Supplementary Figure 2. Phylgenetic trees of myosin sequences. (a) Phylogenetic tree of myosins (gappy/IQ-TREE). The tree was built from the multiple sequence alignment of 286 myosins. Tree scale represents substitution per site. We consider myosin-II as outgroup to root this tree. (b) Phylogenetic tree of myosins (strict/IQ-TREE). The tree was built from the multiple sequence alignment of 286 myosins. Tree scale represents substitution per site. We consider myosin-II as outgroup to root this tree. (c) Phylogenetic tree of myosins (gappy/RAxML). The tree was built from the multiple sequence alignment of 286 myosins. Tree scale represents substitution per site. We consider myosin-II as outgroup to root this tree. (d) Phylogenetic tree of myosins (strict/RAxML). The tree was built from the multiple sequence alignment of 286 myosins. Tree scale represents substitution per site. We consider myosin-II as outgroup to root this tree. (e) Phylogenetic tree of myosins (gappy/IQ-TREE). The tree was built from the multiple sequence alignment of 82 myosins. Tree scale represents substitution per site. We consider myosin-II as outgroup to root this tree.

Supplementary Figure 2a Tree scale: 0.1 C Naegleria gruberi strain NEG-M 2 Naegleria gruberi strain NEG-M 2 Amoeba proteus 49 2 Dictyostelium discoideum AX4 75 59 2 Acanthamoeba castellanii D Contarinia nasturtii 39 100 2 Nasonia vitripennis 2 Fonticula alba 91 51 2 Quercus suber 100 2 Neurospora crassa OR74A 81 23 Oncorhynchus mykiss 69 2 Monosiga brevicollis 98 2 Sphaeroforma arctica JP610 63 2 Capsaspora owczarzaki ATCC 30864 B Monosiga brevicollis 25 1 Karenia brevis NCLDV___TARA_ARC_NCLDV_Bin_278_6 11 5 Cercozoa A Antonospora locustae 7 33 Phytophthora infestans T30-4 36 32 Hyaloperonospora parasitica A Toxoplasma gondii RH 11 A Galdieria sulphuraria 99 31 Rhodosorus marinus M Dictyostelium discoideum AX4 5 N Triparma pacifica 29 G Dictyostelium discoideum AX4 5 Paraphysomonas 13 18 Nasonia vitripennis 2 J Paramecium tetraurelia 100 K Paramecium tetraurelia 34 Isochrysis galbana

5 F Emiliania huxleyi 100 8 Emiliania huxleyi 100 2 Emiliania huxleyi H Emiliania huxleyi 33 31 Hyaloperonospora parasitica 1 20 Nasonia vitripennis 21 17 Quercus suber 100 17 Neurospora crassa OR74A 10 Aureoumbra lagunensis 30 D Emiliania huxleyi CCMP1516 100 7 Emiliania huxleyi 1 B Pavlovales sp. CCMP2436 21 10 Prasinoderma coloniale 6 3 Scrippsiella trochoidea

100 15 Scrippsiella trochoidea 100 7 Polarella glacialis 97 10 Karenia brevis 29 Phytophthora infestans T30-4 22 Spizellomyces punctatus DAOM BR117

9 97 22 Capsaspora owczarzaki ATCC 30864 100 22 Monosiga brevicollis 99 43 22 Nasonia vitripennis I Gloeochaete wittrockiana

36 7 Mayorella sp. JJP-2003 42 I Acanthamoeba castellanii str. Neff 57 I Dictyostelium discoideum AX4 100 22 Cavenderia fasciculata 11 Karenia brevis 100 5 Kryptoperidinium foliaceum 78 2 Karenia brevis

2 M Guillardia theta CCMP2712 100 11 Geminigera cryophila

8 A Micromonas commoda 48 8 Chlamydomonas reinhardtii 97 29 Physcomitrium patens 100 H Phalaenopsis equestris 100 8 Arabidopsis thaliana 24 Plasmodium chabaudi 27 25 Toxoplasma gondii RH 55 14 Toxoplasma gondii RH G Paramecium tetraurelia 7 100 H Paramecium tetraurelia L Tetrahymena thermophila SB210 91 83 I Tetrahymena thermophila SB210 77 M Tetrahymena thermophila SB210 56 N Tetrahymena thermophila SB210 F Paramecium tetraurelia 82 86 C Paramecium tetraurelia 97 E Paramecium tetraurelia 100 D Paramecium tetraurelia F Eutreptiella gymnastica 69 E Trypanosoma cruzi strain CL Brener 91 C Eutreptiella gymnastica

34 A Naegleria gruberi strain NEG-M 58 13 Platyophrya macrostoma 100 13 Leishmania infantum JPCM5 B Toxoplasma gondii RH 9 8 Cercozoa 1 4 Phaeocystis antarctica 100 10 Emiliania huxleyi

11 4 Thecamonas trahens ATCC 50062 4 prasinophyte sp. RCC997 93 100 4 Acanthamoeba castellanii 59 4 Lotharella globosa 2 41 4 Rhizopogon burlinghamii 89 4 Aureococcus anophagefferens 4 Durinskia baltica

23 I Pyramimonas parkeae 34 8 labyrinthulid quahog parasite QPX 100 11 labyrinthulid quahog parasite QPX 1 I Gymnochlora sp. CCMP2014 63 15 Paraphysomonas imperforata 100 7 Paraphysomonas 5 15 Chlorarachniophyceae sp. BC52 100 11 Lotharella globosa 19 S Bigelowiella natans 100 7 Lotharella globosa 31 Emiliania huxleyi 18 2 Chlorarachnion reptans 100 6 Lotharella globosa 26 Toxoplasma gondii RH 30 Emiliania huxleyi 17 4 85 30 Hyaloperonospora parasitica 30 23 Toxoplasma gondii RH

99 23 Pseudo-nitzschia fraudulenta 100 6 Karenia brevis 4 100 8 Karenia brevis 6 Emiliania huxleyi 81 11 Emiliania huxleyi 58 5 Emiliania huxleyi 42 6 Gloeochaete wittrockiana B Fonticula alba 92 92 6 Mayorella sp. JJP-2003 17 96 30 Thecamonas trahens ATCC 50062 1 92 30 Capsaspora owczarzaki ATCC 30864 100 6 Monosiga brevicollis 70 26 Helobdella robusta 100 6 Takifugu rubripes 100 27 Halichoerus grypus 100 30 Galeopterus variegatus 7 Crustomastix stigmatica 33 5 Pyramimonas parkeae 16 11 Palpitomonas bilix 95 I Prymnesium parvum 66 1 Emiliania huxleyi 4 1 Naegleria gruberi strain NEG-M 1 Thecamonas trahens ATCC 50062

