|
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) HPV2 did not cluster together with the rest of the alpha genus
- (2) HPV4 did not cluster together with the rest of the gamma genus
- np: the high divergence values did not allow the algorithm to rend a solution
- 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.
