BetaScan2

BetaScan2 calculates standardized β statistics to detect loci under long-term balancing selection by integrating polymorphism and substitution data.

Key Features:

• β(2) statistic: Implements the β(2) statistic that incorporates both polymorphism and substitution data to detect long-term balancing selection.
• Standardization (βstd): Derives the variance of β statistics to compute standardized β (βstd), enabling comparability across genomic windows and species and reducing confounding influences.
• Locus-Based Calculation: Performs locus-based calculations on predefined windows of interest rather than relying on genome-wide sliding windows.
• Performance: Simulations demonstrate that standardized β statistics outperform existing summary statistics in detecting balancing selection.

Scientific Applications:

• Evolutionary genetics and population genomics: Identifies loci under balancing selection to study mechanisms of genetic diversity maintenance and adaptive evolution.
• Empirical dataset analysis: Applied to the 1000 Genomes Project, revealing high β scores in missense mutations within the ACSBG2 gene.

Methodology:

Computes β(2) from polymorphism and substitution data, derives the variance of β statistics to produce standardized β (βstd), and applies these calculations to predefined genomic windows.