Ecology and Evolutionary Biology

Osborn Memorial Laboratories, 203.432.3837
http://eeb.yale.edu
M.S., Ph.D.

Chair
Thomas Near

Director of Graduate Studies
Erika Edwards

Professors Richard Bribiescas (Anthropology), Nicholas Christakis (Sociology), Michael Donoghue, Casey Dunn, Erika Edwards, Alison Galvani (Public Health), Vivian Irish (Molecular, Cellular, & Developmental Biology), Walter Jetz, Thomas Near, David Post, Jeffrey Powell, Richard Prum, Eric Sargis (Anthropology), Oswald Schmitz (Forestry & Environmental Studies), David Skelly (Forestry & Environmental Studies), Stephen Stearns, Paul Turner, J. Rimas Vaisnys (Electrical Engineering), Günter Wagner

Associate Professors Forrest Crawford (Public Health), James Noonan (Genetics), Jeffrey Townsend (Public Health), David Vasseur

Assistant Professors Craig Brodersen (Forestry & Environmental Studies), Liza Comita (Forestry & Environmental Studies), Alvaro Sanchez, Carla Staver

Senior Lecturer Marta Martínez Wells

Lecturers Adalgisa Caccone, Linda Puth

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 (DGS), 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) E&EB 500 and E&EB 501, Advanced Topics in Ecology and Evolutionary Biology; (2) E&EB 545, a course on the responsible conduct of research; (3) weekly E&EB seminars; and (4) 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); a grade of H must be earned in two of these. Teaching experience is regarded as an integral part of the graduate training program. All students are required to teach three courses, normally at a level 20, typically during their first two years of study.

By the middle of the fourth term of study, each student organizes a formal pre­prospectus consultative meeting with the student’s advisory committee to discuss the planned dissertation research. Before the beginning of the fifth term, students present and defend their planned dissertation research at a prospectus meeting, at which the department determines the viability and appropriateness of the student’s Ph.D. proposal. A successful prospectus meeting and completion of course requirements results 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 Center for Science and Social Science Information.

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.) Students must pass ten graduate-level courses. At least four courses must be taken for a grade, and students must earn Honors in two courses and maintain an overall average of High Pass. Required courses are: E&EB 500 and E&EB 501, Advanced Topics in Ecology and Evolutionary Biology; E&EB 545, Responsible Conduct of Research; E&EB 901, Research Rotation I; and E&EB 902, Research Rotation II. A minimum of five additional graduate-level courses (four taken for a grade) are required.


Additional information on the department, faculty, courses, and facilities is available from Deanna Brunson, 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, deanna.brunson@yale.edu; tel., 203.432.3837; fax, 203.432.2374; website, http://eeb.yale.edu.

Courses

E&EB 500a and E&EB 501b, Advanced Topics in Ecology and Evolutionary BiologyErika Edwards

Topics to be announced. Graded Satisfactory/Unsatisfactory.
M 2:30pm-4:30pm

E&EB 510a, Introduction to Statistics: Life SciencesJonathan Reuning-Scherer and Walter Jetz

Statistical and probabilistic analysis of biological problems, presented with a unified foundation in basic statistical theory. Problems are drawn from genetics, ecology, epidemiology, and bioinformatics.
TTh 1pm-2:15pm

E&EB 515a, Conservation BiologyLinda Puth

An introduction to ecological and evolutionary principles underpinning efforts to conserve Earth's biodiversity. Efforts to halt the rapid increase in disappearance of both plants and animals. Discussion of sociological and economic issues.
MW 10:30am-11:20am

E&EB 520a, General EcologyDavid Vasseur and Ann Staver

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.
MWF 10:30am-11:20am

E&EB 523b, Laboratory for Principles of Evolution, Ecology, and BehaviorMarta Wells

Experimental approaches to organismal and population biology, including study of the diversity of life.
HTBA

E&EB 525b, Evolutionary BiologyAlvaro Sanchez De Andres and Jeffrey Powell

An overview of evolutionary biology as the discipline uniting all of the life sciences. Evolution explains the origin of life and Earth’s biodiversity, and how organisms acquire adaptations that improve survival and reproduction. This course uses reading and discussion of scientific papers to emphasize that evolutionary biology is a dynamic science, involving active research to better understand the mysteries of life. We discuss principles of population genetics, paleontology, and systematics; and application of evolutionary thinking in disciplines such as developmental biology, ecology, microbiology, molecular biology, and human medicine.
TTh 10:30am-11:20am

E&EB 530a, Field EcologyLinda Puth

A field-based introduction to ecological research. Experimental and descriptive approaches, comparative analysis, and modeling are explored through field and small-group projects.
T 1pm-2:15pm, Th 1pm-5pm

