A preprint of my latest manuscript, “Selective sweeps under dominance and self-fertilisation”, is now available on bioRxiv. This work (carried out with Thomas Bataillon) continues my long-standing interest in investigating the mechanisms of adaptation under different reproductive modes. This preprint outlines how the genetic signatures of different adaptive events (for example, whether beneficial mutations arose from new mutation, or from standing variation) are altered by (i) dominance, which is a measure of the fitness effects of individuals carrying one copy of the adaptive gene, compared to the fitness of individuals with two copies; and (ii) self-fertilisation, where individuals can produce both male and female sex cells that are capable of fertilising one another. We show how both these effects impact upon signatures of selection, as well as how to differentiate between scenarios that may produce similar signatures.
You can download the preprint here, with the abstract given below:
A major research goal in evolutionary genetics is to uncover loci experiencing adaptation from genomic sequence data. One approach relies on finding ‘selective sweep’ patterns, where segregating adaptive alleles reduce diversity at linked neutral loci. Recent years have seen an expansion in modelling cases of ‘soft’ sweeps, where the common ancestor of derived variants predates the onset of selection. Yet existing theory assumes that populations are entirely outcrossing, and dominance does not affect sweeps. Here, we develop a model of selective sweeps that considers arbitrary dominance and non-random mating via self-fertilisation. We investigate how these factors, as well as the starting frequency of the derived allele, affect average pairwise diversity, the number of segregating sites, and the site frequency spectrum. With increased self-fertilisation, signatures of both hard and soft sweeps are maintained over a longer map distance, due to a reduced effective recombination rate and faster fixation times of adaptive variants. We also demonstrate that sweeps from standing variation can produce diversity patterns equivalent to hard sweeps. Dominance can affect sweep patterns in outcrossing populations arising from either a single novel mutation, or from recurrent mutation. It has little effect where there is either increased selfing or the derived variant arises from standing variation, since dominance only weakly affects the underlying adaptive allele trajectory. Different dominance values also alters the distribution of singletons (derived alleles present in one sample). We apply models to a sweep signature at the SLC24A5 gene in European humans, demonstrating that it is most consistent with an additive hard sweep. These analyses highlight similarities between certain hard and soft sweep cases, and suggest ways of how to best differentiate between related scenarios. In addition, self-fertilising species can provide clearer signals of soft sweeps than outcrossers, as they are spread out over longer regions of the genome.