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Ecology & Evolution

  • Program Overview

    Ecology and Evolution Department

    The Department of Ecology and Evolution and the Graduate Program in Ecology and Evolution (GPEE) at Stony Brook were the first such units in the United States and have served as models for corresponding units at many other institutions. The Faculty of the GPEE at Stony Brook includes one member of the National Academy of Sciences, several past presidents of national and international societies in ecology, evolution, and systematics, and authors of influential books in these disciplines. Since its inception, the program has emphasized the integration of concepts from ecology and evolutionary biology.

    The faculty and the graduate students in GPEE are engaged in research on Long Island and around the world, including Alaska, the continental US, the Caribbean, Mexico, Central and South America, Africa, and Antarctica. They study terrestrial, freshwater, and marine organisms comprising a wide range of taxa, including fish, amphibians, reptiles, primates, birds, mollusks, insects, vascular plants, fungi, and bacteria. Their research incorporates experimental, comparative, theoretical, and statistical approaches and utilize field, laboratory, and literature survey studies. Research in GPEE includes interspecific interactions, geographical variation and phylogeography, population genetics, experimental evolution, evolutionary genomics, molecular evolution, evolutionary developmental biology, phylogenetics, population dynamics, biological invasions, phenotypic plasticity, ecosystem ecology and paleontology. Many faculty members are active in the application of their research to problems in conservation.

    Our program has students studying toward both master’s and doctoral degrees. Graduates are qualified for positions in academic or research institutions, government agencies, conservation organizations, and environmental consulting companies. Former students have become faculty members in biology, ecology and evolution, agricultural entomology, and marine biology departments at prominent private and public universities as well as selective liberal arts and smaller state colleges. Although GPEE emphasizes basic research, many of its graduates have entered careers that apply ecological and evolutionary principles to problems in such areas as marine toxicology, agricultural entomology, invasive species, natural resource management, conservation, and risk assessment.

    An atmosphere of collegiality and intellectual interchange prevails throughout the GPEE and is fostered by discussion groups and an exciting weekly program of invited speakers during the academic year. A detailed description of the program, including degree requirements, and descriptions of the faculty research interests, and application materials are available on the web at Applicants are strongly encouraged to contact individual faculty members whose interests they share.

    Master of Arts in Biological Sciences (concentrations in Applied Ecology and Applied Evolution)

    The concentration in Applied Ecology provides students with a strong foundation in ecological principles and the quantitative tools necessary for sound assessment of environmental issues. The concentration is intended to address the need for professionals in environmental sciences at federal, state, county, and other levels of government, environmental departments of large industrial companies and smaller environmental consulting firms, and non-governmental conservation and environmental protection organizations. This training is valuable in environmental planning, resource use and regulation, conservation biology, and data analyses for decision makers in government and the private sector.

    The Applied Evolution concentration prepares students for work in these sectors and in fields including biotechnology, forensics, agricultural, pharmaceutical, and biomedicine where genomic, phylogenetic, and population genetics-based analytical skills are required. In particular, the program offers the opportunity to explore both the evolutionary and ecological dimensions of problems such as the evolution of antibiotic or pesticide resistance and genetic contributions to  population decline via inbreeding.

    Both concentrations are useful for further specialized degree programs or careers in education, and are particularly strong in developing quantitative skills, providing enhanced career opportunities.  Courses offered by the Department of Ecology and Evolution provide training in ecology, evolution, genomics, conservation biology, mathematical methods, and statistics, with applications in these fields.

    Ph.D. Program in Ecology and Evolution

    First year students take courses in ecology, evolution, and biometry. A general preliminary examination is given at the end of the first year. Students are encouraged to take specialized courses at Stony Brook and other institutions and to become involved in research during the first summer. Advanced courses and seminars are taken in subsequent years. A temporary advisor is assigned upon entering the program. Students appoint a permanent advisor and advisory committee during the second year. After passing an oral examination that concentrates on the areas of their proposed research and submitting a research proposal to the faculty, students undertake original research that is typically independent of their advisor’s research.

  • Admissions

    Financial Support and Application Deadline

    The application deadline for the PhD Program is December 1 for Fall admission. Applications to the Master’s Program is considered rolling.  Preference will be given to MA applications received by January 15, but we will continue to review all applications submitted by April 15.  The Department does not offer support for MA students; loans and other financial aid may be available through the University. Stony Brook University has among the lowest tuition and fees of any university in the U.S.

