Determining the molecular basis of parasite adaptation to its host is an important component in understanding host–parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short‐ and long‐term adaptive evolution in the eukaryotic parasite Gyrodactylus bullatarudis infecting Caribbean guppies ( Poecilia reticulata ), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyh...