Rearranging Rooted Gene Trees

A molecular phylogeny containing some edges with weak sequence support (low bootstrap values) admits alternate hypotheses through rearrangements around the weak edges. Alternate hypotheses that minimize the number of duplications and losses are of particular interest. Given a rooted gene tree, a species tree and a threshold bootstrap value, Notung-2.6 will generate alternate hypotheses that minimize the D/L Score of the tree without breaking any edge that has a bootstrap score above the threshold, as shown in Fig. 1a-c. This algorithm has been described in Durand, Halldorsson and Vernot [1].

Fig. 1a) A gene phylogeny with low bootstrap support (<90).
Fig. 1b) This shows implied duplications and losses. A poor D/L Score of 5 results from 2 duplications and 2 losses
Fig. 1c) Rearrangement around the weak edge eliminates this problem and yields a more parsimonious tree, with a D/L Score of 1.5

For large, complicated gene trees, identifying optimal rearrangements around weak edges by inspection risks tedium and error. Notung-2.6 allows the user to visualize such alternative hypotheses automatically.

 [1]   A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction.
    D. Durand, B. V. Halldorsson, B. Vernot, 2005. Journal of Computational Biology, 13 (2): 320-335.

[2]   Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1
    A. L. Hughes, 1998. Molecular Biology and Evolution, 15, 854-870.