FAQ for Graduate Life

Unofficial (but who knows more than we do) Graduate Student Guide to EEB Graduate Life

This is what you should be doing each year in EEB.

1st Year-

The key requirements of 1st Year are to do two rotations, take courses, TF, choose a lab, entertain at the retreat, make a poster for the graduate symposium, take advanced topics and make friends.

What is a rotation?

Each semester you will rotate in a lab (you may also choose a summer rotation if that makes sense given your research interests). This should both develop your scientific skills and allow you to see whether you would want to join that lab. Each rotation should involve a scientific project, which you will write a report on at the end of the rotation. The format of the rotation will be decided between you and your rotation supervisor. It is normal to have a desk in the lab office and take part in lab meetings. One of the rotations should be in the lab that you are thinking of joining.

When should I approach a Professor to ask about rotations?

As soon as possible. This will ensure that the PI is willing to have you in their lab.

Can I rotate outside the department?

Yes, if there is a good scientific reason to do so. Check with your main supervisor or the DGS.

How do I choose courses?

When you join the department, you will have an entrance committee consisting of 3 Professors who may assign you courses you have to take to fill any gaps in your scientific education. Otherwise, you are free to take as many courses as you want. You can find all the courses on offer to graduates students (level 500 and above) on the Yale Online Course Information or the Yale Blue Book. You need to take at least 3 courses before you advance to candidacy in addition to advanced topics (EEB500 and EEB501), responsible conduct of research (EEB545), and the rotations (EEB900 and EEB901) .

Grades for graduate courses are Honors, High Pass, Pass, Fail. You need to get at least two Honors and one High Pass in your 3 courses. Most graduate-only courses are graded to give you an opportunity to get Honors to fulfill this requirement. If you get just a Pass, you may have to discuss this with your supervisor.

You can take courses outside of the department but check with your supervisor to make sure they are relevant (and check with other graduate students to see if the course is useful.)

To drop a course or change a course after the deadline, talk to the DGS and/or the Registrar.

What are Advanced Topics?

This is a class just for 1st Years, which is taught by a different professor each week to introduce you to their research. In the second semester, classes will also be dedicated to science writing, research ethics and professionalism, and evaluating proposals.


What departmental events should I take part in?

All years are required to go to departmental seminar on Wednesday afternoon and the brown bottle on Friday afternoon. If possible you should also attend lunch with the seminar speaker on Wednesday as this is a good opportunity to practice talking about your research and meeting Professors. Staying for the happy hour post-Seminar and post-Brown Bottle is also a good way to meet everyone else in the department.

What is the Departmental Retreat?

Each year the whole department takes part in a day-long retreat. It is the responsibility of the 1st Years to plan some entertainment for the whole department. This has normally taken the form of trivia but it doesn’t have to! Talk to some previous years for more information.

What is the Graduate Symposium?

The Graduate Symposium takes place in the Friday of reading week at the end of April or beginning of May. It is a chance for the graduates to present to the whole department. As a 1st Year you will be expected to make a poster. This can be on previous research done as an undergraduate or for a Masters, research done in your rotation project or ideas for research going forward. The poster is not expected to be a ‘finished story’ but is there to give you a chance at practicing to make and present a poster. In previous years, the department has paid for poster printing and workshops have been given to help with poster design.

1st and 2nd Years make posters and 3rd years and above will have the opportunity to give a 15 minute talk.


How do I choose a lab?

Most people come into the department with a supervisor that they want to work with but some people do not. In this case, after your rotations you should talk to your potential supervisor and ask to join their lab. If you are not happy joining one of the labs you rotated in, it is possible to do a 3rd rotation in the summer (or possibly a 4th if you’re still not happy.) Even if you joined the department to work with a particular person, you are not tied to them: If you feel you would be happier in a different lab, join that lab!

Can I be co-advised?

In some cases, it makes sense to be co-advised by 2 PIs. This is not always necessary and it is worth considering whether you could simply have one of the PIs as a committee member.


What does being a TF involve?

Being a TF (Teaching Fellow) differs from class to class. There are different levels of TF. TF level 3, which most EEB TFs are requires a significant amount of work. This may include attending lectures, setting up labs, running section, grading papers, writing exams, grading exams and more. Discuss with the Professor teaching the course. There may be classes to attend to help you become a better teacher.

How many times do I need to TF?

You must TF three times in your graduate career at a level of TF3 or above and an additional time in your fifth year if you do not have external funding. When you TF for a requirement, your payment makes up part of your stipend. If you TF (at any level) after completing requirements, you get paid in addition to your stipend.

Most graduates finish their TF requirements in their first 2 years but it is not problematic to spread this requirement out over more years if needed due to fieldwork or other circumstances.

If I’m a US citizen do I pay tax on my stipend?

