Grad Student Guide

This serves as a guide for graduate students in the department of Ecology and Evolutionary Biology at Yale University. It was written by and is maintained by graduate students in EEB. Generally, it addresses questions not covered in the official list of PhD requirements.

Table of Contents

1st Year

What should I be doing?

Regularly attend speaker lunches and department seminars on Wednesday, and speakeasy on Friday. Staying for happy hour post-seminar and post-speakeasy are also good ways to meet everyone in the department. Your cohort will be responsible for an entertaining activity at the department retreat, and you’ll make a poster for the graduate symposium. Also, take this time to develop healthy habits for the rest of graduate school, and make friends within and beyond the department. 

Many students feel aimless during their first year of graduate school, that’s normal! Graduate school is a much less structured experience than undergraduate degrees are, with much more self-direction and fewer clear objectives. During your first year focus on building skills and figuring out what you’re interested in pursuing for your dissertation research. At this point, that’s the whole point of your coursework, rotations, reading papers, and seminars. Don’t worry if you feel like you’re not getting much research done or data collected, that comes later!

Do I need to pay tax on my stipend?

[Please note that this is not official tax advice, but a description of what some students have learned about taxes. The specifics of each person’s tax situation, such as payment of estimated taxes, can vary. ] Yes. Stipends are taxed like any other income. Although all stipend income is taxed the same, depending on the source from which students are being paid taxes may or may not be withheld automatically. For instance, while students are a TF, or receive their stipend from certain other sources, taxes are withheld automatically. When taxes are not withheld automatically, students will likely need to pay estimated state and/or federal taxes (as appropriate) throughout the year to avoid penalties when they file at the end of the year. Students may receive end of year tax forms from the university listing some or all of the income they received for the previous year, but should file taxes for all of the income they actually received. Students are not required to (but in some cases, may) declare their ‘tuition’, which is paid for them.

Tips for Applying for Fellowships

Nearly all students in the department apply for numerous graduate student fellowships during their time in graduate school, including common fellowships like the NSF GRFP and Ford Foundation Fellowship. If you are applying for a fellowship, reach out to more senior students in the department for examples of applications they’ve submitted!

Tips for Your CV

It’s a good idea to have an up to date academic CV. Why not use David Vasseur’s as a template?

2nd year

I am unhappy with ____, what should I do?

If you are unhappy with some aspect of your graduate training, life in the department, or in general, there are many avenues of recourse. You can talk to your advisor, the DGS, or the Chair of the department. If you don’t feel comfortable discussing with any member of the department, you can contact a dean at the graduate school or any number of extra-departmental resources (e.g., the SHARE center).  

Not all of graduate school will be happy. In fact, there are cycles of typical emotional ups and downs throughout graduate school (e.g., feeling aimless in your first year, feeling like you’re not making progress in your third/fourth year). However, if you are consistently unhappy in your lab and/or feel that you cannot work with your particular advisor, you should switch labs. Sometimes an advisor and a student are not good fits to work with each other, and there is no reason to spend many more years miserable. Students switch labs regularly, and it is easier to do earlier (e.g., before your prospectus) rather than later. Don’t wait and end up wasting more time less productive and happy than you could be. Talk to the DGS and/or the Chair if you feel this could apply to you.

3rd/4th Year

What should I be doing?

You’ve passed the prospectus, congratulations! Take a well-earned break, but don’t expect to coast for the next few years. Your fifth year will sneak up on you sooner than you expect, and keep in mind that if you want to graduate in five years you need to have defended and submitted your thesis with all corrections by the middle of March, meaning all data collection and analysis has to be completed by December of your fifth year. Most people collect much of their data in their fourth and fifth year, so don’t worry if you don’t have much until then.

Try to write up your data and analyses along the way. Even better, try to submit chapters of your dissertation in your 3rd and 4th years. Not only will it help fill out your CV, but it will also mean that chapter is basically done when you need to start putting your dissertation together. To finish, you’re aiming for 4 publishable units. The summer of your 4th year is also an excellent time to go to conferences and start making contacts for what you’ll do after graduating.

Also, back up your work! To at least two different locations, ideally one in the cloud and another in a location different from your usual work space.

Undergraduate mentees

You have a lot of research going on, probably more than you have time for. Why not bring in an undergrad to help out?

Undergrads can interact with you in lab in two main ways. First, they can be hired to assist with specific tasks (e.g. during a summer field season). Talk to your PI if you think an undergrad could help you and advertise via classes in the department. Second, EEB majors are required to complete a senior thesis, often by doing a project in the lab. Keen students will spend time working in the lab before their senior year. This is a good opportunity for an undergrad to complete a side project you don’t have time to finish, or for them to work on a sub-component of one of your dissertation chapters. Keep in mind that undergraduate students will likely require high investment at the beginning to teach them the skills they need, but this can pay off long-term when they begin collecting data you wouldn’t have had time to get. Undergrads who make contributions to research projects you eventually publish should be included as authors if they meet the definitions of authorship, just as you would for any other contributing scientists. This is a win-win, as it can be pointed to as a demonstration of your mentorship and teaching abilities.


Many students collaborate with other labs, both within Yale and between institutions, for both dissertation chapter projects and side projects. If you think a research project would benefit from collaboration, including visiting and working in another lab, ask your PI and the other PI and go for it.