General advice and things to consider when formatting your thesis.
1. Graduate School Requirements
The graduate school has very specific guidelines about thesis formatting, in terms of margins, title page, double spacing, fonts, paper, etc. Their guidelines can be found in this document (or check the Grad School page on theses). They also have templates that you can use that are pre-formatted.
2. Formatting your citations and references
The Grad School does not have any requirements about how to do citations/references, because every discipline and even sub-field has different practices and expectations. The only hard and fast rule is that you need to be consistent throughout your thesis. Your choice of a citation/reference style is completely up to you and your advisor. Some departments may have guidelines, but the Department of Biological Sciences does not. The sciences are generally less dogmatic about styles for citing papers, so we tend to allow any method that works, whereas other fields have more formal systems in place (e.g., APA, MLA).
The most common method for citing papers in the sciences in parenthetical notation with the author(s) and year: ...blah blah blah (Cover et al. 2010).
Some people will use a comma after the authors name, but most do not.
Less common but still accepted is a numbering system, where each citation in the text gets numbered, but there is no mention of the author or any other info in the text: ...blah blah blah (1).
This is the format used by Nature, one of the top science journals, because their articles are so short (~2 pages) and it is easy to glance over at the references section while you are reading the text. However it is not as commonly used for long papers because it requires jumping back to the reference section just to see who the author is. I would not recommend it for a thesis, but if your advisor agrees to it anything goes.
As for the format for listing references, almost anything works as long as it contains the basic info: author names, title, year, journal, volume, page numbers.
Here is one way that is commonly used:
Cover, M. R., C. L. May, W. E. Dietrich, and V. H. Resh. 2008. Quantitative linkages among sediment supply, streambed fine sediment, and benthic macroinvertebrates in northern California streams. Journal of the North American Benthological Society 27:135–149.
Other variations include putting the last name first for all authors, using commas instead of periods, etc.
So, the take home message is:
1. You need to follow the grad school/library guidelines for formatting margins, organization, etc.
2. You can use whatever system you want for references and citations, provided your advisor OKs it and it is a reasonably standard practice in science journals.