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Table 2 Rip coding sequences under strong diversifying positive selection on the protein level

From: Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex

T3E gene Number of strains Alignment length (nt) Population recombination rate,N e r(PLPT)a LRT statistic values for codon model pairsb Proportions of sites in different selection regimesc
     M0 vs M3 M1a vs M2a M7 vs M8 M8a vs M8 Strict negative (ω< 0.15) Relaxed negative (0.15 <ω<0.9) Neutral (0.9<ω<1) Positive (ω>1)
RipAA 10 906 10 (0.33) 134.9 6.2 14.4 13.1 38% (ω=0.04) 56% (ω=0.48) 0% 6% (ω=2.9)
RipAJ 11 936 2 (0.54) 150.5 7.2 11.9 13.3 46% (ω=0.04) 46% (ω=0.49) 9% 7% (ω=3.1)
RipAT 9 1764 0 (0.04) 191.1 11.5 17.3 13.3 38% (ω=0.04) 48% (ω=0.54) 10% 5% (ω=3.3)
RipAW 6 1359 6 (0.00) 177.6 9.4 15.0 20.6 38% (ω=0.02) 48% (ω=0.51) 10% 5% (ω=4.9)
RipAP 7 2400 0 (0.22) 148.6 18.2 21.7 27.6 59% (ω=0.02) 29% (ω=0.48) 10% 2% (ω=10.0)
RipD 11 1971 3 (0.18) 266.5 7.2 16.7 12.7 38% (ω=0.04) 47% (ω=0.47) 9% 6% (ω=2.8)
RipG7 10 2016 10 (0.00) 561.6 28.1 37.6 43.0 46% (ω=0.04) 28% (ω=0.59) 19% 7% (ω=3.4)
RipH3 9 2229 4 (0.81) 145.7 19.5 29.5 25.1 29% (ω=0.07) 57% (ω=0.56) 10% 4% (ω=3.8)
RipS7 7 9570 0 (0.00) 329.0 30.4 34.3 42.2 48% (ω=0.03) 38% (ω=0.44) 10% 5% (ω=4.0)
  1. aValues supporting evidence for recombination are shown in bold.
  2. bFor the presented 9 genes all three LRTs for positive selection were significant, as well as the LRT comparing M0 vs M3 supporting strong variability of selection pressure among sites. Codon models are as described in [74].
  3. cEstimates of selection regimes are according to model M8 if LRT comparing M8a and M8 was significant. Otherwise, selection regimes are reported according to model M8a. For strict and relaxed negative selection, the average omega value over respective selection classes is shown. Note that percentages for the four categories do not always add up to 100% due to rounding.
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