plosone-phylo
pone.0007299.g001.png
Bayesian phylogenetic trees derived from 154 global samples of DENV-3 E gene partial sequences (1023 nucleotides) inferred with MrBayes program.
The posterior probabilities are expressed in percent and indicated at important nodes. DENV-1 (ThD1_0127_80_D4, AY732411), DENV-2 (JAM1983_D2, AY484605) and DENV-4 (1503_YUCATAN_MX_84_D4, DQ341212) were used as outgroup. Horizontal branch lengths are drawn to scale. Aligned sequences were analyzed in the MrModeltest 2.3 program to identify the best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction [23]. The nucleotide substitution model used was under a General Time Reversible model of nucleotide substitution with gamma-distributed rate variation (G = 1.2411) and a proportion of invariable sites (I = 0.3656) (GTR+G+I), using Akaike's Information Criterion (AIC) [24]. Five runs of 4 chains each (one cold and tree heated, temperature = 0.20) were run for 1.5×106 generations, with a burn-in of 6000 generations. Characteristic amino acid substitutions at important nodes are indicated. GenBank accession numbers: BH 16 2003 (EF625832), BH 19 2003 (EF625833), BH 24 2003 (EF625834), BR 00 68784 (AY038605), D3BR RP1 03 (DQ118877), BR74886 02 (AY679147), China 80 2 (AF317645), Cuba21 02 (AY702031), D3BR PV7 03 (EU570161), BR DEN3 RO1 02 (EF629373), BR DEN3 RO2-02 (EF629373), ET ET209 00 (EF440434), ET_D3_Hu_TL129NIID_2005 (AB214882), ET_D3_Hu_TL018NIID_2005 (AB214879), ET_D3_OPD007NIID 2005 (AB219131), ET SV0153 05 (DQ453981), ET SV0160 05 (DQ453980), ET SV0174 05 (DQ453973), ET SV0177 05 (DQ453972), ET SV0193 05 (DQ453970), ET SV0194 05 (DQ453969), ET_D3_TL029NIID_2005 (AB214880), Fiji 92 (L11422), PF89 27643 89 (AY744677), PF89 320219 89 (AY744678), PF90 3050 90 (AY744679), PF90 3056 90 (AY744680), PF90 6056 90 (AY744681), PF92 2956 92 (AY744682), PF92 2986 92 (AY744683), PF94 136116 94 (AY744685), India 84 (L11424), Indo0312a TW 03 (DQ518677), Indo0508a_TW (DQ518678), IN 9108a_Tw 91 (DQ518674), IN 9909a_Tw 99 (DQ518675), IN BA51 04 (AY858037), IN DEN3 98 (AY858039), IN FW01 04 (AY858040), IN FW06 04 (AY858041), IN KJ30i 04 (AY858042), Indo_KJ71 04 (AY858044), ET_D3_Indonésia_NIID01 2005 (AB219137), ET_D3_Indonésia_NIID02 2005 (AB219138), ET_D3_Indonésia_NIID04 2005 (AB219139), IN PH86 04 (AY858045), IN PI64 04 (AY858046), IN Sleman 78 (AY648961), IN TB16 04 (AY858047), IN TB55i 04 (AY858048), Indo_73 (L11425), Indo_78 (L11426), Indo_85 (L11428), JP 73NIID 1973 (AB111085), Malasya 74 (L11429), Malasya 81 (L11427), D3_H_IMTSSA_MART_2000_1567 (AY099338), D3_H_IMTSSA_MART_2000_1706 (AY099339), D3_H_IMTSSA_MART_1999_1243 (AY099337), MG 20 2004 (EF625835), MEX6097_95 (AY146763), 6584_YUCATAN_MX 