Expected pairwise congruence among gene trees under the coalescent model

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Computational Biology

Background:

• Gene trees often deviate from species trees due to evolutionary processes like incomplete lineage sorting (ILS).
• The degree of this gene tree-species tree incongruence is frequently underestimated and seldom quantified.
• Understanding incongruence is crucial for accurate phylogenetic reconstruction and evolutionary inference.

Purpose of the Study:

• To quantify the expected amount of gene tree incongruence arising from incomplete lineage sorting (ILS) within the coalescent process framework.
• To calculate the probability of agreement between two gene trees and the distribution of Robinson-Foulds distances for varying species tree sizes.
• To investigate the influence of species tree-specific factors on the extent of gene tree discordance.

Main Methods:

• Modeling incomplete lineage sorting (ILS) using the coalescent process.
• Computing probabilities of gene tree agreement and Robinson-Foulds distances for species trees with 3 to 8 taxa.
• Analyzing the impact of speciation times and effective population sizes on gene tree discordance.

Main Results:

• Substantial gene tree incongruence is demonstrated to occur even with a small number of species.
• The extent of discordance is significantly influenced by species tree factors, including speciation times and effective population sizes.
• The probability of agreement between randomly sampled gene trees is lower than often assumed.

Conclusions:

• Significant gene tree discordance is a common outcome of incomplete lineage sorting (ILS), even in simplified evolutionary scenarios.
• Current phylogenetic inference methods relying on estimated gene trees may require adjustments to accommodate this inherent variability.
• The findings underscore the importance of considering gene tree incongruence in evolutionary studies and for robust phylogenetic analyses.