Fig. 1

Genomic sample origins and inferred genetic relationships among the Anaplasma phagocytophilum samples examined. a The geographic locations from which the genomic data derived. The left panel shows the US states from which each of the 4 North American samples (Ap-ha variant) were isolated, and the right panel shows the countries from which the 4 European samples (host-generalist ecotype) were isolated. Also shown in the right panel is the roe-deer specialist ecotype sample, used for outgroup comparisons. This sample was isolated from France. b PCA of North American Ap-ha variant samples (in green), European host-generalist ecotype samples (in blue) and European roe deer-specialist ecotype samples (in red). Both axes are labeled with the percent of genetic variance explained. c Approximate maximum-likelihood phylogeny [37] based on multi-locus sequence typing data using unique haplotypes from Huhn et al. [6], with the addition of the orthologous sequences from the 9 focal genomes. Also included are samples from the burrowing-mammal specialist. Genome data are labeled in the figure. Colors correspond to the variant/ecotype and are the same as in the PCA. Numbers next to the nodes corresponding to divergences between ecotypes/variants indicate support values from 10,000 ultrafast bootstrap (UFBoot) replicates [40], and 10,000 replicates of the Shimodaira-Hasegawa-like approximate likelihood ratio test (SH-aLRT; [41,42,43]). PCA, Principal component analysis