The Doctoral Program in Ecology and Evolution

This document gives a summary of the Graduate School's requirements and also includes additional requirements and explanations relevant to graduate students in the Ecology and Evolution Ph.D. Program.

The Graduate Bulletin gives an official statement of degree requirements and can be found here. General information for new and current graduate students is available here.

The First Year—Coursework & Research

During their first year, graduate students take three core courses: Principles of Ecology, Principles of Evolution, and Biometry. These courses provide an extensive background in ecology, evolutionary biology, and quantitative procedures.

Throughout the fall semester, students attend BEE 556, Research Areas in Ecology and Evolution, a seminar with presentations by the faculty members in the program. The goal of the course is to acquaint students with research opportunities and to provide a chance to meet all faculty members in the graduate program. There are no formal lab rotation requirements.

During the spring semester of their first year students take Biometry, finishing their core course requirements, and GRD 500 (seminar on responsible conduct of research). Another elective course or seminar may also be taken at this time.

After the SBU Spring Break, students will take the General Written Prelim Exam, which is test of general knowledge in Ecology and Evolution.  The first year class sits for the exam together, over a weekend in April. A reading list for the exam may be found here [insert link].

The First Year—Advisors

Incoming students are assigned a Temporary Advisor during the admissions process. Over the course of their first year, students will meet with their Temporary Advisor and at least one other faculty member to discuss research objectives and the coursework required to prepare students to start their dissertation research. Ideally, students will begin research projects during the first year under the direction of their Temporary Advisor.  These interactions can also take the form of Tutorials and Research for credit during the academic year.

Under the guidance of their Temporary Advisor or another faculty member, students should prepare for a productive summer, either by conducting research or taking an off-campus course that will provide them with skills necessary to conduct their dissertation research.

Also during their first year, students meet with the Graduate Program Coordinator to discuss academic procedures, and with the Graduate Program Director to discuss academic requirements and expectations.

The First Year—Additional Information

Eligible students (most domestic students who have not previously completed a Masters) are strongly encouraged to apply for an NSF Graduate Research Fellowship. The deadline is usually in early November. These fellowships pay a stipend for three years and provide a "Cost of Education Supplement". They also provide funds for travel and supercomputer access. Check the NSF website) for details. It is important to try in your first year because the comments you receive will help you prepare for another try in your second year.During their first year, domestic Ph.D. students must work towards establishing New York state residency. Details about establishing residency can be found on the Bursar’s website. Domestic students with tuition scholarships should note that the scholarship is limited to in-state tuition starting their second year.

You may find the essays by Stephens C. Stearns (Yale University) and John N. Thompson ( UC Santa Cruz) helpful as you start your graduate career. They are available as PDF files. "Some modest advice for graduate students" and "On being a successful graduate student in the sciences."

The Second Year

The focus of the second year is to develop and defend a project that will be the doctoral dissertation.

It is a busy year and by the end, students should:

  1. Formalize a relationship with a program faculty member who will serve as a "permanent" Advisor for the student's dissertation research (fall semester)
  2. Appoint a permanent dissertation committee that includes at least two additional program faculty members (fall semester)
  3. Hold a meeting of their dissertation committee (fall semester)
  4. Pass their oral preliminary exam (spring semester)
  5. Complete a dissertation proposal (spring semester)
  6. Finish taking three elective courses (by the end of the spring semester)
  7. Submit the paperwork required to advance to candidacy (by the end of the spring semester)

Details on these tasks are as follows:

