BetaScan2: Standardized statistics to detect balancing selection utilizing substitution data

Abstract

The recently reported statistic {beta} 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 {beta} statistic framework. We show that this approach outperforms existing summary statistics in simulations. We also present the variance of {beta} with and without substitution data, allowing calculation of a standardized score. Besides providing a measure of significance, this enables a proper comparison of {beta} values across varying underlying parameters, a feature lacking from some related methods.