selscan 2.0: scanning for sweeps in unphased data

Abstract

Summary: Several popular haplotype-based statistics for identifying recent or ongoing positive selection in genomes require knowledge of haplotype phase. Here, we provide an update to selscan which implements a re-definition of these statistics for use in unphased data.

Availability and implementation: Source code and binaries are freely available at https://github.com/szpiech/selscan, implemented in C/C++, and supported on Linux, Windows, and MacOS.

Figure 1.

Unphased power. Power curves for unphased implementations of iHS (A), nSL (B), XP-EHH (C), and XP-nSL (D), and power difference between unphased implementations of iHS (E), nSL (F), XP-EHH (G), and XP-nSL (H) and phased implementations. Blue curves represent the power difference between the unphased and phased statistics when applied to unphased data (UN). Red curves represent the power difference between the unphased and phased statistics when applied to perfectly phased data (PH). Values greater than 0 indicate the unphased statistic had higher power. All panels represent analyses with demographic history Demo 1 and n = 100, 50, 20, or 10 diploid samples. For these plots the selection coefficient is set at $s=0.01$, the frequency at which selection began is set at $e=0$ (i.e. a hard sweep), and the divergence time in generations is set at $t_d=2000$. $f$ is the frequency of the adaptive allele at time of sampling, $g$ is the number of generations at time of sampling since fixation.