    To apply, fill out an online application on the Graduate School website.

    Applicants will also need to provide:

    1. Official transcripts of undergraduate and (if applicable) graduate course work

    2. Official Graduate Record Examination (GRE) scores (Stony Brook's code for score reporting is 2548)

    3. Three letters of recommendation

    4. A non-refundable application fee of $100.00. (Please note that applications will not be processed without the $100.00 fee)

    5. Foreign students are required to take the TOEFL test for proficiency in English.

    PhD applicants should also have:

    1. A bachelor’s degree in biology, chemistry, mathematics, or other courses of study that provide an appropriate background for advanced training in ecology and evolution.

    2. Formal coursework in genetics, ecology, evolution and the biology of a particular group of organisms is strongly recommended. Prior biological research experience also strongly influences the likelihood of admission.

    3. Prior correspondence with GPEE Faculty member(s) to discuss research interests and possibilities is strongly recommended.

    All incoming students will need to be accepted by both the Graduate School and the Department of Ecology & Evolution.

    For more information on applying, contact the Ecology and Evolution Graduate Program Coordinator.


  • Degree Requirements

    Requirements for the M.A. Degree in Biological Sciences

    Concentration in Applied Ecology

    Required Graduate Courses:

    1. BEE 576 - Principles of Applied Ecology and Evolution (4 cr.)
    2. BEE 587 - Applied Ecology and Conservation Biology Laboratory (3 cr.)
    3. BEE 555 - Mathematical Methods in Population Biology (3 cr.)
    4. BEE 574 - Landscape Ecology Laboratory (3 cr.) or Ecology Laboratory (3 cr.)
    5. BEE 552 - Biometry (4 cr.)

    Electives include:

    1. BEE 554 - Population Genetics and Evolution (3 cr.)
    2. MAR 522 - Environmental Toxicology and Public Health (3 cr.)
    3. MAR 536 - Environmental Law and Regulation (3 cr.)
    4. BEE 586 - Introduction to Ecological Modeling (3 cr.)
    5. BEE 550 - Principles of Ecology (4 cr.)

    Concentration in Applied Evolution

    Required Graduate Courses:

    1. BEE 576 - Principles of Applied Ecology and Evolution (4 cr.)
    2. BEE 554 - Population Genetics and Evolution (3 cr.) or an equivalent approved by the Program Director
    3. CSE 549 - Computational Biology (3 cr.) or AMS 533 - Numerical Methods and Algorithms in Computational Biology (3 cr.)
    4. Molecular Diversity Laboratory (3 cr.)
    5. BEE 552 - Biometry (4 cr.)

    Electives include:

    1. BEE 555 - Mathematical Methods in Population Biology (3 cr.)
    2. BEE 587 - Applied Ecology and Conservation Biology Laboratory (3 cr.)
    3. BEE 551 - Principles of Evolution (4 cr.)
    4. AMS 536 - Molecular Modeling of Biological Molecules (3 cr.)
    5. AMS 589 - Quantitative Genetics (3 cr.)
    6. ANT 565 - Human Evolution (4 cr.)
    7. ANT 564 - Primate Evolution (4 cr.)
    8. HBA 550 - Vertebrate Evolution (4 cr.)
    9. HBM 503 - Molecular Genetics (3 cr.)

    Requirements for the Ph.D. Degree in Ecology and Evolution

    A. Course Requirements

    1. In the first year in residence, students are normally required to take BEE550 Principles of Ecology, BEE551 Principles of Evolution, BEE552 Biometry, and BEE556 Research Areas in Ecology and Evolution.

    2. In later semesters, students must take a minimum of three other graduate courses, other than seminars, within this or other programs of this or other universities.  Upon the recommendation of a student’s dissertation committee and with the approval of the Graduate Program Director, one elective course may be waived.

    3. BEE671 and BEE672, Colloquium in Ecology and Evolution must be taken each semester in residence.

    4. Four graduate seminar courses are required under normal circumstances.

    5. Most students will require advanced training in various ancillary disciplines appropriate to their chosen field of research. Requirements will be determined by the student’s advisory committee and may include a foreign language or advanced studies in mathematics, statistics, computer science, molecular biology, taxonomy, or other areas.

