Ecology and Evolutionary Biology
Osborn Memorial Laboratories, Rm 101, 165 Prospect Street, 432.3837
www.eeb.yale.edu/
M.S. (en route to the Ph.D.), Ph.D.
Chair
Günter Wagner
Director of Graduate Studies
Paul Turner
Professors
Leo Buss, Michael Donoghue, Jacques Gauthier (Geology & Geophysics), Willard Hartman (Emeritus), Vivian Irish (Molecular, Cellular & Developmental Biology), Kenneth Kidd (Genetics; Psychiatry), Gene Likens (Cary Arboretum), Jeffrey Powell, Richard Prum (on leave [F]), Charles Remington (Emeritus), Oswald Schmitz (Forestry & Environmental Studies), David Skelly (Forestry & Environmental Studies), Stephen Stearns, J. Rimas Vaisnys (Electrical Engineering), Günter Wagner
Associate Professor
Paul Turner
Assistant Professors
Suzanne Alonzo (on leave), Antonia Monteiro, Thomas Near, David Post, Melinda Smith (on leave), Jeffrey Townsend
Lecturers
Adalgisa Caccone, Marta Martinez Wells
Fields of Study
The Department of Ecology and Evolutionary Biology (E&EB) 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. All first-year students carry out two research rotations. Students have the option of a rotation over their first summer. Students must participate in (1) a program of ethics of research and authorship; (2) weekly E&EB seminars; and (3) symposia of faculty and graduate student research. In addition, during their first two years of study, graduate students must enroll in a minimum of three additional graduate-level courses (numbered 500 and above). Teaching experience is regarded as an integral part of the graduate training program. All students are required to teach two courses, normally at the TF 2 level, during their first two years of study.
In the third term of study each student takes qualifying examinations 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 admission to 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.
In cases where the dissertation committee decides that preliminary field work during the summer after the fourth term is necessary prior to the prospectus, the prospectus meeting can be delayed by one term. A request for a delay must come from the dissertation committee adviser and must be approved by the DGS. In these exceptional cases admission to candidacy may not be required for registration for the third year of graduate 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 E&EB department also requires an average grade of at least High Pass in course work during the first two years of study.
Master’s Degree
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; e-mail, maureen.cunningham@yale.edu; phone, 203.432.3837; fax: 203.432.2374; Web site: www.eeb.yale.edu/.
Courses
E&EB 500a/b, Advanced Topics in Ecology and Evolutionary Biology. Staff.
2 HTBA
Topics to be announced.
E&EB 510au, Introduction to Statistics: Life Sciences. Günter Wagner.
M 2.30–4.20
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. Also STAT 501au.
E&EB 520au, General Ecology. David Post, Leo Buss.
MWF 10.30–11.20
A broad consideration of the theory and practice of ecology, including the ecology of individuals, population dynamics and regulation, community structure, ecosystem function, and ecological interactions on broad spatial and temporal scales. Topics such as climate change, fisheries management, and infectious disease are placed in an ecological context.
E&EB 522bu, Principles of Evolution, Ecology, and Behavior. Stephen Stearns.
MWF 11.35–12.25
The major principles of evolution, ecology, and behavior explained and illustrated by recent advances that have changed the field. Emphasis on major events in the history and key transitions in the organization of life. Ecological processes from organisms through populations and communities to the biosphere. Foraging, mating, and selfish and cooperative behavior placed in evolutionary and ecological context.
E&EB 523Lbu, Laboratory for Principles of Evolution, Ecology, and Behavior. Marta Wells.
TWTh 1.30
Experimental approaches to organismal and population biology, including study of the diversity of life.
E&EB 525bu, Evolutionary Biology. Paul Turner, Jeffrey Townsend.
TTh 11.35–12.50
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. Adalgisa Caccone.
W 1.30
The companion laboratory to E&EB 525b. Study of patterns and processes of evolution, including collection and interpretation of molecular and morphological data in a phylogenetic context. Focus on methods of analysis of species-level and population-level variation in natural populations.
E&EB 530au, Field Ecology. David Post.
Th 1–5
A field-based introduction to ecological research. Experimental and descriptive approaches, comparative analysis, and modeling are explored using field and small-group projects relevant to major topics in ecology. Concurrently with or after E&EB 520a or by permission of the instructor. Limited enrollment.
[E&EB 540au, Animal Behavior.]
