SUPPLEMENTARY INFORMATION Doi:10.1038/Nature21072

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.

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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

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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

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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

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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

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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

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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

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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

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xx59-235 1050 451 ？ 2 110 88 Y Y - - - 10 3 ? N

xx61-27 1251 968 3 ? 330 245 Y Y ------N

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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.

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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 "" " "" "

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&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 """" "

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&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 " " "" " """""

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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. 3 Bilateral symmetry Absent (0), present (1). Absent in cnidarians. Echinoderms were originally bilateral in symmetry (see ref. 36). Absent (0), present (1). Acoelomorphs and cnidarians lack a true coelom. The kinorhynchs and most priapulids have a pseudocoelom. All vetulicolians (Vetulicola 37, Beidazoon 38, Ooedigera 32, Pomatrum 39, Xidazoon 40, Didazoon 8, Yuyuanozoon 41, Banffia 42 and Heteromorphus39) 4 Coelom and the vetulocystids (Vetulocystis, Dianchicystis)10 are suggested to have a coelom on account of the intestine being located on mid -line of the tail, indicating that the intestine was attached by mesodermal muscles are derived from coelom (see ref. 43). Schizocoely (0), enterocoely (1). Develop of coelom by schizocoely in Arthropoda, Onychophora, and Annelida; the coelom of Echinodermata, 5 Coelom formation Enteropneusta, Urochordata, Cephalochordata, and Vertebrata is derived from the endodermal intestine (enterocoely) (see ref. 43). 6 Tripartite coelom Absent (0), present (1). Echinoderms and hemichordates exhibit three coeloms. Such coeloms may not be homologous.

7 Protonephridia Absent (0), present or with metanephridia (1). Cnidarians and acoelomorphs lacks protonephridia (see ref. 43) Uniparitite body (0), Bipartite (1), Tripartite (2). The body in vetulicolians and vetulocystids can be subdivided into an anterior pharygeal region 8 Body division and a posterior tail. Urochordate larvae have a posterior tail. The body of cephalochordates can be superficially subdivided into an anterior pharygeal region and a posteriorpharygeal region. Ventral (0), ventral terminal (1), terminal (2). Acoelomorphs and Saccorhytus have ventral mouth. Stem-group onychophorans have a terminal mouth see refs. 44,45. Crown-group onychophorans have a ventral terminal mouth. Cycloneuralians have terminal mouth; Arthropoda, Annelida and Mollusca have ventral-terminal mouth. The mouth in echinoderms is ventral (Crinoida, Asterioda, Ophiuroida) or terminal (Holothuroida). 9 Position of mouth All vetulicolians have terminal mouth. The mouth of urochordates is coded as "?" (See ref. 43). The correlation of body axis (i.e. the anterior-posterior, dorsal-ventral) between cnidarians and bilaterians remains unresolved (see ref. 46), thus we coded the position of mouth in cnidarians as (?). Mouth surrounded by oral Absent (0), present (1). Mouth surrounded by oral folds are present in acoelomorphs, scalidophorans, extant onychophorans and Saccorhytus, 10 folds or plates Pomatrum, Xidazoon, Didazoon, and Banffia, hence coded as (1). Multi-circlets of oral 11 Absent (0), present (1), valved (2). Pomatrum, Xidazoon and Saccorhytus are coded as (1). folds

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12 Introvert Absent (0), present (1).