  1. Formalize a relationship with a program faculty member who will serve as a permanent advisor
    Paperwork to complete this is available from the Graduate Program Coordinator.
  1. Appoint a permanent dissertation committee that includes at least two additional program faculty members
    Paperwork to complete this is available from the GPC.
  1. Hold a meeting of the dissertation committee
    The goal of this meeting is to discuss and outline the student’s research plan.
  1. Pass the oral preliminary exam
    The oral examination will be given by all program members on the student's committee and, optionally, the external committee member. Oral exams should be scheduled only during the academic year. It is the student's responsibility to plan for and schedule this exam. The idea behind the oral exam is not only to assess the feasibility and scientific merit of the thesis proposal, but also to assess the student’s depth of knowledge in relevant fields and the ability of the student to formulate answers to questions on the spot. Students should therefore expect that some questions during the oral examination will address the proposal specifically, while others will relate to any area deemed relevant to the particular student’s research program. The exact line of questioning is the prerogative of the committee. Faculty differ in the guidance they provide to students regarding preparation, so students should meet with their advisors and committee members well before the exam.
  1. Complete the dissertation proposal and submit the dissertation proposal abstract for approval by the Graduate Program faculty
    A finished dissertation proposal (approved by the advisor) is presented to the committee at least two weeks in advance of the oral examination date. The dissertation proposal should include a substantial component of literature review and should present an important and original scientific question that the student plans to pursue (see "Proposal Guidelines"). The committee-approved abstract will be submitted to the Graduate Program faculty for approval. 51% of Graduate Program faculty must approve the proposal abstract. The Graduate Program Coordinator can assist with the paperwork and distribution of the abstract.
  1. Finish taking three elective courses
    Also during their second year, students are expected to finish their three required electives. Upon the recommendation of a student’s dissertation committee and with the approval of the Graduate Program Director, one elective course may be waived. The dissertation committee will consider the scope and depth of the previously completed coursework in the context of the student's projected trajectory when recommending to the Graduate Program Director to waive one elective course requirement. The Graduate Program Director may consult with the executive committee, and/or the graduate program faculty in making this decision. Courses offered by the Department that are designed for Master's students will not count towards this requirement. Graduate courses at other institutions are generally not accepted for credit in the GPEE program. Exceptions can be granted but only if preapproved by the Graduate Program Director.
  1. Submit the paperwork required to advance to candidacy
    To submit the paperwork, graduate students must have passed their oral preliminary exam, have an approved research proposal, have an approved abstract of the research proposal, have the abstract approved by 51% of the graduate program faculty and complete three elective courses.
    Advancement to candidacy must take place at least two semesters before the completion of the Ph.D. degree. The Graduate Program Director will recommend advancement to the Dean of Graduate School after all requirements are completed. If the paperwork to advance to candidacy is received after day 10 of a semester then it will not take effect until following semester. Note: after the tenth day of the semester the Graduate Program Director can still provide a statement for an NSF Doctoral Dissertation Improvement Grant, DDIG, saying that all requirements have been satisfied and that a request for advancement has been submitted to the Graduate School.

The deadline for advancing to candidacy is June 15th following the second semester of the third year. Students who do not advance to candidacy by this deadline will result in termination from the program.

The Third Year and Beyond

By the spring of the third year (5th semester), students are required to add an external committee member to their Dissertation Committee. A Dissertation Committee must include at least 3 members from the E&E program faculty in addition to the outside member. In most cases, the Dissertation Examining Committee consists of the members of the Oral Exam Committee plus an outside member.

The members of the dissertation committee should be submitted to the Graduate School for approval. The Graduate Program Coordinator can provide the paperwork. 

From the third year onwards, the student must hold at least one committee meeting each year. Committee meetings should be held during the academic year and not in the summer. In general it is recommended that students hold committee meetings or meet with members individually whenever there is a significant problem or change in the research plan.

Students are encouraged to attend relevant professional meetings and make oral and poster presentations. The Graduate Student Organization's Research Access Program provides small grants to help offset the costs. See the GSO Research Access Program for more information and the application form. The E&E Graduate Program can also help cover the costs of attending meetings, workshops, and special courses such as those offered by the Organization for Tropical Studies.

Beginning in their second year, graduate students who are in residence at Stony Brook may enroll in seminar courses. Each student is required to take a total of four graduate seminar courses during their time in E&E. Within the department, at least four BEE seminar courses are offered each year, in the general areas of ecology and evolution. This requirement may also be met by taking suitable courses or seminars in other departments and universities, but credit for these courses will only be applied if preapproved by the Graduate Program Director. Waiving of the seminar requirement because of absence from the University because of field work must be approved by the Graduate Program Director.

