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Table 3 Insertion/deletion rates among different phylogenetic groups estimated in rate variation model. Estimation was based on the common-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 0.147413 0.39 3.89 -40017 0.44 -40278 261*
Brucella 4 2.1 0.000275 0.035 382.06 -1264 44.50 -1387 123*
Burkholderia 7 3.8 0.044985 0.18 181.93 -17467 2.14 -18391 924*
Candidatus 4 1.3 0.433912 0.49 -4722 0.49 -4722 0
Chlamydophila 7 1.2 0.096709 0.39 0.30 -1439 0.19 -1466 27*
Clostridium 5 3.3 0.151053 0.52 8.49 -9529 7.23 -9756 227*
Corynebacterium 5 3.0 0.223104 1.19 2.48 -8492 0.49 -8509 17*
Ehrlichia 5 1.5 0.063546 0.24 -831 0.24 -831 0
Escherichia 7 5.0 0.006966 0.31 13.43 -10654 4.82 -11006 352*
Helicobacter 5 1.7 0.189516 0.52 1.75 -3961 1.05 -4109 148*
Lactobacillus 6 2.2 0.331530 0.33 -9241 0.33 -9241 0
Mycobacterium 6 4.2 0.087643 0.23 191.03 -14660 1.63 -14718 25*
Mycoplasma 12 0.9 0.244815 0.22 -8214 0.22 -8214 0
Prochlorococcus 5 1.9 0.319829 2.56 0.19 -4413 0.17 -4419 6*
Pseudomonas 8 6.3 0.083078 1.91 1.06 -26994 0.91 -27130 136*
Rhodopseudomonas 4 5.3 0.109002 0.52 1.75 -9352 0.77 -9459 107*
Rickettsia 5 1.3 0.054524 0.35 3.49 -3181 1.36 -3310 129*
Salmonella 5 4.8 0.003016 0.080 96.48 -5214 7.97 -5351 137*
Shigella 6 4.6 0.004433 0.17 131.93 -9784 11.39 -10327 543*
Staphylococcus 13 2.8 0.047252 0.085 279.41 -11390 14.76 -14581 3191*
Streptococcus 19 2.0 0.053313 0.29 18.71 -24327 13.19 -26553 2226*
Synechococcus 5 2.6 0.310236 0.33 -7531 0.33 -7531 0
Vibrio 5 3.2 0.196671 0.17 10.02 -8642 0.37 -8939 260*
Xanthomonas 6 5.1 0.026682 0.59 6.33 -9385 2.73 -9541 156*
Yersinia 6 4.6 0.000355 0.060 221.14 -3172 31.15 -3467 295*
  1. *Significant improvement