Cand. Korarchaeum cryptofilum OPF8
KORARCHAEOTA
100
99
98
100
100
69
Ignisphaera aggregans DSM 17230
Thermosphaera aggregans DSM 11486
100
Desulfurococcus kamchatkensis 1221n
100
Desulfurococcus mucosus DSM 2162
100
99
Hyperthermus butylicus DSM 5456
100
Pyrolobus fumarii 1A
Ignicoccus hospitalis KIN4
96
Desulfurococcales
Aeropyrum pernix K1
83
Acidilobus saccharovorans 345 15
100
100
Sulfolobales
Staphylothermus marinus F1
98
99
100
100
Acidilobus saccharovorans 345 15
9
Ignicoccus hospitalis KIN4
99
100
Desulfurococcus kamchatkensis 1221
100
Thermosphaera aggregans DSM 11486
Staphylothermus marinus F1
100
75
Thermoproteus neutrophilus V24Sta
Pyrobaculum islandicum DSM 4184
99
Thermoproteus tenax Kra 1
Ignisphaera aggregans DSM 17230
Thermofilum pendens Hrk 5
Thermoproteales
Vulcanisaeta moutnovskia 768 28
Caldiarchaeum subterraneum
Cenarchaeum symbiosum A
100
Nitrosopumilus maritimus SCM1
100
Nitrosoarchaeum koreensis MY1
100
Nitrosoarchaeum limnia SFB1
100
Nanoarchaeum equitans Kin4M
100
Nst1
AIGARCHAEOTA
Caldivirga maquilingensis IC 167
NANOARCHAEOTA
Cenarchaeum symbiosum A
Caldiarchaeum subterraneum
Methanobrevibacter ruminantium M1
100
100
Methanothermobacter marburgensis Marburg
100
Methanobacterium SWAN 1 uid67359
Methanobacterium AL 21 uid63623
100
100
Methanosphaera stadtmanae DSM 3091
Methanothermus fervidus DSM 2088
Methanothermococcus okinawensis IH1
100
Methanococcus maripaludis X1
Methanococcus aeolicus Nankai 3
Methanococcus maripaludis C5
100
100
Methanococcus maripaludis C6
99
94
Methanococcus maripaludis C7
100
95
96 100
Ferroplasma acidarmanus fer1
Methanocaldococcus jannaschii DSM 2661
70
100
Methanocaldococcus FS406 22
95
100
Methanocaldococcus fervens AG86
Archaeoglobus profundus DSM 5631
Archaeoglobus fulgidus DSM 4304
92
Halogeometricum borinquense DSM 11551
100 97
Haloquadratum walsbyi DSM 16790
Halorubrum lacusprofundi ATCC 49239
halophilic archaeon DL31
99
100
99
Halalkalicoccus jeotgali B3
99
Halopiger xanaduensis SH
Natrialba magadii ATCC 43099
100
Haloterrigena turkmenica DSM 5511
67
Natronomonas pharaonis DSM 2160
99 98
Halorhabdus utahensis DSM 12940
Halomicrobium mukohataei DSM 12286
100
Haloarcula hispanica ATCC 33960
100
42
100
Methanocaldococcus vulcanius M7
Methanocaldococcus infernus ME
Methanocorpusculum labreanum Z
100
Candidatus Methanoregula boonei 6A8
Methanosphaerula palustris E1 9c
68
99
Methanoculleus marisnigri JR1
Methanoplanus petrolearius DSM 11571
17
Methanococcoides burtonii DSM 6242
19
100
Methanosalsum zhilinae DSM 4017
Methanohalobium evestigatum Z 7303
100
98
100
100
Methanosaeta thermophila PT
100
uncultured methanogenic archaeon RC I
Halobacterium salinarum R1
Methanocella paludicola SANAE
100
Methanocorpusculum labreanum Z
1
99
Halobacterium NRC 1
Halorhabdus utahensis DSM 12940
83
Methanospirillum hungatei JF 1
96 100
Methanoplanus petrolearius DSM 11571
