WordNet sense 1 (be a distinctive feature, attribute, or trait; sometimes in a very positive sense):

distinguish, mark

WordNet sense 2 (mark as different):

separate, tell, secern, secernate, severalise, severalize, separate, tell apart

WordNet sense 3 (evolve so as to lead to a new species or develop in a way most suited to the environment):

specialize, specialise, speciate