Supertrees Based on the Subtree Prune-and-Regraft Distance.

Area of Science:

• Computational Biology and Bioinformatics
• Evolutionary Biology
• Phylogenetics

Background:

• Supertree methods aim to combine multiple phylogenetic trees into a single evolutionary history.
• Existing supertree methods often struggle with conflicting evolutionary signals caused by artifacts and lateral gene transfer (LGT).
• Current optimality criteria may not accurately reflect evolutionary processes and can be biased by LGT.

Purpose of the Study:

• To introduce a new supertree construction method utilizing the subtree prune-and-regraft (SPR) distance as an optimality criterion.
• To develop a computationally efficient method for reconciling phylogenetic trees, even in the presence of significant LGT.
• To assess the performance of SPR-based supertrees against existing methods using simulated and real-world phylogenomic data.

Main Methods:

• Developed novel maximum agreement forest-based algorithms to efficiently calculate rooted SPR distances, enabling iterative searches.
• The method accommodates phylogenetic trees with multifurcating nodes, representing uncertain relationships.
• Evaluated performance on simulated datasets with varying LGT rates and a large-scale phylogenomic dataset of bacterial genomes.

Main Results:

• SPR supertrees demonstrated higher similarity to true species histories compared to supertrees constructed using parsimony or Robinson-Foulds distances.
• Successfully constructed a supertree from over 40,000 gene trees across 244 bacterial genomes.
• The SPR-based approach enabled direct inference of gene transfer highways, identifying specific genes involved in long-distance LGT between bacterial taxa.

Conclusions:

• The SPR distance provides a more biologically relevant optimality criterion for supertree construction than traditional methods.
• The developed method offers a scalable and accurate approach for reconciling complex evolutionary histories, including those shaped by LGT.
• This work facilitates deeper insights into prokaryotic phylogeny and the dynamics of horizontal gene transfer.