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Graph theoretical insights into evolution of multidomain proteins.
We study properties of multidomain proteins from a graph theoretical perspective. In particular, we demonstrate connections between properties of the domain overlap graph and certain variants of Dollo parsimony models. We apply our graph theoretical results to address several interrelated questions: do proteins acquire new domains infrequently, or often enough that the same combinations of domains will be created repeatedly through independent events? Once domain architectures are created do they persist? In other words, is the existence of ancestral proteins with domain compositions not observed in contemporary proteins unlikely? Our experimental results indicate that independent merges of domain pairs are not uncommon in large superfamilies.