13 Scalids Absent (0), present (1).

14 Anus Absent (0), present (1). Anus is absent in cnidarians, acoelomorphs and Saccorhytus.

Anterior to the tail (0). Terminal anus (1). Hemichordates, echinoderms and vetulicolians and vetulocystids were coded as (1). Chordates 15 Position of anus (urochordates, cephalochordates and vertebrates coded as (0)). Not applicable in cnidarian, acoelomorphs and Saccorhytus. Segmentation or 16 Absent (0), present (1). Some aplacophoran postlarva showing distinct metamerism (see ref. 47), we coded it as {01}. metamerism Body divided into 13 Absent (0), present (1). Most vetulicolians have 13 body segments (see ref. 31). Kinorhyncha has 13 segments but not homologous (see ref. 43), 17 segments coded as (0). Terminal addition during Absent (0), present (1). Addition of posterior segments during ontogeny along the anterior-posterior body axis is seen in arthropods, priapulids, 18 ontogeny annelids, mollusks, but no evidence in cnidarians, acoelomorphs, kinorhynchs, vetulicolians, vetulocystids, and Saccorhytus. Anterior segments fused and condensed into a 19 Absent (0), present (1). The heads of arthropods and stem-group onychophorans are formed by fusion of anterior segments. head region with sensory or feeding organs Anterior body with fused 20 dorsal and ventral Absent (0), present (1). Dorsal and ventral marginal of the anterior body in vetulicolians are fused together forming a longitudinal narrow zone. marginal zones Shape of anterior body 21 Ovoid (0), subquadrate present (1). This character is from Aldridge et al. and only applicable for vetulicolians region Shape of pharyngeal 22 Doliform (0); globular (1). This character is only appliable for vetulicolians, vetulocystids and Saccorhytus region Posterior body with Absent (0), present (1). In Banffia and Heteromorphus, there are many fine annulations between the anterior and the posterior body. Such 23 numerous narrow annulations are absent in other genera of vetulicolians. segments/annulations Endoskeleton Absent (0), present (1). The hard tissue under the surface membrane of vetulicolians is interpreted as endoskeleton homologous with crown-group 24 mesodermally derived deuterostomes (see ref. 8). Surface membrane Absent (0), present (1). The soft, labile (decay-prone) surface membrane can be observed in most specimens of various vetulicolian taxa, which 25 (epidermis) renders a new cuticle after moultingas unlikely. In addition, no other Chengjiang arthropods are preserved with such an outermost layer. Here

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interpreted as epidermis (the membrane) underlain by endoskeleton (the plates). The chevron pattern in Saccorhytus is interpreted as a surface membrane. Surface cuticle (or 26 exoskeleton) underlain by Absent (0), present (1). Besides ecdysozoans, annelids have cuticle. epidermis Cuticle mainly made of 27 Absent (0), present (1). Į-chitin cuticle is present in arthropods and onychophorans. Į-chitin Growth by ecdysis 28 Absent (0), present (1). No evidence of moulting in vetulicolians, vetulocystids and Saccorhytus. (molting) 29 Three-layered cuticle Absent (0), present (1). Present in ecdysozoans. (see ref. 33).

30 Trilaminate epicuticle Absent (0), present (1). Present in ecdysozoans. (see ref. 33).

31 Circumpharyngeal brain Absent (0), present (1). Present in ecdysozoans. (see ref. 33).

32 Chaetae Absent (0), present (1). Chaetae are present in Mollusca and Annelida. (see seatae in ref. 33).

33 Diffuse nerve net Absent (0), present (1). Present in cnidarians and acoelomorphs. (see ref. 33).

Absent (0), present (1). Arthropods, onychophorans, priapulids, kinorhychs, annelids and mollusks are coded as (1). Hemichordates have dorsal Longitudinal ventral 34 and ventral nerve cords, coded as (1). Longitudinal ventral nerve cord is seen Xidazoon 40. Saccorhytus has a relatively large ventral mouth, but nerve cord(s) somewhat shorter than the body length, thus assumed no space for the ventral nerve cord, we code it as (0). Longitudinal dorsal nerve 35 Absent (0), present (1). Unique in chordates. Hemichordates have both ventral and dorsal nerve cords. Saccorhytus is coded as (?). cord(s) Longitudinal lateral Absent (0), present (1). Two longitudinal lateral grooves where the gill pouches situated are present in Vetulicola, Beidazoon, and Ooedigera. 36 grooves (median zone). These genera are coded as (1). They are not obvious in Heteromorphus and Banffia (see ref. 32), but should be coded as (1). Absent (0), present (1). Pharyngeal gill slits were regarded as a synapomorphy of extant deuterostomes. Vetulicolians and vetulocystids have 37 Pharyngeal gill slits. pharyngeal gill slits (see ref. 1). The body cones in Saccorhytus are attested as pecursors of pharyngeal gill slits (see main text). 38 Body cones Absent (0), present (1). Body cones with radial 39 Absent (0), present (1). folds 40 Orientation of body cones Perpendicular to the body surface(0); anteriorly directed (1)

41 Number of body cones 5 pairs (0), two (1), 4 pairs (2)

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42 Gill bars/arches Absent (0), present (1). Present in hemichordates and chordates.

