Generalist species in rodents: Multilocus analyses indicate inadequate resolution of established markers.

Intracellular parasites of the genus are described as tissue/host-specific. Phylogenetic classification of rodent suggested that some species have a broader host range than previously assumed. We explore whether spp. infecting house mice are misclassified by the most widely used molecular markers due to a lack of resolution, or whether, instead, these parasite species are indeed infecting multiple host species.With the commonly used markers (18S/COI), we recovered monophyletic clades of and from that included identified in other rodent host species ( spp. and ). A lack of internal resolution in these clades could suggest the existence of a species complex with a wide host range infecting murid and cricetid rodents. We question, however, the power of COI and 18S markers to provide adequate resolution for assessing host specificity. In addition to the rarely used marker ORF470 from the apicoplast genome, we present multilocus genotyping as an alternative approach. Phylogenetic analysis of 35 nuclear markers differentiated from house mice from isolates from hosts. Isolates of from are still found in clusters interspersed with non- isolates, even with this high-resolution data.In conclusion, we show that species-level resolution should not be assumed for COI and 18S markers in coccidia. Host-parasite cospeciation at shallow phylogenetic nodes, as well as contemporary coccidian host ranges more generally, is still open questions that need to be addressed using novel genetic markers with higher resolution.