Despite their important ecological role, questions remain on mechanisms structuring parasite assemblages. We present an endemic and species‐poor parasite–host system of two species of clupeid fishes Limnothrissa miodon, Stolothrissa tanganicae) and two species of monogenean parasites (Kapentagyrus, Dactylogyridae) from Lake Tanganyika as a model to study parasite distribution patterns and co‐infection dynamics in nature. We modelled spatiotemporal dynamics of parasite–host interaction using infection data along the north–south axis of Lake Tanganyika (660 km) over the course of two seasons and four years (1730 fish, 3710 parasites). We found temporal stability of parasite infection, which contrasts with previously reported seasonally driven fluctuations of fish host abundances. We found a difference in spatial structure between the parasite species which follows the contrasting dispersal pattern of their respective host species. On L. miodon, the host species that is infected by the two parasite species, we discovered a positive correlation with host body size for one parasite species, and a negative correlation for the other species. The apparent host‐size related replacement in the two parasite species infecting L. miodon contrasts with the beneficial influence that each of the parasite species has on the other. Parasites have been reported in previous studies to change habitat depending on host size/age. Differences in abundance and prevalence here reported between parasite species infecting the same host species related to the host body length further illustrate the parasites' dependence on changes in lifestyle of the host during its ontogenetic development. Also, possible mechanisms underlying the reported facilitation of infection are discussed. In conclusion, we show that in this closed, species‐poor system parasite infection dynamics are dependent on a combination of host mobility, host lifestyle changes over ontogenetic development, and interspecific interactions between parasites.
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