b16537 Natronomonas pharaonis DSM2160

1. Supplementary figure 1A 75 b16537 Natronomonas pharaonis DSM2160 57 b13618 Halomicrobium mukohataei DSM12286 b13621 Halorhabdus utahensis DSM12940 100 b13496 Natrialba magadii ATCC43099 94 b16175 Haloterrigena turkmenica DSM5511 97 100 b16531 Halogeometricum borinquense DSM11551 b3658 Haloferax volcanii DS70 84 b16534 Haloquadratum walsbyi DSM16790 100 b13344 Halorubrum lacusprofundi ATCC49239 88 b7203 Haloarcula marismortui ATCC43049 b13623 Halorhabdus utahensis DSM12940 b13345 Halorubrum lacusprofundi ATCC49239 85 100 b3641 Haloferax volcanii DS70 86 60 b16529 Halogeometricum borinquense DSM11551 63 b3673 Halobacterium sp. NRC-1 Halobacteriales 100 b16177 Haloterrigena turkmenica DSM5511 100 b13495 Natrialba magadii ATCC43099 b13622 Halorhabdus utahensis DSM12940 78 b13620 Halomicrobium mukohataei DSM12286 67 57 b16535 Natronomonas pharaonis DSM2160 b16532 Haloquadratum walsbyi DSM16790 100 83 b3640 Haloferax volcanii b16530 Halogeometricum borinquense DSM11551 b10356 Halorubrum lacusprofundi ATCC49239 72 b3659 Halobacterium salinarum NRC-1 100 b13497 Natrialba magadii ATCC43099 68 b16176 Haloterrigena turkmenica DSM5511 68 83 b16536 Natronomonas pharaonis DSM2160 b13619 Halomicrobium mukohataei DSM12286 100 100 b16510 Haloarcula marismortui ATCC43049 100 b13624 Halorhabdus utahensis DSM12940 b16533 Haloquadratum walsbyi DSM16790 b6388 Uncultured marine group II euryarchaeote b15788 Candidatus Methanoregula boonei 6A8 100 78 b15786 Candidatus Methanoregula boonei 6A8 78 b12720 Methanosphaerula palustris E1-9c b10034 Methanocorpusculum labreanum Z 75 b9320 Methanoculleus marisnigri JR1 b7758 Methanospirillum hungatei JF-1 95 b4670 Methanosarcina mazei Goe1 100 100 Euryarchaeota b4666 Methanosarcina acetivorans C2A 100 b5708 Methanosarcina barkeri fusaro b5053 Methanococcoides burtonii DSM6242 90 b4672 Methanosarcina mazei Goe1 100 b4664 Methanosarcina acetivorans C2A 91 Methanomicrobiales b5700 Methanosarcina barkeri fusaro b5052 Methanococcoides burtonii DSM6242 100 100 b4665 Methanosarcina acetivorans C2A 100 b4671 Methanosarcina mazei Goe1 b5707 Methanosarcina barkeri fusaro 86 b9321 Methanoculleus marisnigri JR1 58 50 b12721 Methanosphaerula palustris E1-9c 89 b15784 Candidatus Methanoregula boonei 6A8 b10033 Methanocorpusculum labreanum Z 100 52 91 b7759 Methanospirillum hungatei JF-1 b15785 Candidatus Methanoregula boonei 6A8 86 b8459 Methanothrix thermophila PT b8460 Methanothrix thermophila PT 72 b8458 Methanothrix thermophila PT Methanopyrales b3678 Methanopyrus kandleri AV19 77 b15782 Methanococcus maripaludis C6 b10133 Methanococcus maripaludis C7 100 b9969 Methanococcus maripaludis C5 93 b5023 Methanococcus maripaludis strain S2 100 b10040 Methanococcus vannielii SB 92 b16538 Methanococcus voltae A3 Methanococcales 100 b3649 Methanothermococcus thermolithotrophicus DSM2095 b15789 Methanococcus aeolicus Nankai-3 100 62 b3672 Methanocaldococcus jannaschii DSM2661 100 b14367 Methanocaldococcus fervens AG86 100 b14497 Methanocaldococcus vulcanius M7 82 Methanocaldococcus infernus ME 100 b16515 Methanobrevibacter ruminantium M1 92 b15388 Methanobrevibacter smithii DSM2374 55 b16513 Methanosphaera stadtmanae DSM3091 100 Methanobacteriales 100 b16514 Methanobrevibacter ruminantium M1 90 b15387 Methanobrevibacter smithii DSM2374 81 b16512 Methanosphaera stadtmanae DSM3091 Nanoarchaeota b4788 Nanoarchaeum equitans Kin4-M 90 b9343 Uncultured Euryarchaeote sp. Alv-FOS5 0.1

