How to distinguish between a genetic bottleneck and directional selection? Genetic bottlenecks and directional selection should have relatively similar genetic signals: reduced heterozygosity and greater genetic divergence (Fst?) in contemporary populations compared to the past How would one be able to distinguish between these two evolutionary forces if their signals are so similar?

Population bottleneck will have genome-wide effect while directional selection will affect only the locus (and closely linked loci via a selective sweep).

You can typically screen through the genome and calculate Tajima's D. Under a bottleneck scenario, Tajima's D will be expected to be negative everywhere. Under a directional selection scenario, Tajima's D would be negative only at the locus (and closely linked loci) to the one that is under selection.

There are of course a whole lot series of technics but the above is probably the simplest and most straight-forward (it probably lacks in power though).