Figures
Figure 1. Map of Europe showing the geographic origin and the infection status of our samples based on the host species: (A) European rabbit (Oryctolagus cuniculus ), (B) European brown hare (Lepus europaeus ), (C) mountain hare (Lepus timidus ), (D) Corsican hare (Lepus corsicanus ). Red squares indicate positive and black triangles represent negative tested animals. Coloured geographic range overlays provide information on the distribution of the different lagomorph species according to the International Union for Conservation of Nature (IUCN) Red List of Threatened Species (https://www.iucnredlist.org). The distribution charts were modified to include the UK to the species distribution of L. europaeus(Marques, Ferreira et al., 2017). Green = mountain hare, red = European brown hare, yellow = Iberian hare (Lepus granatensis ). The map was created in QGIS v. 3.20 using Bing Aerial (http://ecn.t3.tiles.virtualearth.net/tiles/a{q}.jpeg?g=1) as a map source with TM World Borders 0.3 overlay (https://thematicmapping.org/downloads/world_borders.php).
Figure 2. Maximum-likelihood tree based on the concatenated alignment (tp0488 and tp0548). The tree was constructed with IQ-TREE with the best-fit model (GTR+F+R3) based on the Bayesian Information Criterion and 1,000 bootstrap replicates. We included 194 sequences, containing 156 parsimony-informative sites and 48 singletons. Only bootstrap values > 90% are shown. Scale bar represents substitutions per nucleotide site. The circle colour indicates the geographic origin of the sample: magenta = USA, yellow = Sweden, cyan = Northern Germany, black = Southern Germany, green = Central and Western Germany, orange = The Netherlands, wine-red = Italy, pink = Czech Republic and red = United Kingdom. Text colour indicates the host species: black = Lepus europaeus , yellow = Lepus timidus , blue = Lepus corsicanus and red = Oryctolagus cuniculus . The tree was rooted using T. pallidum subsp.endemicum strain Iraq B (GenBank CP032303.1).
Figure 3. Illustration of the tp0548 gene variable regions and repeat types. A. Overview about the two identified variable regions (V1-2) at a minimum variant frequency of 0.25. The colours in V2 are coding for the flanking regions of the repeats upstream (blue) and downstream (red). The grey area indicates the location of the repeats.B. Sequence information of the identified repeat types I-XIV. Changes from the Type I repeat are highlighted in bold. C . Truncated violine plot of the frequency distribution of the five most abundant repeat types identified in our set of sequences. In red, the bold dashed lines indicate the median, the smaller dotted lines represent the quartiles. Individual data are superimposed with a grey cross. The total number of strains with the respective repeat type is shown on the right. Only repeat types occurring > three and which contain only a single repeat type are shown. Figure S4 provides further information on other repeat patterns. Violin plots were created in GraphPad PRISM 9.3.1.