Fig. 2

Phylogenetic analysis of T. equi sequences obtained from clinically infected horses (triangles) and subclinically infected horses (open circles) using three genes (sample names as detailed in Additional file 1: Table S1). a Analysis of 1079 nucleotide positions of T. equi 18S rRNA gene, from 6 clinical and 40 subclinical samples, along with additional published sequences (GenBank ID/parasite/host/location). The phylogenetic tree was constructed based on the Tamura-Nei model with gamma distribution (+G). b Analysis of 400 nucleotide positions of T. equi ema-1 gene sequences obtained from four clinical and five subclinical samples, along with additional published sequences (GenBank ID/parasite/host/location). The classification of each sample according to its 18S rRNA gene is states near the sample name (− 18SX). The phylogenetic tree was constructed based on the Kimura 2-parameter model with consideration on invariable sites (+ I). c Analysis of 782 nucleotide positions of T. equi ema-2 gene sequences obtained from six clinical and four subclinical samples, along with all 19 additional published sequences (GenBank ID/parasite/host/location). The classification of each sample according to its 18S rRNA gene is states near the sample name (− 18SX). The phylogenetic tree was constructed by based on the Kimura 2-parameter model with consideration on invariable sites (+ I). All phylogenetic trees were constructed using maximum likelihood method and 1000 bootstrap replicates. The percentage of trees in which the associated samples clustered together is shown next to the branches when it was above 70%. The analysis was constructed in MEGA7