Background Microsporidians are obligate endoparasites infecting taxonomically diverse hosts. Both vertical (from mother to eggs) and horizontal (between conspecifics or between species) transmission routes are known. While the former may promote co-speciation and host-specificity, the latter may promote shifts between host species. Among aquatic arthropods, freshwater amphipod crustaceans are hosts for many microsporidian species. However, despite numerous studies, no general pattern emerged about host specificity and co-diversification. In south-eastern Europe, the gammarid Gammarus roeselii is composed of 13 cryptic lineages of Miocene to Pleistocene age but few genotypes of one lineage have spread postglacially throughout north-western Europe. Based on nearly 100 sampling sites covering its entire range, we aim to: (i) explore the microsporidian diversity present in G. roeselii and their phylogenetic relationships, especially in relation to the parasites infecting other Gammaridae; (ii) test if the host phylogeographical history might have impacted host–parasite association (e.g. co-diversifications or recent host shifts from local fauna). Methods We used part of the small subunit rRNA gene as source of sequences to identify and determine the phylogenetic position of the microsporidian taxa infecting G. roeselii . Results Microsporidian diversity was high in G. roeselii with 24 detected haplogroups, clustered into 18 species-level taxa. Ten microsporidian species were rare, infecting a few individual hosts in a few populations, and were mostly phylogenetically related to parasites from other amphipods or various crustaceans. Other microsporidians were represented by widespread genera with high prevalence: Nosema , Cucumispora and Dictyocoela. Two contrasting host association patterns could be observed. First, two vertically transmitted microsporidian species, Nosema granulosis and Dictyocoela roeselum , share the pattern of infecting G. roeselii over most of its range and are specific to this host suggesting the co-diversification scenario. This pattern contrasted with that of Dictyocoela muelleri , the three species of Cucumispora , and the rare parasites, present only in the recently colonised region by the host. These patterns suggest recent acquisitions from local host species, after the recent spread of G. roeselii . Conclusions Microsporidians infecting G. roeselii revealed two scenarios of host–parasite associations: (i) ancient associations with vertically transmitted parasites that probably co-diversified with their hosts, and ...

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