96 (DQ341203), Nicaragua 94 (AY702033), Panama 94 (DQ341209), Philip 56 H87 (L11423), Philp_05_0508aTw (DQ518673), Philp_96_9609aTw (DQ518668), Philp_98_9808aTw (DQ518671), Philp_98_9809aTw (DQ518669), PtoRico 63 (L11433), D3PY AS10 03 (DQ118883), SAMOA_86 (L11435), SOMALIA 93 S142 (DQ341208), SriLan 99 9912a (DQ518679), D3_H_IMTTSSA_Sri_2000_1266 (AY099336), SriLanka 81 (L11431), SriLanka 85 (L11436), SriLanka 89 (L11437), SriLanka 91 (L11438), Venez_C02 003_Maracay_2001 (DQ367720), Venez C23 009 Maracay_2001 (DQ367721), Venz_LARD5990_00 (AY146764), In_98901437 DSS DV_3_98 (AB189126), In_98901517 DHF DV_3_98 (AB189127), In_98901403 DSS DV_3_98 (AB189125), NAMRU_2 98901620 (AY265857), Tw_05_812KH0508a_Tw (DQ518672), ET_SV0171_05 (DQ453974), In_den3_88 (AY858038), Thail_D88_303_88 (AY145714), In_98902890 DF DV_3_98 (AB189128), 95TW466_95(DQ675519), Tw_94_813KH9408a_Tw (DQ518667), In_InJ_I6_82 (DQ401694), PF92_4190_92 (AY744684), Taiwan_739079A (AY776329), BR_D3BR_ST14_04 (DQ118882), PY_D3PY_AS12_02 (DQ118884), Cuba580_01 (AY702030), 6883_YUCATAN_MX_97 (DQ341204), 4841_YUCATAN_MX_95 (DQ341202), Ja_00_28_1HuNIID_00 (AB111081), PtoRico_77_1339 (AY146761), Tahiti_65 (L11439), ThD3_1687_98 (AY676348), ThD3_0115_99 (AY676387), ThD3_1959_01 (AY676402), ThD3_0328_02 (AY676383), ThD3_0989_00 (AY676414), ThD3_0077_98 (AY676389), ThD3_0654_01 (AY676394), ThD3_0111_02 (AY676420), ThD3_0188_91 (AY676367), ThD3_0182_96 (AY676369), Thail_03_0308a_Tw (DQ518660), TW_05_807KH0509a_Tw (DQ518659), VietN_BID V1018_2006 (EU482462), Thal_D93_044_93 (AY145720), Ja_00_40_1HuNIID_00 (AB111082), Ja_96_17_1HuNIID_96(AB111084), BDH_Apu_01 (AY656672), Thail_D92_423_92 (AY145718), Thail_D94_283_94 (AY145723), Thail_D95_0014 _95(AY145724), Thail_D97_0144_97 (AY145729), Thail_D93_674 _93 (AY145721), Thail_D94_122 _94(AY145722), Thail_D97_0291 _97(AY145730), Thail_D95_0400 _95 (AY145725), Ja_00_27_1HuNIID_00 (AB111080), BDH02_1_02 (AY496871), Myan_05_0508a_Tw, DQ518666), Mal_LN7933_94 (AY338494), Ma_LN2632_93 (AF147459), Sing_8120_95 (AY766104), ThD3_0029_90 (AY676421), ThD3_0183_85 (AY676368), Thail_87_1384_87 (AF533079), Thail_D91_538_91 (AY145717), Thail_D92_431_92 (AY145719), ThD3_0065_86 (AY676354), ThD3_0040_80 (AY676359), 98TW182_98 (DQ675520), Thail_PaH881_88 (AF349753), ThD3_0046_83 (AY676358), Thail_D89_273_89 (AY145715), ThD3_0137_84 (AY676371), ThD3_0059_81 (AY676356), ThD3_285M_77 (AY676384), ThD3_0059_82 (AY676355), ThD3_0033_74 (AY676360), 1503_YUCATAN_MX_84_D4 (DQ341212), JAM1983_D2 (AY484605), ThD1_0127_80 _D1 (AY732411).
pone.0007299.g001.png
Bayesian phylogenetic trees derived from 154 global samples of DENV-3 E gene partial sequences (1023 nucleotides) inferred with MrBayes program.