43 Gill cowls (hoods) Absent (0), present (1). Seen in PomatrumǃXidazoonǃDidazoonǃYuyuanozoon. Filter feeding Absent (0), present (1). Vetulicolians have been demonstrated as filtering feeders using their pharynx (see ref. 45). The body cones of Saccorhytus 44 accomplished within indicate a filtering feeding habit although a predatory potential cannot be excluded. pharynx Endostyle, epibranchial ridge, or thyroid that Absent (0), present (1). Present in all major groups of deuterostomes except echinoderms. The stomochord of enteropneust hemichordates taken 45 accumulates iodine and to be homologous to the pharyngeal endostyle (see ref. 48). secretes mucus Absent (0), present (1). Pharyngeal food-transport grooves are present in ventral side of hemichordates, dorsal side of urochordates and Pharyngeal food-transport 46 cephalochordates. Vetulicolians proposed to have food-transport grooves on both the dorsal and ventral sides of the pharyngeal region (see ref. groove 48). Absent (0), present (1). Crown-group hemichordates, cephalochordates and urochordates have peripharyngeal atrium. The peripharyngeal atrium 47 Peripharyngeal atrium. in vetulicolians remains controversial (see ref. 7, 49). We coded vetulicolians, vetulocystids and Saccorhytus as (?). 48 Notochord Absent (0), present (1). Present only in chordates. X-shaped mark around 49 the antero-posterior Absent (0), present (1). In Banffia and Heteromorphus, there is an X-type torsion between the anterior and the posterior body. junction ?Lenticulate respiratory Absent (0), present (1). In Vetulocystis and Dianchicystis, there is a lenticulate structure between the anterior and the posterior body that has been 50 organ interpreted as a respiratory organ (see ref. 10) V- or W-shaped V- or W-shaped myomeres. Absent (0), present (1). Such myomeres are unique to cephalochordates and vertebrates. No such myomeres are 51 myomeres visible in vetulicolians, vetulicystids and Saccorhytus. Absent (0), present (1). Neural crest cells have been considered unique to vertebrates, but recently this feature has been reportedly developed also 52 Neural crest cells in urochordate embryos (see ref. 50) Absent (0), present (1). Neurogenic placodes was traditionally considered as a innovation of vertebrates, but recently this feature has been 53 Neurogenic placodes reportedly developed also in urochordates (see ref. 50) 54 Tornaria-like larva Absent (0), present (1). Tornaria-like larvae are present only in echinoderms and hemichordates (see refs. 51,52).

55 Trochophore Absent (0), present (1). A trochophore larva is present in both Mollusca and Annelida.

56 Oxygen transport proteins Absent (0), present (1) (see ref. 53)

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57 tRNA Lys Absent (0), present (1) (see ref. 33).

58 Lox2/4 Absent (0), present (1) (see ref. 33).

59 Abd-B duplication Absent (0), present (1) (see ref. 33).

60 Antp Absent (0), present (1) (see ref. 33).

61 HRP Absent (0), present (1). An immunoreactive marker, horseradish peroxidase (HRP), is present in all ecdysozoans (see ref. 54).

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(d) PAUP commands

#NEXUS

Begin Data;

Dimensions nTax=25 nChar=61;

FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="0123" INTERLEAVE=YES;

Matrix

Cnidaria 1 1 0 0 - 0 0 0 ? 0 0 0 0 0 - 0 - 0 0 0 - - 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 - - - - - 0 - - 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Acoelomorpha 0 1 1 0 0 - 0 0 0 1 0 0 0 0 - 0 ------0 0 0 - - 0 0 0 0 1 0 0 0 0 0 - - - - - 0 - - 0 0 - 0 0 0 0 0 0 0 ? ? ? ? 0

Arthropoda - 1 1 1 0 0 1 2 2 0 0 0 0 1 1 1 0 1 1 - - - - 0 0 1 1 1 1 1 0 1 0 1 0 0 0 0 - - - - - 0 - - 0 0 - 0 0 0 0 0 0 1 ? 0 0 1 1

Onychophora - 1 1 1 0 0 1 0 {12} 1 0 0 0 1 1 1 0 1 1 - - - - 0 0 1 1 1 1 1 0 1 0 1 0 0 0 0 - - - - - 0 - - 0 0 - 0 0 0 0 0 0 1 ? 0 0 1 1

