Persistent Melira

Consider these questions, all if which are related in some manner:

1. Assume you control Melira, Sylvok Outcast, you give her persist (for example with Cauldron Haze), and she dies. When she comes back, will she have a -1/-1 counter?
2. Assume you control Melira's Keepers, you give it persist, and it dies. When it comes back, will it have a -1/-1 counter?
3. You control a Clone (it doesn't really matter what it's copying) and Melira's Keepers, you give the Clone persist, and it dies. When it comes back, you make it be a copy of Melira's Keepers. Will it have a -1/-1 counter?
4. You control a Volrath's Shapeshifter, the top card of your library is Melira's Keepers, you give the Shapeshifter persist, and it dies. When it comes back, will it have a -1/-1 counter?

These questions deal with some of the most obscure parts of the rules of the game. Let's examine the first two.

Melira, Sylvok Outcast has a static ability which states that creatures you control can't have -1/-1 counters placed on them. Melira's Keepers is somewhat similar, except that it affects only itself (and stops any kind of counters from being placed on it, although in this case that's inconsequential).

So there are two interesting questions here: When they gain persist and die, do they come back with a -1/-1 counter or without one, and do they behave differently in this regard?

Quite curiously their type of static ability does make a difference in this case. In particular, Melira, Sylvok Outcast will return with a -1/-1 counter, while Melira's Keepers will return without one. The reason for this may not be apparent, and it is, as said, one of the more obscure parts of the rules.

A static ability that affects all creatures behaves differently from a static ability that only affects the specific creature itself. The effect (in this case persist) that makes the creature enter the battlefield with an additional characteristic (in this case a -1/-1 counter) will be affected by a static ability that says something about the creature itself, but will not be affected by any generic effect that applies to all creatures (even if that effect is in the card being evaluated.) In a sense, one could think of it as the generic effect not affecting the creature until it's on the battlefield (and thus doesn't affect how creatures enter it.)

What about the Clone?

When the Clone is entering the battlefield, you choose what it copies. In this case we are choosing Melira's Keepers. So the question becomes: What happens first, the persist effect giving it a -1/-1 counter, or Clone acquiring the Keepers' ability that stops counters from being put onto it?

The correct answer is that Clone becomes a copy of Keepers before the persist effect tries to put a -1/-1 counter on it, and therefore it gets no counter. (This is, if anything, an even more obscure and hard to find consequence of the rules of the game.)

And finally, Volrath's Shapeshifter (and Melira's Keepers being the top card of your graveyard):

Now this is a really tricky one, and can confuse even judges. (It doesn't help that the official rulings for this card and how it interacts with enters-the-battlefield replacement effects have changed over time.)

At first it might look like this is just the same thing as with the Clone, but their abilities are a bit different. While Clone specifically says that it "enters the battlefield as a copy" of something, this card does not say anything about entering the battlefield with the characteristics of the top card of the graveyard.

This is such an obscure case that there may be some disagreement even among experts, but the majority consensus seems to be that Shapeshifter is considered to have the characteristics of the top graveyard card as it enters, and will therefore not have a -1/-1 counter put on it by persist. (However, this interpretation shouldn't be taken as set-in-stone until an official ruling from Wizards of the Coast can be cited.)