97 E Capsaspora owczarzaki ATCC 30864 99 69 1 Monosiga brevicollis 58 33 Synchytrium microbalum 55 1 Capsaspora owczarzaki ATCC 30864 70 100 1 Nasonia vitripennis 1 Lotharella globosa 1 Trichosphaerium sp. ATCC 40318 51 1 Acanthamoeba castellanii 82 1 Palpitomonas bilix

82 29 1 Leishmania infantum JPCM5 59 1 Hyaloperonospora parasitica

11 1 Fonticula alba 42 1 Dictyostelium discoideum AX4

21 1 Quercus suber 100 1 Neurospora crassa OR74A 97 1 prasinophyte sp. RCC997 98 1 Gloeochaete wittrockiana 15 prasinophyte sp. RCC997 G Capsaspora owczarzaki ATCC 30864

27 10 Capsaspora owczarzaki ATCC 30864 100 10 Monosiga brevicollis 94 10 Takifugu rubripes 35 Takifugu rubripes 59 11 12 Trichinella spiralis 47 15 Nasonia vitripennis 4 42 15 Capsaspora owczarzaki ATCC 30864 38 15 Monosiga brevicollis 25 11 Amphimedon queenslandica 53 7 Monosiga brevicollis G Necator americanus 35 100 7 Nasonia vitripennis 50 7 Rhodamnia argentea 6 55 32 Biomphalaria glabrata 76 U Colius striatus

100 I Chlamydotis macqueenii 99 13 Paramormyrops kingsleyae 79 14 Gymnodraco acuticeps 100 29 Gymnodraco acuticeps G Trypanosoma rangeli 9 Nasonia vitripennis 12 P Monosiga brevicollis C Strongylocentrotus purpuratus 29 82 28 Xenopus tropicalis H Monosiga brevicollis 10 100 G Monosiga brevicollis 62 30 L Monosiga brevicollis

92 I Monosiga brevicollis 61 M Monosiga brevicollis 60 J Monosiga brevicollis 29 16 Takifugu rubripes

13 N Monosiga brevicollis 82 O Monosiga brevicollis 100 28 Salpingoeca rosetta B Strongylocentrotus purpuratus 4 14 F Monosiga brevicollis 46 E Monosiga brevicollis 100 D Monosiga brevicollis

4 K Monosiga brevicollis 42 C Monosiga brevicollis 38 A Monosiga brevicollis 8 O Hydra vulgaris 21 Nasonia vitripennis 65 63 K Acyrthosiphon pisum 100 3 Nasonia vitripennis 63 J Scyliorhinus canicula 100 L Scyliorhinus canicula 100 N Bos taurus 72 M Erpetoichthys calabaricus 11 Gloeochaete wittrockiana F Hyaloperonospora parasitica 45 H Hyaloperonospora parasitica 93 24 J Thalassiosira pseudonana CCMP1335 65 G Hyaloperonospora parasitica 33 E Hyaloperonospora parasitica

71 D Hyaloperonospora parasitica 79 C Hyaloperonospora parasitica 71 B Hyaloperonospora parasitica 97 A Hyaloperonospora parasitica 19 Takifugu rubripes 5 100 24 Anolis carolinensis 100 33 Zootoca vivipara

51 5 Capsaspora owczarzaki ATCC 30864 36 5 Neurospora crassa OR74A

92 5 Monosiga brevicollis H Acyrthosiphon pisum 94 92 A Nasonia vitripennis 92 5 Nasonia vitripennis 85 Q Carassius auratus 28 99 F Colius striatus 100 E Desmodus rotundus 5 Acanthamoeba castellanii str. Neff 100 5 Trichosphaerium sp. ATCC 40318 63 5 Dictyostelium discoideum AX4 B Volvox carteri f. nagariensis 34 51 11 Acetabularia peniculus R Daucus carota subsp. sativus 3 99 5 Lactuca sativa 99 58 F Syzygium oleosum 100 S Lupinus angustifolius 100 B Cajanus cajan 100 11 Arabidopsis thaliana

98 27 Malus domestica 98 31 Prosopis alba 54 I Ipomoea triloba 58 Q Capsicum annuum B Guillardia theta CCMP2712 11 Goniomonas 100 34 Guillardia theta CCMP2712 99 100 8 Rhodomonas lens 88 8 Cryptomonas curvata 100 8 Cryptophyta sp. CCMP2293

97 5 Cryptophyta sp. CCMP2293 100 5 Rhodomonas lens 15 100 11 Cryptophyta sp. CCMP2293 93 11 Cryptomonas curvata 27 Toxoplasma gondii RH T Hyaloperonospora parasitica 58 U Hyaloperonospora parasitica I Thalassiosira pseudonana CCMP1335 18 18 34 Hyaloperonospora parasitica 37 41 Q Hyaloperonospora parasitica 20 R Hyaloperonospora parasitica 32 S Rhizopogon burlinghamii 27 S Hyaloperonospora parasitica 16 NCLDV___GVMAG_M_3300025707_20 NCLDV___Moniruzzaman_MM15_ERX556043_42 60 NCLDV___GVMAG_M_3300009706_33 NCLDV___TARA_ARC_NCLDV_Bin_172_2 12 39 NCLDV___GVMAG_M_3300020185_49 71 100 NCLDV___TARA_PSW_NCLDV_Bin_50_13 31 NCLDV___GVMAG_S_3300005613_53 NCLDV___GVMAG_M_3300020187_27 99 NCLDV___GVMAG_S_1017745_26 71 100 28 NCLDV___Moniruzzaman_MM07_SRX802073_62 61 NCLDV___GVMAG_M_3300020169_51 100 NCLDV___Moniruzzaman_MM01_ERX555965_5 NCLDV___TARA_PSW_NCLDV_Bin_89_8 NCLDV___TARA_RED_NCLDV_Bin_76_1 56 NCLDV___TARA_PSW_NCLDV_Bin_173_3 9 100 NCLDV___GVMAG_M_3300020185_18 100 NCLDV___TARA_MED_NCLDV_Bin_341_9 59 NCLDV___Moniruzzaman_MM11_ERX552257_96 NCLDV___TARA_PON_NCLDV_Bin_110_3 48 NCLDV___TARA_ARC_NCLDV_Bin_340_2 100 100 NCLDV___GVMAG_S_3300000115_46 100 NCLDV___Moniruzzaman_MM13_SRX803008_78 92 NCLDV___TARA_ARC_NCLDV_Bin_340_3 Supplementary Figure 2b Tree scale: 0.1 2 Amoeba proteus

