Selective sweeps under dominance and self-fertilisation
A major research goal in evolutionary genetics is to uncover loci experiencing positive selection. One approach involves finding selective sweeps patterns, which can either be hard sweeps formed by de novo mutation, or soft sweeps arising from recurrent mutation or existing standing variation. Existing theory generally assumes outcrossing populations, and it is unclear how dominance affects soft sweeps. We consider how arbitrary dominance and inbreeding via self-fertilisation affect hard and soft sweep signatures. With increased self-fertilisation, they are maintained over longer map distances due to reduced effective recombination and faster beneficial allele fixation times. Dominance can affect sweep patterns in outcrossers if the derived variant originates from either a single novel allele, or from recurrent mutation. These models highlight the challenges in distinguishing hard and soft sweeps, and propose methods to differentiate between scenarios.