Table 2. Phylogenetic patterns of gene distribution in selected Proteobacteria. Values were calculated for the 1000 partitions of the species phylogenetic tree.

Genea	Db	P(D > 0)c	P(D < 1)c	Phylogenetic signal strength
pqqB	0.05 (0.01/0.07)	0.16/0.41	0	Strong
pqqC	0.04 (0.00/0.07)	0.16/0.45	0	Strong
pqqD	0.04 (0.00/0.07)	0.16/0.45	0	Strong
pqqE	0.04 (0.01/0.07)	0.17/0.45	0	Strong
pqqF	−0.17 (−0.20/−0.15)	0.95/0.99	0	Very strong
pqqG	−0.18 (−0.21/−0.17)	0.95/0.98	0	Very strong
phlA	−0.40 (−0.76/−0.06)	0.48/0.88	0.00/0.04	Very strong
phlB	−0.40 (−0.75/−0.05)	0.49/0.89	0.00/0.04	Very strong
phlC	−0.40 (−0.75/−0.06)	0.48/0.88	0.00/0.03	Very strong
phlD	−0.24 (−0.36/−0.12)	0.63/0.86	0	Very strong
hcnA	−0.18 (−0.30/−0.06)	0.62/0.95	0	Strong
hcnB	−0.18 (−0.30/−0.05)	0.61/0.95	0	Strong
hcnC	−0.18 (−0.29/−0.06)	0.61/0.94	0	Strong
budA	−0.34 (−0.37/−0.30)	0.98/0.99	0	Very strong
budB	−0.34 (−0.37/−0.30)	0.98/0.99	0	Very strong
budC	−0.02 (−0.08/−0.03)	0.40/0.70	0	Strong
nirK	−0.05 (−0.09/−0.02)	0.60/0.89	0	Very strong
ipdC	−0.33 (−0.41/0.28)	0.96/0.99	0	Very strong
ppdC	−0.34 (−0.27/−0.47)	0.65/0.80	0	Very strong
acdS	0.10 (0.07/0.13)	0.05/0.19	0	Moderate
nifD	0.28 (0.23/0.33)	0.01/0.05	0	Weak
nifH	0.28 (0.24/0.33)	0.00/0.04	0	Weak
nifK	0.28 (0.23/0.33)	0.00/0.04	0	Weak

^aThe genes studied are involved in phosphate solubilization (pyrroloquinoline quinone; pqqBCDEFG), 2,4-diacetylphloroglucinol synthesis (phlACBD), hydrogen cyanide synthesis (hcnABC), induced systemic resistance (acetoine and 2,3-butanediol; budAB and budC, respectively), NO synthesis (copper nitrite reductase; nirK), IAA synthesis (indole-3-pyruvate decarboxylase/phenylpyruvate decarboxylase; ipdC/ppdC), plant ethylene regulation (ACC deamination; acdS), and nitrogen fixation (nitrogenase; nifHDK).

^bMedian value (with the minimum and maximum values in parenthesis).

^cMinimum and maximum values when different.