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> Active Directory

Microsoft has differing documentation on preferred domain naming.

Regarldess. It's not a good idea to make your root domain point to your actual domain. You should point it to a subdomain. That way, you can serve the root domain directly, or redirect it wherever.

anr.msu.edu
ad.anr.msu.edu
mail.anr.msu.edu
ns.anr.msu.edu
www.anr.msu.edu


> www

You will get dinged by search engines for having duplicate content on 2 domains.

msu.edu
www.msu.edu

One should redirect to the other. Either way is common. My personal opinion is that everything future is www, so there's no reason to add it. The default service is http. There's even a whole movement dedicated <http://no-www.org>.