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.