Resolving Non-binary Gene Trees

Although true gene trees are inherently binary, phylogeny reconstruction may yield non-binary trees given noisy data or short branch lenghths. Notung-2.6 can be used to resolve non-binary gene tree with duplication/loss parsimony by fitting it to a binary species tree.

Two possible resolutions of the non-binary gene tree in Fig. 1a are shown in Figs. 1c and 1d. Notung determines the most parsimonious resolution of the non-binary node(s) using duplication/loss parsimony. Resolutions with fewer duplications and losses (Fig. 1c) are more plausible than those with more duplications and losses (Fig. 1d).

Fig. 1: Resolving a Non-Binary Node

Fig. 1a: Gene Tree	Fig. 1c: One resolution. D/L Score = 1D
Fig. 1b: Species Tree	Fig. 1d: Another resolution. D/L Score = 2D+2L