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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