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Positive selection distorts the structure of genealogies and hence alterspatterns of genetic variation within a population. Most analyses of thesedistortions focus on the signatures of hitchhiking due to hard or softselective sweeps at a single genetic locus. However, in linked regions ofrapidly adapting genomes, multiple beneficial mutations at different loci cansegregate simultaneously within the population, an effect known as clonalinterference. This leads to a subtle interplay between hitchhiking andinterference effects, which leads to a unique signature of rapid adaptation ongenetic variation both at the selected sites and at linked neutral loci. Here,we introduce an effective coalescent theory (a "fitness-class coalescent") thatdescribes how positive selection at many perfectly linked sites alters thestructure of genealogies. We use this theory to calculate several simplestatistics describing genetic variation within a rapidly adapting population,and to implement efficient backwards-time coalescent simulations which can beused to predict how clonal interference alters the expected patterns ofmolecular evolution.

Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations