TABLE 1.

Nestedness and modularity of PVY-plant infectivity matrices

Parameter and algorithm	Value for the parameter in:a
	PVY mutants		PVY isolates
	Including susceptible plant genotypes	Excluding susceptible plant genotypes	Including susceptible plant genotypes	Excluding susceptible plant genotypes
Nestedness
binmatnest2b	0.80 (0.032*, 0.193)	0.71 (0.301, 0.541)	0.93 (0.021*, 0.106)	0.77 (0.340, 0.579)
NODF2c	0.71 (0.011*, 0.172)	0.56 (0.231, 0.397)	0.85 (0.009**, 0.028*)	0.73 (0.128, 0.267)
WINEd	0.61 (0.011*, 0.117)	0.53 (0.059, 0.332)	0.64 (0.015*, 0.070)	0.47 (0.289, 0.400)
Modularity
leading.eigenvector.communitye	0.22 (0.371, 0.326)	0.25 (0.316, 0.292)	0.18 (0.374, 0.343)	0.19 (0.077, 0.255)
spinglass.communityf	0.20 (NA, NA)	0.22 (NA, NA)	0.18 (NA, NA)	0.22 (NA, NA)
optimal.communityg	0.23 (0.765, 0.516)	0.27 (0.433, 0.328)	0.18 (0.734, 0.468)	0.19 (0.107, 0.327)
edge.betweenness.communityh	0.11 (0.527, 0.373)	0.25 (0.191, 0.178)	0	0
infomap.communityi	0	0	0	0

^aNestedness and modularity were estimated with different algorithms of the R software package, and estimation values are indicated separately for PVY VPg mutants or field isolates and including or excluding the Capsicum annuum and Solanum habrochaites susceptible reference genotype plants that were infected by all PVY variants (Fig. 1d and e). Values in parentheses are the frequencies of matrices simulated under the Bernoulli null model and the probabilistic degree null model, respectively, showing higher nestedness or modularity estimates than the experimental infectivity matrices, except when no module was detected (modularity indicated as 0). Totals of 10,000 (nestedness) or 1,000 (modularity) matrices were simulated independently under the two null models. Nestedness was significant at the 5% (*) and 1% (**) type I error threshold (in bold). NA, not available (the method cannot work with unconnected graphs, many of which were obtained in the matrices simulated under the null models).

^bR function according to Rodríguez-Gironés and Santamaría (19).

^cR function according to Almeida-Neto et al. (20).

^dR function according to Galeano et al. (21).

^eR function according to Newman (22).

^fR function according to Newman and Girvan (24), Reichardt and Bornholdt (25), and Traag and Bruggeman (26).

^gR function according to Brandes et al. (27).

^hR function according to Newman and Girvan (24).

ⁱR function according to Rosvall and Bergstrom (28).