TABLE 2.
Results of PERMDISP2, ANOSIM, and PERMANOVA testsa.
| Group | PERMDISP2 Raw P-Value (F)b | ANOSIM Raw P-Value (R)c | PERMANOVA Raw P-Value (R2)d |
| Pan-genome element presence/absence (n = 4,102)e | |||
| Serotype | 2.0E-4 (14.3)* | <1.0E-4 (0.99)* | <1.0E-4 (0.93)* |
| Farm | <1.0E-4 (4.43)* | <1.0E-4 (0.54)* | <1.0E-4 (0.73)* |
| Source | 0.071 (3.40) | 0.99 (−0.07) | 0.32 (0.01) |
| Antimicrobial resistance and stress response gene presence/absence (n = 28)f | |||
| Serotype | 0.013 (4.46) | <1.0E-4 (0.79)* | <1.0E-4 (0.85)* |
| Farm | <1.0E-4 (5.52)* | <1.0E-4 (0.30)* | <1.0E-4 (0.54)* |
| Source | 0.74 (0.01) | 0.79 (−0.03) | 0.31 (0.01) |
aAll tests were performed using a Jaccard dissimilarity metric and 10,000 permutations; raw P-values are reported for all tests, with significant P-values (P < 0.05 after a Bonferroni correction was applied to all values) denoted with an asterisk (*).
bANOVA-like permutation test applied to results obtained using the PERMDISP2 procedure for the analysis of multivariate homogeneity of group dispersions (i.e., variances), obtained using the betadisper and permutest functions in the vegan package in R; betadisper is a multivariate analog of Levene’s test for homogeneity of variances.
cAnalysis of similarities (ANOSIM) test results obtained using the ANOSIM function in the vegan package in R.
dPermutational analysis of variance (PERMANOVA) test results obtained using the adonis2 function in the vegan package in R.
eIdentified using Roary and a 70% protein BLAST (BLASTP) identity threshold.
fDetected using AMRFinderPlus.