53 2 Naegleria gruberi strain NEG-M 41 2 Dictyostelium discoideum AX4 56 2 Acanthamoeba castellanii 2 Fonticula alba 33 2 Quercus suber 100 2 Neurospora crassa OR74A 73 D Contarinia nasturtii 100 2 Nasonia vitripennis 40 2 Sphaeroforma arctica JP610

86 2 Capsaspora owczarzaki ATCC 30864 62 23 Oncorhynchus mykiss 80 2 Monosiga brevicollis M Guillardia theta CCMP2712 100 11 Geminigera cryophila

22 2 Chlorarachnion reptans 100 6 Lotharella globosa 37 5 Kryptoperidinium foliaceum 100 2 Karenia brevis 46 11 Karenia brevis B Monosiga brevicollis 21 1 Karenia brevis I Pyramimonas parkeae 6 5 Cercozoa C Naegleria gruberi strain NEG-M 17 17 Neurospora crassa OR74A 100 17 Quercus suber 31 Emiliania huxleyi 7 A Galdieria sulphuraria 100 31 Rhodosorus marinus A Toxoplasma gondii RH 10 15 Chlorarachniophyceae sp. BC52 100 11 Lotharella globosa M Dictyostelium discoideum AX4 4 N Triparma pacifica 26 G Dictyostelium discoideum AX4 34 Isochrysis galbana

8 F Emiliania huxleyi 100 8 Emiliania huxleyi 100 2 Emiliania huxleyi 15 prasinophyte sp. RCC997

4 4 Durinskia baltica 33 8 labyrinthulid quahog parasite QPX 100 11 labyrinthulid quahog parasite QPX A Antonospora locustae 5 Paraphysomonas 6 32 18 Nasonia vitripennis 8 33 Phytophthora infestans T30-4 29 32 Hyaloperonospora parasitica G Trypanosoma rangeli

10 3 Scrippsiella trochoidea 100 15 Scrippsiella trochoidea 100 7 Polarella glacialis 91 10 Karenia brevis 20 Nasonia vitripennis C Eutreptiella gymnastica 8 36 13 Platyophrya macrostoma 100 13 Leishmania infantum JPCM5 87 A Naegleria gruberi strain NEG-M 42 F Eutreptiella gymnastica 46 E Trypanosoma cruzi strain CL Brener 10 Aureoumbra lagunensis 15 D Emiliania huxleyi CCMP1516 100 7 Emiliania huxleyi 1 8 Cercozoa

6 B Toxoplasma gondii RH 17 4 Phaeocystis antarctica 97 10 Emiliania huxleyi 7 Crustomastix stigmatica 77 33 10 Prasinoderma coloniale H Emiliania huxleyi 1 62 31 Hyaloperonospora parasitica 5 5 Pyramimonas parkeae

47 11 Palpitomonas bilix 83 I Prymnesium parvum 70 1 Emiliania huxleyi 15 Paraphysomonas imperforata 100 7 Paraphysomonas 22 I Gymnochlora sp. CCMP2014 42 S Bigelowiella natans 100 2 7 Lotharella globosa 4 Thecamonas trahens ATCC 50062 4 prasinophyte sp. RCC997 81 96 4 Acanthamoeba castellanii 49 4 Lotharella globosa 56 4 Rhizopogon burlinghamii 70 4 Aureococcus anophagefferens 25 Toxoplasma gondii RH 41 24 Plasmodium chabaudi 47 14 Toxoplasma gondii RH G Paramecium tetraurelia 14 100 H Paramecium tetraurelia L Tetrahymena thermophila SB210 71 41 I Tetrahymena thermophila SB210 80 M Tetrahymena thermophila SB210 51 N Tetrahymena thermophila SB210 F Paramecium tetraurelia 86 74 C Paramecium tetraurelia 79 E Paramecium tetraurelia 100 D Paramecium tetraurelia 11 Emiliania huxleyi 55 5 Emiliania huxleyi 95 6 Emiliania huxleyi 5 B Pavlovales sp. CCMP2436 11 Gloeochaete wittrockiana 16 H Hyaloperonospora parasitica 16 32 J Thalassiosira pseudonana CCMP1335 82 G Hyaloperonospora parasitica 95 F Hyaloperonospora parasitica

33 D Hyaloperonospora parasitica 85 E Hyaloperonospora parasitica 56 C Hyaloperonospora parasitica 61 B Hyaloperonospora parasitica 91 A Hyaloperonospora parasitica 30 Emiliania huxleyi 88 30 Hyaloperonospora parasitica 25 23 Toxoplasma gondii RH

98 23 Pseudo-nitzschia fraudulenta 99 6 Karenia brevis 5 100 8 Karenia brevis 26 Toxoplasma gondii RH 6 Gloeochaete wittrockiana 17 B Fonticula alba 3 65 65 6 Mayorella sp. JJP-2003 86 30 Thecamonas trahens ATCC 50062

58 30 Capsaspora owczarzaki ATCC 30864 100 6 Monosiga brevicollis 50 26 Helobdella robusta 98 6 Takifugu rubripes 100 27 Halichoerus grypus 100 30 Galeopterus variegatus A Micromonas commoda 83 8 Chlamydomonas reinhardtii 98 29 Physcomitrium patens 100 H Phalaenopsis equestris 98 8 Arabidopsis thaliana 11 Acetabularia peniculus B Volvox carteri f. nagariensis 93 R Daucus carota subsp. sativus 10 97 5 Lactuca sativa 68 59 F Syzygium oleosum 100 S Lupinus angustifolius 100 B Cajanus cajan 100 11 Arabidopsis thaliana 92 Q Capsicum annuum 14 47 I Ipomoea triloba 57 27 Malus domestica 89 31 Prosopis alba 5 Acanthamoeba castellanii str. Neff 99 5 Trichosphaerium sp. ATCC 40318 64 5 Dictyostelium discoideum AX4 19 Takifugu rubripes 24 100 24 Anolis carolinensis 100 33 Zootoca vivipara

