Monomorphic Trypanozoon : towards reconciling phylogeny and pathologies

2. Abstract Trypanosoma brucei evansi and Trypanosoma brucei equiperdum are animal infective trypanosomes conventionally classified by their clinical disease presentation, mode of transmission, host range, kDNA composition and geographic distribution. Unlike other members of the subgenus Trypanozoon , they are non-tsetse transmitted and predominantly morphologically uniform (monomorphic) in their mammalian host. Their classification as independent species or subspecies has been long debated and genomic studies have found that isolates within T. b. evansi and T. b. equiperdum have polyphyletic origins. Since current taxonomy does not fully acknowledge these polyphyletic relationships, we re-analysed publicly available genomic data to carefully define each clade of monomorphic trypanosome. This allowed us to identify, and account for, lineage specific variation. We included a recently published isolate, IVM-t1, which was originally isolated from the genital mucosa of a horse with dourine and typed as T. equiperdum . Our analyses corroborate previous studies in identifying at least four distinct monomorphic T. brucei clades. We also found clear lineage specific variation in the selection efficacy and heterozygosity of the monomorphic lineages, supporting their distinct evolutionary histories. The inferred evolutionary position of IVM-t1 suggests its reassignment to the T. b. evansi type B clade, challenging the relationship between the Trypanozoon species, the infected host, mode of transmission and the associated pathological phenotype. The analysis of IVM-t1 also provides the first evidence of the expansion of T. b. evansi type B, or a 5 th monomorphic lineage represented by IVM-t1, outside of Africa, with important possible implications for disease diagnosis. 3. Impact statement Trypanosoma brucei are unicellular parasites typically transmitted by tsetse flies. Subspecies of T. brucei cause human African trypanosomiasis and the animal diseases, nagana, surra and dourine. T. b. evansi and T. b. equiperdum have branched from T. brucei and, by foregoing tsetse transmission, expanded their geographic range beyond the sub-Saharan tsetse belt. These species can only reproduce asexually and exhibit morphological uniformity in their host (‘monomorphism’). T. b. evansi and T. b. equiperdum have historically been classified based on fragmentary information on the parasites’ transmission routes, geographic distribution, kDNA composition and disease phenotypes. Our analysis of genome sequencing data from monomorphic T. brucei supports at least four independent origins with distinct evolutionary histories. One isolate, IVM-t1, typed as T. equiperdum , is a closer relative to T. b. evansi , highlighting the risk of using pathognomonic descriptors for subspecies assignment. We show clear lineage specific variation in the selection efficacy in monomorphic T. brucei . Using the evolutionary relationships between lineages, we suggest it would be beneficial to reconcile phylogeny and pathology in monomorphic trypanosomes. 4. Data summary The data used in this study is available from the Sequence Read Archive or the Wellcome Sanger Institute. The accessions can be found in Supplementary file 1.