Dogs are pack animals. They definitely follow a pecking order.

Cats are territorial and they form a 'club' when they live together.

There can be an Alpha male as well as an Alpha female, at the same time.

The other statuses are: Laid Back, non-agressive, scardey, and pariah.

The Laid Back cat has no aspirations of being Alpha, but could become Alpha if the current Alpha is removed. They are easy to get along with cats, more commonly altered males.

The non-agressive cat knows its place, but will stand up for itself.

The scardey cat is fearful and wants nothing to do with the social order.

The Pariah, or victim cat will run from the other more dominant cats, and not stand up to them. The others will take advantage of this, and chase and pick on this type of cat.
They are best living alone.


As far as your litter box situation, the cat who goes and does not cover is definitely daclaring himself Alpha.

More litterboxes will help. Give the cat that is afraid to go in the box a new box in a new location, which she can be first to use. And if you can keep the Alpha away, at least for a while, it might help her relax.