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In large fields most schools have a PhD program. Ivy League and top tier research institutions tend to make sure that they have good programs.
It's a question of numbers. If you have 200 good faculty in a field you can bet that many more of the top 10% will be at schools top-rated in lots of areas. They have money, tenure lines, facilities. They're big and impressive. They have a certain critical mass.
But if you have 10 good faculty in a field, what are the chances they're at the top-rated schools? Odds are many of the top-rated schools won't even have a program for them to fit into--or, if they would make room, there's nothing in it for the researcher unless he really wants to have the name recognition after having had a lesser institution support him (or her) for years. So if you get a few really good faculty in a lesser school, that program is top rated in the field. Only the dean and people in the field would know this.
This creates an anti-feedback loop, as far as those programs are concerned. If you're in ling or psych and want to go into psycholinguistics, what are the odds that your undergrad faculty know the best grad programs? Probably not great. So you'd be attracted to the default "brand name" schools. So a lot of lesser schools get the best students, at least to start. Then you find that the big names in your field are elsewhere and you have to transfer or settle. A consequence is that those programs have more or less two tiers to their grad program--the top notch students who knew where to go because they actively researched the field prior to applying, and those who went to the school more or less by accident; the first tend to be brilliant, the second not so much.
Of course, in the last 15 years a lot of smaller schools have cut out minor, "unnecessary" programs, some of which were excellent as they directed resources to the cheap popular fields--English, history, etc.
You're right: There is a hierarchy. But it's a funny amalgam of overall reputation + field-specific reputation. Some is deserved, some isn't. As a prof in my MA program said that reputations are funny, they tend to lag reality by a number of years. So I was going to apply to Harvard and he said not to waste my time--even if I got in and everything was paid for, I shouldn't waste my time because U. Illinois Urbana-Champaign was far better. I found out later that Harvard had lost two of their top faculty a couple of years earlier because Harvard's prickly with tenure; while neither went to U Ill., it still meant that U. Ill. (and a couple of other non-Ivy League schools) had the largest concentration of top faculty in my field. I should've gone there.
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