Student Handbook

use ecological and evolutionary knowledge to advance empirical and theoretical understanding of the natural world.
identify and address societally relevant problems in fundamental and applied ecology and evolution.
employ appropriate quantitative methods and approaches to develop and test hypotheses, predictions and models.
effectively communicate research findings by using written and oral disciplinary discourse practices and norms.
use evidence-based practices to teach and inspire the next generation of scientists, environmental stewards, and citizens.

PhD Students Your First Year

The First Year—Coursework & Research

During their first year, PhD students take three core courses: Principles of Ecology [BEE 550], Principles of Evolution [BEE 551], and Biometry [BEE 552]. These courses provide an extensive background in ecology, evolutionary biology, and quantitative procedures.

Throughout the fall semester, students attend Research Areas in Ecology and Evolution [BEE 556], a seminar with presentations and discussion by/with the faculty members in the program. Through exposure to the diverse research questions and methodologies employed by the Graduate Program in Ecology & Evolution [GPEE] faculty, students will develop a richer and more expansive understanding of the field and the research possibilities offered by our program.

During the spring semester of their first-year students take Biometry [BEE 552], finishing their core course requirements. GRD 500 [seminar on responsible conduct of research] is registered for each semester. This course tracks complete of Responsible Conduct of Research, which is completed in lab groups. Another elective course or seminar may also be taken at this time.

After the SBU Spring Break, students will take the General Written Preliminary Exam [Prelim], which is a test of general knowledge in Ecology and Evolution. The first-year class sits for the exam together, over a two-day period in April, at a mutually agreed upon time. Information on preparing for the exam is distributed each October.

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 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. Please refer to NSF for the current rules and we advise consulting with your advisor. Other fellowships that PhD students have been successful with include NASA FINESST, the U.S. Department of Energy (DOE) Office of Science Graduate Student Research (SCGSR) program, and the NOAA National Estuarine Research Reserve Graduate Research Fellowship. Recent successful and honorable mention application packets are available to consult (please speak with the GPC).

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.

Our program adopted the mentoring documents developed by the graduate school. The student and mentor should discuss the expectations for mentor and mentee responsibilities and document if there are any expectations that both parties cannot agree to. Secondly, mentees and mentors should fill out the mentoring plan together to prompt open communication. In addition, the Student Advisor Expectation Scale can be used. The worksheet lists 16 pairs of statements describing end points on a continuum, and individuals may differ as to the position they take reflecting variation in educational philosophy, personality, and disciplinary norms. Making expectations explicit and having regular conversations about expectations minimizes understanding.

It could be useful to revisit the second two of these document yearly as the research relationship evolves.

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. "Some modest advice for graduate students" and "On being a successful graduate student in the sciences."

Your Second Year

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

It is a busy year and by the end, students are expected to:

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

Details on these tasks are as follows:

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.

Appoint a dissertation committee that includes at least two additional program faculty members Paperwork to complete this is available from the Graduate Program Coordinator.

Hold a meeting of the dissertation committee. The goal of this meeting is to discuss and outline the student’s dissertation research plan.

Complete the dissertation proposal and submit the dissertation proposal abstract for circulation to the Graduate Program faculty, after approval of committee.

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 is expected to include a substantial component of literature review and 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 circulation to the Graduate Program faculty. The Graduate Program Coordinator can assist with the paperwork and distribution of the abstract.

Pass the oral 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 dissertation proposal, but also to assess the student’s depth of knowledge in relevant fields and the ability of the student to formulate answers. Students are advised 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.

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 elective requirement, although on a case-by-case basis courses they may be accepted if approved by the student's advisor and the Graduate Program Director. Graduate courses at other institutions are accepted for credit in the GPEE program if preapproved by the Graduate Program Director and the student's advisor. Students in their second year are also encouraged to enroll in relevant seminar courses. Four seminar courses are required prior to graduation.

Submit the paperwork required to advance to candidacy

For the program to submit paperwork to advance a graduate student to candidacy the, the student must have passed their oral exam, have an approved research proposal, have an approved abstract of the research proposal, have the abstract circulated to the graduate program faculty, and complete three elective courses (or two, if one was waived).

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 five of a semester then it will not take effect until the following semester.

The target date for completing the proposal and exam is the second semester of the second year. The final deadline for advancing to candidacy is June 15th following the second semester of the third year. Students who have not advanced to candidacy by this date will be dismissed from the program.