2. Supplementary figure 1A (continued) 100 Methanobacteriales b3642 Methanothermobacter thermoautotrophicum Delta H b3643 Methanothermobacter thermoautotrophicum Delta H 99 b12728 Thermococcus sp. AM4 100 b14185 Thermococcus gammatolerans EJ3 76 b16511 Thermococcus onnurineus NA1 96 100 b3631 Thermococcus kodakaraensis KOD1 85 b12727 Thermococcus sp. AM4 87 b14186 Thermococcus gammatolerans EJ3 100 Thermococcales b3650 Thermococcus kodakaraensis KOD1 95 b12692 Thermococcus onnurineus NA1 100 b3677 Pyrococcus furiosus DSM3638 100 b3648 Pyrococcus horikoshii OT3 100 b3668 Pyrococcus abyssi GE5 b4070 Thermococcus litoralis 100 b16539 Thermococcus sibiricus MM739 87 b16540 Thermococcus sibiricus MM739 b4069 Thermococcus litoralis 60 Euryarchaeota b12533 Thermococcus barophilus MP 100 b12534 Thermococcus barophilus MP 55 b15277 Ferroglobus placidus DSM10642 100 Archaeoglobales 100 b15278 Ferroglobus placidus DSM10642 b16179 Archaeoglobus profundus DSM5631 72 b16178 Archaeoglobus profundus DSM5631 100 b3644 Archaeoglobus fulgidus DSM4304 100 b3661 Archaeoglobus fulgidus DSM10642 100 b5705 Ferroplasma acidarmanus DR1 70 Thermoplasmatales b5504 Picrophilus torridus DSM9790 100 b3674 Thermoplasma acidophilum DSM1728 100 99 b3796 Thermoplasma volcanium GSS1 100 b3660 Thermoplasma acidophilum DSM1728 b3797 Thermoplasma volcanium GSS1 98 b5706 Ferroplasma acidarmanus DR1 b5503 Picrophilus torridus DSM9790 94 100 b12538 Aciduliprofundum boonei T469 Thaumarchaeota b12539 Aciduliprofundum boonei T469 76 b10386 Candidatus Nitrosopumilus maritimus SCM1 100 b10385 Candidatus Nitrosopumilus maritimus SCM1 100 b9532 Cenarchaeum symbiosum A 100 76 b9531 Cenarchaeum symbiosum A b16522 Sulfolobus islandicus L.D.8.5 100 b3632 Sulfolobus shibatae DSM5389 99 Sulfolobales b3664 Sulfolobus solfataricus P2 80 b14379 Sulfolobus solfataricus 98/2 100 b4035 Acidianus tengchongenses s5 100 98 99 b3653 Sulfolobus acidocaldarius DSM639 b3671 Sulfolobus tokodaii strain 7 98 b3665 Sulfolobus solfataricus P2 b14377 Sulfolobus solfataricus 98/2 100 98 b16524 Sulfolobus islandicus L.D.8.5 90 b3670 Sulfolobus tokodaii strain 7 Desulfurococcales 100 b9565 Metallosphaera sedula DSM5348 100 b12676 Staphylothermus marinus F1 b16432 Staphylothermus hellenicus DSM12710 81 64 b12778 Desulfurococcus kamchatkensis 1221n 95 b3646 Pyrodictium occultium PL-19 91 b16518 Hyperthermus butylicus DSM5456 100 100 b3651 Aeropyrum pernix K1 Thermoproteales b16516 Ignicoccus hospitalis KIN4/I 52 b3676 Pyrobaculum aerophilum IM2 Crenarchaeota b16528 Pyrobaculum islandicum DSM4184 b10704 Thermoproteus neutrophilus V24Sta 100 100 b15794 Pyrobaculum calidifontis JCM11548 100 b16525 Caldivirga maquilingensis IC-167 Sulfolobales b9318 Thermofilum pendens Hrk 5 100 58 93 b9319 Thermofilum pendens Hrk 5 86 b14378 Sulfolobus solfataricus 98/2 100 b3663 Sulfolobus solfataricus P2 100 b16523 Sulfolobus islandicus L.D.8.5 100 100 b3669 Sulfolobus tokodaii strain 7 b3654 Sulfolobus acidocaldarius DSM639 Desulfurococcales 100 b9564 Metallosphaera sedula DSM5348 87 b12779 Desulfurococcus kamchatkensis 1221n b3655 Desulfurococcus mobilis 65 b12677 Staphylothermus marinus F1 56 b16431 Staphylothermus hellenicus DSM12710 100 Thermoproteales b16519 Hyperthermus butylicus DSM5456 100 b3647 Pyrodictium occultium PL-19 b16517 Ignicoccus hospitalis KIN4/I 97 b3652 Aeropyrum pernix K1 Korarchaetoa b10703 Thermoproteus neutrophilus V24Sta b15793 Pyrobaculum calidifontis JCM11548 b3675 Pyrobaculum aerophilum IM2 b16527 Pyrobaculum islandicum DSM4184 b16526 Caldivirga maquilingensis IC-167 b12417 Korarchaeum cryptofilum OPF8 b12416 Korarchaeum cryptofilum OPF8 0.1

