It is no secret that Pinkie Pie really hopes the Pies and Apples are related, as it gives her an excuse to have the Apples all be friends with her family. But even if the genealogical records are in doubt, there are other ways to tell. For instance, two related earth pony families should respond to the earth in similar ways.

The Pies are known for their abilities with rocks. Finding, sculpting, evaluating - if it can be done with rocks, the Pies can do it.

The Apples grow things, none of them rocks. (Notwithstanding the occasional apple that rots into something hard.)

Pinkie Pie feels her hopes deflating. But Maud does not seem worried, even if she can be hard to read sometimes.

In the popular box on 11/4/15! Thanks for the views and votes!