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Table 2 Insertion/deletion rates among different phylogenetic groups estimated in rate variation model. Estimation was based on the select-genes trees.

From: Uncovering rate variation of lateral gene transfer during bacterial genome evolution

Group Taxa Genome Size Branch Length Rate Variation Constant Rate ΔLnL
     α value MLE LnL MLE LnL  
Bacillus 13 4.9 0.126886 0.39 4.79 -40187 0.51 -40545 358*
Brucella 4 2.1 0.000775 0.053 126.82 -1214 22.77 -1253 39*
Burkholderia 7 3.8 0.028971 0.35 25.58 -17258 3.54 -17717 459*
Candidatus 4 1.3 0.608223 0.36 -4635 0.36 -4635 0
Chlamydophila 7 1.2 0.081640 0.41 0.36 -1427 0.22 -1451 25*
Clostridium 5 3.3 0.123806 0.50 11.93 -9544 9.84 -9769 225*
Corynebacterium 5 3.0 0.172207 0.79 2.48 -8537 0.71 -8600 63*
Ehrlichia 5 1.5 0.059080 0.27 -832 0.27 -832 0
Escherichia 7 5.0 0.002852 0.23 51.34 -10689 12.53 -11236 547*
Helicobacter 5 1.7 0.232504 0.47 1.75 -3966 1.16 -4133 167*
Lactobacillus 6 2.2 0.250368 0.44 -9302 0.44 -9302 0
Mycobacterium 6 4.2 0.070373 0.41 19.94 -14693 1.63 -14718 25*
Mycoplasma 12 0.9 0.441286 0.13 -8448 0.13 -8448 0
Prochlorococcus 5 1.9 0.356990 2.42 0.17 -4414 0.15 -4421 7*
Pseudomonas 8 6.3 0.057175 1.66 2.09 -27117 1.32 -27231 114*
Rhodopseudomonas 4 5.3 0.060450 0.59 2.73 -9342 1.43 -9433 91*
Rickettsia 5 1.3 0.055962 0.33 3.70 -3172 1.30 -3302 130*
Salmonella 5 4.8 0.002930 0.37 12.19 -5283 7.97 -5356 73*
Shigella 6 4.6 0.003188 0.37 39.69 -9753 16.25 -10064 311*
Staphylococcus 13 2.8 0.034391 0.090 407.56 -12283 19.77 -14514 2231*
Streptococcus 19 2.0 0.041459 0.34 12.76 -24015 9.39 -26146 2131*
Synechococcus 5 2.6 0.364362 0.31 -7320 0.31 -7320 0
Vibrio 5 3.2 0.104170 0.21 11.72 -8623 0.74 -8883 260*
Xanthomonas 6 5.1 0.024790 0.33 18.00 -9388 3.21 -9714 326*
Yersinia 6 4.6 0.000263 0.064 261.75 -3236 46.77 -3606 370*
  1. *Significant improvement