The key reason to take a PhD program is to learn research techniques that will turn you into a researcher. If you want to make paleo related research a key factor should be going to some University where a well known paleo researcher teaches, so you could have his/her direction when you start writing your dissertation. So perhaps you should look at the main names in the field in terms of research, like Loren Cordain (Colorado), Staffan Lindeberg (Sweden), Rob Wolff, etc and find out whether they work with graduate students. Good luck!

What coursework does each path entail? I agree with Drew that studying physical antrhopology will provide you with valuable knowledge. Perhaps the other will teach some useful physiology though?

The most important aspect of PhD training is your thesis. You should choose a topic that reflects your interests and abilities. Then, you choose classes to give you the background to adequately understand & address that topic.

Personally, I'd buy some books on anthropology and read them on your own time. The guided questioning that a program provides would probably be more useful in the physiology program.

And from a purely practical perspective, it's a lot more solid to get into a PhD vs. a master's program.

P.Evil - I was going to say the opposite. I agree with the PhD > master's though.

I have a BS in exercise science with a sports medicine concentration, and I feel I have learned more since graduating and working in the field than I did during my studies. I could have learned the anatomy, nutrition, and physiology parts on my own (without the misleading information as well!).

I think the interning experience you get in the anthropology program would be enlightening, and you can pick up some anatomy, nutrition, and physiology books to supplement your studies.

Much luck A.J. and if you ever start that program I will be certainly be researching it further!

Don't forget to think about your job prospects and what each degree would prepare you for!