Methanocella paludicola SANAE
84
100
100
100
100
Methanosarcina barkeri Fusaro
10095
Methanosarcina acetivorans C2A
Methanohalophilus mahii DSM 5219
Methanosalsum zhilinae DSM 4017
99
99 6
100
100
Methanobacterium AL 21
Archaeoglobus profundus DSM 5631
100
Ferroglobus placidus DSM 10642
100
Thermoplasma volcanium GSS1
Methanobrevibacter smithii ATCC 35061
Thermococcus AM4
100
79
Thermococcus gammatolerans EJ3
100
96
Thermococales
95
Pyrococcus furiosus DSM 3638
100
100
87
0.2
Thermococcus onnurineus NA1
99
Pyrococcus yayanosii CH1
100
Thermococcus kodakarensis KOD1
Thermococcus 4557
Thermococcus 4557
Thermococcus kodakarensis KOD1
Thermococcus AM4
89
100
Thermococcus onnurineus NA1
100
Thermococcus gammatolerans EJ3
100
Thermococcus sibiricus MM 739
93
Thermoplasma acidophilum DSM 1728
Aciduliprofundum boonei T469
Methanothermobacter thermautotrophicus Delta H
Thermococcus barophilus MP
72
100
100
100
Methanothermobacter marburgensis Marburg
100
Picrophilus torridus DSM 9790
100
Methanobrevibacter ruminantium M1
100
Ferroplasma acidarmanus fer1
100
Methanosphaera stadtmanae DSM 3091
100
Haloferax volcanii DS2
Archaeoglobus fulgidus DSM 4304
76
Methanobacterium SWAN 1
99
Haloquadratum walsbyi DSM 16790
Halogeometricum borinquense DSM 11551
Archaeoglobus veneficus SNP6
29
Methanopyrus kandleri AV19
Methanothermus fervidus DSM 2088
99
halophilic archaeon DL31
100
99
Methanohalobium evestigatum Z 7303
91
Natrialba magadii ATCC 43099
Halalkalicoccus jeotgali B3
Halorubrum lacusprofundi ATCC 49239
Methanococcoides burtonii DSM 6242
100
Haloterrigena turkmenica DSM 5511
Halopiger xanaduensis SH 6
86
Methanosarcina mazei Go1
100
Halomicrobium mukohataei DSM 122
100
Methanosaeta concilii GP6
100
Haloarcula hispanica ATCC 33960
87
Methanosaeta thermophila PT
96
Haloarcula marismortui ATCC 430
100
uncultured methanogenic archaeon RC I
100
Natronomonas pharaonis DSM 2160
63
20
Methanosphaerula palustris E1 9c
100
Halobacterium salinarum R1
0
Methanoregula boonei 6A8
88
81
100
Methanosarcina barkeri Fusaro
Methanosaeta concilii GP6
55
Haloarcula marismortui ATCC 43049
Methanosarcina mazei Go1
Methanosarcina acetivorans C2A
99
Methanoculleus marisnigri JR1
100
75
Methanohalophilus mahii DSM 5219
96
Halobacterium NRC 1
100
Methanospirillum hungatei JF 1
100 76
EURYARCHAEOTA
100
EURYARCHAEOTA
Haloferax volcanii DS2
100
97
Archaeoglobus veneficus SNP6
100
Methanococcus voltae A3
Methanotorris igneus Kol 5
Ferroglobus placidus DSM 10642
100
Methanococcus maripaludis C6
Methanococcus vannielii SR
100
Thermoplasma volcanium GSS1
Picrophilus torridus DSM 9790
100
Methanococcus maripaludis C5
Methanococcus maripaludis C7
100
Thermoplasma acidophilum DSM 1728
100
Methanococcus maripaludis S2
100
Aciduliprofundum boonei T469
100
Methanococcus maripaludis XI
89
100
Methanococcus aeolicus Nankai 3
100
100
100
Methanothermococcus okinawensis IH1