E&EB 546bu, Plant Diversity and Evolution. Staff.
MW 1–2.15
Introduction to the evolutionary relationships of plant lineages. Exploration of the complexity, diversity, and characteristics of the major plant groups, including the green algae, mosses, ferns, conifers, and flowering plants, within a phylogenetic context.
E&EB 547Lbu, Laboratory for Plant Diversity and Evolution. Staff.
T 1
Local flora field research; hands-on experience with the plant groups examined in the accompanying lectures.
E&EB 548bu, Insect Development and Evolution. Antonia Monteiro.
TTh 1–2.15
This course focuses on the diversity of developmental mechanisms that give rise to the spectacular diversity in insect form. Topics range from the study of the evolution of key innovations such as wings, butterfly wing scales, or the process of metamorphosis, to the control of alternative casts or seasonal forms within a species by hormonal mechanisms. We cover basic developmental processes of insect body plan determination (body segments, wings, legs), as well as more detailed mechanisms of color patterning butterfly wings. Focus on how variation in these developmental processes affects the shape, color, and form of insects.
E&EB 549Lbu, Laboratory for Insect Development and Evolution. Antonia Monteiro.
Th 2.30
Focus is on experiments with live butterflies, examining mechanisms of development and developmental plasticity and of micro-evolution. Experiments range from (1) classical perturbations of signaling groups of cells that differentiate certain wing color patterns during pupal wing development, to (2) extracting wing discs from larvae and visualizing gene expression patterns on the wings, to (3) rearing cohorts of larvae at different temperatures to study phenotypic plasticity of the wing patterns, to (4) visualizing the shift in the mean size of a certain morphological trait in a population by the application of artificial selection to that trait.
[E&EB 550au, Biology of Terrestrial Arthropods.]
[E&EB 551Lau, Laboratory for Biology of Terrestrial Arthropods.]
[E&EB 555b, Invertebrates I.]
[E&EB 556Lb, Laboratory for the Invertebrates I.]
[E&EB 557b, Invertebrates II.]
[E&EB 558Lb, Laboratory for Invertebrates II.]
[E&EB 560a, Seminar in Invertebrate Zoology I.]
E&EB 564au, Ichthyology. Thomas Near.
MWF 1.30–2.20
A survey of fish diversity including jawless vertebrates, chimaeras and sharks, lungfishes, and ray-finned fishes. Topics include the evolutionary origin of vertebrates, the fossil record of fishes, evolutionary diversification of major extant fish lineages, biogeography, ecology, and reproductive strategies of fishes.
E&EB 565au, Laboratory for Ichthyology. Thomas Near.
T 1–4
Laboratory and field studies of fish diversity, form, function, behavior, and classification. The course primarily involves study of museum specimens and of living and fossil fishes. Must be taken concurrently with E&EB 564.
[E&EB 616Lau, Laboratory in Molecular Systematics.]
[E&EB 620bu, Conservation Genetics.]
E&EB 626au, Molecular Ecology. Adalgisa Caccone.
TTh 11.35–12.50
This course provides an overview of molecular genetic tools used to investigate ecological and evolutionary processes in natural populations. The use of molecular markers is explored through the hierarchy of life from studies of genetic individuality, parentage, kinship, population substructure, species boundaries, phylogenetics of closely related species.
E&EB 640b, Community Ecology. Oswald Schmitz.
HTBA
The course provides students in-depth understanding of theory on multiple species interactions and dynamics including predation, competition, food chain, and food web interactions. Considerable emphasis is placed on mathematical modeling to formalize ideas about how species interactions structure ecological communities and to specify the appropriate focus of empirical research, study design, and data gathering. The course addresses contemporary issues in community ecology including scaling from individual behavior to community dynamics, the link between biodiversity and system stability, alternative dynamic regimes, spatially extended systems, and metacommunities.
[E&EB 660bu, Wildlife Conservation Ecology.]
E&EB 665au, Landscape Ecology. David Skelly.
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 564a.
E&EB 670au, Aquatic Ecology. David Skelly.
T 1–2.15, lab Th 1–5
An intensive introduction to the ecology of populations and communities in freshwater systems. Concepts, patterns, and organisms important in lakes and streams; techniques of information collection and analysis. Weekly field trips to gather data. Also F&ES 560a.
E&EB 672bu, Ornithology. Richard Prum.
