PMC

Phylogenetic reconstruction of 25 B. microti samples. Bayesian maximum clade credibility phylogeny of complete apicoplast genome sequences (28.7 Kb) from the 25 B microti samples calculated from the posterior distribution of trees generated by Bayesian MCMC coalescent analysis in BEAST []. Bayesian coalescent analysis was performed with a substitution rate of 1.2 × 10⁻⁸ substitutions per site per year (1.2 % per million years). Branches defining major clades are displayed in different colors, which correspond to the colors in Fig.  (b, c). Divergence dates (median estimates and 95 % HPD) are given in parenthesis for major nodes. Posterior probabilities > 0.65 are indicated at each node. The timescale is indicated below the phylogeny. Babesia microti-human derived samples are marked with “*”

Population structure of B. microti in the continental U.S. a Map showing the geographic origin and the proportions of sample belonging to each cluster for each sampling site in the continental U.S. as determined by the DAPC analysis. Area of the circle is proportional to the sample size for the site. b Scatter plot showing the first two discriminant functions of the discriminant analysis of principal components applied to the B. microti genome-wide SNPs data set from the 25 samples (K = 4). Circles represent individual samples. B. microti samples originated from Nantucket Island (cluster 1) are indicated in dark blue, mainland Northeast sites (CT) Maine (ME), Long Island (NY) and New Hampshire (NH) (cluster 2) in orange, southeastern portion of Massachusetts, specifically Marta’s Vineyard Island and Cape Cod (MA) (cluster 2) in light blue, and the upper Midwestern samples (Wisconsin) (cluster 4) in green. The histogram shows the two principal components of PCA (x-axis) which contained 58 % of the data variance (y-axis) using K =4 as a prior clustering. c. Bar plots showing for each sample ancestral probability using ADMIXTURE on the genome-wide SNP dataset (K = 4) (14 tick-derived strains and 11 clinical isolates from human patients marked with “*”)