E&EB 535a, Evolution and MedicineStephen Stearns

Introduction to the ways in which evolutionary science informs medical research and clinical practice. Diseases of civilization and their relation to humans’ evolutionary past; the evolution of human defense mechanisms; antibiotic resistance and virulence in pathogens; cancer as an evolutionary process. Students view course lectures online; class time focuses on discussion of lecture topics and research papers.
TTh 11:35am-12:50pm

E&EB 545a, Responsible Conduct of ResearchErika Edwards

This five-week discussion seminar considers issues related to the responsible conduct of research. Topics addressed include research misconduct, plagiarism, data acquisition and management, mentoring and collaboration, authorship and peer review, the use of animals and humans in scientific research, sexual harassment, diversity, and balancing professional and personal life. Graded Satisfactory/Unsatisfactory.  0 Course cr
M 2:30pm-4:30pm

E&EB 546a, Plant Diversity and EvolutionMichael Donoghue

Introduction to the major plant groups and their evolutionary relationships, with an emphasis on the diversification and global importance of flowering plants.
MW 1pm-2:15pm

E&EB 547La, Laboratory for Plant Diversity and EvolutionMichael Donoghue

Hands-on experience with the plant groups examined in the accompanying lectures; local field trips.
HTBA

E&EB 550a, Biology of Terrestrial ArthropodsMarta Wells

Evolutionary history and diversity of terrestrial arthropods (body plan, phylogenetic relations, fossil record); physiology and functional morphology (water relations, thermo-regulation, 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).
TTh 11:35am-12:50pm

E&EB 551La, Laboratory for Biology of Terrestrial ArthropodsMarta Wells

Comparative anatomy, dissections, identification, and classifications of terrestrial arthropods; specimen collection; field trips.
W 1:30pm-4:30pm

E&EB 555a, InvertebratesCasey Dunn

An overview of animal diversity that explores themes including animal phylogenetics (evolutionary relationships), comparative studies of evolutionary patterns across species, organism structure and function, and the interaction of organisms with their environments. Most animal lineages are marine invertebrates, so marine invertebrates are the focus of most of the course. Must be taken concurrently with E&EB 556.
MWF 9:25am-10:15am

E&EB 556a, Laboratory for InvertebratesCasey Dunn

The study of invertebrate anatomy and diversity in a laboratory and field setting. Activities include examination of live animals and museum specimens, as well as local field trips. Some field trips fall on weekends. Must be taken concurrently with E&EB 555.  ½ Course cr
Th 1pm-4pm

E&EB 564a, IchthyologyRichard Harrington

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.
TTh 1pm-2:15pm

E&EB 565La, Laboratory for IchthyologyRichard Harrington


W 1pm-4pm

E&EB 626b, Plant Structure and FunctionErika Edwards

An examination of the relationship between the structure of plants and their physiological systems, and the role of the environment in shaping the evolution and diversity of vascular plants. Lectures focus on exploring the basics of plant morphology, and the anatomical and physiological adaptations of leaves, stems, and roots to different habitats. A comparative, phylogenetic approach is emphasized. This is a hybrid lecture/lab course: the first two-thirds of the course consists of chalkboard lectures by the instructor and the last third is an intensive period of data collection and analysis, providing students with firsthand experience in measuring and interpreting plant functional traits. Students work on a set of group projects that are designed to test long-standing assumptions about the evolution and adaptive nature of certain plant traits. Projects differ from year to year, and although the general theme is chosen by the instructor, students are expected to play a large role in experimental design and focus. Students leave the class with a solid foundation both in plant anatomy and ecophysiology and in applying a phylogenetic comparative approach to studies of organismal biology; and they gain firsthand experience in data collection, experimental design, data analysis, and the collaborative presentation of a scientific study. Permission of the instructor required. Must be taken in conjunction with E&EB 627L.
TTh 1pm-2:15pm

E&EB 627Lb, Plant Structure and Function LabErika Edwards

An examination of the relationship between the structure of plants and their physiological systems, and the role of the environment in shaping the evolution and diversity of vascular plants. Lectures focus on exploring the basics of plant morphology, and the anatomical and physiological adaptations of leaves, stems, and roots to different habitats. A comparative, phylogenetic approach is emphasized. This is a hybrid lecture/lab course: the first two-thirds of the course consists of chalkboard lectures by the instructor and the last third is an intensive period of data collection and analysis, providing students with firsthand experience in measuring and interpreting plant functional traits. Students work on a set of group projects that are designed to test long-standing assumptions about the evolution and adaptive nature of certain plant traits. Projects differ from year to year, and although the general theme is chosen by the instructor, students are expected to play a large role in experimental design and focus. Students leave the class with a solid foundation both in plant anatomy and ecophysiology and in applying a phylogenetic comparative approach to studies of organismal biology; and they gain firsthand experience in data collection, experimental design, data analysis, and the collaborative presentation of a scientific study. Must be taken in conjunction with E&EB 626.  ½ Course cr
HTBA