37 5 Capsaspora owczarzaki ATCC 30864 62 5 Neurospora crassa OR74A

61 5 Monosiga brevicollis H Acyrthosiphon pisum 69 55 A Nasonia vitripennis 57 5 Nasonia vitripennis 53 Q Carassius auratus 96 F Colius striatus 100 E Desmodus rotundus B Guillardia theta CCMP2712 11 Goniomonas 92 8 Rhodomonas lens 92 100 8 Cryptomonas curvata 56 34 Guillardia theta CCMP2712 99 8 Cryptophyta sp. CCMP2293

96 5 Cryptophyta sp. CCMP2293 100 5 Rhodomonas lens 90 11 Cryptophyta sp. CCMP2293 89 11 Cryptomonas curvata 3 R Hyaloperonospora parasitica

6 S Rhizopogon burlinghamii 14 T Hyaloperonospora parasitica 56 U Hyaloperonospora parasitica 7 S Hyaloperonospora parasitica 25 27 Toxoplasma gondii RH 2 I Thalassiosira pseudonana CCMP1335 38 Q Hyaloperonospora parasitica 5 47 34 Hyaloperonospora parasitica J Paramecium tetraurelia 100 K Paramecium tetraurelia NCLDV___TARA_ARC_NCLDV_Bin_278_6

10 NCLDV___Moniruzzaman_MM15_ERX556043_42 58 NCLDV___GVMAG_M_3300009706_33 11 NCLDV___TARA_PSW_NCLDV_Bin_89_8 19 21 NCLDV___GVMAG_M_3300025707_20 NCLDV___TARA_ARC_NCLDV_Bin_172_2 NCLDV___GVMAG_M_3300020185_49 14 98 NCLDV___TARA_PSW_NCLDV_Bin_50_13 39 52 NCLDV___GVMAG_S_3300005613_53 NCLDV___GVMAG_M_3300020187_27 96 NCLDV___GVMAG_S_1017745_26 80 100 NCLDV___Moniruzzaman_MM07_SRX802073_62 79 9 NCLDV___GVMAG_M_3300020169_51 99 NCLDV___Moniruzzaman_MM01_ERX555965_5 NCLDV___TARA_RED_NCLDV_Bin_76_1 72 NCLDV___TARA_PSW_NCLDV_Bin_173_3 95 NCLDV___GVMAG_M_3300020185_18 99 NCLDV___TARA_MED_NCLDV_Bin_341_9 36 NCLDV___Moniruzzaman_MM11_ERX552257_96 NCLDV___TARA_PON_NCLDV_Bin_110_3 33 NCLDV___TARA_ARC_NCLDV_Bin_340_2 100 100 NCLDV___GVMAG_S_3300000115_46 100 NCLDV___Moniruzzaman_MM13_SRX803008_78 84 NCLDV___TARA_ARC_NCLDV_Bin_340_3 1 Naegleria gruberi strain NEG-M E Capsaspora owczarzaki ATCC 30864

87 1 Thecamonas trahens ATCC 50062 86 37 1 Monosiga brevicollis 45 33 Synchytrium microbalum 50 1 Capsaspora owczarzaki ATCC 30864 53 95 1 Nasonia vitripennis 1 Lotharella globosa 1 Trichosphaerium sp. ATCC 40318 61 1 Quercus suber 100 1 Neurospora crassa OR74A 76 90 1 prasinophyte sp. RCC997 58 1 Gloeochaete wittrockiana 67 1 Palpitomonas bilix 32 1 Dictyostelium discoideum AX4 24 1 Acanthamoeba castellanii

2 8 1 Fonticula alba 30 1 Leishmania infantum JPCM5 74 1 Hyaloperonospora parasitica 29 Phytophthora infestans T30-4 7 Mayorella sp. JJP-2003

9 28 I Acanthamoeba castellanii str. Neff 29 I Dictyostelium discoideum AX4 99 29 22 Cavenderia fasciculata I Gloeochaete wittrockiana

20 22 Spizellomyces punctatus DAOM BR117 86 22 Capsaspora owczarzaki ATCC 30864 100 22 Monosiga brevicollis 92 22 Nasonia vitripennis

1 10 Capsaspora owczarzaki ATCC 30864 99 10 Monosiga brevicollis 93 10 Takifugu rubripes 35 Takifugu rubripes 43 12 Trichinella spiralis 32 15 Capsaspora owczarzaki ATCC 30864 56 15 Monosiga brevicollis 47 5 15 Nasonia vitripennis 8 G Capsaspora owczarzaki ATCC 30864 7 Nasonia vitripennis 12 G Necator americanus 98 7 Rhodamnia argentea 41 78 32 Biomphalaria glabrata 11 Amphimedon queenslandica 35 81 7 Monosiga brevicollis 4 23 U Colius striatus

98 13 Paramormyrops kingsleyae 91 I Chlamydotis macqueenii 51 14 Gymnodraco acuticeps 100 29 Gymnodraco acuticeps 9 Nasonia vitripennis C Strongylocentrotus purpuratus 70 28 Xenopus tropicalis 26 16 Takifugu rubripes

9 N Monosiga brevicollis 58 O Monosiga brevicollis 43 100 28 Salpingoeca rosetta 21 Nasonia vitripennis O Hydra vulgaris 36 10 K Acyrthosiphon pisum 46 100 3 Nasonia vitripennis

65 J Scyliorhinus canicula 100 L Scyliorhinus canicula 98 N Bos taurus 3 71 M Erpetoichthys calabaricus P Monosiga brevicollis

15 K Monosiga brevicollis 26 C Monosiga brevicollis 44 A Monosiga brevicollis B Strongylocentrotus purpuratus 2 16 F Monosiga brevicollis 29 E Monosiga brevicollis 100 D Monosiga brevicollis 7 H Monosiga brevicollis 100 G Monosiga brevicollis 23 L Monosiga brevicollis