Preparation Deadlines

Second year PhD students should be mindful of the following deadlines. These deadlines are in addition to regular communication and consultation with your advisor and committee:

Dec 15: Deadline to form a committee for the oral exam. Please email the graduate program coordinator and GPD the names of the members of your committee by this date. You need at least two committee members in addition to your advisor, and they must be members of our Graduate Program
20: Deadline to submit* an outline of your dissertation proposal to the program (we understand this is subject to change as you continue to write).
March 15: Deadline to submit* a draft of your proposal to the program (we understand this is subject to change as you continue to write).
April 15: Deadline to inform us of the scheduled date for your oral exam with your committee. If a date for the oral exam is not scheduled by April 15, your advisor will be asked to set the date. Scheduling is challenging, so taking care of this at the beginning of the spring semester is highly advised.
April 25: Deadline to submit your dissertation research proposal to your committee (but at least a week before your scheduled exam date). Your committee may have seen previous versions.
May 1-May 30: Oral exams should be scheduled to be completed no later than May 1- May 30.
June 1 - Deadline to submit* your approved proposal abstract to the program. The program will circulate the abstract to program members. You are expected to submit your Abstract upon completion of your oral exam and it must have the approval of all of your committee members. The final approved proposal is also due upon completion of your oral exam and with the approval of your committee.

*Please email the graduate program coordinator and the GPD a copy of these documents.

You are welcome to move faster than these deadlines. In order to meet each of these deadlines, you will need to work collaboratively and actively with your advisor. They are in charge of assisting you in planning and preparing for these, and all documents are expected to meet with their approval before submission.

Dissertation Proposal Guidelines

We recommend that students follow this format of sections in the preparation of their dissertation plan and that faculty committees use it as a jumping off for the oral exam. In terms of length and organization, the format is roughly based in NSF proposal structure.

Overview

Proposals follow NSF application guidelines. Any requirements suggested below may be superseded by referring to the current NSF Guidelines.

Format

In a typical NSF-style proposal, formatting guidelines include using a standard font like Arial or Times New Roman at a font size of 11 points or larger, with at least 1-inch margins on all sides. The text is single spaced. The page limit is 15 pages, including figures, figure legends, and tables. The page limit does not include the literature cited.

Sections:

Introduction and Background.

(NOTE: This section should be ~ 5 pages.) This section should state the general problem that you will be addressing and its intellectual relevance. The background should involve a succinct review of the relevant literature that sets up the entire proposal by defining key concepts related to the general topic, describing important patterns and generalities, outlining intellectual and detailing relevant methodological concerns that are relevant to the proposed work. The relative emphasis on these different elements will depend on the field and topic of interest. By the end of this section, the reader should have a clear sense of why the questions you will be asking are in some way interesting and feasible.

Questions, Rational, and Significance

This section should introduce the specific questions and hypotheses to be addressed in the dissertation. It should provide a concise statement of the goals of the dissertation work. The intellectual merit of the proposed questions and goals should be related to the information provided in the Background section. You should state what you expect the general expected or alternative outcomes will be. Discuss the logical interpretation of these outcomes to make it clear how they relate to your initial questions/hypotheses.

Finally address the significance of these outcomes in light of the background material. NOTE: If this dissertation is part of a larger collaborative effort in a lab you need to define your role in the group effort.

The Research Plan and Design

The Research Plan should discuss the general plan of effort. You must provide a clear explanation and sketch of experimental methods, forms of analysis, and technical procedures that will be used along with supporting references. You need to explain and justify these approaches. Among things that should also be addressed are:

What is the time-line for completion of the various tasks outlined in the research plan.
Do you need further training? Are these methods and expertise currently available in the department or university? How will you gain access to needed expertise and resources not present at Stony Brook?
It is very important to point out early on any potential problems, or alternative strategies. By definition one can’t always anticipate what will happen in research. Identify benchmarks that will indicate success of specific approaches and may serve as signposts for possible “forks in the road” where different directions or emphasis may be entertained.
You should be clear when advice from experts has shaped your decisions, so these decisions can be properly evaluated.
If your research is in the early stages, describe any steps required to establish feasibility. What are the high-risk aspects of the dissertation? Are they essential to success of the project and your career goals?

Budget

A separate budget section is encouraged but not required. A rough breakdown of possible expenses will provide insight into the practicality of the research. Discuss any needs for travel, materials, etc. In addition, this section may address what financial resources may be available to cover these expenses.

