The genetic diversity of a species is shaped by its recent evolutionary
history and can be used to infer demographic events or selective sweeps. Most
inference methods are based on the null hypothesis that natural selection is a
weak or infrequent evolutionary force. However, many species, particularly
pathogens, are under continuous pressure to adapt in response to changing
environments. A statistical framework for inference from diversity data of such
populations is currently lacking. Toward this goal, we explore the properties
of genealogies in a model of continual adaptation in asexual populations. We
show that lineages trace back to a small pool of highly fit ancestors, in which
almost simultaneous coalescence of more than two lineages frequently occurs.
While such multiple mergers are unlikely under the neutral coalescent, they
create a unique genetic footprint in adapting populations. The site frequency
spectrum of derived neutral alleles, for example, is non-monotonic and has a
peak at high frequencies, whereas Tajima's D becomes more and more negative
with increasing sample size. Since multiple merger coalescents emerge in many
models of rapid adaptation, we argue that they should be considered as a
null-model for adapting populations.Comment: to appear in PNA
