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Table 1 Mitochondrial gene data sets and HGTs postulated by Bergthorsson et al. and those computed by the MP analysis (NEPAL). 'donor' denotes the group from which the gene was transferred (in all cases, the recipient is Amborella).

From: Bootstrap-based Support of HGT Inferred by Maximum Parsimony

 

Bergthorsson et al .[21]

MP analysis

Gene

#HGTs

donor

SH

b1

b2

b3

b4

#HGTs

F?

cox2

3

M

<0.001

100

38

-

-

1

Y

  

E

NS

     

Y

  

E

NS

      

nad2

2

M

<0.001

100

62

-

-

1

Y

  

E

NS

     

Y

nad4(exons)

1

M

<0.001

99

98

44

-

2

Y

nad4(ex4)

1

E

NS

58

 

-

-

0

Y

nad5

2

M

<0.001

100

95

84

35

3

Y

  

A

0.025

     

Y

nad6

1

B

<0.001

100

26

-

-

1

Y

nad7

2

M

<0.001

99

64

-

-

1

Y

  

E

NS

     

Y

atp1

1

E

0.001

98

33

-

-

1

Y

atp8

1

E

0.008

75

38

-

-

1

Y

ccmB

1

E

NS

39

-

-

-

0

Y

ccmC

1

E

0.03

68

-

-

-

0

Y

ccmFN1

1

E

0.004

80

86

37

-

2

Y

cox3

1

A

NS

69

-

-

-

0

N

nad1

1

E

<0.001

100

88

25

-

2

Y

rpl16

1

E

NS

46

 

-

-

0

Y

rps19

1

E

0.003

100

61

-

-

1

Y

sdh4

1

E

NS

35

 

-

-

0

Y

nad2intron

1

M

-

66

 

-

-

0

Y

nad5intron

1

M

-

97

41

-

-

1

Y

nad7intron

1

M

-

100

67

-

-

1

Y

  1. 'SH' denotes support of the HGT events as computed by the Shimodaira-Hasegawa (SH) test and reported by Bergthorsson et al. (values lower than 0.05 indicate high support, and NS indicates support is not significant). The 'b1', 'b2', 'b3', and 'b4' columns correspond to the support values from Formula 3 for adding the first, second, third, and fourth HGT edges inferred by the MP analysis. Since adding HGT edges stops once a weakly supported edge is encountered, a '-' entry under these columns indicates that adding HGT edges was stopped before. B = Bryophyte, M = Moss, E = Eudicot, and A = Angiosperm.