Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors.

Area of Science:

• Evolutionary biology
• Genomics
• Population genetics

Background:

• Interspecific gene flow is widespread, but detection methods often assume a molecular clock.
• Rate variation across lineages challenges the molecular clock assumption.
• The impact of rate heterogeneity on introgression detection in closely related taxa is poorly understood.

Purpose of the Study:

• To evaluate the robustness of widely used introgression detection methods (D-statistic, HyDe) to rate variation.
• To assess the effect of rate heterogeneity on phylogenetic timescales, particularly shallow ones.
• To understand how rate variation influences false-positive rates in gene flow detection.

Main Methods:

• Theoretical analyses and simulations were employed.
• The study focused on site pattern methods like the D-statistic and HyDe.
• Simulations incorporated varying degrees of rate variation and phylogenetic depths.

Main Results:

• Both D-statistic and HyDe methods are highly sensitive to minor molecular clock deviations at shallow evolutionary timescales.
• Rate variation can substantially inflate false-positive rates, especially in young phylogenies with small population sizes.
• Using a more distant outgroup exacerbates these spurious signals.

Conclusions:

• Summary tests for introgression are vulnerable to minor rate variations.
• Existing methods may generate false signals of gene flow due to rate heterogeneity.
• Advanced methodologies are crucial for accurately distinguishing genuine introgression from rate-induced artifacts.