3. 81 Supplementary figure 1B b13618 Halomicrobium mukohataei DSM12286 60 b16537 Natronomonas pharaonis DSM2160 b13621 Halorhabdus utahensis DSM12940 100 b16175 Haloterrigena turkmenica DSM5511 82 b13496 Natrialba magadii ATCC43099 99 98 b16531 Halogeometricum borinquense DSM11551 b3658 Haloferax volcanii DS70 63 b16534 Haloquadratum walsbyi DSM16790 63 100 b13344 Halorubrum lacusprofundi ATCC49239 b7203 Haloarcula marismortui ATCC43049 b13623 Halorhabdus utahensis DSM12940 b13345 Halorubrum lacusprofundi ATCC49239 97 b3641 Haloferax volcanii DS70 b16529 Halogeometricum borinquense DSM11551 100 b13495 Natrialba magadii ATCC43099 b16177 Haloterrigena turkmenica DSM5511 98 b3673 Halobacterium salinarum NRC-1 Halobacteriales b13620 Halomicrobium mukohataei DSM12286 b13622 Halorhabdus utahensis DSM12940 b16535 Natronomonas pharaonis DSM2160 70 b16536 Natronomonas pharaonis DSM2160 b10356 Halorubrum lacusprofundi ATCC49239 93 b3640 Haloferax volcanii DS70 b16530 Halogeometricum borinquense DSM11551 58 b3659 Halobacterium salinarum NRC-1 100 91 b13497 Natrialba magadii ATCC43099 70 b16176 Haloterrigena turkmenica DSM5511 97 100 b13619 Halomicrobium mukohataei DSM12286 97 b16510 Haloarcula marismortui ATCC43049 b13624 Halorhabdus utahensis DSM12940 b16533 Haloquadratum walsbyi DSM16790 b16532 Haloquadratum walsbyi DSM16790 b6388 Uncultured marine group II euryarchaeote 71 b4664 Methanosarcina acetivorans C2A 100 b5700 Methanosarcina barkeri fusaro 99 b4672 Methanosarcina mazei Goe1 59 b5052 Methanococcoides burtonii DSM6242 100 b4671 Methanosarcina mazei Goe1 100 b4665 Methanosarcina acetivorans C2A Euryarchaeota b5707 Methanosarcina barkeri fusaro 59 b12721 Methanosphaerula palustris E1-9c 57 b9321 Methanoculleus marisnigri JR1 91 Methanomicrobiales b15784 Candidatus Methanoregula boonei 6A8 100 b7759 Methanospirillum hungatei JF-1 70 b10033 Methanocorpusculum labreanum Z b15785 Candidatus Methanoregula boonei 6A8 b8460 Methanothrix thermophila PT b8459 Methanothrix thermophila PT 99 b15788 Candidatus Methanoregula boonei 6A8 68 b15786 Candidatus Methanoregula boonei 6A8 60 b12720 Methanosphaerula palustris E1-9c 100 b10034 Methanocorpusculum labreanum Z b9320 Methanoculleus marisnigri JR1 b7758 Methanospirillum hungatei JF-1 100 b4670 Methanosarcina mazei Goe1 100 b4666 Methanosarcina acetivorans C2A 100 b5708 Methanosarcina barkeri fusaro b5053 Methanococcoides burtonii DSM6242 b8458 Methanothrix thermophila PT Methanopyrales b3678 Methanopyrus kandleri AV19 100 Methanobacteriales b3643 Methanothermobacter thermoautotrophicus Delta H b3642 Methanothermobacter thermoautotrophicus Delta H 92 b12728 Thermococcus sp. AM4 100 b14185 Thermococcus gammatolerans EJ3 b16511 Thermococcus onnurineus NA1 53 78 b3631 Thermococcus kodakaraensis KOD1 100 b3677 Pyrococcus furiosus DSM3638 100 b3648 Pyrococcus horikoshii OT3 b3668 Pyrococcus abyssi GE5 100 b12727 Thermococcus sp. AM4 68 Thermococcales b14186 Thermococcus gammatolerans EJ3 100 b3650 Thermococcus kodakaraensis KOD1 100 b12692 Thermococcus onnurineus NA1 100 b4069 Thermococcus litoralis 76 b16540 Thermococcus sibiricus MM739 b12533 Thermococcus barophilus MP 54 99 b16539 Thermococcus sibiricus MM739 b4070 Thermococcus litoralis 73 b12534 Thermococcus barophilus MP 0.1

