Fig. 4 Canonical correspondence analysis (CCA) plot, showing the correspondence (~influence) of main environmental factors (blue arrows; cf. Table 4) with the vegetation composition of the plots (black crosses; vegetation types R1, R2, B1 and B2 of the plots are indicated).
Taking more samples per plot to more adequately represent the plant community composition of the plots was not possible due to the time necessary for taking and analyzing further samples.
The third source of uncertainty arises due to the composition of the Dalitz plot.
We were interested in determining (i) whether there were differences in the composition of the plant community in plots with and without Carduus, (ii) whether particular species were associated with the presence of Carduus and (iii) whether these associations differed between sites.
Nonmetric multidimensional scaling analysis and partial Mantel tests showed that the floristic composition of the two plots was distinct, even after accounting for the underlying spatial gradient in composition.
The possible maximum number of the two indices is 100%, indicating that the species composition of the compared plots is exactly the same.
To evaluate whether the pangenome (sum of all the genes of all the collected strains) (Medini et al. 2005; Tettelin et al. 2008) of the species has been fully represented, we determined the ortholog groups, analyzed the composition of the pangenome, and plotted the evolution of the coregenome (set of genes shared by all the strains) versus the pangenome from 1 to 50 strains (fig. 1).
Inclusion of the good-colonizing group, legumes, created a more dichotomous pattern, with colonists being either distantly or closely related to existing plot species (3 and 7 plots, respectively); this result was driven by initial experimental composition of plots and whether plots had legumes or not.
Structural composition of the historical and recent plots was compared through the total amount of stems, mean DBH and basal area for stems with minimum DBH of 10��cm, and for stems and basal area of the DBH class 10 to 20 cm.
