Figure 1

Phylogenetic tree used to simulate genome evolution including a directed highway of gene sharing. Two different trees were tested, one having a slightly longer internal branch of 0.05 substitutions per site compared to the other tree with only 0.01 substitutions per site. Genome B' was used as a donor for genes transferred into the lineage leading to genome F. Genome B' was not included in the phylogenetic reconstruction and genes from genome B' were used as replacements for their orthologs in genome F. The simulations were repeated with increasing amount of transfers from genome B' to F. The genome sequences were generated using Evolver from the PAML package [113]. Each simulated genomes contained a total of 100 genes, each 300 amino acids long.