SUPPLEMENTARY INFORMATION doi:10.1038/nature21072 1. Supplementary Table 1. List and measurements of the specimens of Saccorhytus 2. Phylogenetic position of Saccorhytus within Deuterostomia. The sources and analytical methods were mostly based on refs 31–33. The analysis was performed by PAUP* 4.0b10 (ref. 34) and TNT1.1 (ref. 35). (a) Data matrix in nexus format, including 25 taxa and 61 characters. (b) Description of characters. (c) References cited in Description of characters. (d) PAUP4.0 commands. Cnidaria is set as an out group. (e) Log file performing the commands. WWW.NATURE.COM/NATURE | 1 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Table 1. List and measurements of the specimens of Saccorhytus number of number of spines cones diameter of oral chevron width of Specimen diameter of nodular length of circular rectangle photos of specimens length(μm) width(μm) cone protuber pattern(μ chevron(μ number cones (μm) rugae spines(μm) pores pore aperture(μm) ances m) m) right left right left XX23-248 1011.81 629.92 0 0 ? ? Y Y - - - 5.15 2.06 - N XX25-62 557.78 513.33 0 2 77.78 74.86 51.11 36.00 Y Y - - - 3.43 2.29 11.92 N XX26-170 1210.74 537.19 ?3 ?4 - - Y Y - - - 11.72 4.69 30.39 N >52.66 XX27-168 987.8 788.62 2 2 195.65 177.03 65.22 62.5 Y Y 2 2 >86.41 - - 26.47 N >81.30 109.09 33.06 153.72 56.20 79.34 71.07 168.67 XX34-298 1078.51 752.07 4 3 264.46 181.82 N Y 1 1 11.05 4.07 15.15 Y 250.00 >46.88 328.13 195.31 101.56 WWW.NATURE.COM/NATURE | 2 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION XX35-228 1164.44 637.04 1 0 223.91 116.3 N ？ - - >96.77 - - - N 160.19 247.30 47.57 74.32 >63.73 XX36-22 920 500 2 1 Y Y 1 1 - - 18.33 N 147.24 79.75 >50.00 82.71 83.33 54.14 27.45 284.15 78.95 103.66 35.53 XX42-83 929.69 722.66 4 4 Y N 1 1 55.74 57.84 5.63 3.52 - N 178.86 78.13 76.42 31.25 174.83 360.66 78.32 73.68 XX42-323 800 793.89 147.37 84.21 N N - - - - - 16.91 N 37.92 83.53 132.09 193.46 52.73 40.73 330.92 140.35 XX44-273 1198.29 695.8 4 4 34.46 N Y - - - - - 42.66 N 71.74 366.87 245.09 38.89 72.64 88.72 41.16 39.20 90.82 164.35 187.57 XX44-301 1064.16 823.02 2 2 64.44 N ？ - - - 84.2 8.93 - N 130.30 212.03 150.19 WWW.NATURE.COM/NATURE | 3 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION 66.96 93.75 187.5 119.64 126.83 50 XX45-1 1071.43 1010.21 3 3 91.06 28.34 Y Y - - - 11.27 2.38 22 55.6 N 107.90 84.64 151.93 105.45 32.48 83.06 133.9 101.92 XX45-20 991.47 753.55 3 4 244.46 63.51 210.07 Y Y - 1 22.97 9.92 4.51 29.2 N 118.81 225.64 33.48 97.95 186.54 27.21 125.56 60.13 207.54 223.65 323.27 65.63 XX45-56 1156.51 861.55 3 4 37.42 Y Y - - - 13.21 6.19 27.53 N 194.25 319.62 117.63 224.06 196.52 152.84 72.54 73.52 91.03 94.13 XX46-27 760.66 686.36 4 215.75 Y Y - - - 14.45 8.64 - N 238.03 179.75 143.21 54.25 70.32 77.70 116.39 156.64 91.07 XX47-498 1107.28 949.18 3 3 213.66 112.15 Y Y - - - - - 22.46 N 148.71 203.66 362.06 281.20 WWW.NATURE.COM/NATURE | 4 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION 72.89 94.45 130.46 105.04 XX47-558 731.46 564.89 4 Y Y - - - 11.19 6.8 18.76 N 259.48 205.25 198.37 185.16 90.77 142.99 48.08 90.90 XX48-64 985.73 778.58 3 3 206.34 71.37 152.00 40.96 Y Y - - - 8.28 4.14 24.32 N 113.94 92.54 42.50 53.18 26.31 32.99 XX48-288 960.4 518.92 3 ？ N Y - - - - - 22.67 N 108.95 71.35 37.71 84.80 266.91 176.06 XX48-399 949.87 722.34 3 3 345.08 116.69 267.99 Y Y - - - - - 20.06 N 134.02 336.20 61.16 93.48 248.08 XX49-183 798.42 672.12 3? ？ 188.66 130.33 Y Y - - - - - 23.18 N 119.48 XX50-360 548.94 425.9 1 1 144.47 171.17 N Y - - - 11.74 7.03 - N 74.78 106.98 212.54 47.42 59.86 XX51-326 969.38 729.59 3 ？ N N - - - - - - N 75.18 35.90 WWW.NATURE.COM/NATURE | 5 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION 20.46 XX51-334 1005.1 785.71 - - - - Y N - - - - - N 32.26 XX52-68 632.35 361.47 - - - - Y Y - - - 9.66 5.08 23.97 N XX53-232 855.54 754.77 - - - - N N - - - - - 14.27 N XX54-109 676.62 683.00 1 ？ 