Figure 2

Comparison of supermatrix and supertree approaches for recovering the correct tree following horizontal genetic transfer. Horizontal genetic transfer was simulated between lineage B' and F (Figure 1) with an internal branch of 0.05 (A) or 0.01 substitutions per site (B). The frequency with which the correct tree is recovered from supermatrix and supertree approaches from data that include increasing amounts of genes transferred along a single highway of gene sharing was tested. Each simulated genome contained a total of 100 genes, each 300 amino acids long. Genes were concatenated into a single sequence from each simulated genome for the supermatrix tree calculation or alternatively, gene trees were calculated individually from each gene for the supertree approach. The sequences were not realigned to avoid any additional artifact potentially introduced from alignment algorithms. Neighbor-joining trees were calculated with Kimura correction in ClustalW version 2.0.12 [114]. Maximum likelihood trees were calculated with PhyML V.3.0 [115] with Pinvar, JTT model and estimated gamma distribution under 4 categories. The embedded quartet trees [116] as well as the resulting plurality trees (supertree) were calculated from the individual gene family trees using Quartet Suite v.1.0 [117]. The simulations were repeated 100 times to measure the reproducibility of the different tree reconstruction methods in recovering the original tree topology.