69 M Monosiga brevicollis 54 J Monosiga brevicollis 40 I Monosiga brevicollis Supplementary Figure 2c Tree scale: 0.1 2 Naegleria gruberi strain NEG-M 2 Amoeba proteus 2 Acanthamoeba castellanii 2 Dictyostelium discoideum AX4 2 Nasonia vitripennis D Contarinia nasturtii 18 Nasonia vitripennis 2 Fonticula alba 2 Neurospora crassa OR74A 2 Quercus suber 2 Sphaeroforma arctica JP610 2 Capsaspora owczarzaki ATCC 30864 23 Oncorhynchus mykiss 2 Monosiga brevicollis F Emiliania huxleyi 2 Emiliania huxleyi 8 Emiliania huxleyi 8 Chlamydomonas reinhardtii A Micromonas commoda 29 Physcomitrium patens 8 Arabidopsis thaliana H Phalaenopsis equestris 11 Geminigera cryophila M Guillardia theta CCMP2712 11 Karenia brevis 2 Karenia brevis 5 Kryptoperidinium foliaceum B Guillardia theta CCMP2712 11 Goniomonas 34 Guillardia theta CCMP2712 8 Rhodomonas lens 8 Cryptomonas curvata 8 Cryptophyta sp. CCMP2293 5 Cryptophyta sp. CCMP2293 5 Rhodomonas lens 11 Cryptophyta sp. CCMP2293 11 Cryptomonas curvata 27 Toxoplasma gondii RH T Hyaloperonospora parasitica U Hyaloperonospora parasitica S Rhizopogon burlinghamii S Hyaloperonospora parasitica R Hyaloperonospora parasitica I Thalassiosira pseudonana CCMP1335 Q Hyaloperonospora parasitica 34 Hyaloperonospora parasitica 11 Gloeochaete wittrockiana B Pavlovales sp. CCMP2436 F Hyaloperonospora parasitica H Hyaloperonospora parasitica J Thalassiosira pseudonana CCMP1335 G Hyaloperonospora parasitica E Hyaloperonospora parasitica D Hyaloperonospora parasitica C Hyaloperonospora parasitica B Hyaloperonospora parasitica A Hyaloperonospora parasitica 19 Takifugu rubripes 24 Anolis carolinensis 33 Zootoca vivipara 5 Capsaspora owczarzaki ATCC 30864 5 Neurospora crassa OR74A 5 Monosiga brevicollis Q Carassius auratus F Colius striatus E Desmodus rotundus H Acyrthosiphon pisum A Nasonia vitripennis 5 Nasonia vitripennis 5 Acanthamoeba castellanii str. Neff 5 Trichosphaerium sp. ATCC 40318 5 Dictyostelium discoideum AX4 B Volvox carteri f. nagariensis 11 Acetabularia peniculus S Lupinus angustifolius F Syzygium oleosum R Daucus carota subsp. sativus 5 Lactuca sativa 11 Arabidopsis thaliana B Cajanus cajan 27 Malus domestica 31 Prosopis alba I Ipomoea triloba Q Capsicum annuum 2 Chlorarachnion reptans 6 Lotharella globosa 26 Toxoplasma gondii RH 30 Emiliania huxleyi 30 Hyaloperonospora parasitica 23 Toxoplasma gondii RH 23 Pseudo-nitzschia fraudulenta 8 Karenia brevis 6 Karenia brevis 6 Emiliania huxleyi 5 Emiliania huxleyi 11 Emiliania huxleyi 6 Gloeochaete wittrockiana B Fonticula alba 6 Mayorella sp. JJP-2003 30 Thecamonas trahens ATCC 50062 30 Capsaspora owczarzaki ATCC 30864 6 Monosiga brevicollis 26 Helobdella robusta 6 Takifugu rubripes 27 Halichoerus grypus 30 Galeopterus variegatus 31 Emiliania huxleyi 31 Hyaloperonospora parasitica H Emiliania huxleyi 5 Pyramimonas parkeae 7 Crustomastix stigmatica 11 Palpitomonas bilix 1 Emiliania huxleyi I Prymnesium parvum 15 prasinophyte sp. RCC997 A Toxoplasma gondii RH A Antonospora locustae B Monosiga brevicollis 32 Hyaloperonospora parasitica 33 Phytophthora infestans T30-4 A Galdieria sulphuraria 31 Rhodosorus marinus 34 Isochrysis galbana 3 Scrippsiella trochoidea 15 Scrippsiella trochoidea 7 Polarella glacialis 10 Karenia brevis 10 Prasinoderma coloniale 10 Aureoumbra lagunensis 7 Emiliania huxleyi D Emiliania huxleyi CCMP1516 B Toxoplasma gondii RH 10 Emiliania huxleyi 4 Phaeocystis antarctica 4 Durinskia baltica I Pyramimonas parkeae 11 labyrinthulid quahog parasite QPX 8 labyrinthulid quahog parasite QPX 15 Chlorarachniophyceae sp. BC52 11 Lotharella globosa 7 Lotharella globosa S Bigelowiella natans I Gymnochlora sp. CCMP2014 15 Paraphysomonas imperforata 7 Paraphysomonas 8 Cercozoa 4 Thecamonas trahens ATCC 50062 4 prasinophyte sp. RCC997 4 Acanthamoeba castellanii 4 Lotharella globosa 4 Aureococcus anophagefferens 4 Rhizopogon burlinghamii 29 Phytophthora infestans T30-4 7 Mayorella sp. JJP-2003 I Acanthamoeba castellanii str. Neff 22 Cavenderia fasciculata I Dictyostelium discoideum AX4 I Gloeochaete wittrockiana 22 Spizellomyces punctatus DAOM BR117 22 Capsaspora owczarzaki ATCC 30864 22 Monosiga brevicollis 22 Nasonia vitripennis 10 Capsaspora owczarzaki ATCC 30864 10 Takifugu rubripes 10 Monosiga brevicollis G Capsaspora owczarzaki ATCC 30864 15 Nasonia vitripennis 35 Takifugu rubripes 15 Monosiga brevicollis 15 Capsaspora owczarzaki ATCC 30864 7 Monosiga brevicollis 11 Amphimedon queenslandica G Necator americanus 7 Nasonia vitripennis 32 Biomphalaria glabrata 7 Rhodamnia argentea U Colius striatus I Chlamydotis macqueenii 13 Paramormyrops kingsleyae 14 Gymnodraco acuticeps 29 Gymnodraco acuticeps 9 Nasonia vitripennis P Monosiga brevicollis E Monosiga brevicollis D Monosiga brevicollis C Strongylocentrotus purpuratus 28 Xenopus tropicalis H Monosiga brevicollis G Monosiga brevicollis L Monosiga brevicollis I Monosiga brevicollis M Monosiga brevicollis J Monosiga brevicollis N Monosiga brevicollis 28 Salpingoeca rosetta O Monosiga brevicollis C Monosiga brevicollis A Monosiga brevicollis K Monosiga brevicollis B Strongylocentrotus purpuratus F Monosiga brevicollis 21 Nasonia vitripennis 16 Takifugu rubripes O Hydra vulgaris 3 Nasonia vitripennis K Acyrthosiphon pisum J Scyliorhinus canicula L Scyliorhinus canicula