Kinorhyncha ? 1 1 0 - 0 1 0 2 1 0 1 1 1 1 1 0 0 0 - - - - 0 0 1 0 1 1 1 0 1 0 1 0 0 0 0 - - - - - 0 - - 0 0 - 0 0 0 0 0 0 1 ? ? ? ? 1

Priapulida 1 1 1 {01} - 0 1 0 2 1 0 1 1 1 1 0 - 1 0 - - - - 0 0 1 0 1 1 1 0 1 0 1 0 0 0 0 - - - - - 0 - - 0 0 - 0 0 0 0 0 0 1 ? 0 0 1 1

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Mollusca 0 {01} 1 1 0 0 1 0 1 0 0 0 0 1 1 {01} 0 1 0 - - - - 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 - - - - - 0 - - 0 0 - 0 0 0 0 0 1 1 0 0 0 0 0

Annelida 0 {01} 1 1 0 0 1 0 1 0 0 0 0 1 1 1 0 1 0 - - - - 0 0 1 0 0 0 0 1 0 0 1 0 0 0 0 - - - - - 0 - - 0 0 - 0 0 0 0 0 1 1 0 0 0 0 0

Echinodermata 1 0 1 1 1 1 1 2 {02} 0 0 0 0 1 {01} 0 - 0 - - - {01} - 1 1 0 - 0 0 0 0 0 0 0 0 0 {01} 0 - - - - - 0 - - ? 0 - 0 0 0 0 1 0 1 1 1 1 0 0

Enteropneusta 1 0 1 1 1 1 1 2 1 0 0 0 0 1 1 0 - 0 - - - - - 1 1 0 - 0 0 0 0 0 0 1 1 0 1 0 - - - 1 0 1 1 1 1 0 - 0 0 0 0 1 0 1 1 1 1 0 0

Urochordata - 0 1 1 1 0 1 1 ? 0 0 0 0 1 0 ? - 0 0 - - - - 0 0 0 - 0 0 0 0 0 0 0 1 0 1 0 - - - 1 0 1 1 1 1 1 0 0 0 1 1 0 0 1 0 1 1 0 0

Cephalochordata 1 0 1 1 1 0 1 1 1 0 0 0 0 1 0 1 - 0 0 - - - - 1 1 0 - 0 0 0 0 0 0 0 1 0 1 0 - - - 1 0 1 1 1 1 1 - 0 1 0 0 0 0 1 0 1 1 0 0

Vertebrata 1 0 1 1 1 0 1 0 1 0 0 0 0 1 0 1 - 0 0 - - - - 1 1 0 - 0 0 0 0 0 0 0 1 0 1 0 - - - 1 0 0 1 0 0 1 - 0 1 1 1 0 0 1 0 1 1 0 0

Vetulicola ? ? 1 1 ? ? ? 1 2 0 2 0 0 1 1 1 1 0 0 1 1 0 0 1 1 0 ? 0 - - 0 ? 0 ? 0 1 1 1 0 1 0 0 0 1 ? 1 ? 0 0 0 0 ? ? ? ? ? ? ? ? ? ?

Beidazoon ? ? 1 1 ? ? ? 1 2 0 2 0 0 1 1 1 1 0 0 1 1 0 0 1 1 0 ? 0 - - 0 ? 0 ? 0 1 1 1 0 1 0 0 0 1 ? 1 ? 0 0 0 0 ? ? ? ? ? ? ? ? ? ?

Ooedigera ? ? 1 1 ? ? ? 1 2 0 2 0 0 1 1 1 1 0 0 1 0 0 0 1 1 0 ? 0 - - 0 ? 0 ? 0

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1 1 1 0 1 0 0 0 1 ? 1 ? 0 0 0 0 ? ? ? ? ? ? ? ? ? ?

Pomatrum ? ? 1 1 ? ? ? 1 2 1 1 0 0 1 1 1 1 0 0 1 0 0 0 1 1 0 ? 0 - - 0 ? 0 ? 0 1 1 1 0 1 0 0 1 1 ? 1 ? 0 0 0 0 ? ? ? ? ? ? ? ? ? ?

Xidazoon ? ? 1 1 ? ? ? 1 2 1 1 0 0 1 1 1 1 0 0 1 0 0 0 1 1 0 ? 0 - - 0 ? 0 1 0 1 1 1 0 1 0 0 1 1 ? 1 ? 0 0 0 0 ? ? ? ? ? ? ? ? ? ?

