Fig. 1.

—Phylogeny reconstruction and genealogy variation using a codon model. (A) Cumulative distribution of number of genes per topology. Numbers indicate the frequencies of the six most frequent topologies. The middle horizontal dotted line indicates half of the genes under study. (B) Four most frequent topologies with their corresponding frequency. Genealogies are examples of genes taken for each topology class. (C) Species tree obtained by combining all gene trees using the Super Distance Matrix method.