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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.