MWF 9.25–10.15
Structure, function, behavior, evolution, and diversity of birds. A general overview of avian biology and evolution. Topics include the evolutionary origin of birds, avian phylogeny, anatomy, physiology, neurobiology, behavior, breeding systems, and biogeography.
E&EB 673Lbu, Laboratory for Ornithology. Richard Prum.
T 2
Laboratory and field studies of avian morphology, diversity, phylogeny, classification, identi-fication, and behavior. Must be taken concurrently with E&EB 672bu.
[E&EB 675bu, Molecular Approaches to Systematics, Conservation Genetics, and Behavioral Ecology.]
[E&EB 678b, Mathematical Models and Quantitative Methods in Evolution and Ecology.]
E&EB 690bu, Evolution of Development. Antonia Monteiro.
TTh 9–10.15
An introduction to the ways that developmental mechanisms change through time to give rise to organismal diversity. Topics include how mutations influence the processes of gene regulation, tissue growth, and cell and organ differentiation.
[E&EB 691b, Developmental Evolution of Body Plans, Homology, and Evolutionary Innovations.]
E&EB 710a, Seminar in Evolutionary Functional Genomics. Jeffrey Townsend.
HTBA
Discussion of the burgeoning new literature on the evolution of gene expression especially focused on genomic approaches to understanding organismal biology. Topics include population variation in genome-wide gene expression, molecular evolution of gene expression, models of the evolution of gene expression, and consideration of how the “central dogma” of molecular biology (DNA->RNA->Proteins) constrains or facilitates evolution of adaptive traits. This graduate course is composed of a mix of instructor- and student-led discussions of key papers. Students are expected to present a paper on a topic and to actively participate in the discussions.
[E&EB 728bu, Ecology and Evolution of Infectious Diseases.]
E&EB 729a, Microbial Ecology and Evolution. Paul Turner.
Th 9.25–11.15
This course examines the ecology and evolution of microbes, with an emphasis on prokaryotes (bacteria, Archaea) and viruses. Microorganisms came into existence over 3.8 billion years ago and they are found everywhere today. The ecological roles of these organisms in the environment have been finely honed by evolutionary processes over the complete span of life on earth. Most evolutionary and ecological theory has been developed with macro-organisms as the focus. Considering that evolution has been acting on microbes longer than all other organisms, this course emphasizes that evolution and ecology insights can be obtained through microbial research. The evolutionary ecology of microorganisms is studied from individual, population, and community perspectives. Species interactions including competition, predation, parasitism, and mutualism as well as microbial communication through quorum sensing is examined through the lens of evolutionary ecology. Sex and reprod!
uction, genome architecture and reduction, novel evolutionary mechanisms, and life in extreme environments are examined from a microbial perspective. The result is an understanding of microbes in their natural habitats, and of the power in using microbes to elucidate fundamental principles in ecology and evolution.
E&EB 810b, Dynamics of Evolving Systems. J. Rimas Vaisnys.
TTh 11.35–12.50
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 826bu, Phylogenetics and Macroevolution. Thomas Near.
MWF 2.30–3.45
The tools of phylogeny reconstruction have had a dramatic impact on evolutionary biology. This course describes the methods of phylogenetic inference, provides the student with practical experience in reconstructing evolutionary histories from comparative data, especially molecular sequence data, and applies these techniques to understanding selected issues in macroevolution—evolution above the species level. Phylogenetics has become the organizing principle for macroevolutionary studies, and it has provided new levels of quantitative understanding and rigor, especially in problems relating to the tempo and mode of evolutionary change. The course emphasizes development of quantitative skills, conceptual understanding, and appreciation for biological examples ranging from the evolution of viral pathogens to the origin of major clades of animals and green plants.
E&EB 827Lbu, Laboratory for Phylogenetics and Macroevolution. Thomas Near.
T 1–4
The course emphasizes methodological approaches to phylogenetic analyses that are used in many research areas of ecology and evolutionary biology. Introduction to methods of phylogeny reconstruction and evolutionary comparative analysis. Computer-lab-based exercises and lessons provide experience obtaining genetic data from Internet resources, and the tools used to build phylogenetic trees. Additional topics and methods include biogeographic analyses, estimating divergence times with molecular data, and independent contrast analysis.
E&EB 900a–b, First-Year Introduction to Research and Rotations. Richard Prum.
E&EB 930a, Seminar in Systematics. Staff.
E&EB 950a or b, Second-Year Research.
By arrangement with faculty.
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