Long-range linkage effects in adapting sexual populations

Abstract

AbstractIn sexual populations, closely-situated genes have linked evolutionary fates, while genes spaced far in genome are commonly thought to evolve independently due to recombination. In the case where evolution depends essentially on supply of new mutations, this assumption has been confirmed by mathematical modeling. Here I examine it in the case of pre-existing genetic variation, where mutation is not important. A haploid population with$$N$$Ngenomes,$$L$$Lloci, a fixed selection coefficient, and a small initial frequency of beneficial alleles$${f}_{0}$$f0is simulated by a Monte-Carlo algorithm. When the number of loci,L, is larger than a critical value of$${\text{4log}}^{2} \left( {Nf_{0} } \right),$$4log2Nf0,simulation demonstrates a host of linkage effects that decrease neither with the distance between loci nor the number of recombination crossovers. Due to clonal interference, the beneficial alleles become extinct at a fraction of loci$$1-2\mathrm{log}\left(N{f}_{0}\right)/{L}^{0.5}$$1-2logNf0/L0.5. Due to a genetic background effect, the substitution rate varies broadly between loci, with the fastest value exceeding the one-locus limit by the factor of$${[{L}^{0.5}/\mathrm{log}\left(Ns\right)]}^{0.75}.$$[L0.5/logNs]0.75.Thus, the far-situated parts of a long genome in a sexual population do not evolve as independent blocks. A potential link between these findings and the emergence of new Variants of Concern of SARS-CoV-2 is discussed.