2.6 Statistical analyses
The slopes of the dynamics of the percentages of Dickeya -,Pectobacterium -, D. solani - and D.
dianthicola -positive fields were analyzed using F-tests and ANCOVAs
using GraphPad Prism version 8.4.2 for MacOS, GraphPad Software
(www.graphpad.com). A Chi-squared method
was used to test the non-random distribution of taxa in each field.
In all the plant assays, the non-inoculated plants and tubers remained
asymptomatic, and this control condition was not considered in
statistical analyses. The two symptom levels (with or without symptoms)
of potato plants and hyacinths virulence assays, the five symptom
classes in tuber aggressiveness assays, and gene expression levels were
compared among treatments (the different pathogens) by Kruskal-Wallis
tests (α = 0.05) because the data significantly deviated from normality.
Then, post-hoc Tukey tests were run to assess what pairwise differences
were significant. When the bacterial strains were inoculated separately
on plants and tubers, we compared the D. solani and D.
dianthicola species traits using each bacterial strain as a replicate
of the considered species. When the bacterial strains were inoculated
altogether to constitute an experimental population, we compared theD. solani and D. dianthicola species traits using at least
two independent replicates of the experiments.
In competition assays, the hypothesis of balanced abundances of the two
competitors was tested by comparing the calculated CI values to one
using a Kruskal-Wallis test. Analyses were carried out with the software
R (http://www.R-project.org) using the packages RcmdR and
nparcomp.