E&EB 672b, OrnithologyRichard Prum

An overview of avian biology and evolution, including the structure, function, behavior, and diversity of birds. The evolutionary origin of birds, avian phylogeny, anatomy, physiology, neurobiology, breeding systems, and biogeography.
MWF 9:25am-10:15am

E&EB 673Lb, Laboratory for OrnithologyRichard Prum

Laboratory and field studies of avian morphology, diversity, phylogeny, classification, identification, and behavior. Must be taken concurrently with E&EB 672.  ½ Course cr
T 1:30pm-4:30pm

E&EB 678a, Mathematical Models and Quantitative Methods in Evolution and EcologyAlvaro Sanchez De Andres

In this course, we focus on how quantitative approaches are used to allow scientific inference. We discuss general principles for generating hypotheses that are testable (i.e., quantifiable). The course also examines a variety of approaches used to model population-level processes in evolution and ecology, including an overview of population genetics, quantitative genetics, optimality models, game theory, and population dynamic equations. We also discuss experimental design, statistical analyses, inference, and other quantitative methods. The course assumes a basic background in algebra, calculus, probability theory, and statistics. Please address any questions regarding the course to alvaro.sanchez@yale.edu.
W 1pm-2:50pm

E&EB 680b, Life History EvolutionStephen Stearns

Life history evolution studies how the phenotypic traits directly involved in reproductive success are shaped by evolution to solve ecological problems. The intimate interplay between evolution and ecology.
TTh 11:35am-12:50pm

E&EB 713b, Concepts and Methods in Global Biodiversity Change Research in the Age of Big DataWalter Jetz

Biodiversity and the many functions it provides are changing worldwide, creating a critical need for a better understanding of mechanisms underpinning this change and the development of new information products to help monitoring and mitigation. New technologies, data, and methods, as well as conceptual advances, increasingly enable work addressing this challenge for species and communities at a global scale. We discuss these new opportunities and familiarize ourselves with recent research and new approaches to global biodiversity change. The course combines in-depth discussion of recent empirical work and hands-on examples of biodiversity change analysis workflows. On the technical front, we explore the use of remote sensing though Google Earth Engine (GEE) and work through R-based scripted examples of species distribution and community change modeling. The course is offered in collaboration with the Yale Center for Biodiversity and Global Change (https://bgc.yale.edu) and includes seminars and discussions with guest speakers.
Th 3:30pm-5:20pm

E&EB 725a, Scientific Writing for Ecology and Evolutionary BiologyAnn Staver

This course provides guidance and practice for graduate students in grant and manuscript writing in the fields of ecology and evolutionary biology. Students produce one grant application (NSF GRFP/DDIG or similar) and one manuscript for publication (on a topic of their choice, to contribute to their thesis or other ongoing work).
Th 4pm-6pm

E&EB 810b, Dynamics of Evolving SystemsJ. Rimas Vaišnys

An introduction to the ways evolving biological systems can be described, modeled, and analyzed by using a dynamical systems approach. To use currently fashionable terminology, we develop an individual-based model of the behavior of biological populations, which leads to evolution as an emergent property. In this approach it is possible to construct populations of varying individuals, which can then be combined into larger assemblages, and to modify both the overall environment and the environments at the lower levels, so that aspects often neglected in modeling evolution can be explored and related to any available observational data. Extensive use of the software package Mathematica, but prior experience with the program is not required.
TTh 9am-10:15am

E&EB 842b / ANTH 835b, Primate Diversity and EvolutionEric Sargis

The diversity and evolutionary history of living and extinct primates. Focus on major controversies in primate systematics and evolution, including the origins and relationships of several groups. Consideration of both morphological and molecular studies. Morphological diversity and adaptations explored through museum specimens and fossil casts.
MW 2:30pm-3:45pm

E&EB 900a or b, First-Year Introduction to Research and RotationsErika Edwards


HTBA

E&EB 901a, Research Rotation IErika Edwards


HTBA

E&EB 902b, Research Rotation IIErika Edwards


HTBA

E&EB 903b, Independent StudyErika Edwards

By arrangement with faculty. Approval of DGS required.
HTBA

E&EB 930a or b / G&G 703a or b, Seminar in SystematicsJacques Gauthier

A seminar on using molecular evolutionary models in Bayesian phylogenetic analyses. Topics are chosen by the participants but may include “models” in phylogenetics, understanding and comparison of model selection criteria, effects of model under- and overparameterization on parameter value estimates and phylogenetic inferences, and accommodating model uncertainty and model-averaging.
HTBA

E&EB 950a or b, Second-Year ResearchErika Edwards

By arrangement with faculty.
HTBA