One question; and I hope it doesn't throw a big monkey wrench into the problem for you; but what about formerly seperated colonies re-connecting?

a a a
a b a -- time=0
a a a


a a a
b b b -- time=1
c c c


a a a
b a b -- time=2
c c c


If the newly formed colony is shown as seperate (as above), then at time=1 they split into 3 colonies, not 2... they then remain 3 colonies through time=2. If, on the other hand, inheritance is an important part of your simulation (genetic code, etc..); then they would be time(0)=2 colonies, time(1)=3 colonies, and time(2)=2 colonies again...that might make it a bit more difficult to establish exactly which colonies are actually seperate from time frame to time frame.

Are the individual colonies tagged with their appropriate parentage? That might make it a little easier to determine when a previously seperate colony was reconnected.