The posterior probabilities are expressed in percent and indicated at important nodes. DENV-1 (ThD1_0127_80_D4, AY732411), DENV-2 (JAM1983_D2, AY484605) and DENV-4 (1503_YUCATAN_MX_84_D4, DQ341212) were used as outgroup. Horizontal branch lengths are drawn to scale. Aligned sequences were analyzed in the MrModeltest 2.3 program to identify the best fit-model of nucleotide substitution for Bayesian phylogenetic reconstruction [23]. The nucleotide substitution model used was under a General Time Reversible model of nucleotide substitution with gamma-distributed rate variation (G = 1.2411) and a proportion of invariable sites (I = 0.3656) (GTR+G+I), using Akaike's Information Criterion (AIC) [24]. Five runs of 4 chains each (one cold and tree heated, temperature = 0.20) were run for 1.5×106 generations, with a burn-in of 6000 generations. Characteristic amino acid substitutions at important nodes are indicated. GenBank accession numbers: BH 16 2003 (EF625832), BH 19 2003 (EF625833), BH 24 2003 (EF625834), BR 00 68784 (AY038605), D3BR RP1 03 (DQ118877), BR74886 02 (AY679147), China 80 2 (AF317645), Cuba21 02 (AY702031), D3BR PV7 03 (EU570161), BR DEN3 RO1 02 (EF629373), BR DEN3 RO2-02 (EF629373), ET ET209 00 (EF440434), ET_D3_Hu_TL129NIID_2005 (AB214882), ET_D3_Hu_TL018NIID_2005 (AB214879), ET_D3_OPD007NIID 2005 (AB219131), ET SV0153 05 (DQ453981), ET SV0160 05 (DQ453980), ET SV0174 05 (DQ453973), ET SV0177 05 (DQ453972), ET SV0193 05 (DQ453970), ET SV0194 05 (DQ453969), ET_D3_TL029NIID_2005 (AB214880), Fiji 92 (L11422), PF89 27643 89 (AY744677), PF89 320219 89 (AY744678), PF90 3050 90 (AY744679), PF90 3056 90 (AY744680), PF90 6056 90 (AY744681), PF92 2956 92 (AY744682), PF92 2986 92 (AY744683), PF94 136116 94 (AY744685), India 84 (L11424), Indo0312a TW 03 (DQ518677), Indo0508a_TW (DQ518678), IN 9108a_Tw 91 (DQ518674), IN 9909a_Tw 99 (DQ518675), IN BA51 04 (AY858037), IN DEN3 98 (AY858039), IN FW01 04 (AY858040), IN FW06 04 (AY858041), IN KJ30i 04 (AY858042), Indo_KJ71 04 (AY858044), ET_D3_Indonésia_NIID01 2005 (AB219137), ET_D3_Indonésia_NIID02 2005 (AB219138), ET_D3_Indonésia_NIID04 2005 (AB219139), IN PH86 04 (AY858045), IN PI64 04 (AY858046), IN Sleman 78 (AY648961), IN TB16 04 (AY858047), IN TB55i 04 (AY858048), Indo_73 (L11425), Indo_78 (L11426), Indo_85 (L11428), JP 73NIID 1973 (AB111085), Malasya 74 (L11429), Malasya 81 (L11427), D3_H_IMTSSA_MART_2000_1567 (AY099338), D3_H_IMTSSA_MART_2000_1706 (AY099339), D3_H_IMTSSA_MART_1999_1243 (AY099337), MG 20 2004 (EF625835), MEX6097_95 (AY146763), 6584_YUCATAN_MX 