As a split-off from http://www.worldofmeeroos.com/index.php?q=node/2966 to discuss eyes specifically since it seems we're all on to something :).

I would really like to thank Freyja for posting about her findings in public. Too often in the forums there's a "I think I'm on to something... but I'm not sharing!", which isn't helpful to anyone.

From her post on the other thread:
"I was quickly able to see that pairings of two clears with different colours yielded dusty every time, as predicted (since a/a + b/b can only yield a mixed eye) and that pairings of two dusty with the same colour yielded clears on a number of occasions."

In addition after starting to work out visible/recessive for my own meeroos I noticed that for a dusty eyeset, the visible colour always seems to come from the mother.

If that holds true in general then:
* Female: Colour 1 / Clear
* Male: Colour 2 / Clear
=> Nest: Colour 1 / Dusty

And for breeding specific eye colour:
* Female: Colour A / Clear
=> Nest: Colour A
(Or: if all you want are dusty eyes then the eye colour of the father doesn't matter)

If it's a general rule then it makes working out the dormant eye-colour very easy:
* Female: Colour A / Dusty
=> Nest: Colour B

This would mean that mom has Colour A (visible) / Colour B markers.

(Of course any randomness from "reaching back" aside, but I guess if it works out like this it should be true for almost all of our individual Meeroos)