4. Supplementary figure 1B (continued) 100 b16179 Archaeoglobus profundus DSM5631 67 b16178 Archaeoglobus profundus DSM5631 100 Archaeoglobales b15278 Ferroglobus placidus DSM10642 98 b15277 Ferroglobus placidus DSM10642 b3661 Archaeoglobus fulgidus DSM10642 82 b3644 Archaeoglobus fulgidus DSM4304 67 b9969 Methanococcus maripaludis C5 67 b5023 Methanococcus maripaludis strain S2 100 b15782 Methanococcus maripaludis C6 73 b10133 Methanococcus maripaludis C7 94 b10040 Methanococcus vannielii SB 94 Methanococcales b16538 Methanococcus voltae A3 99 b3649 Methanothermococcus thermolithotrophicus DSM2095 b15789 Methanococcus aeolicus Nankai-3 96 84 b14497 Methanocaldococcus vulcanius M7 100 b3672 Methanocaldococcus jannaschii DSM2661 100 b14367 Methanocaldococcus fervens AG86 63 b16885 Methanocaldococcus infernus ME Euryarchaeota 55 b15387 Methanobrevibacter smithii DSM2374 91 b16512 Methanosphaera stadtmanae DSM3091 b16514 Methanobrevibacter ruminantium M1 Methanobacteriales 64 83 b15388 Methanobrevibacter smithii DSM2374 91 b16515 Methanobrevibacter ruminantium M1 b16513 Methanosphaera stadtmanae DSM3091 Nanoarchaeota b4788 Nanoarchaeum equitans Kin4-M b9343 Uncultured Euryarchaeote sp. Alv-FOS5 100 b5706 Ferroplasma acidarmanus DR1 100 b5503 Picrophilus torridus DSM9790 100 b3660 Thermoplasma acidophilum 59 Thermoplasmatales b3797 Thermoplasma volcanium GSS1 82 b5705 Ferroplasma acidarmanus DR1 100 b5504 Picrophilus torridus DSM9790 88 100 b3796 Thermoplasma volcanium GSS1 b3674 Thermoplasma acidophilum DSM1728 b12538 Aciduliprofundum boonei T469 b12539 Aciduliprofundum boonei T469 64 b9531 Cenarchaeum symbiosum A 87 b9532 Cenarchaeum symbiosum A Thaumarchaeota 97 b10386 Candidatus Nitrosopumilus maritimus SCM1 b10385 Candidatus Nitrosopumilus maritimus SCM1 100 b14379 Sulfolobus solfataricus 98/2 100 b3664 Sulfolobus solfataricus P2 b16522 Sulfolobus islandicus L.D.8.5 b3632 Sulfolobus shibatae DSM5389 99 Sulfolobales b4035 Acidianus tengchongenses s5 54 b3671 Sulfolobus tokodaii strain 7 b3653 Sulfolobus acidocaldarius DSM639 100 b14377 Sulfolobus solfataricus 98/2 100 58 b3665 Sulfolobus solfataricus P2 90 b16524 Sulfolobus islandicus L.D.8.5 b3670 Sulfolobus tokodaii strain 7 90 b9565 Metallosphaera sedula DSM5348 100 b12676 Staphylothermus marinus F1 91 b16521 Staphylothermus hellenicus DSM12710 b12778 Desulfurococcus kamchatkensis 1221n 100 b16519 Hyperthermus butylicus DSM5456 81 b3647 Pyrodictium occultium PL-19 Desulfurococcales 100 b3646 Pyrodictium occultium PL-19 b16518 Hyperthermus butylicus DSM5456 84 67 b3651 Aeropyrum pernix K1 b16516 Ignicoccus hospitalis KIN4/I 99 b3652 Aeropyrum pernix K1 b16517 Ignicoccus hospitalis KIN4/I 80 Crenarchaeota b16528 Pyrobaculum islandicum DSM4184 84 b3676 Pyrobaculum aerophilum IM2 100 Thermoproteales b10704 Thermoproteus neutrophilus V24Sta 82 b15794 Pyrobaculum calidifontis JCM11548 82 b16525 Caldivirga maquilingensis IC-167 b9318 Thermofilum pendens Hrk 5 100 b3663 Sulfolobus solfataricus P2 100 b14378 Sulfolobus solfataricus 98/2 55 Sulfolobales b16523 Sulfolobus islandicus L.D.8.5 99 b3669 Sulfolobus tokodaii strain 7 100 b3654 Sulfolobus acidocaldarius DSM639 94 b9564 Metallosphaera sedula DSM5348 99 b3655 Desulfurococcus mobilis 84 b12779 Desulfurococcus kamchatkensis 1221n Desulfurococcales 100 b12677 Staphylothermus marinus F1 b16520 Staphylothermus hellenicus DSM12710 63 b15793 Pyrobaculum calidifontis JCM11548 52 b10703 Thermoproteus neutrophilus V24Sta 100 Thermoproteales b3675 Pyrobaculum aerophilum IM2 82 b16527 Pyrobaculum islandicum DSM4184 b16526 Caldivirga maquilingensis IC-167 b9319 Thermofilum pendens Hrk 5 Korarchaetoa b12416 Korarchaeum cryptofilum OPF8 b12417 Korarchaeum cryptofilum OPF8 0.1