100
THAUMARCHAEOTA
AIGARCHAEOTA
Methanothermobacter thermautotrophicus Delta H
Methanococcus vannielii SB
100
Methanobrevibacter smithii ATCC 35061
100
47
Methanococcus maripaludis S2
100
Nitrosoarchaeum koreensis MY1
Nitrosopumilus maritimus SCM1
100
Methanococcus voltae A3
100
Nitrosoarchaeum limnia SFB1
100
100
100
Methanotorris igneus Kol 5
100
Vulcanisaeta moutnovskia 768 28
100
Methanocaldococcus jannaschii DSM 2661
98
Thermoproteales
Vulcanisaeta distributa DSM 14429
77
THAUMARCHAEOTA
Methanocaldococcus vulcanius M7
100
Pyrobaculum arsenaticum DSM 13514
Pyrobaculum aerophilum IM2
99
Methanocaldococcus FS406 22
90
Pyrobaculum islandicum DSM 4184
95
100
Methanocaldococcus fervens AG86
100
Thermoproteus neutrophilus V24Sta
100
99
Methanocaldococcus infernus ME
100
Pyrobaculum calidifontis JCM 11548
98
Caldivirga maquilingensis IC 167
100
Thermoproteus uzoniensis 768 20
100
94
Vulcanisaeta distributa DSM 14429
100
Thermoproteus tenax Kra 1
100
Thermoproteus uzoniensis 768 20
100
100
Desulfurococcales
Staphylothermus hellenicus DSM 12710
100
Pyrobaculum arsenaticum DSM 13514
100
100
Desulfurococcus mucosus DSM 2162
100
Pyrobaculum aerophilum IM2
91
Aeropyrum pernix K1
100
99
Sulfolobales
Pyrolobus fumarii 1A
Hyperthermus butylicus DSM 5456
99
100
Pyrobaculum calidifontis JCM 11548
99
KORARCHAEOTA
Acd1
100
Thermofilum pendens Hrk 5
100
Metallosphaera sedula DSM 5348
Metallosphaera cuprina Ar 4
Acidianus hospitalis W1
Sulfolobus islandicus M 16 4
Sulfolobus islandicus M 16 27
99 Sulfolobus islandicus M 14 25
Sulfolobus islandicus L D 8 5
Sulfolobus islandicus L S 2 15
10091 Sulfolobus islandicus Y N 15 51
Sulfolobus islandicus Y G 57 14
Sulfolobus solfataricus P2
Sulfolobus tokodaii 7
Sulfolobus acidocaldarius DSM 639
100
Staphylothermus hellenicus DSM 12710
100
100
Methanopyrus kandleri AV19
85
NANOARCHAEOTA
CRENARCHAEOTA
99
Nst1
Cand. Korarchaeum cryptofilum OPF8
CRENARCHAEOTA
Sulfolobus acidocaldarius DSM 639
Sulfolobus tokodaii 7
Sulfolobus solfataricus P2
Sulfolobus islandicus M 16 27
100
Sulfolobus islandicus L D 8 5
100 Sulfolobus islandicus L S 2 15
100
Sulfolobus islandicus Y G 57 14
Sulfolobus islandicus Y N 15 51
85
Sulfolobus islandicus M 14 25
Sulfolobus islandicus M 16 4
Acidianus hospitalis W1
Metallosphaera cuprina Ar 4
100
Metallosphaera sedula DSM 5348
Nanoarchaeum equitans Kin4M
100
Acd1
100
100
Pyrococcus horikoshii OT3
Pyrococcus abyssi GE5
100
Pyrococcus horikoshii OT3
99
Pyrococcus NA2 uid66551
100
Pyrococcus abyssi GE5
Thermococales
Pyrococcus furiosus DSM 3638
Pyrococcus yayanosii CH1
Thermococcus barophilus MP
Thermococcus sibiricus MM 739
Pyrococcus NA2
43 ribosomal proteins
(6527 positions)
91
0.1
4 subunits RNA polymerase
(2629 positions)
Additional file 3. Maximum likelihood phylogenies of the Archaea based on concatenated ribosomal protein gene sequences
and RNA polymerase subunits.