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

Area of Science:

• Evolutionary biology
• Phylogenetics
• Genomics

Background:

• Phylogenetic tree rooting is crucial for understanding evolutionary history.
• Tree reconciliation methods are increasingly used for rooting species trees.
• These methods depend on the gene transfer to gene duplication (T:D) ratio, often estimated during analysis.

Purpose of the Study:

• To evaluate the accuracy of T:D ratios estimated by tree reconciliation methods.
• To investigate the impact of T:D ratio accuracy on species tree root inference.
• To compare T:D estimates from reconciliation with independent methods.

Main Methods:

• Performed over 10,000 gene tree reconciliations for bacterial and eukaryotic datasets.
• Varied T:D ratios to assess their effect on root placement.
• Compared T:D ratios estimated by the ALE method with independent estimates.

Main Results:

• ALE-estimated T:D ratios were consistently different (10- to 100-fold) from independent estimates.
• Species tree root inferences using ALE were highly sensitive to the T:D ratio.
• Increased T:D ratios led to more inferred roots, including incorrect ones, with gene duplications having a greater impact than gene transfers or losses.

Conclusions:

• Current tree reconciliation methods may produce inaccurate species tree roots due to unreliable T:D ratio estimation.
• Accurate root inference with ALE requires abundant gene duplications and low false positive rates.
• The T:D ratio significantly impacts phylogenetic root inference, necessitating careful consideration in evolutionary analyses.