5. Supplementary figure 1C 98 Halogeometricum borinquense DSM11551 99 Haloquadratum walsbyi DSM16790 Haloferax volcanii DS70 100 Haloterrigena turkmenica DSM5511 Natrialba magadii ATCC43099 Halobacteriales Halorhabdus utahensis DSM12940 Halobacterium salinarum NRC-1 Haloarcula marismortui ATCC43049 100 Halomicrobium mukohataei DSM12286 Halorubrum lacusprofundi ATCC49239 Natronomonas pharaonis DSM2160 99 Methanosarcina acetivorans C2A 100 100 Methanosarcina barkeri fusaro 100 Methanosarcina mazei Goe1 100 Methanococcoides burtonii DSM6242 Methanothrix thermophila PT 67 100 Candidatus Methanosphaerula palustris E1-9c Methanomicrobiales Candidatus Methanoregula boonei 6A8 89 Methanoculleus marisnigri JR1 100 Methanocorpusculum labreanum Z Methanospirillum hungatei JF-1 Methanobrevibacter smithii ATCC35061 Methanobrevibacter ruminantium M1 76 Methanobacteriales Methanosphaera stadtmanae DSM3091 Methanothermobacter thermoautotrophicum Delta H 100 Picrophilus torridus DSM9790 100 Ferroplasma acidarmanus DR1 Thermoplasmatales 100 Thermoplasma volcanium GSS1 Thermoplasma acidophilum DSM1728 66 Euryarchaeota Uncultured marine group II euryarchaeote Aciduliprofundum boonei T469 68 95 Methanococcus maripaludis C6 72 Methanococcus maripaludis S2 100 Methanococcus maripaludis C5 59 Methanococcus maripaludis C7 100 Methanococcus vannielii SB 90 Methanococcus voltae A3 100 Methanococcales Methanococcus aeolicus Nankai-3 Methanothermococcus thermolithotrophicus DSM2095 94 100 Methanocaldococcus jannaschii DSM2661 92 Methanocaldococcus fervens AG86 100 Methanocaldococcus vulcanius M7 Methanocaldococcus infernus ME 63 Thermococcus kodakaraensis KOD1 57 Thermococcus gammatolerans EJ3 98 Thermococcus onnurineus NA1 Thermococcus sp. AM4 Archaeoglobales 99 Thermococcus sibiricus MM739 64 Thermococcus litoralis 100 Thermococcus barophilus MP 100 Pyrococcus horikoshii OT3 100 Pyrococcus abyssi GE5 Pyrococcus furiosus DSM 3638 83 Methanopyrales Methanopyrus kandleri AV19 Nanoarchaeota Nanoarchaeum equitans Kin4-M 100 Ferroglobus placidus DSM10642 100 Thermococcales Archaeoglobus profundus DSM5631 Archaeoglobus fulgidus DSM4304 Uncultured Euryarchaeote sp. Alv-FOS5 Sulfolobus solfataricus 98/2 85 Sulfolobus solfataricus P2 100 Sulfolobus islandicus L.D.8.5 91 Sulfolobus shibatae DSM5389 Sulfolobales 100 Sulfolobus tokodaii strain 7 100 Sulfolobus acidocaldarius DSM639 100 Acidianus tengchongenses s5 Metallosphaera sedula DSM5348 100 Staphylothermus hellenicus DSM12710 99 83 Staphylothermus marinus F1 100 Desulfurococccus mobilis Crenarchaeota Desulfurococcus kamchatkensis 1221n Desulfurococcales 100 Hyperthermus butylicus DSM5456 80 Pyrodictium occultium PL-19 100 Aeropyrum pernix K1 Ignicoccus hospitalis KIN4/I Thermoproteus neutrophilus V24Sta 60 Pyrobaculum aerophilum IM2 100 Pyrobaculum islandicum DSM4184 100 Thermoproteales Pyrobaculum calidifontis JCM11548 97 Caldivirga maquilingensis IC-167 Thermofilum pendens Hrk 5 100 Nitrosopumilus maritimus SCM1 Thaumarchaeota Cenarchaeum symbiosum A Korarchaetoa Korarchaeum cryptofilum OPF8 0.1

6. Supplementary figure 2

7. Supplementary Figure 3

8. Supplementary figure 4A TCPREG B12 ** * TCPDRY E10 TCPREG F08 TCPDRY F07 ** TCPDRY E09 TCPDRY C06 TCPDRY F11 ** TR3 * TCPREG F01 ** TCPDRY B09 TCPDRY C05 ** tcpreg3 2 TCPREG C10 * tcpdry10 5 TCPDRY D02 tcpreg9 3 TCPDRY D08 * TCPDRY D11 ** TCPREG F11 ** TCPDRY B05 TCPDRY E12 ** * tcpreg7 2 ** TCPREG H11 * b16515 Methanobrevibacter ruminantium M1 TCPDRY H11 ** ** TCPREG E10 ** TCPDRY D12 TCPDRY E05 ** tcpreg4 2 ** TCPDRY G01 ** TCPREG H10 b15388 Methanobrevibacter smithii DSM2374 TD7 ** * TCPREG G02 tcpdry1 7 tcpreg2 12 TD6 TCPREG