Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed.
Different lineages evolve independently.
The probability of a base substitution at a given site is small over the lengths of time involved in a branch of the phylogeny. The expected amounts of change do not vary enough among sites that two changes in one site are more probable than one change in another. Change from an occupied site to a deletion is counted as one change. Reversion from a deletion to an occupied site is allowed and is also counted as one change. Note that this in effect assumes that a deletion N bases long is N separate events.