167.75 132.84 Y Y - - - 12.27 6.47 11.05 N ?128.77 ?90.27 XX54-249 829.31 645.97 3? ？ 223.89 149.03 Y N - - - - - - N ?118.36 ?76.29 121.68 152.34 XX54-354 898.35 857.44 2 ？ 157.87 182.13 Y N 2 - - - ?48.66 N 130.09 184.18 71.50 214.28 36.26 64.49 XX54-387 934.7 567.48 3 ？ Y N - - - 20.03 10.62 - N 140.21 23.13 WWW.NATURE.COM/NATURE | 6 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION XX55-43 1084.58 856.23 2 ？ 210.08 261.00 179.35 82.45 Y N - - - 12.34 8.03 - N 189.31 XX55-310 1024.35 906.88 2 ？ 281.17 181.92 Y Y - - - - - 23.71 N 118.57 50.52 125.22 17.09 70.10 XX55-338 951.72 570.98 3 ？ Y Y 1 113.19 - - 9.12 N 95.46 58.39 XX56-192 961.33 473.21 2 ？ 171.86 227.82 77.32 69.57 Y Y - - - - - - N XX56-493 1045.57 783.4 2? ？ 165.37 59.17 128.50 49.23 Y Y - - - 7.9 5.6 32.7 N XX57-80 1059.84 537.91 - - - - Y Y - - - - - - N XX57-198 743.56 394.7 1 ？ 135.89 52.05 Y N - - - 8.35 6.25 - N WWW.NATURE.COM/NATURE | 7 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION XX57-351 848.92 492.98 2 ？ 57.16 162.40 30.70 66.29 Y N 1 89.2 12.33 8.31 - N XX57-371 1152.72 745.52 2 ？ 188.62 77.75 94.95 58.69 Y N - - - 9.33 6.13 - N XX57-473 847.29 658.12 - - - - N N - - - - - 16.3 N xx58-118 1160 830 2 ？ 175 278 150 180 Y ? 1 150 - - 20 N xx58-125 1326 697 ？ 4 318 151 N ? - - - 3 ? N xx58-331 1108 897 4 ？ 231 166 N ? - - - 10 3 25 N WWW.NATURE.COM/NATURE | 8 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION xx59-235 1050 451 ？ 2 110 88 Y Y - - - 10 3 ? N xx61-27 1251 968 3 ? 330 245 Y Y - - - - - - N WWW.NATURE.COM/NATURE | 9 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Information 2: Phylogenetic position of Saccorhytus within Deuterostomia. The sources and analytical methods were mostly based on refs 31–33. The analysis was performed by PAUP* 4.0b10 (ref. 34) and TNT1.1 (ref. 35). (a) Data matrix in nexus format, including 25 taxa and 61 characters. (b) Description of characters. (c) References cited in Description of characters. (d) PAUP4.0 commands. Cnidaria is set as an out group. (e) Log file performing the commands. WWW.NATURE.COM/NATURE | 10 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION D 'DWDPDWUL[ &QLGDULD " $FRHORPRUSKD $UWKURSRGD 2Q\FKRSKRUD ^` .LQRUK\QFKD " 3ULDSXOLGD ^` 0ROOXVFD ^` ^` $QQHOLGD ^` (FKLQRGHUPDWD ^` ^` (QWHURSQHXVWD 8URFKRUGDWD " " &HSKDORFKRUGDWD 9HUWHEUDWD Vetulicola " " "" " Beidazoon " " "" " Ooedigera " " "" " Pomatrum " " "" " Xidazoon "" "" " Didazoon " " "" " Yuyuanozoon " " "" " Heteromorphus " " "" " Banffia " " "" " Vetulocystis " " " "" " " "" Dianchicystis " " " "" " " "" Saccorhytus "" " "" " WWW.NATURE.COM/NATURE | 11 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION &QLGDULD $FRHORPRUSKD $UWKURSRGD 2Q\FKRSKRUD .LQRUK\QFKD 3ULDSXOLGD 0ROOXVFD $QQHOLGD (FKLQRGHUPDWD ^` ^` (QWHURSQHXVWD 8URFKRUGDWD &HSKDORFKRUGDWD 9HUWHEUDWD Vetulicola """ Beidazoon """ Ooedigera """ Pomatrum """ Xidazoon "" Didazoon """ Yuyuanozoon """ Heteromorphus """ Banffia """" Vetulocystis """" " Dianchicystis """" " Saccorhytus """" " WWW.NATURE.COM/NATURE | 12 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION &QLGDULD $FRHORPRUSKD """" $UWKURSRGD " 2Q\FKRSKRUD " .LQRUK\QFKD """" 3ULDSXOLGD " 0ROOXVFD $QQHOLGD (FKLQRGHUPDWD " (QWHURSQHXVWD 8URFKRUGDWD &HSKDORFKRUGDWD 9HUWHEUDWD Vetulicola " " """ " " """"" Beidazoon " " """ " " """"" Ooedigera " " """ " " """"" Pomatrum " " """ " " """"" Xidazoon " " """ " " """"" Didazoon " """ " " """"" Yuyuanozoon " " """ " " """"" Heteromorphus " " """ " " """"" Banffia " " """ " " """"" Vetulocystis "" " """ " " """"" Dianchicystis "" " """ " " """"" Saccorhytus " " "" " """"" WWW.NATURE.COM/NATURE | 13 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION (b) Description of characters Characters Description of characters 1 Cleavage. Spiral cleavage (0), radial cleavage (1). 2 Fate of blastopore Anus (0), non-anus (closure, mouth, or both anus and mouth after lateral closure) (1). See ref. 33.