How do researchers handle hypotheses? In my field (biology), the end of the introduction in a research article generally ends with a list of hypotheses that the researchers tested. A common structure of this part of a research paper is:

 'We tested (1) hypothesis X (2) hypothesis Y and (3) hypothesis Z'. 


The research papers I read often test between two and four hypotheses. I'm interested in how the researchers generally arrive at this list of two and four hypotheses. Do they start with a list of 10+ hypotheses, and tick off the ones that they fail to say anything useful about? Or do they stick with the same two to four hypotheses throughout a research project? Or do researchers not begin with any hypotheses, and fit some suitable hypotheses after checking their results?
In my field, Physics, I have only focussed on a single, yet detailed, hypothesis.  This has been true for my thesis and published papers.

I find that it has been and is easier for me to concentrate and explore one single hypothesis thoroughly, any new hypotheses that arise from from this form the basis of several sie projects and further research.