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:
<script type="text/javascript" src="species.js"></script>
<script type="text/javascript" src="fishycode.js"></script>
etc. ad nauseum.