BetaScan2: Standardized statistics to detect balancing selection utilizing substitution data

Abstract

The recently reported statistic β detects balanced haplotypes without the need for genomic data from an outgroup species. Here we present an extension to the method that incorporates between-species substitution data into the β statistic framework. We show that this approach outperforms existing summary statistics in simulations. We also present the variance of β with and without substitution data, allowing calculation of a standardized score. Besides providing a measure of significance, this enables a proper comparison of β values across varying underlying parameters, a feature lacking from some related methods.