Whoops...missed JMrker's post.
Yes, you can indeed separate the species stuff into it's own JS file.
You could have several JS files, in fact, if you wanted.
I would still put them all at the *bottom* of the page, not in the <head>.
So if you had the species stuff in one JS file and the actual code in another, then just before the </body> tag you would do:
etc. ad nauseum.