A11 ** tcpreg5 3 ** TD1 ** TCPDRY H09 b16513 Methanosphaera stadtmanae DSM3091 TCPDRY H07 * TR6 tcpreg11 4 tcpreg12 4 TCPDRY F06 TR2 ** TCPREG F03 TR8 TCPREG E03 TCPDRY B07 TCPDRY A11 ** TCPREG E11 TR5 tcpdry4 11 TCPDRY F03 TCPDRY G04 * TCPDRY B08 TCPREG G03 tcpdry7 2 * tcpdry2 2 * TCPDRY A07 * * tcpdry9 2 * TCPREG H06 TCPREG D12 tcpdry3 2 ** TR4 ** TCPREG A04 ** TCPDRY B11 ** b15387 Methanobrevibacter smithii DSM2374 * tcpreg8 2 * TCPREG H02 ** ** TCPDRY D01 ** TCPDRY G05 ** b16514 Methanobrevibacter ruminantium M1 b16512 Methanosphaera stadtmanae DSM3091 b4788 Nanoarchaeum equitans Kin4-M b9969 Methanococcus maripaludis C5 * b15782 Methanococcus maripaludis C6 * ** ** b5023 Methanococcus maripaludis strain S2 ** b10133 Methanococcus maripaludis C7 ** b10040 Methanococcus vannielii SB * b16538 Methanococcus voltae A3 b3649 Methanothermococcus thermolithotrophicus DSM2095 b15789 Methanococcus aeolicus Nankai-3 ** b3672 Methanocaldococcus jannaschii DSM2661 ** b14497 Methanocaldococcus vulcanius M7 ** ** b14367 Methanocaldococcus fervens AG86 Methanocaldococcus infernus ME b3642 Methanothermobacter thermoautotrophicum Delta H ** b3643 Methanothermobacter thermoautotrophicum Delta H b16178 Archaeoglobus profundus DSM5631 b12720 Methanosphaerula palustris E1-9c b9320 Methanoculleus marisnigri JR1 b15788 Candidatus Methanoregula boonei 6A8 ** * b15786 Candidatus Methanoregula boonei 6A8 * b10034 Methanocorpusculum labreanum Z b7758 Methanospirillum hungatei JF-1 b4666 Methanosarcina acetivorans C2A ** b4670 Methanosarcina mazei Goe1 ** ** b5708 Methanosarcina barkeri fusaro b5053 Methanococcoides burtonii DSM6242 b3640 Haloferax volcanii b9531 Cenarchaeum symbiosum A b3631 Thermococcus kodakaraensis KOD1 b3678 Methanopyrus kandleri AV19 b8458 Methanothrix thermophila PT b8459 Methanothrix thermophila PT b8460 Methanothrix thermophila PT b12721 Methanosphaerula palustris E1-9c * * b9321 Methanoculleus marisnigri JR1 * * b15784 Candidatus Methanoregula boonei 6A8 * b7759 Methanospirillum hungatei JF-1 * b10033 Methanocorpusculum labreanum Z b15785 Candidatus Methanoregula boonei 6A8 b4665 Methanosarcina acetivorans C2A ** ** b4671 Methanosarcina mazei Goe1 b5707 Methanosarcina barkeri fusaro b4664 Methanosarcina acetivorans C2A ** b5700 Methanosarcina barkeri fusaro ** b4672 Methanosarcina mazei Goe1 b5052 Methanococcoides burtonii DSM6242 b3674 Thermoplasma acidophilum DSM1728 b14379 Sulfolobus solfataricus 98/2 ** b12778 Desulfurococcus kamchatkensis 1221n b12416 Korarchaeum cryptofilum OPF8 0.1

9. Supplementary figure 4B ** TCPRA3 D04 TCPRA3 C05 tcprat13 7 * tcprat19 3 TCPRA3 F08 ** tcprat20 5 ** tcprat4 2 TCPRA3 G04 b16515 Methanobrevibacter ruminantium M1 * tcprat17 4 ** TCPRA3 H01 ** tcprat1 2 tcprat21 2 * ** tcprat3 2 ** tcprat6 3 * tcprat24 3 b15388 Methanobrevibacter smithii DSM2374 ** tcprat5 9 b16513 Methanosphaera stadtmanae DSM3091 tcprat14 5 * tcprat2 6 ** tcprat12 5 * tcprat18 4 * tcprat26 2 ** TCPRA4 C03 TCPRA3 A04 * tcprat15 2 ** TCPRA4 B08 b15387 Methanobrevibacter smithii DSM2374 ** TCPRA3 G05 * * TCPRA4 B04 tcpra25 11 tcprat23 5 ** ** tcprat9 14 ** TCPRA4 B11 b16514 Methanobrevibacter ruminantium M1 ** b16512 Methanosphaera stadtmanae DSM3091 b4788 Nanoarchaeum equitans Kin4-M * b5023 Methanococcus maripaludis strain S2 b9969 Methanococcus maripaludis C5 ** b15782 Methanococcus maripaludis C6 * b10133 Methanococcus maripaludis C7 ** b10040 Methanococcus vannielii SB * ** b16538 Methanococcus voltae A3 b3649 Methanothermococcus thermolithotrophicus DSM2095 * ** b14497 Methanocaldococcus