Myriad ecological and evolutionary factors can influence whether a
particular parasite successfully transmits to a new host during a
disease outbreak, with consequences for the structure and diversity of
parasite populations. However, even though the diversity and evolution
of parasite populations is of clear fundamental and applied importance,
we have surprisingly few studies that track how genetic structure of
parasites changes during naturally occurring outbreaks in non-human
populations. Here, we used population genetic approaches to reveal how
genotypes of a bacterial parasite, Pasteuria ramosa, change over time,
focusing on how infecting P. ramosa genotypes change during the course
of epidemics in Daphnia populations in two lakes. We found evidence for
genetic change – and, therefore, evolution – of the parasite during
outbreaks. In one lake, P. ramosa genotypes structured by sampling date;
in both lakes, genetic distance between groups of P. ramosa isolates
increased with time between sampling. Diversity in parasite populations
remained constant over epidemics, though one epidemic (which was large)
had low genetic diversity while the other epidemic (which was small) had
high genetic diversity. Our findings demonstrate that patterns of
parasite evolution differ between outbreaks; future studies exploring
the feedbacks between epidemic size, host diversity, and parasite
genetic diversity would improve our understanding of parasite dynamics
and evolution.