Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers

Area of Science:

• Evolutionary genetics
• Population genetics
• Molecular evolution

Background:

• Accurately identifying genetic signatures of soft selective sweeps from nucleotide variation patterns is challenging.
• Recent studies proposed statistical identifiability and evolutionary prevalence of soft selective sweeps in Drosophila and HIV.

Purpose of the Study:

• To provide counterarguments to recent claims regarding the identification and role of soft selective sweeps.
• To critically evaluate the methodologies and interpretations used in studies of soft selective sweeps.

Main Methods:

• Re-evaluation of statistical models for detecting selection.
• Analysis of competing evolutionary models.
• Critique of interpretations of empirical data, particularly outliers.

Main Results:

• Claims of soft selective sweep identifiability may stem from overlooking alternative evolutionary models.
• Empirical outliers might be misinterpreted, inflating the perceived role of soft selective sweeps.
• New definitions of evolutionary processes can obscure common mechanisms.

Conclusions:

• Fitting evolutionary models requires careful consideration of common processes before invoking rare or episodic ones.
• The tendency to assume pervasive positive selection may lead to biased interpretations in evolutionary genetics.
• Robust methods are needed to distinguish soft selective sweeps from other evolutionary forces.