Recombination and phylogenetic inference

Area of Science:

• Evolutionary biology
• Phylogenetics
• Population genetics

Background:

• Recombination presents challenges for inferring evolutionary history.
• Two common methods, concatenation and species tree inference, handle recombination differently.

Purpose of the Study:

• To evaluate the impact of recombination on phylogenetic inference methods.
• To assess strategies for addressing recombination in phylogenetics.

Main Methods:

• Reviewed statistical robustness of methods ignoring recombination.
• Examined methods accommodating recombination by identifying recombinant regions.
• Considered methods inferring varying gene trees across the genome.

Main Results:

• Recombination is more detrimental to concatenation methods than species tree inference.
• Species tree methods show minimal impact on topology and divergence time estimates.
• Eliminating recombinant loci may introduce bias in parameter estimates.

Conclusions:

• Species tree inference methods are robust to recombination.
• Recombination detection may be unnecessary for species tree inference.
• Developing methods to combine varying gene trees with recombination remains a challenge.