Each genospecies display unique structuring
Borrelia bavariensis displayed the strongest geographic structuring between the European and Asian samples (FST (Nei, 1987) = 0.744;AMOVAcontinent (Excoffier et al., 1992) = 69.7% of molecular variance (σ)) followed by B. afzelii(FST = 0.570;AMOVAcontinent = 40.2% of σ) (Table 1 & 2). Regions (defined as country or sampling locality if known, see Table S1 & S3) within continents further explained variation in B. afzelii samples (AMOVARegion = 23.6% of σ; Table 2) and structuring was observed between randomly sampled B. afzelii isolates from the islands of Hokkaido (ASA) and Honshu (NAG) (FST = 0.379; Table S2). Honshu and HokkaidoB. afzelii isolates do form two reciprocally monophyletic clades, with the notable exception of one Hokkaido isolate belonging to the Honshu clade (Figure 2A) suggesting some level of migration. Of interest however, this trend was not observed for B. bavariensis(AMOVARegion = 0.99% of σ; Table 2) and, indeed, randomly sampled B. bavariensis isolates from the islands of Hokkaido and Honshu did not show geographic structuring (FST = 0.057; Table S2) even though both B. bavariensis and B. afzelii are rodent adapted (Kurtenbach et al., 2006; Gabriele Margos et al., 2019, 2011). Furthermore, AsianB. bavariensis displayed a low divergence clade containing samples from Japan (including isolates from distinct islands), China, and Russia (Figure 1B) suggestive of relatively high migration between Asian regions. Less geographic structuring by continent was observed inB. garinii (FST = 0.13;AMOVAContinent = 8.7% of σ; Table 1 & 2) as expected as B. garinii displayed little geographic structuring throughout the phylogeny with mixing of samples from different geographic origins (Figure 2C).