Descriptive analyses
We began with descriptive analyses and illustration of the virus
co-occurrence structure. We assessed the nestedness of the data by
organising the virus community matrix based on overlap in virus
presences among plants and decreasing fill (Almeida-Neto et al.2008). We calculated C-scores (Stone & Roberts 1990) for the virus
community at the level of individual host plants and populations (Figure
2). We calculated the numbers of pairwise virus co-occurrence
combinations in host plants, as well as the pairs of viruses that never
co-occur. We used the full dataset of 25 viruses (See Results) for these
descriptive analyses.
We quantified the relationship between the cumulative virus richness and
co-occurrence patterns with respect to increasing area sampled by
calculating the mean species–area–curve and mean coexistence–curve
(Hart et al. 2017). Both curves were constructed by randomly
selecting one sampled host plant, and then increasing the spatial scale
and sample by including the next closest plant to the species richness
or co-occurrence calculation. We calculated the mean curves by repeating
this 100 times, selecting a different initial plant for each round. We
also calculated the maximum number of co-occurring virus pairs from the
number of taxa observed thus far. For more details, see Supplementary
Material and Methods and Supplementary Results Figure S2-3.