Weak seed banks influence the signature and detectability of selective sweeps

Seed banking (or dormancy) is a widespread bet-hedging strategy, generating a form of population overlap, which decreases the magnitude of genetic drift. The methodological complexity of integrating this trait means it is ignored when developing tools to detect selective sweeps. But, as dormancy lengthens the ancestral recombination graph, increasing times to fixation, it can radically change the genomic signals of selection. To detect genes under positive selection in seed banking species it is important to 1) determine whether the efficacy of selection is affected, and 2) predict the patterns of nucleotide diversity at and around positively selected alleles. We present the first tree sequence-based simulation program integrating a weak seed bank to examine the dynamics and genomic footprints of beneficial alleles in a finite population. We find that seed banking generally decreases the probability of fixation and magnifies (respectively decreases) the efficacy of selection for alleles under strong (respectively weak) selection. As seed banking increases the effective recombination rate, footprints of sweeps appear more narrow around the selected sites and are detectable for longer periods of time. The developed simulation tool can be used to predict the footprints of selection and draw statistical inference of past evolutionary events in plants, invertebrates, or fungi with seed banks.