Literature Cited

By this stage you should have established a reference management system (e.g. Mendeley, Endnote, or Reference Manager). Several are provided free of charge on the university’s Department of Information Technology website. Provide an informative bibliography of all references cited in the proposal, including those used in figures and tables. Recognize that in the oral exam you may be asked to elaborate on any of the cited work. Do not use numbered in-text citation formats in the proposal; rather, use name & date formats common in scientific society journals like Ecology or Evolution. In the bibliography, use reference formats that include names of all authors (in the same sequence in which they appear in the publication), the article and journal title, book title, volume number, page numbers, and year of publication (not necessarily in that order).

FAQs about the Written Dissertation Proposal

What is the format of the written dissertation proposal?

The format of the proposal is in NSF style, 15 pages single spaced, not including references but including figures and tables.

How do I know when my written proposal is ready to submit?

Your proposal is expected to be developed in concert with your advisor, and your advisor's feedback informs when you solicit external feedback, and send out draft or final copies.

When do I write and circulate the abstract of my proposal to the program faculty?

Once your committee approves the proposal abstract you should send it to the GPC for circulation to the faculty.

Where can I find examples of previous written dissertation proposals?

Please speak with the GPC, who can provide examples shared by current and previous students. Samples are also available on the shared student google drive.

What are the possible outcomes after I submit the written dissertation proposal to my committee?

If your committee does not find your proposal acceptable, there is a possibility that your oral exam might be delayed to allow time for significant revisions. However, usually a student works closely with their advisor and committee to develop a satisfactory research plan.

FAQs about the Oral Exam

How do I know when I am ready to take the oral exam?

You are expected to take the oral exam at the end of the fourth semester.

How should I prepare for the oral exam? What should I read, and how should I divide my time between writing my proposal and preparing for the oral exam? What topics will be covered on the oral exam? How does this intersect with the topics that are covered in my proposal? Should I organize a meeting of my committee before my oral exam? What happens at this meeting? What is the format of the oral exam? Who is in charge? Do I present at the beginning?

The answers to these questions are largely decided by mutual agreement between you and your committee, and it depends on how knowledgeable your committee is regarding your proposed dissertation research. Students often have a couple of meetings with their committee prior to the oral exam to discuss the outlines of the proposed work and address any major concerns. Having met and discussed your proposed research prior to the oral exam, the oral exam can focus on the exam itself rather than a detailed discussion of the dissertation proposal. Under these circumstances, a presentation at the oral exam is unnecessary. The chair of your committee will oversee this meeting (who is not your advisor). In some cases, due to scheduling and other timing considerations, it is not possible for the committee to meet sufficiently before the oral exam to address concerns with the proposal itself, and in these cases the oral exam involves both a detailed discussion of the proposal and an examination of the relevant subject matter. In these cases, the student should prepare a presentation that walks the committee through the proposed research, though it is worth noting that under these circumstances, the oral exam can take quite a long time and should be scheduled for a sufficiently long block of time that the committee can both discuss the proposal and evaluate the students readiness for the proposed research.

What are the possible outcomes of the oral exam?

Ideally, the student passes the oral exam without qualifications, and the dissertation proposal is approved. However, it may be that the student passes the exam, but the proposal itself needs further revision, or the student is found to have gaps in their knowledge that need to be addressed. In some cases, the exam will be suspended and reconvened sometime in the future after the student has addressed gaps in their knowledge or background. A second meeting may be required to go over elements of the proposal or to assess whether gaps in a student's knowledge have been addressed.

Failure to pass the oral exam could be considered failure to make academic progress and cause for dismissal.

Your Third Year and Beyond

The dissertation committee must consist of a minimum of four people: (1) the chairperson of the defense, who is a member of the Ecology & Evolution program, (2) the dissertation advisor, who is a member of the Ecology & Evolution program, (3) a third member who is a part of the Ecology & Evolution graduate program, and (4) a fourth member who is external to the E&E graduate program.

Note that one of the members must have no conflict of interest to the student. Conflicts of interest may, but are not limited to, financial or professional relationship between the student and committee member. In practice this means that the person does not pay your GA/RA salary or any supplemental salary and at the point of dissertation defense, you do not have any joint publications. In most cases, the Dissertation Examining Committee consists of the members of the Oral Exam Committee plus an outside member.

Graduate students are required to complete four seminar courses prior to graduation. 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. As a matter of course, students take courses from other Stony Brook departments. Credit for courses outside the institution should be 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.

The members of the dissertation committee will be submitted to the Graduate School for approval by the Graduate Program Coordinator. Please send the GPC the names of all committee members, indicating the advisor and chair, the name of the external committee member and a copy of the external committee member’s CV. The members of the dissertation committee should be submitted to the Graduate School for approval between when the committee is finalized, and at least a month prior to the dissertation defense.

