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Table 4 Statistically significant results of analysis of natural selection with codeml site models and FUBAR as well as recombination breakpoints detected with GARD for groups of NLR subfamilies CNL and TNL

From: Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms

Group na LRT M1:M2 P b LRT M7:M8 P b Estimates for M8c M8 BEB sitesd FUBAR positivee FUBAR positive partitionsf FUBAR negativee FUBAR negative partitionsf GARD break pointsg
CNL
 GC1 9 147.05 <0.001 165.85 <0.001 ω = 5.77; p1 = 0.05 16 26 28 72 65 2 (7)
 GC2 13 22.85 <0.001 45.72 <0.001 ω = 2.00; p1 = 0.07 4 2 1 280 266 2 (7)
 GC3 5 127.18 <0.001 129.00 <0.001 ω = 8.65; p1 = 0.08 36 32 30 26 22 2 (9)
 GC4 6 87.78 <0.001 111.74 <0.001 ω = 4.06; p1 = 0.09 17 13 16 20 44 1 (8)
 GC5 12 125.11 <0.001 152.85 <0.001 ω = 3.44; p1 = 0.08 19 22 14 145 122 5 (6)
 GC6 5 50.57 <0.001 57.46 <0.001 ω = 5.17; p1 = 0.07 7 13 4 31 28 0 (7)
 GC7 10 64.06 <0.001 108.68 <0.001 ω = 2.51; p1 = 0.10 19 13 13 183 170 1 (7)
TNL
 GT1 21 174.03 <0.001 209.33 <0.001 ω = 2.73; p1 = 0.07 21 3 12 316 302 1(3)
 GT2 8 22.84 <0.001 44.70 <0.001 ω = 2.19; p1 = 0.1 3 11 4 137 110 1 (8)
 GT3 13 218.48 <0.001 259.31 <0.001 ω = 3.10; p1 = 0.1 43 10 23 214 189 3 (5)
 GT5 6 77.90 <0.001 90.03 <0.001 ω = 5.72; p1 = 0.05 17 15 13 118 83 2 (7)
 GT6 11 24.74 <0.001 52.40 <0.001 ω = 1.82; p1 = 0.17 14 9 14 237 221 2 (6)
 GT11 9 113.42 <0.001 126.25 <0.001 ω = 4.17; p1 = 0.07 15 5 10 79 42 1 (7)
 GT14 8 34.66 <0.001 44.31 <0.001 ω = 3.09; p1 = 0.07 7 4 3 65 58 4 (7)
 GT15 7 71.62 <0.001 82.99 <0.001 ω = 3.13; p1 = 0.09 21 19 4 96 63 4 (7)
 GT21 6 25.63 <0.001 39.91 <0.001 ω = 2.83; p1 = 0.09 5 1 3 93 81 0 (7)
 GT22 6 95.80 <0.001 106.74 <0.001 ω = 4.76; p1 = 0.07 11 32 21 71 43 5 (8)
  1. aNumber of sequences in the group
  2. b P-values are corrected for multiple comparisons with the Benjamini-Hochberg procedure employing a False Discovery Rate of 0.10. Values in bold represent significant tests in which ω is inferred to be >1.0
  3. cω is dN:dS estimated under M8; p1 is the inferred proportion of positively selected sites. Positions under positive selection are provided in Additional file 13: Data 8
  4. dNumber of codon position under positive selection with P > 0.9
  5. eAccording to FUBAR analysis this is the number of codon positions under positive or negative selection with P > 0.9
  6. fResults obtained with FUBAR analysis based on the partitions of all breakpoints detected with GARD regardless of their statistical significance
  7. gNumber of breakpoints with significant phylogenetic topological incongruence at p ≤ 0.1, between parentheses is the total number of breakpoints detected
  8. N.E. means no evidence for recombination was detected. For such groups a second FUBAR analysis was not performed