Departmental Colloquium

All members of the Department of Ecology and Evolution attend the department's weekly colloquium on Wednesday afternoons. Attendance is required of all graduate students. The colloquium features speakers visiting from outside the University who present the results of their research. Receptions follow most colloquium presentations, sometimes later in the evening, and provide an opportunity for students to meet informally with visiting scientists. Graduate students may suggest speakers they wish to invite, and play an active role in hosting speakers.

Informal Seminar

The graduate students run an informal seminar series on Tuesdays at noon in which they present research results or discuss new ideas. This provides an excellent way for new students to get feedback on their work and get to know their colleagues. Most students give at least one presentation during their tenure in the program.


All graduate students are required to complete at least one semester as a teaching assistant. Students must register for Teaching Practicum in order for a semester of teaching to count towards the teaching requirement. Typically, this involves helping to operate the labs for an undergraduate course. Exceptional graduate teaching assistants are recognized each year with a program award for Best Teaching Assistance and the Graduate School’s President's Award for Excellence in Teaching, which provides a cash prize.

Grade Point Averages

Graduate students must maintain at least a 3.0 grade point average. Grades of I, NR, P, S, U, and R are excluded from this computation but grades of I are treated as an F in determining whether a student should be placed on probation. Graduate student may repeat course but the credits are counted only once. The most recent grade is used in the computation of the GPA, though both grades will appear on the student’s transcript.

Time Limits

We expect students to finish in 5-6 years. The Graduate School has a limit of seven years if the student is admitted with an Master’s degree in a closely related field. If the student enters without a Master’s degree, the Graduate School’s time limit is 7 years after completion of two full-time semesters (i.e., a total of 8 years). The student may petition for an extension of an additional semester or a year if it is submitted before this limit is reached.

Leave of Absence

A student who, for any reason, would like to take leave of absence for one or more semesters must submit an application to the Graduate School before leaving. This avoids a re-admission fee. Papers for re-admission must be submitted before the start of the semester of re-joining. Students may initially apply for a maximum leave of one year, which may be renewed for a second year. Students must be registered during the previous semester. Readmission requests must be made 3 months in advance of the student's return.

Dissertation Defense

Students formally announce their dissertation defense (and set the defense date, time, and location) at least 1 month in advance. The student must submit his or her dissertation to the dissertation committee at least 1 month before the defense. If this deadline is missed, the defense must be rescheduled. A dissertation defense announcement must be submitted to the Graduate School at least 3 weeks before the defense. The Graduate School requires this document be on a special form available from their forms download page. The dissertation defense must take place on campus during the regular academic year and requires participation of the full dissertation examining committee (exceptions require the approval of the Dean of the Graduate School). Dissertation defenses will be allowed during the summer period only under exceptional circumstances. The public part of the defense should be open to the entire University community and should be widely advertised. The Graduate School also places restrictions on remote attendance (e.g., via Skype) of committee members; the student must consult the Graduate School before making such arrangements.

The Graduate School also defines a procedure to apply for graduation, as well as guidelines and templates for the submission of the dissertation.

To be eligible for the hooding ceremony, the student must either successfully complete an oral defense of their dissertation or provide a written statement from the GPD that the defense will take place prior to the start of the next term (excluding summer). A student may register for no more than one semester following the completion of the defense. The scheduling, announcement, and planning of the dissertation defense are the responsibility of the student.

As of May 2014, a student is allowed up to three months after their defense to submit their dissertation to the Graduate School. A student must be enrolled during the semester in which they are graduating. If a dissertation needs 'major revisions', it may require a second defense before it is approved. The three-month time limit would then be based on the second defense. Registered degree candidates maintain their student status (with housing and library privileges, visa status, etc.) until their final semester is over, regardless of when they turn in their dissertation during that semester.

State University of New York at Stony Brook is an affirmative action/equal opportunity educator and employer.

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