If you TF tax is taken out automatically. For any money not from teaching i.e. from your regular stipend, you should declare this on your tax form as other income and pay taxes on it. You do not need to declare your ‘tuition,’ which is paid for you.

Applying for the NSF Pre-doc-

If you are a US citizen with less than two full years of graduate school (i.e. do not have a Masters), you should apply for the NSF for a pre-doctoral fellowship. You can apply in either your first or second year or both. If successful you will get a bonus from Yale but you will not be allowed to teach for money when you are taking NSF money. You can pass on the bonus in your 5th year to have guaranteed 6th year funding. If applying there are many examples of successful NSF applications in the department so please ask for them. Also, make sure your recommenders submit in plenty of time and make sure you have a copy of an official transcript submitted in time.

This website is helpful for all grant writing- http://theprofessorisin.com/2011/07/05/dr-karens-foolproof-grant-template/.

Graduate Student Responsibilities

The graduates are responsible for a number of different things. These include running speaker lunch, helping to run the brown bottle, running the graduate symposium, being in charge of beer, planning for and inviting the graduate student speakers and planning the prospective students’ visit. These positions are often shared between more than one person. There is also the option for a student to be the EEB representative to the GSA. At the moment 1st years are in charge of speaker lunch, 2nd -4th years are in charge of everything else. 2nd years are responsible for telling 1st years everything they need to know. Don’t ask a 5th or 6th year to be in charge of anything or do- make my day.

2nd year-

The key requirements of 2nd year are to finish your courses, pick a committee, have a preprospectus, do preliminary research, have a prospectus. In addition you can apply for the NSF, apply for the Chair’s fund and will be a TF once or twice.

Chair’s Fund

You have two opportunities to apply for the chair’s fund: before and after your prospectus. It is normal to first apply at the beginning of your second year. The chair’s fund gives you ~1500-2000 to spend on whatever scientific purpose you want. Use it for fieldwork, reagents or more likely to go to an awesome foreign conference. The deadline is October 15th and the application only requires a paragraph or two about what you will use the money for and a simple budget.

How do I choose a committee?

You need a thesis committee who will be in charge of your progression through your PhD. Your committee consists of your supervisor and at least two other faculty members. You should aim to have 3 faculty members from EEB on your committee. You can have faculty members from other departments on your committee if it will be helpful. There is not a limit to the number of people you can have on your committee but if you want to plan meetings with more than 4 professors, you probably haven’t thought this through.

You should aim to ask people to be on your committee in January. This assumes that you have worked out a general field of research by the end of the Fall semester, 2nd Year.

What is the Preprospectus?

The Preprospectus is your first meeting with your committee where you will outline the plan for your PhD. Your committee will determine whether what you have suggested is feasible and assign you areas of required reading and possibly data to gather before the Prospectus. Different professors may require different formats for the Prospectus. You should aim to do your Preprospectus in March though if you have fieldwork plans, you may have to do this earlier.

You should prepare a document (~6 single space pages) and a Powerpoint presentation of 15-20 slides. 

The key to the Preprospectus is to demonstrate that you have a novel idea and a way to test it. You should show that you have background knowledge in the field, identify the question you are going to ask and then propose experiments to test the question. I recommend having three main experiments (or one main experiment and two potential follow-ups). Your experiments should all be thematically linked though it is not technically required. Having three chapter ideas, gives you some buffer room if your committee decides that one of your experiments is infeasible. In any case, you most likely won’t get to present the 3rd idea and you won’t have time for it in your PhD either.

You do not need preliminary data for your Preprospectus but include it if you have it.

The biggest mistake you can make with the Preprospectus is to be too vague and not propose specific experiments. Don’t just survey the literature and identify problems without also proposing the experiments you will do to fix them.

The second biggest mistake is to jump straight into describing specific experiments without demonstrating that you understand how your specific questions relate to larger questions in Ecology and Evolutionary Biology.

The faculty of EEB has also provided here suggested guidelines for preparing your preprospectus and prospectus.

Following the Preprospectus, your committee will give you specific areas to study and may suggest changes before the Prospectus.

What is the Prospectus?

The prospectus is the exam that will allow you to advance to candidacy: becoming a PhD candidate. The prospectus is similar to the Preprospectus with the added component of an oral examination on general EEB concepts and specific areas assigned by your committee. The document submitted should probably be a few pages longer than your Preprospectus. If your committee was happy with your ideas in the Preprospectus, they do not need to change substantially for the Prospectus. Following the Preprospectus, your committee may have required you to collect preliminary data or to flesh out particular points so you should definitely do that.

You can schedule the prospectus 2 months after your Preprospectus or longer if you need more time to gather preliminary data. If your committee is unhappy with aspects of your prospectus you may be given a conditional pass and have to present a second time. You must have passed your prospectus before the beginning of 3rd year or you will not be able to register as a student and get paid. If you fail your prospectus, you will be asked to leave the program. However, this has not happened in the last 5 years.

