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Table 5 Significant results of analysis of natural selection with codeml site models and FUBAR as well as recombination breakpoints detected with GARD for groups of DEFL genes

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

CRP groupsa Group 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
CRP0260 S125 12.03 0.03 12.08 0.04 ω = 4.92 p1 = 0.2 5 4 3 2 2 0 (3)
CRP0340 S43 44.01 0.01 24.85 0.01 ω = 5.42 p1 = 0.22 8 6 6 3 3 0 (1)
CRP0360 S81 16.99 0.01 19.27 0.01 ω = 5.66 p1 = 0.16 3 2 3 3 2 0 (2)
CRP0360 S87 38.60 0.01 44.39 0.01 ω = 5.25 p1 = 0.28 14 4 6 2 2 0 (2)
CRP0560 S14 22.32 0.01 10.52 0.05 ω = 3.25 p1 = 0.53 7 3 3 2 2 0 (4)
CRP0580 S65 7.64 0.03 9.57 0.06 ω = 3.66 p1 = 0.08 2 2 N.A. 3 N.A. N.E.
CRP0830 S63 9.30 0.10 9.52 0.06 ω = 9.65 p1 = 0.04 3 7 8 3 4 0 (2)
CRP1110 S68 16.57 0.01 16.68 0.01 ω = 5.45 p1 = 0.16 7 5 5 2 4 0 (1)
  1. aCysteine Rich Peptide groups (CRPs) of defensin and defensin-like genes (DEFLs) as defined for A. thaliana in [29]
  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 M8 inferred with Bayes Empirical Bayes analysis with P > 0.9
  5. eAccording to the FUBAR procedure 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. N.E. means no evidence for recombination was detected. For such groups a second FUBAR analysis was not performed (N.A.)