TABLE 2.

SD% for RP, PHX, PMX, and PA genesa

GenomebRPPHXPMXPAβcSEd
No. of genesSD%No. of genesSD%No. of genesSD%No. of genesSD%
ESCCO5775.430671.63,32157.126940.90.710.12
HAEIN5782.514075.71,32851.66048.31.820.26
VIBCH5680.417264.02,90747.517444.80.510.14
PSEAE5787.712882.84,83669.127465.30.770.19
CAMJE5492.611979.01,35157.11145.52.090.42
HELPY5481.57383.61,28758.12755.63.540.79
RICPR5450.04131.772817.902.971.17
NEIME5784.29183.51,36848.420940.21.900.28
CHLPN5375.58562.486440.71450.03.200.63
CHLTR5170.65269.276645.4933.32.660.83
BORBU*5479.67167.670050.700.980.59
TREPA5198.09973.779159.22634.62.330.60
BACSU**62100.014793.23,29289.417284.90.330.26
MYCGE**5122.42714.841910.500.091.31
MYCPN5334.05728.154617.05010.02.811.00
UREUR5284.67273.646955.01154.52.310.64
MYCTU5574.556055.42,93946.415846.20.960.27
SYNSQ5749.138037.62,32924.518621.51.540.29
DEIRA5585.533758.52,32939.525442.51.160.14
AQUAE5692.923369.51,17443.57454.13.180.39
THEMA5498.117493.71,44389.96484.42.350.78
METJA*6287.111354.91,32548.52835.70.530.29
METTH6085.016071.31,39359.67659.21.660.46
ARCFU5978.034359.81,60143.513343.62.350.36
PYRAB6096.724180.51,35170.58959.61.870.36
PYRHO5481.217369.91,68055.713429.91.520.38
THEAC4985.714933.61,14022.99414.92.240.83
HALSP*5853.432824.11,28327.414025.7−0.820.45
SULSO6558.565427.11,76021.732221.41.290.42
PYRAE**6633.35925.41,98523.39214.10.451.01
  • a See text for definitions of PHX, PMX, and PA gene classes. For the gene classes RP, PHX, and PA, SD% in bold indicates a significant increase over the group PMX, while underlining signifies a significant decrease (P < 0.05 for a χ2 test using the Yates correction). The P value of the logistic regression (for a likelihood ratio test of the regression) was <0.01 for all genomes except those marked with * (0.05 < P < 0.1) and ** (P > 0.1).

  • b See Fig. 2 legend for abbreviations.

  • c Estimated coefficient for the logistic regression model (β1 in equation 5).

  • d Standard error of the estimated β.