    B. Entering Student Advising and Evaluation

    Early in the first semester of study, each student meets with his or her advisor and other faculty member(s) as needed to discuss additional courses beyond required first-year courses. At the end of the second semester, a Preliminary Examination is given testing students' knowledge in the fields of ecology and evolution.

    C. Oral Examination

    In the second year of study, each student takes an Oral Examination tailored to the student’s interests and administered by his or her advisory committee. The student and his or her committee decide in advance on the areas to be covered in this examination. This examination is concurrent with the submission of a Dissertation Research Proposal that is written by the student and must be approved by the advisory committee before advancement to Ph.D. candidacy. As part of his or her dissertation proposal, each student writes a substantial review of the topic of the dissertation

    D. Advancement to Candidacy

    The faculty will recommend a student to the Graduate School for advancement to candidacy upon satisfactory completion of the Oral Examination and any language requirement established for the student, and upon acceptance of the written Dissertation Research Proposal by the faculty.

    E. Research and Dissertation

    A dissertation is required for the Ph.D. degree. It must contain the results of original and significant investigation. A student’s progress in research is monitored by regular evaluations by the faculty in meetings held twice a year. Continued lack of progress may result in probation or dismissal.

    F. Dissertation Committee

    Students select a temporary advisor during the first semester and a permanent advisor at the beginning of the third semester. The advisory committee, consisting of the permanent advisor and at least two other GPEE faculty members, is nominated by the student in consultation with his or her permanent advisor and must be approved by the Graduate Program Director. Additional members from outside GPEE and/or the University may be appointed to the dissertation committee.

    G. Final Examination

    The dissertation must be approved by the student’s advisory committee. A dissertation examining committee (which must include an external examiner) is then approved by the Dean of the Graduate School. A formal public oral dissertation defense is held, at which the student presents his or her findings and is questioned by members of the audience and then by the examining committee in a meeting immediately following the presentation.

    H. Teaching Requirement

    All graduate students completing a doctoral degree will function as teaching assistants during at least one semester of their graduate careers.

    I. Residence Requirement

    At least two consecutive semesters of full-time graduate study are required. The demands of the course of study usually necessitate a longer period of residence.

    J. Time Limit

    The time limit imposed by the Graduate School is observed by GPEE. Students must satisfy all requirements for the Ph.D. degree within seven years after completing 24 credit hours of graduate courses in GPEE.

  • Facilities

    Facilities of the Ecology and Evolution Department

    Ample laboratory, greenhouse, and environmental facilities and all of the standard laboratory equipment for molecular, microbiological, and genomic studies are available. The department houses laboratories working with model organisms including Drosophila and yeast. Field and marine study areas are at Flax Pond, a University-affiliated laboratory near campus. Some terrestrial studies are performed at the Ashley Schiff Nature Preserve, a 26-acre forested area on campus. The University is a member of the Organization for Tropical Studies, which maintains field stations in Costa Rica. There are other opportunities for field studies both in this country and abroad; faculty members have continuing projects at Friday Harbor Marine Labs in Washington, Cook Inlet in Alaska, Ranomafana National Park in Madagascar, Cajas National Park in Ecuador, the Antarctic Peninsula and through various oceanographic cruises. Collaboration is possible with scientists at Brookhaven National Laboratory, Cold Spring Harbor Laboratory, and the New York Genome Center. Opportunities are also available for projects at field stations maintained by other university centers and colleges of the State University of New York. The School of Marine and Atmospheric Sciences is located on campus. Stony Brook is close enough to New York City and Washington, D.C. for arrangements to be made for consultation and work at museums and other institutions in those cities.

  • Faculty
  • Contact

    Ecology and Evolution

    Robert Thacker, Life Sciences Building 650, (631) 632-8600

    Ph.D. Graduate Program Director
    Stephen Baines, Life Sciences Building 636, (631) 632-1092

    M.A. Graduate Program Director
    Joshua Rest, Life Sciences Building 676, (631) 632-1916

    Graduate Program Coordinator
    Melissa J. Cohen, Life Sciences Building 640, (631) 632-8604

    Degrees Awarded
    M.A. in Biological Sciences: Concentration in Applied Ecology or Concentration in Applied Evolution
    Ph.D. in Ecology and Evolution

    Web site


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