Figure and table legends
Figure 1. A schematic representation of direct and indirect
associations between viruses in the context of their hosts and
environment. Within plant populations, individual plants host viruses.
The viruses have associations with each other, either through direct
mutualistic or antagonistic interactions (bold font), or indirect
associations mediated by another virus, shared vector, and/or host
immunological responses (small font). The environment can influence the
(co-)occurrences either directly or through host effects at the level of
host populations or individuals, or via the vectors (capital font). The
solid bold arrow represents the direct association between two viruses,
whereas the dashed arrows show the confounding indirect associations.
The additional conditioning explanatory variables included in our
constrained models are illustrated. The indirect effects (mediator
species, changes and variation in host immune response) are included in
the models implicitly through spatial variables and the model structure.
Figure 2 . Virus communities by population. In A, each
pie chart represents the virus community of a host plant population,
overlayed on the map of Ă…land. Infection load is shown with greyscale,
as indicated in the legend. Sliced portions of same shade of grey show
plants with equal number of viruses, but in different combinations. B)
Nestedness of the virus communities when aggregated to host population
level. Two most contrasting communities are shown in more detail in C
and D. In these barplots, the within-host virus community composition of
a virus-rich plant host population 861 (D) and virus-poor population
3222 (C) is shown with different colours indicating different virus
taxa, as shown in legend.
Figure 3. Viral co-occurrence structure. A) Virus occurrences
(diagonal) and co-occurrences (off-diagonals), organised according to
the first principal component of the incidence matrix. The colouring of
the font intensifies with the value. The diagonal elements show the
overall number of occurrences of the focal virus, whereas the
off-diagonal elements show the numbers of host plants where the two
viruses co-occur. The numbers inside brackets next to virus names
indicate the number of single infections. B) Species-area curve and
coexistence curves. The uppermost black dotted line indicates the
species-area curve, the grey dashed line indicates the maximum amount of
possibly coexisting pairs (calculated from the species-area-curve), and
the black solid line shows the actual average coexistence curve.
Figure 4. Virus networks. A) Markov random field co-occurrence
network, representing direct pairwise associations between viruses,
after accounting for the rest of the community (MRF). B) Constrained
Markov random field co-occurrence network, representing direct pairwise
associations between viruses, after accounting for the rest of the
community as well as all environmental and spatial effects (CRFfull). C)
Direct associations explained by host-related variables
(CRFhost); D) direct associations explained by habitat-related
variables (CRFhabitat); and E) direct associations explained by
spatial variables (CRFspat). The viruses closer in space have stronger
positive associations with each other and edge thickness is scaled by
the strength of association. In summary, when the associations in panels
C-D are subtracted from all the associations in panel A, the
associations in panel B are left. Hence, the dashed lines in C-D
represent associations that disappear from panel A after adding the
explanatory variable group in question, resulting in the permanent
associations illustrated with solid lines in panel B.
Table 1. Explanatory conditioning variables. See
Supplementary Material and Methods for more thorough description and
justification of the explanatory variables.
Table 2. The direct effects of the additional explanatory
variables on the virus occurrence probabilities and the indirect effects
of the additional explanatory variables through their influence on the
association between a focal pair of viruses. Effects\(\geq|\)0.25| are highlighted with bold font. All
mean coefficient estimates are significant (based on bootstrapping and a
90% confidence interval).