M Erpetoichthys calabaricus N Bos taurus C Eutreptiella gymnastica E Trypanosoma cruzi strain CL Brener F Eutreptiella gymnastica A Naegleria gruberi strain NEG-M 13 Platyophrya macrostoma 13 Leishmania infantum JPCM5 J Paramecium tetraurelia K Paramecium tetraurelia NCLDV___GVMAG_M_3300020185_18 NCLDV___TARA_MED_NCLDV_Bin_341_9 NCLDV___TARA_PSW_NCLDV_Bin_173_3 NCLDV___TARA_RED_NCLDV_Bin_76_1 NCLDV___Moniruzzaman_MM11_ERX552257_96 NCLDV___TARA_PON_NCLDV_Bin_110_3 NCLDV___GVMAG_S_3300000115_46 NCLDV___TARA_ARC_NCLDV_Bin_340_2 NCLDV___TARA_ARC_NCLDV_Bin_340_3 NCLDV___Moniruzzaman_MM13_SRX803008_78 NCLDV___TARA_ARC_NCLDV_Bin_172_2 NCLDV___GVMAG_M_3300020185_49 NCLDV___TARA_PSW_NCLDV_Bin_50_13 NCLDV___TARA_PSW_NCLDV_Bin_89_8 NCLDV___GVMAG_M_3300009706_33 NCLDV___Moniruzzaman_MM15_ERX556043_42 NCLDV___GVMAG_M_3300025707_20 NCLDV___GVMAG_S_3300005613_53 NCLDV___GVMAG_M_3300020187_27 NCLDV___Moniruzzaman_MM01_ERX555965_5 NCLDV___GVMAG_M_3300020169_51 NCLDV___GVMAG_S_1017745_26 NCLDV___Moniruzzaman_MM07_SRX802073_62 1 Naegleria gruberi strain NEG-M 1 Lotharella globosa 1 Thecamonas trahens ATCC 50062 E Capsaspora owczarzaki ATCC 30864 1 Monosiga brevicollis 33 Synchytrium microbalum 1 Capsaspora owczarzaki ATCC 30864 1 Nasonia vitripennis 1 Trichosphaerium sp. ATCC 40318 1 Acanthamoeba castellanii 1 Palpitomonas bilix 1 Leishmania infantum JPCM5 1 Hyaloperonospora parasitica 1 Dictyostelium discoideum AX4 1 Fonticula alba 1 Quercus suber 1 Neurospora crassa OR74A 1 Gloeochaete wittrockiana 1 prasinophyte sp. RCC997 20 Nasonia vitripennis 5 Cercozoa 12 Trichinella spiralis G Trypanosoma rangeli NCLDV___TARA_ARC_NCLDV_Bin_278_6 1 Karenia brevis 14 Toxoplasma gondii RH 25 Toxoplasma gondii RH 24 Plasmodium chabaudi C Naegleria gruberi strain NEG-M 17 Neurospora crassa OR74A 17 Quercus suber M Dictyostelium discoideum AX4 G Dictyostelium discoideum AX4 N Triparma pacifica 5 Paraphysomonas H Paramecium tetraurelia G Paramecium tetraurelia L Tetrahymena thermophila SB210 I Tetrahymena thermophila SB210 M Tetrahymena thermophila SB210 N Tetrahymena thermophila SB210 F Paramecium tetraurelia C Paramecium tetraurelia E Paramecium tetraurelia D Paramecium tetraurelia Supplementary Figure 2d Tree scale: 0.1 2 Amoeba proteus 2 Naegleria gruberi strain NEG-M 2 Dictyostelium discoideum AX4 2 Acanthamoeba castellanii 2 Fonticula alba 2 Neurospora crassa OR74A 2 Quercus suber 2 Nasonia vitripennis D Contarinia nasturtii 2 Sphaeroforma arctica JP610 2 Capsaspora owczarzaki ATCC 30864 23 Oncorhynchus mykiss 2 Monosiga brevicollis B Pavlovales sp. CCMP2436 NCLDV___TARA_ARC_NCLDV_Bin_278_6 F Emiliania huxleyi 2 Emiliania huxleyi 8 Emiliania huxleyi H Hyaloperonospora parasitica J Thalassiosira pseudonana CCMP1335 G Hyaloperonospora parasitica F Hyaloperonospora parasitica D Hyaloperonospora parasitica E Hyaloperonospora parasitica C Hyaloperonospora parasitica B Hyaloperonospora parasitica A Hyaloperonospora parasitica 11 Gloeochaete wittrockiana A Micromonas commoda 8 Chlamydomonas reinhardtii 29 Physcomitrium patens 8 Arabidopsis thaliana H Phalaenopsis equestris 11 Acetabularia peniculus B Volvox carteri f. nagariensis S Lupinus angustifolius F Syzygium oleosum R Daucus carota subsp. sativus 5 Lactuca sativa 11 Arabidopsis thaliana B Cajanus cajan Q Capsicum annuum I Ipomoea triloba 27 Malus domestica 31 Prosopis alba 5 Acanthamoeba castellanii str. Neff 5 Trichosphaerium sp. ATCC 40318 5 Dictyostelium discoideum AX4 A Antonospora locustae 19 Takifugu rubripes 24 Anolis carolinensis 33 Zootoca vivipara 5 Neurospora crassa OR74A 5 Capsaspora owczarzaki ATCC 30864 5 Monosiga brevicollis Q Carassius auratus F Colius striatus E Desmodus rotundus H Acyrthosiphon pisum 5 Nasonia vitripennis A Nasonia vitripennis 27 Toxoplasma gondii RH S Hyaloperonospora parasitica I Thalassiosira pseudonana CCMP1335 Q Hyaloperonospora parasitica 34 Hyaloperonospora parasitica T Hyaloperonospora parasitica U Hyaloperonospora parasitica S Rhizopogon burlinghamii R Hyaloperonospora parasitica B Guillardia theta CCMP2712 11 Goniomonas 8 Rhodomonas lens 8 Cryptomonas curvata 34 Guillardia theta CCMP2712 8 Cryptophyta sp. CCMP2293 5 Cryptophyta sp. CCMP2293 5 Rhodomonas lens 11 Cryptophyta sp. CCMP2293 11 Cryptomonas curvata 30 Hyaloperonospora parasitica 30 Emiliania huxleyi 26 Toxoplasma gondii RH 23 Toxoplasma gondii RH 23 Pseudo-nitzschia fraudulenta 8 Karenia brevis 6 Karenia brevis 6 Emiliania huxleyi 5 Emiliania huxleyi 11 Emiliania huxleyi 6 Gloeochaete wittrockiana B Fonticula alba 6 Mayorella sp. JJP-2003 30 Thecamonas trahens ATCC 50062 30 Capsaspora owczarzaki ATCC 30864 6 Monosiga brevicollis 26 Helobdella robusta 6 Takifugu rubripes 27 Halichoerus grypus 30 Galeopterus variegatus 7 Crustomastix stigmatica 10 Prasinoderma coloniale 31 Emiliania huxleyi 10 Aureoumbra lagunensis 7 Emiliania huxleyi D Emiliania huxleyi CCMP1516 34 Isochrysis galbana 1 Karenia brevis B Monosiga brevicollis 11 Geminigera cryophila M Guillardia theta CCMP2712 2 Chlorarachnion reptans 6 Lotharella globosa 5 Kryptoperidinium foliaceum 2 Karenia brevis 11 Karenia brevis 25 Toxoplasma gondii RH 24 Plasmodium chabaudi 14 Toxoplasma gondii RH L Tetrahymena thermophila SB210 I Tetrahymena thermophila SB210 M Tetrahymena thermophila SB210 G Paramecium