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I have to provide 3 references for OMSAS and I have 4 to choose from:

1. A professor I published a paper with, over 2 weeks of 12-hour days of field and lab research in undergrad, who likes me but had admittedly little face to face time. Fish physiological research, 3rd author.

2. My volunteer coordinator at the local hospital, 140 hours, 2 years, just loves me, and has very high praise from the head nurses of the wards I've volunteered in.

3. A program coordinator and technician who teaches an entomology field research course I attended. Field research, 2 weeks, 2 other courses with him. Easily my #1 fan, would be a spectacular reference with high praise, but not a professor.

4. My graduate thesis supervisor. Medical science, diabetes and atherosclerosis. Just an amazing guy but I don't think he likes me very much. Its been an unusually hard year, I've struggled with family issues, anxiety and depression and as a result I've performed uncharacteristically poorly. Missing days without notice, coming in late, slow pace of research. He has every right to be annoyed. The lab, colleagues and supervisor have all been spectacular, but I've just really struggled to make a good impression with everything going on. I've spoken to him several times to check in and while he was pleased with my progress until recently, in the last two months he's seemed pretty frustrated. I've proactively apologized for missing days but haven't told him about the anxiety and depression. 

Anyway, TLDR: my supervisor and I have a complicated relationship. Would it be better to use references 1,2, and 3? Would it hurt if I didn't include him?

(I know UofT required him as a reference, but I'm asking mostly for other schools)

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This is a tough call. You have to balance between how it will look omitting the person who should presumably be your best and strongest reference between the reality of obtaining a lacklustre review from them. I think the omission of your graduate supervisor in favor of either 1 or 3 would be an error, considering they would hardly know you in comparison. I might be cynical, but I believe reviewers would assume the worst about your relationship with your supervisor at that point, which is not a good thing. It is a huge red flag to use someone you have spent  a couple weeks with versus someone you have worked for full-time. 

You should have an honest and frank conversation with your supervisor about your performance and see how they feel about writing the letter. 

Also keep in mind that professors are generally not interested in doing more work than necessary. They have likely written a letter for you in the past that they will modify as necessary and copy/paste, so chances are your more recent issues may not even be addressed or reflected in their letter.

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I can't really speak too much about how excluding your graduate supervisor would look at other schools, because I don't know how those letters are evaluated. That being said, have you considered being honest with your supervisor about your anxiety, and straight up asking him if he would provide you a positive letter? If he says no, then obviously look elsewhere, but if he's understanding and says he will support you then I do think its a better option. Just looking at your first reference, and the importance of tangible examples in reference letters, it doesn't seem like that is a great option. 2 weeks with little face time doesn't lend itself to a good reference letter regardless of the fact you have published with him and worked long days. Your graduate supervisor is in a better position to truly assess you and provide a useful evaluation of your capabilities (provided he says he will support you).

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