Realistic Gene Transfer to Gene Duplication Ratios Identify Different Roots in the Bacterial Phylogeny Using a Tree Reconciliation Method.

On the other hand, the average gene loss rate has no significant influence on the number of inferred roots (rho ≈ 0.08 and p ≈ 0.4 for bacteria; rho ≈ 0.01 and p ≈ 0.9 for fungi-metazoan), while the gene transfer rate shows a weak correlation with the number of roots which is only marginally significant (rho = 0.09 and p = 0.04 for bacteria; rho = −0.17 p ≈ 0.05, for fungi-metazoan).

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