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Table 1 Phylogenetic coherence of different papillomavirus taxa according to the L1 and E7 genes, and to the URR.

From: Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

L1

Clustalw

Dialign

Tcoffee

consensus

 

dnapars

Fitch

NJ

UPGMA

Protpars

Fitch

NJ

UPGMA

Protpars

Fitch

NJ

UPGMA

 

α

77

100

77

94

80

100

100

87

52

100

100

93

71

β

100

100

100

100

100

100

100

100

100

100

100

100

100

γ

94

92

100

58

94

77

100

98

97

91

99

98

95

δ

60

43

100

79

100

100

100

100

54

100

100

100

37

β+γ

52

82

50

99

70

77

82

84

48

95

77

76

64

δ+ξ

100

100

68

15

77

100

38

-

100

49

69

-

72

κ

100

100

100

100

100

100

100

100

100

100

99

99

100

λ

68

100

100

100

88

100

100

100

66

100

100

100

89

μ

95

100

100

100

92

99

100

100

97

95

99

99

97

μ+κ+λ

42

92

97

88

49

99

94

95

33

100

98

89

35

E7

Clustalw

Dialign

Tcoffee

consensus

 

Protpars

Fitch

NJ

UPGMA

Protpars

Fitch

NJ

UPGMA

Protpars

Fitch

NJ

UPGMA

 

α

54

90

86

99

-

92

84

89

63

85

84

97

30

β

26

96

89

94

99

92

89

84

64

85

96

88

57

γ

58

53

99

96

94

100

83

72

96

94

98

100

81

δ

55

15

-

-

-

47

-

-

-

55

25

-

35

β+γ

-

100

-

-

-

-

-

-

-

-

-

-

-

δ+ξ

            

-

κ

-

-

-

-

38

-

-

-

88

-

29

-

33

λ

-

95

96

99

99

95

94

96

84

86

91

91

94

μ

100

93

91

99

100

92

94

97

92

96

99

100

92

μ+κ+λ

-

-

-

-

-

-

-

-

-

-

-

-

-

URR

Clustalw

Dialign

Tcoffee

consensus

 

dnapars

Fitch

NJ

UPGMA

dnapars

Fitch

NJ

UPGMA

dnapars

Fitch

NJ

UPGMA

 
  

K2/ML

K2/ML

K2/ML

 

K2/ML

K2/ML

K2/ML

 

K2/ML

K2/ML

K2/ML

 

α

-

-/62

-/-

-/91(1)

99

-/-

np/-

np/-

20

-/15(1)

-/-

89(1)/88(1)

19(1)

β

98

100/100

100/100

100

-

-/-

np/-

np/-

97

-/30

-/-

97/96

51

γ

-

100(2)/100(2)

100(2)/100(2)

100(2)/100(2)

-

-/-

np/-

np/-

-

-/-

-/-

-/-

66(2)

δ

96*

69/62

100

100/100

99

-/-

np/30

np/44

94

85/49

100/99

100/100

80

β+γ

-

-/-

-/-

-/-

-

-/-

np/-

np/-

-

-/-

-/-

-/-

-

δ+ξ

-

-/-

-/-

-/-

-

-/-

np/-

np/-

-

-/-

-/-

-/-

-

κ

-

-/-

-/-

-/-

-

-/-

np/-

np/-

81

-/-

-/-

-/-

-

λ

100

73/-

68

99

-

-/-

np/-

np/-

93

61/49

-/-

98/92

-

μ

-

75/74

58

100/99

-

-/-

np/-

np/-

86

97/98

97/99

100/99

64

μ+κ+λ

-

-/-

-/-

-/-

-

-/-

np/-

np/-

-

-/-

-/-

-/-

-

  1. (1) HPV2 did not cluster together with the rest of the alpha genus
  2. (2) HPV4 did not cluster together with the rest of the gamma genus
  3. np: the high divergence values did not allow the algorithm to rend a solution
  4. Phylogenies were reconstructed with three different alignments, CLUSTALW, DIALIGN and TCOFFEE, subsequently analysed with four different phylogenetic algorithms: a parsimony based algorithm – PROTPARS for protein sequences and DNAPARS for DNA sequences -, and three different matrix-based algorithms: FITCH, Neighbor-Joining (NJ), and UPGMA. Matrices were generated with PROTDIST or DNADIST. For DNA, two different nucleotide substitution models were used, the Kimura-two parameter model (K2) or a maximum-likelihood model (ML). Numbers refer to the percentage of times a given group is recovered in the consensus tree for each reconstruction method, after a bootstrap of 1000 cycles. The column "consensus" gathers the output of the CONSENSE programme with trees from all independent algorithms as input. Some algorithms could not work with the DIALIGN alignment as input, due to the extreme divergence between the sequences. This fact is marked as "np" in the corresponding columns. The support values decrease in the order L1>E7>URR. This reflects the diversity of the evolutionary pressures along the genome of the papillomaviruses. Some of the genera stably recovered according to the L1 protein phylogeny appear with a lower support for the E7 protein phylogeny, and do not appear as definite groups for the URR phylogeny. This is the case for genera alpha, kappa or lambda. Some other genera appear confidently with independence of the element analysed. This is the case for genera beta, gamma and delta. This shows that there are differences in the evolutionary patterns between the members of different clades.