Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement...

Area of Science:

• Evolutionary biology
• Bioinformatics
• Genomics

Background:

• Recombination creates mosaic genomes with varying ancestral histories.
• Reconstructing ancestral recombination graphs (ARGs) from genomic data is computationally complex.

Purpose of the Study:

• To develop a method for reconciling discordant phylogenetic trees to reconstruct ARGs.
• To improve the accuracy and efficiency of ARG reconstruction.

Main Methods:

• Utilized maximum agreement forests (MAFs) to identify concordant subtrees between discordant phylogenetic trees.
• Developed a reconciliation approach to retain supported discordances and minimize phylogenetic noise.
• Combined MAFs and reconciliation to select optimal local trees across the genome for ARG construction.

Main Results:

• The heuristic ARG reconstruction method is computationally efficient and comparable in accuracy to exact methods.
• Reconstructed ARGs accurately estimate demographic parameters like recombination rates.
• Successfully applied the method to Potyvirus RNA viruses, distinguishing true recombination from noise.

Conclusions:

• The MAF-based approach offers an efficient and accurate method for ARG reconstruction.
• This method aids in understanding complex evolutionary histories shaped by recombination.
• The approach is valuable for analyzing viral evolution and distinguishing biological signals from data artifacts.