PT  - JOURNAL ARTICLE
AU  - Víctor Hugo Jarquín-Díaz
AU  - Alice Balard
AU  - Anna Mácová
AU  - Jenny Jost
AU  - Tabea Roth von Szepesbéla
AU  - Karin Berktold
AU  - Steffen Tank
AU  - Jana Kvičerová
AU  - Emanuel Heitlinger
TI  - Generalist <em>Eimeria</em> species in rodents: multilocus analyses indicate inadequate resolution of established markers
AID  - 10.1101/690487
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 690487
4099  - http://biorxiv.org/content/early/2019/07/02/690487.short
4100  - http://biorxiv.org/content/early/2019/07/02/690487.full
AB  - Intracellular parasites of the genus Eimeria are described as tissue/host specific. Phylogenetic classification of rodent Eimeria suggested that some species have a broader host range than previously assumed. We explore if Eimeria spp. infecting house mice are misclassified by the most widely used molecular markers due to a lack of resolution, or if, instead, these parasite species are indeed infecting multiple host species.With the commonly used markers (18S/COI), we recovered monophyletic clades of E. falciformis and E. vermiformis from Mus that included E. apionodes identified in other rodent host species (Apodemus spp., Myodes glareolus, and Microtus arvalis). 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 E. falciformis from house mice from isolates from Apodemus hosts. Isolates of E. vermiformis from Mus are still found in clusters interleaved with non-Mus 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 co-speciation at shallow phylogenetic nodes, as well as contemporary coccidian host ranges more generally, are still open questions that need to be addressed using novel genetic markers with higher resolution.