Didazoon ? ? 1 1 ? ? ? 1 2 1 2 0 0 1 1 1 1 0 0 1 0 0 0 1 1 0 ? 0 - - 0 ? 0 ? 0 1 1 1 0 1 0 0 1 1 1 1 ? 0 0 0 0 ? ? ? ? ? ? ? ? ? ?

Yuyuanozoon ? ? 1 1 ? ? ? 1 2 0 2 0 0 1 1 1 1 0 0 1 0 0 0 1 1 0 ? 0 - - 0 ? 0 ? 0 1 1 1 0 1 0 0 1 1 ? 1 ? 0 0 0 0 ? ? ? ? ? ? ? ? ? ?

Heteromorphus ? ? 1 1 ? ? ? 1 2 1 2 0 0 1 1 1 0 0 0 1 0 0 1 1 1 0 ? 0 - - 0 ? 0 ? 0 1 1 1 0 1 0 0 0 1 ? 1 ? 0 1 0 0 ? ? ? ? ? ? ? ? ? ?

Banffia ? ? 1 1 ? ? ? 1 2 1 2 0 0 1 1 1 0 0 0 1 0 0 1 1 ? 0 ? 0 - - 0 ? 0 ? 0 1 1 1 0 1 0 0 0 1 ? 1 ? 0 1 0 0 ? ? ? ? ? ? ? ? ? ?

Vetulocystis ? ? 1 ? ? ? ? 1 ? ? ? 0 0 1 1 1 0 0 0 0 - 1 1 1 1 ? ? 0 - - 0 ? 0 ? ? 0 1 1 1 0 1 0 0 1 ? ? ? 0 0 1 0 ? ? ? ? ? ? ? ? ? ?

Dianchicystis ? ? 1 ? ? ? ? 1 ? ? ? 0 0 1 1 1 0 0 0 0 - 1 1 1 1 ? ? 0 - - 0 ? 0 ? ? 0 1 1 1 0 1 0 0 1 ? ? ? 0 0 1 0 ? ? ? ? ? ? ? ? ? ?

Saccorhytus ? ? 1 ? ? ? ? 0 0 1 1 0 0 0 - 0 - 0 0 0 - 1 0 1 1 ? ? 0 - - 0 ? ? 0 ? 0 1 1 2 0 2 0 0 1 ? 0 ? 0 - 0 0 ? ? 0 0 ? ? ? ? ? ?

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;

End;

Begin Paup;

Log File=Log_saccorhytus.txt;

Cstatus;

Outgroup Cnidaria;

Set Criterion=Parsimony Maxtrees=1000 Increase=No Autoclose=Yes;

BandB;

DescribeTrees /Plot=Phylogram BrLens=Yes;

SaveTrees File=MPTrees.tre Root=Yes BrLens=Yes SaveBootp=BrLens;

Pscores /TL=Yes CI=Yes RI=Yes RC=Yes HI=Yes ScoreFile=Score_MPTrees.txt;

ConTree All/Strict=No MajRule=Yes TreeFile=MajorityConTree.tre;

BootStrap nReps=1000 ConLevel=50;

SaveTrees File=BootstrapMajorityConTree.tre Root=Yes BrLens=Yes Savebootp=Both From=1 To=1;

HSearch;

ReWeight;

HSearch;

ReWeight;

SaveTrees File= MPTrees_Weighted.tre Root=Yes BrLens=Yes SaveBootp=BrLens;

Pscores /TL=Yes CI=Yes RI=Yes RC=Yes HI=Yes ScoreFile=Score_MPTrees_Weighted.txt;

ConTree All/Strict=Yes MajRule=N TreeFile=StrictConTree_Weighted.tre;

Log Stop;

End;

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(e) Log file performing the PAUP commands.

P A U P * Version 4.0b10 for 32-bit Microsoft Windows Tue Oct 04 11:05:05 2016

------NOTICE------This is a beta-test version. Please report any crashes, apparent calculation errors, or other anomalous results. There are no restrictions on publication of results obtained with this version, but you should check the WWW site frequently for bug announcements and/or updated versions. See the README file on the distribution media for details. ------

Character-status summary: Current optimality criterion = parsimony No characters are excluded Of 61 total characters: All characters are of type 'unord' All characters have equal weight 1 character is constant 1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59

Outgroup status changed: 1 taxon transferred to outgroup Total number of taxa now in outgroup = 1 Number of ingroup taxa = 24