tetraurelia H Paramecium tetraurelia N Tetrahymena thermophila SB210 F Paramecium tetraurelia C Paramecium tetraurelia E Paramecium tetraurelia D Paramecium tetraurelia 31 Hyaloperonospora parasitica H Emiliania huxleyi 5 Pyramimonas parkeae 11 Palpitomonas bilix 1 Emiliania huxleyi I Prymnesium parvum 8 Cercozoa 10 Emiliania huxleyi 4 Phaeocystis antarctica B Toxoplasma gondii RH 3 Scrippsiella trochoidea 15 Scrippsiella trochoidea 7 Polarella glacialis 10 Karenia brevis 15 Paraphysomonas imperforata 7 Paraphysomonas I Gymnochlora sp. CCMP2014 7 Lotharella globosa S Bigelowiella natans 15 Chlorarachniophyceae sp. BC52 11 Lotharella globosa 4 Durinskia baltica 11 labyrinthulid quahog parasite QPX 8 labyrinthulid quahog parasite QPX 4 Thecamonas trahens ATCC 50062 4 prasinophyte sp. RCC997 4 Acanthamoeba castellanii 4 Lotharella globosa 4 Aureococcus anophagefferens 4 Rhizopogon burlinghamii 29 Phytophthora infestans T30-4 J Paramecium tetraurelia K Paramecium tetraurelia A Toxoplasma gondii RH A Galdieria sulphuraria 31 Rhodosorus marinus C Eutreptiella gymnastica F Eutreptiella gymnastica E Trypanosoma cruzi strain CL Brener A Naegleria gruberi strain NEG-M 13 Platyophrya macrostoma 13 Leishmania infantum JPCM5 NCLDV___TARA_PSW_NCLDV_Bin_173_3 NCLDV___TARA_RED_NCLDV_Bin_76_1 NCLDV___GVMAG_M_3300020185_18 NCLDV___TARA_MED_NCLDV_Bin_341_9 NCLDV___Moniruzzaman_MM11_ERX552257_96 NCLDV___TARA_PON_NCLDV_Bin_110_3 NCLDV___GVMAG_S_3300000115_46 NCLDV___TARA_ARC_NCLDV_Bin_340_2 NCLDV___TARA_ARC_NCLDV_Bin_340_3 NCLDV___Moniruzzaman_MM13_SRX803008_78 NCLDV___GVMAG_M_3300009706_33 NCLDV___Moniruzzaman_MM15_ERX556043_42 NCLDV___TARA_PSW_NCLDV_Bin_89_8 NCLDV___GVMAG_M_3300025707_20 NCLDV___TARA_ARC_NCLDV_Bin_172_2 NCLDV___GVMAG_M_3300020185_49 NCLDV___TARA_PSW_NCLDV_Bin_50_13 NCLDV___GVMAG_S_3300005613_53 NCLDV___GVMAG_M_3300020187_27 NCLDV___Moniruzzaman_MM01_ERX555965_5 NCLDV___GVMAG_M_3300020169_51 NCLDV___GVMAG_S_1017745_26 NCLDV___Moniruzzaman_MM07_SRX802073_62 M Dictyostelium discoideum AX4 5 Cercozoa 12 Trichinella spiralis N Triparma pacifica G Dictyostelium discoideum AX4 20 Nasonia vitripennis I Pyramimonas parkeae 33 Phytophthora infestans T30-4 18 Nasonia vitripennis 32 Hyaloperonospora parasitica 5 Paraphysomonas C Naegleria gruberi strain NEG-M 17 Neurospora crassa OR74A 17 Quercus suber 1 Naegleria gruberi strain NEG-M E Capsaspora owczarzaki ATCC 30864 1 Thecamonas trahens ATCC 50062 1 Monosiga brevicollis 33 Synchytrium microbalum 1 Capsaspora owczarzaki ATCC 30864 1 Nasonia vitripennis 1 Lotharella globosa 1 Trichosphaerium sp. ATCC 40318 1 prasinophyte sp. RCC997 1 Gloeochaete wittrockiana 1 Quercus suber 1 Neurospora crassa OR74A 1 Dictyostelium discoideum AX4 1 Fonticula alba 1 Acanthamoeba castellanii 1 Palpitomonas bilix 1 Leishmania infantum JPCM5 1 Hyaloperonospora parasitica 7 Mayorella sp. JJP-2003 I Acanthamoeba castellanii str. Neff 22 Cavenderia fasciculata I Dictyostelium discoideum AX4 I Gloeochaete wittrockiana 15 prasinophyte sp. RCC997 22 Spizellomyces punctatus DAOM BR117 22 Capsaspora owczarzaki ATCC 30864 22 Monosiga brevicollis 22 Nasonia vitripennis 10 Capsaspora owczarzaki ATCC 30864 10 Takifugu rubripes 10 Monosiga brevicollis 7 Nasonia vitripennis G Necator americanus 7 Rhodamnia argentea 32 Biomphalaria glabrata 7 Monosiga brevicollis 11 Amphimedon queenslandica U Colius striatus 13 Paramormyrops kingsleyae I Chlamydotis macqueenii 14 Gymnodraco acuticeps 29 Gymnodraco acuticeps G Capsaspora owczarzaki ATCC 30864 15 Capsaspora owczarzaki ATCC 30864 35 Takifugu rubripes 15 Nasonia vitripennis 15 Monosiga brevicollis 9 Nasonia vitripennis 28 Xenopus tropicalis C Strongylocentrotus purpuratus P Monosiga brevicollis E Monosiga brevicollis D Monosiga brevicollis H Monosiga brevicollis G Monosiga brevicollis L Monosiga brevicollis M Monosiga brevicollis I Monosiga brevicollis J Monosiga brevicollis N Monosiga brevicollis 28 Salpingoeca rosetta O Monosiga brevicollis G Trypanosoma rangeli 16 Takifugu rubripes 21 Nasonia vitripennis K Monosiga brevicollis A Monosiga brevicollis C Monosiga brevicollis B Strongylocentrotus purpuratus F Monosiga brevicollis O Hydra vulgaris 3 Nasonia vitripennis K Acyrthosiphon pisum J Scyliorhinus canicula L Scyliorhinus canicula M Erpetoichthys calabaricus N Bos taurus Supplementary Figure 2e Tree scale: 1 2 Neurospora crassa OR74A 2 Nasonia vitripennis 19 Takifugu rubripes 100 24 Anolis carolinensis 100 33 Zootoca vivipara 91 5 Capsaspora owczarzaki ATCC 30864 5 Neurospora crassa OR74A 93 5 Monosiga brevicollis 47 H Acyrthosiphon pisum 99 98 A Nasonia vitripennis 99 5 Nasonia vitripennis 95 41 Q Carassius auratus 99 F Colius striatus 100 E Desmodus rotundus 5 Acanthamoeba castellanii str. Neff 100 5 Trichosphaerium sp. ATCC 40318 54 5 Dictyostelium discoideum AX4 B Volvox carteri f. nagariensis 40 45 11 Acetabularia peniculus R Daucus carota subsp. sativus 100 5 Lactuca sativa 100 54 F Syzygium oleosum 100 S Lupinus angustifolius 100 B Cajanus cajan 100 11 Arabidopsis thaliana 100 98 27 Malus domestica 98 31 Prosopis alba 53 I Ipomoea triloba 65 Q Capsicum annuum 11 Gloeochaete wittrockiana F Hyaloperonospora parasitica 71 41 J Thalassiosira pseudonana CCMP1335 68 G Hyaloperonospora parasitica 100 H Hyaloperonospora parasitica

