Detecting bottlenecks and selective sweeps from DNA sequence polymorphism

A coalescence-based maximum-likelihood method is presented that aims to (i) detect diversity-reducing events in the recent history of a population and (ii) distinguish between demographic (e.g:, bottlenecks) and selective cau ses (selective sweep) of a recent reduction of genetic variability. The for mer goal is achieved by taking account of the distortion in the shape of ge ne genealogies generated by diversity-reducing events: gene trees tend to b e more star-like than under the standard coalescent. The latter issue is ad dressed by comparing patterns between loci: demographic events apply to the whole genome whereas selective events affect distinct regions of the genom e to a varying extent. The maximum-likelihood approach allows one to estima te the time and strength of diversity-reducing events and to choose among c ompeting hypotheses. An application to sequence data from an African popula tion of Drosophila melanogaster shows that the bottleneck hypothesis is unl ikely and that one or several selective sweeps probably occurred in the rec ent history of this population.