96 (DQ341203), Nicaragua 94 (AY702033), Panama 94 (DQ341209), Philip 56 H87 (L11423), Philp_05_0508aTw (DQ518673), Philp_96_9609aTw (DQ518668), Philp_98_9808aTw (DQ518671), Philp_98_9809aTw (DQ518669), PtoRico 63 (L11433), D3PY AS10 03 (DQ118883), SAMOA_86 (L11435), SOMALIA 93 S142 (DQ341208), SriLan 99 9912a (DQ518679), D3_H_IMTTSSA_Sri_2000_1266 (AY099336), SriLanka 81 (L11431), SriLanka 85 (L11436), SriLanka 89 (L11437), SriLanka 91 (L11438), Venez_C02 003_Maracay_2001 (DQ367720), Venez C23 009 Maracay_2001 (DQ367721), Venz_LARD5990_00 (AY146764), In_98901437 DSS DV_3_98 (AB189126), In_98901517 DHF DV_3_98 (AB189127), In_98901403 DSS DV_3_98 (AB189125), NAMRU_2 98901620 (AY265857), Tw_05_812KH0508a_Tw (DQ518672), ET_SV0171_05 (DQ453974), In_den3_88 (AY858038), Thail_D88_303_88 (AY145714), In_98902890 DF DV_3_98 (AB189128), 95TW466_95(DQ675519), Tw_94_813KH9408a_Tw (DQ518667), In_InJ_I6_82 (DQ401694), PF92_4190_92 (AY744684), Taiwan_739079A (AY776329), BR_D3BR_ST14_04 (DQ118882), PY_D3PY_AS12_02 (DQ118884), Cuba580_01 (AY702030), 6883_YUCATAN_MX_97 (DQ341204), 4841_YUCATAN_MX_95 (DQ341202), Ja_00_28_1HuNIID_00 (AB111081), PtoRico_77_1339 (AY146761), Tahiti_65 (L11439), ThD3_1687_98 (AY676348), ThD3_0115_99 (AY676387), ThD3_1959_01 (AY676402), ThD3_0328_02 (AY676383), ThD3_0989_00 (AY676414), ThD3_0077_98 (AY676389), ThD3_0654_01 (AY676394), ThD3_0111_02 (AY676420), ThD3_0188_91 (AY676367), ThD3_0182_96 (AY676369), Thail_03_0308a_Tw (DQ518660), TW_05_807KH0509a_Tw (DQ518659), VietN_BID V1018_2006 (EU482462), Thal_D93_044_93 (AY145720), Ja_00_40_1HuNIID_00 (AB111082), Ja_96_17_1HuNIID_96(AB111084), BDH_Apu_01 (AY656672), Thail_D92_423_92 (AY145718), Thail_D94_283_94 (AY145723), Thail_D95_0014 _95(AY145724), Thail_D97_0144_97 (AY145729), Thail_D93_674 _93 (AY145721), Thail_D94_122 _94(AY145722), Thail_D97_0291 _97(AY145730), Thail_D95_0400 _95 (AY145725), Ja_00_27_1HuNIID_00 (AB111080), BDH02_1_02 (AY496871), Myan_05_0508a_Tw, DQ518666), Mal_LN7933_94 (AY338494), Ma_LN2632_93 (AF147459), Sing_8120_95 (AY766104), ThD3_0029_90 (AY676421), ThD3_0183_85 (AY676368), Thail_87_1384_87 (AF533079), Thail_D91_538_91 (AY145717), Thail_D92_431_92 (AY145719), ThD3_0065_86 (AY676354), ThD3_0040_80 (AY676359), 98TW182_98 (DQ675520), Thail_PaH881_88 (AF349753), ThD3_0046_83 (AY676358), Thail_D89_273_89 (AY145715), ThD3_0137_84 (AY676371), ThD3_0059_81 (AY676356), ThD3_285M_77 (AY676384), ThD3_0059_82 (AY676355), ThD3_0033_74 (AY676360), 1503_YUCATAN_MX_84_D4 (DQ341212), JAM1983_D2 (AY484605), ThD1_0127_80 _D1 (AY732411).