Gene Tree Discordance Causes Apparent Substitution Rate Variation.

Area of Science:

• Evolutionary biology
• Phylogenetics
• Genomics

Background:

• Substitution rates vary across genes, chromosomes, species, and lineages.
• Gene tree discordance, often due to incomplete lineage sorting (ILS), is common in genomic data.
• Analyzing substitutions on discordant gene trees within a fixed species tree can create technical biases.

Purpose of the Study:

• To identify and characterize a novel source of substitution rate variation stemming from gene tree discordance.
• To investigate the impact of this bias, termed Substitutions Produced by ILS (SPILS), on phylogenetic inference and evolutionary analyses.
• To demonstrate the presence and implications of SPILS in empirical data.

Main Methods:

• Simulations were used to model the effects of varying levels of ILS on substitution rate inference.
• Analysis of discordant gene tree topologies to predict erroneous branch length estimations.
• Testing for positive selection under fixed species tree topologies using simulated and empirical data.

Main Results:

• SPILS increases with higher levels of ILS and larger numbers of taxa.
• Specific species tree branches are consistently miscalculated in length due to SPILS.
• Fixing species tree topology inflates false positive rates in tests for positive selection, particularly for genes with high discordance.

Conclusions:

• SPILS represents a significant technical bias in phylogenetic analyses, particularly in scenarios with high ILS.
• This bias can lead to erroneous inferences of evolutionary rates, convergence, and accelerated evolution.
• Addressing SPILS is crucial for accurate character mapping and understanding evolutionary processes in rapid radiations.