vulcanius M7 ** b3672 Methanocaldococcus jannaschii DSM2661 ** ** b14367 Methanocaldococcus fervens AG86 Methanocaldococcus infernus ME b15789 Methanococcus aeolicus Nankai-3 ** b3643 Methanothermobacter thermoautotrophicum Delta H b3642 Methanothermobacter thermoautotrophicum Delta H b16178 Archaeoglobus profundus DSM5631 ** b15788 Candidatus Methanoregula boonei 6A8 * b15786 Candidatus Methanoregula boonei 6A8 * b12720 Methanosphaerula palustris E1-9c b7758 Methanospirillum hungatei JF-1 ** b9320 Methanoculleus marisnigri JR1 b10034 Methanocorpusculum labreanum Z ** b4670 Methanosarcina mazei Goe1 ** b4666 Methanosarcina acetivorans C2A ** b5708 Methanosarcina barkeri fusaro b5053 Methanococcoides burtonii DSM6242 b8458 Methanothrix thermophila PT b8460 Methanothrix thermophila PT b8459 Methanothrix thermophila PT b3678 Methanopyrus kandleri AV19 b3640 Haloferax volcanii b3631 Thermococcus kodakaraensis KOD1 b9531 Cenarchaeum symbiosum A * b5700 Methanosarcina barkeri fusaro * ** b4664 Methanosarcina acetivorans C2A ** b4672 Methanosarcina mazei Goe1 b5052 Methanococcoides burtonii DSM6242 ** b4665 Methanosarcina acetivorans C2A ** b4671 Methanosarcina mazei Goe1 b5707 Methanosarcina barkeri fusaro * b12721 Methanosphaerula palustris E1-9c * b9321 Methanoculleus marisnigri JR1 b15784 Candidatus Methanoregula boonei 6A8 * b7759 Methanospirillum hungatei JF-1 b10033 Methanocorpusculum labreanum Z b15785 Candidatus Methanoregula boonei 6A8 b3674 Thermoplasma acidophilum DSM1728 ** b12778 Desulfurococcus kamchatkensis 1221n b14379 Sulfolobus solfataricus 98/2 b12416 Korarchaeum cryptofilum OPF8 0.1

10. Supplementary figure 4C * 16Sreg9 3 16D1 16D8 16SREG C07 16D3 16Sdry2 21 ** 16Sreg5 5 16SDRY F01 * 16Sreg1 6 ** 16Sdry3 4 16D7 16SDRY H08 16D6 16SDRY D10 16Sreg8 3 * 16Sreg4 13 16Sdry1 17 16Sdry7 2 16SDRY B11 Methanobrevibacter smithii ATCC35061 16D2 * 16SREG E05 16D5 16R2 * 16D4 16Sreg2 2 * 16Sreg3 17 * 16Sdry8 4 * Methanobrevibacter ruminantium M1 16R7 * 16R6 ** 16SREG H12 * 16R3 16SREG G06 ** 16Sreg10 3 16SDRY G04 * 16SREG C09 16SREG H08 16SDRY G12 ** 16Sdry4 3 ** * 16SREG G02 Methanosphaera stadtmanae DSM3091 * 16SDRY A07 ** 16SDRY A05 * 16SDRY F08 16SREG E02 16SREG D02 16SREG E03 16SDRY C03 * 16SREG C01 16Sdry11 2 16SREG A07 ** 16SDRY A01 16SREG F05 16SREG D09 Methanothermobacter thermoautotrophicum Delta H 16SDRY E12 * Halogeometricum borinquense DSM11551 ** Haloferax volcanii Haloquadratum walsbyi DSM16790 Natronomonas pharaonis DSM2160 ** Natrialba magadii ATCC43099 * Haloterrigena turkmenica DSM5511 * ** Halobacterium sp. NRC-1 Halorhabdus utahensis DSM12940 * Halomicrobium mukohataei DSM12286 Haloarcula marismortui ATCC43049 Halorubrum lacusprofundi ATCC49239 * Methanosarcina barkeri fusaro ** ** Methanosarcina acetivorans C2A ** Methanosarcina mazei Goe1 Methanococcoides burtonii DSM6242 * Methanothrix thermophila PT * * Methanocorpusculum labreanum Z * Methanoculleus marisnigri JR1 * Candidatus Methanosphaerula palustris E1-9c Candidatus Methanoregula boonei 6A8 ** Methanospirillum hungatei JF-1 ** 16Sdry6 4 ** 16SDRY B09 16SDRY A02 ** Ferroplasma acidarmanus DR1 ** Picrophilus torridus DSM9790 ** ** Thermoplasma acidophilum DSM1728 ** Thermoplasma volcanium GSS1 Aciduliprofundum boonei T469 Uncultured marine group II euryarchaeote * Methanococcus maripaludis C7 ** Methanococcus maripaludis C5 * Methanococcus maripaludis C6 * Methanococcus maripaludis S2 Methanothermococcus thermolithotrophicus DSM2095 ** Methanococcus vannielii SB Methanococcus aeolicus Nankai-3 * Methanococcus