23 E Hyaloperonospora parasitica 72 D Hyaloperonospora parasitica 88 C Hyaloperonospora parasitica 53 B Hyaloperonospora parasitica 98 A Hyaloperonospora parasitica 57 B Guillardia theta CCMP2712 11 Goniomonas 100 34 Guillardia theta CCMP2712 98 100 8 Rhodomonas lens 90 8 Cryptomonas curvata 100 8 Cryptophyta sp. CCMP2293

100 5 Cryptophyta sp. CCMP2293

46 100 5 Rhodomonas lens 100 11 Cryptophyta sp. CCMP2293 85 11 Cryptomonas curvata 27 Toxoplasma gondii RH T Hyaloperonospora parasitica 68 U Hyaloperonospora parasitica 82 I Thalassiosira pseudonana CCMP1335 27 Q Hyaloperonospora parasitica 31 34 Hyaloperonospora parasitica 31 15 S Rhizopogon burlinghamii 32 S Hyaloperonospora parasitica 32 R Hyaloperonospora parasitica NCLDV___GVMAG_M_3300025707_20 20 NCLDV___Moniruzzaman_MM15_ERX556043_42 56 NCLDV___GVMAG_M_3300009706_33

17 NCLDV___TARA_ARC_NCLDV_Bin_172_2 NCLDV___GVMAG_M_3300020185_49 98 30 100 NCLDV___TARA_PSW_NCLDV_Bin_50_13 56 NCLDV___GVMAG_S_3300005613_53 NCLDV___GVMAG_M_3300020187_27 99 NCLDV___GVMAG_S_1017745_26 37 71 100 NCLDV___Moniruzzaman_MM07_SRX802073_62 59 NCLDV___GVMAG_M_3300020169_51 99 NCLDV___Moniruzzaman_MM01_ERX555965_5 NCLDV___TARA_PSW_NCLDV_Bin_89_8 NCLDV___Moniruzzaman_MM11_ERX552257_96 20 NCLDV___TARA_RED_NCLDV_Bin_76_1 61 NCLDV___TARA_PSW_NCLDV_Bin_173_3 57 100 NCLDV___GVMAG_M_3300020185_18 100 NCLDV___TARA_MED_NCLDV_Bin_341_9 41 NCLDV___TARA_PON_NCLDV_Bin_110_3 NCLDV___GVMAG_S_3300000115_46 100 100 NCLDV___TARA_ARC_NCLDV_Bin_340_2 100 NCLDV___Moniruzzaman_MM13_SRX803008_78 94 NCLDV___TARA_ARC_NCLDV_Bin_340_3