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. 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. The Department of Ecology and Evolution's 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 through awards.

Departmental Colloquium

All members of the Department of Ecology and Evolution are required to attend the department's weekly colloquium on Wednesday afternoons. Attendance is required of all graduate students. The colloquium features speakers, generally visiting from outside the University, who present the results of their research. Receptions may follow 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. A pizza lunch with colloquium speakers targeted at graduate students is usually offered.

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. Students are required to give at least one presentation during their tenure in the program.

PLAID form

At the end of each semester, students must submit a PLAID [Program Learning and Information Document] form. This form records academic activities, accomplishments, and plans for the coming term, and serves as a basis for documenting and evaluating student progress and scientific development by the full program faculty. Students are expected to review their submission with their advisor. Completion of the PLAID form is required every semester.

Teaching

All graduate students are required to complete at least one semester as a teaching assistant. Students must register for Teaching Practicum for a semester of teaching to count towards the teaching requirement.

Graduate students have the opportunity to serve as teaching assistants (TAs). 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 students may repeat courses, 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.

According to the policies of the Graduate School, students are unable to register for classes after two semesters on academic probation with a GPA of below 3.0. This results in defacto dismissal. The Graduate School enforces this requirement strictly.

Time Limits

We expect doctoral students to finish in five to six years. Students must satisfy all requirements for the Ph.D. degree within seven years after completing 24 credit hours of graduate courses in GPEE.

Leaves of Absence and Withdrawals

Graduate students may request a leave of absence by submitting a Request for Leave Absence form to the Graduate School. The process of withdrawing from the University is a formal procedure that the student must initiate. A student finding it necessary to withdraw from the University must submit a letter of intention to the graduate program director and the Graduate School. Please find more information about Leaves of Absence and Withdrawals in the Graduate Bulletin.

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 their dissertation to the dissertation committee at least one 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 three 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 zoom) of committee members; please consult the Graduate Program Coordinator prior to the defense where members are planning to be present remotely.

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

Doctoral candidates who have completed their degree requirements by the Ceremony Registration deadline are eligible to participate in the May Doctoral Hooding Ceremony. August, December and January candidates are permitted to attend by emailing the Graduate School. More information on eligibility is on the Graduate School’s website. 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.

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.

Department Retreat

The purpose of the annual Ecology and Evolution retreat is to share and discuss scientific research interests, projects, and findings, to exchange ideas and insights, to network with other department and program members, and to recognize and celebrate accomplishments of our community. Participation by all program/department graduate students, faculty, post-docs, and researchers is highly encouraged. Participation may include simply attending or giving a lightning or regular talk. Participants are encouraged to help with the various committees needed for this event. In addition to the scientific and networking aspects of the retreat, it also serves as an important opportunity to highlight the program and department to prospective students.

Department Roles

The Graduate Program Coordinator - The Graduate Program Coordinator (GPC) at Stony Brook University is the primary departmental staff member who manages the day-to-day operations of Master's and PhD programs. GPCs guide students from the admissions process all the way to graduation clearance, handling course enrollments, Teaching/Research Assistant (TA/RA) appointments, and degree progress. The GPC provides advising and support, helps to process forms related to academic and registration, and funding and payroll.

The Graduate Program Director - is a faculty member elected to lead the departments Graduate Program. Ecology and Evolution as a director for the MA program and a PhD program director. The PhD Graduate Program Director assigns TAs, leads the Program Meetings, held once a semester, where student progress is discussed by the full faculty, is responsible for communicating this information formally via Program Progress letters, is the chair of the Graduate Program Executive Committee, and approves seminar topics. If you are having problems in the program, both the GPC and GPD are appropriate people to discuss concerns with, as well as your advisor, and other folks that may be helpful (the University ombudsperson). If your concern involves another individual, we encourage you to address the issue informally as an initial step, through open and respectful communication.

The Department Chair is the bridge between the faculty and students and University administration, responsible for leadership, curriculum planning, and securing resources. In the Ecology and Evolution Program, the department chair is responsible for scheduling courses and assigning instructors, appointing committees and committee chairs, and evaluating and supporting faculty.

The Graduate Program Executive Committee is composed of the department chair, the two program directors, and two elected members, one from inside the department, and one external, and a graduate student member. The GPEE discusses and votes on policies and issues that affect the Graduate Program.

DOCTORAL GRADUATE PROGRAM IN ECOLOGY AND EVOLUTION

Program Goals