voltae A3 * Methanocaldococcus fervens AG86 ** ** Methanocaldococcus jannaschii DSM2661 Methanocaldococcus vulcanius M7 Methanocaldococcus infernus ME Methanopyrus kandleri AV19 * Thermococcus kodakaraensis KOD1 * * Thermococcus onnurineus NA1 Thermococcus gammatolerans EJ3 ** * Thermococcus sp. AM4 Pyrococcus furiosus DSM 3638 ** Pyrococcus abyssi GE5 ** Pyrococcus horikoshii OT3 Thermococcus barophilus MP * ** Thermococcus sibiricus MM739 Thermococcus litoralis Nanoarchaeum equitans Kin4-M Uncultured Euryarchaeote sp. Alv-FOS5 ** Archaeoglobus profundus DSM5631 ** Ferroglobus placidus DSM10642 Archaeoglobus fulgidus DSM4304 ** Cenarchaeum symbiosum A Nitrosopumilus maritimus SCM1 ** Staphylothermus marinus F1 Staphylothermus hellenicus ** Desulfurococcus kamchatkensis 1221n * Desulfurococccus mobilis ** Hyperthermus butylicus DSM5456 ** Pyrodictium occultium PL-19 Ignicoccus hospitalis KIN4/I Aeropyrum pernix K1 * * Sulfolobus solfataricus P2 * ** Sulfolobus solfataricus 98/2 Sulfolobus islandicus L.D.8.5 * Sulfolobus shibatae DSM5389 * ** Sulfolobus tokodaii strain 7 Sulfolobus acidocaldarius DSM639 ** ** Metallosphaera sedula DSM5348 Acidianus tengchongenses s5 Thermoproteus neutrophilus V24Sta ** Pyrobaculum islandicum DSM4184 ** Pyrobaculum aerophilum IM2 * Pyrobaculum calidifontis JCM11548 Caldivirga maquilingensis IC-167 Thermofilum pendens Hrk 5 Korarchaeum cryptofilum OPF8 0.1

11. Supplementary figure 4D mcrdry7 7 * MCRREG F03 MCRREG F12 MCRREG C08 MCRREG G06 * mcrdry10 2 MCRDRY D10 MD7 ** mcrreg3 2 * mcrreg9 2 MCRREG E09 MCRDRY A03 MCRREG D05 * mcrreg6 2 MCRREG C10 MCRREG E02 MCRREG G04 MCRDRY F11 MCRREG B03 mcrdry4 2 ** * MCRDRY G05 MCRDRY B08 MCRREG D08 MR5 * ** MR1 MCRDRY E09 * MCRREG B05 * MCRREG E05 * mcrdry 1 4 MCRREG F01 MCRDRY E06 ** MCRDRY C03 MCRREG A06 * Methanobrevibacter smithii DSM2375 Methanobrevibacter smithii ATCC35061, alpha1 Methanobrevibacter smithii DSM2374 MCRDRY D11 MCRDRY G12 * MCRREG G05 MCRDRY H05 MR3 mcrreg11 6 MCRDRY C05 * MR7 mcrreg1 12 MR8 MCRREG B10 MCRDRY A02 MCRREG A03 MCRREG E03 MCRREG B12 MR4 mcrdry6 14 mcrreg4 9 * MCRDRY E01 * * MCRREG F09 ** * MCRREG G01 MCRDRY F10 MCRDRY G01 ** MD1 Methanobrevibacter ruminantium M1 ** mcrreg8 2 ** * MCRDRY H11 MCRREG C06 ** MR6 * MCRREG H08 MCRDRY B02 mcrreg10 5 ** MCRDRY A08 MCRREG D07 ** MD2 ** MCRREG C12 MCRDRY C02 MD6 mcrdry9 2 ** MD5 ** MCRDRY H03 mcrdry8 2 mcrreg7 6 MCRREG D04 * mcrdry 3 9 ** MCRREG F05 MCRDRY E05 MCRDRY F07 ** * Methanosphaera stadtmanae DSM3091 (mrtA) MD8 ** * Methanococcus maripaludis S2 * ** * MCRDRY E08 Methanococcus vannielii SB * Methanococcus maripaludis C5 Methanococcus maripaludis C7 * ** Methanococcus maripaludis C6 * Methanococcus voltae A3 Methanococcus aeolicus Nankai-3 Methanocaldococcus jannaschii DSM2661 * Methanocaldococcus fervens AG86 Methanocaldococcus vulcanius M7, alpha1 Methanocaldococcus vulcanius M7, alpha2 * Methanobrevibacter smithii ATCC35061, alpha2 * MCRREG H01 * Methanothermobacter thermautotrophicus str. Delta H ** MD3 MD4 mcrdry 2 1 ** MCRDRY E11 * MCRDRY D04 ** Methanocorpusculum labreanum Z, alpha1 Methanocorpusculum labreanum Z, alpha2 ** Methanoculleus marisnigri JR1, alpha1 Methanoculleus marisnigri JR1, alpha2 Methanospirillum hungatei JF-1 * Candidatus Methanoregula boonei 6A8 ** Candidatus Methanosphaerula palustris E1-9c ** MCRREG H03 Methanosarcina acetivorans C2A Methanosarcina mazei Go1 Methanosarcina barkeri str. fusaro Methanococcoides burtonii DSM6242 Methanothrix thermophila PT Methanopyrus kandleri AV19 0.1

12. Supplementary figure 5