Molecular phylogenies suggest the oocyst residuum can be used to distinguish two independent lineages of Eimeria spp in rodents.

Using plastid 23S and nuclear 18S rDNA partial sequences for 16 Eimeria species from rodents, we compared their molecular phylogenetic inferences with morphological features and host specificity. The 16 ingroup taxa included Eimeria species which had different morphological features, but were from the same host genus or species, and species which had similar morphological features, but were from different host families or genera. Molecular phylogenies grouped the 16 rodent Eimeria species into two major lineages with high bootstrap support: lineage A included E. albigulae (from Neotoma), E. arizonensis (Peromyscus, Reithrodontomys), E. chaetodipi (Chaetodipus), E. chobotari (Dipodomys), E. dipodomlysis (Dipodomys), E. leucopi (Peromyscus), E. onychomysis (Onychomys), E. peromysci (Peromyscus) and E. reedi (Perognathus); and lineage B included E. falciformis (Mus), E. langebarteli (Peromyscus, Reithrodontomys), E. nieschulzi (Rattus), E. papillata (Mus), E. scholtysecki (Dipodomys), E. separata (Rattus) and E. sevilletensis (Onychomys). Examination of the morphological features of all 16 Eimeria species indicates that only the oocyst residuum shows a clear correlation to the phylogenetic relationships determined by the molecular data. Species in lineage A all contain one (or more) oocyst residuum in their sporulated oocysts, while species in lineage B lack an oocyst residuum in their sporulated oocysts. Considering that the host range of the Eimeria species used in this study includes nine genera in two families and that each eimeriid lineage contains species from both families, it seems likely that the two Eimeria lineages split before their host families diverged.