden Markov models, Bayesian networks, support vector machines and kernel methods, and perhaps other topics to be determined. For each topic, instructors present introductory lectures on the statistical theory, models, and methods of analysis. Students work on projects and present results, which may include computer implementations of the statistical techniques, analyses of biological sequence and gene expression data using available programs, and reports on research papers. Although there are no specific prerequisites, the course makes substantial use of probability theory, statistics, introductory biology, and computation; students without background in some of these areas may need to do additional work and should consult the instructors before enrolling. Open to undergraduates with permission of instructors.

E&EB 810a, Dynamics of Evolving Systems. J. Rimas Vaisnys. Tues/Thurs 11.30-12.45
An introduction to the ways in which the structure and behavior of evolving biological systems can be described, modeled, and analyzed. Examination of model systems as well as modeling of laboratory and field phenomena.

[E&EB 827b, Advanced Topics of Computational Biology: Emergence and Evolutionary Innovation.]

E&EB 845a, Advanced Evolutionary Theory. Sean Rice. Tues/Thurs 4-5.30
A lecture course covering the mathematical and conceptual basis of the major branches of evolutionary theory, including traditional and emerging areas. Emphasis on the biological insights that are gained from the theory. Open to undergraduates with permission of the intructor.

E&EB 900a-b, First-Year Introduction to Research and Rotations. Margaret Riley.

E&EB 950a or b, Second-Year Research.
By arrangement with faculty.

Next: Economic History