You should expect your prospectus to last about 2 hours with an hour of oral examination followed by an hour to present your research ideas.

Brown Bottle

You should present at brown bottle every year from your second year onwards. This is normally a 20 minute presentation on an aspect of your research.

I am unhappy with my lab, what should I do?

If you are unhappy with some aspect of life in the department or in general, there are many avenues of recourse. The first is to talk to the DGS or alternatively the Chair of the department. If you have a problem, which you are unhappy to bring up to any member of the department, talk to a dean at the graduate school who can help you.

Not all of graduate life will be happy all of the time but I cannot stress the following point enough: If you are consistently unhappy in your lab and feel that you cannot work with your particular supervisor, SWITCH LABS. Sometimes a supervisor is not a good fit for a particular student, there is no reason to spend 4 more years being miserable. Students switch labs regularly so it is not uncommon and it is easier to do earlier (i.e. before your prospectus) rather than later. Anecdotally, I knew a student (not in EEB) whose interactions with their supervisor had broken down by the end of first year but it took another year before they finally switched labs. Hopefully, you won’t be in this situation but if you are, don’t make this mistake. Talk to your DGS or the Chair if you feel this could apply to you.

3rd/4th Year

You’ve probably been in the department long enough to know how things work but here is some advice anyway – back up your work on an external hard drive.

Passed the Prospectus, should I coast for a few years?

Nope. Fifth year will sneak up on you, catlike and come sooner than you expect. Bear in mind if you want to officially graduate in five years, you need to have defended and submitted your thesis with all corrections by the middle of March. This effectively means that all your experiments should be finished and data collected and analyzed by the end of December of your fifth year. However, many people collect most of their data in their fourth and fifth year as it takes time to work out kinks in experimental systems.

Try to write up some of your data along the way. This won’t work for everyone but if you can submit a paper in your 3rd or 4th year, it will help you in multiple ways. Good experience, good CV points, a chapter in the bag, etc. To finish, you should be aiming for 4 publishable units. Ideally, these should be relatively clear by the middle of your 4th Year and certainly by the beginning of 5th year.

The summer of your 4th year is also an excellent time to go to a conference and make contacts that could lead to a Post-doc.

Committee Meetings

You should aim to have a committee meeting before April in your 3rd and 4th Year. You will not be required to write a document as for the prospectus rather just present the progress (or lack) you have made to your committee. Bring the forms each time. You may also add additional members to your committee if needed due to the direction your research has taken.


It’s a good idea to have an up to date academic CV. Why not use David Vasseur’s as a template? http://vasseurlab.yale.edu/sites/default/files/files/Vasseur%20CV.pdf

Graduate Symposium

Sign up to give a talk. Sign up to run it if you like. Even if you don’t like, you have to sign up to run something…


Have a lot of menial jobs to do? Why not hire an undergrad?

Undergrads can interact with you in lab in two main ways. Firstly, they can be hired to assist with specific tasks (e.g. over the summer) in the lab or in the field. Talk to your PI if you think an undergrad could help you and advertise in the department/classes you TF. However, they can require a lot of training/supervision….

Secondly, EEB majors will often complete a senior thesis by doing a project in the lab, which you may end up supervising. Keen students will spend time working in the lab before their senior year. This can be a good opportunity to get an undergrad to complete a side project you don’t have time for.

If you have good undergrads, it is advantageous to them to put them as authors on any papers that they have contributed to. This is also beneficial to you as it demonstrates an ability to mentor undergrads and can be used as evidence on a teaching statement. You may need to take additional harassment training if supervising paid undergrads.


If you think you would benefit from working with or in a different lab in Yale or further afield, ask the other PI, ask permission from your PI and go for it.

5th/6th Year

TF unless you have external funding.

This is a list of things which we need to add to the wiki!

  • Getting a Masters.
  • DDIG
  • Other funding opportunities
  • External Member
  • Auditing courses
  • 5th Year
  • 6th Year
  • How to Defend


1st Year Fall Semester –

August- Entrance Committee, Choose Classes, Start 1st Rotation

September- Entertainment for the retreat,

October- (Apply for NSF)

December- Finish and write up 1st rotation.

1st Year Spring Semester –

January- Start 2nd Rotation, Take classes, TF,

April- Make a poster for the Symposium,

May- Finish and write up 2nd rotation, choose a lab.

2nd Year Fall Semester – Work out what you want to research, TF.

2nd Year Spring Semester

January- Choose a committee

March- Preprospectus

May/June- Prospectus.

3rd Year – Work.

4th Year – Work harder.

5th Year – Do not rile: prickly.

6th Year – Do not ask them when they will defend.