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Updated: Jan 17, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Recombination and phylogenetic inference.

Bruce Rannala¹

¹Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, United States.

Evolutionary Journal of the Linnean Society

|September 22, 2025

Summary

This summary is machine-generated.

Recombination significantly impacts phylogenetic tree inference. Species tree methods are more robust to recombination than concatenation methods, suggesting recombination detection may not always be necessary.

Keywords:

ancestral recombination graph coalescent recombination species tree inference

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Published on: June 25, 2013

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.