MaxTrees reset to 1000

Branch-and-bound search settings: Optimality criterion = parsimony Character-status summary: Of 61 total characters: All characters are of type 'unord' All characters have equal weight 1 character is constant 1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59 Gaps are treated as "missing" Multistate taxa interpreted as uncertainty Initial upper bound: unknown (compute heuristically) Addition sequence: furthest 'MaxTrees' setting = 1000 (will not be increased) Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted

Branch-and-bound search completed: Score of best tree found = 96 Number of trees retained = 144 Time used = 0.82 sec

Tree description:

Unrooted tree(s) rooted using outgroup method Optimality criterion = parsimony Character-status summary: Of 61 total characters: All characters are of type 'unord' All characters have equal weight 1 character is constant

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1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59 Gaps are treated as "missing" Multistate taxa interpreted as uncertainty Character-state optimization: Accelerated transformation (ACCTRAN)

Tree number 1 (rooted using user-specified outgroup)

Branch lengths and linkages for tree #1 (unrooted)

Assigned Minimum Maximum Connected branch possible possible Node to node length length length ------Cnidaria (1)* 48 1 1 1 26 48 4 1 6 Acoelomorpha (2) 26 0 0 1 Saccorhytus (25) 26 6 6 9 47 48 10 6 12 31 47 2 1 3 29 31 8 6 9 27 29 2 2 2 Arthropoda (3) 27 2 1 2 Onychophora (4) 27 0 0 1 28 29 3 2 4 Kinorhyncha (5) 28 1 1 2 Priapulida (6) 28 1 1 1 30 31 3 3 4 Mollusca (7) 30 1 0 1 Annelida (8) 30 0 0 1 46 47 10 5 14 35 46 3 1 9 32 35 5 5 5 Echinodermata (9) 32 3 1 4 Enteropneusta (10) 32 1 0 3 34 35 3 2 6 33 34 2 2 2 Urochordata (11) 33 3 2 3 Vertebrata (13) 33 4 4 5 Cephalochordata (12) 34 0 0 1 45 46 3 1 7 43 45 4 4 9 41 43 2 1 3 40 41 0 0 1 36 40 1 1 1 Vetulicola (14) 36 0 0 0 Beidazoon (15) 36 0 0 0 39 40 1 1 2 38 39 1 1 2 37 38 1 1 2 Pomatrum (17) 37 0 0 0 Xidazoon (18) 37 0 0 1 Didazoon (19) 38 0 0 0 Yuyuanozoon (20) 39 0 0 0 Ooedigera (16) 41 0 0 0 42 43 2 2 3 Heteromorphus (21) 42 0 0 0 Banffia (22) 42 0 0 0 44 45 3 1 4 Vetulocystis (23) 44 0 0 0 Dianchicystis (24) 44 0 0 0 ------Sum 96

Tree length = 96 Consistency index (CI) = 0.6771 Homoplasy index (HI) = 0.3229 CI excluding uninformative characters = 0.6737

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HI excluding uninformative characters = 0.3263 Retention index (RI) = 0.8394 Rescaled consistency index (RC) = 0.5683

144 trees saved to file "F:\deuterostomes\OneDrive\phylogeny\final 18 1004\MPTrees.tre"

Lengths and fit measures of trees in memory: Character-status summary: Of 61 total characters: All characters are of type 'unord' All characters have equal weight 1 character is constant 1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59 Gaps are treated as "missing" Multistate taxa interpreted as uncertainty

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Tree lengths written to file "F:\deuterostomes\OneDrive\phylogeny\final 18 1004\Score_MPTrees.txt"

Sum of min. possible lengths = 65 Sum of max. possible lengths = 258

Tree # 1 2 3 4 5 6 7 8 9 10 11 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 12 13 14 15 16 17 18 19 20 21 22 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 23 24 25 26 27 28 29 30 31 32 33 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 34 35 36 37 38 39 40 41 42 43 44 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 45 46 47 48 49 50 51 52 53 54 55 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 56 57 58 59 60 61 62 63 64 65 66 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 67 68 69 70 71 72 73 74 75 76 77 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 78 79 80 81 82 83 84 85 86 87 88 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 89 90 91 92 93 94 95 96 97 98 99 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568

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HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 100 101 102 103 104 105 106 107 108 109 110 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 111 112 113 114 115 116 117 118 119 120 121 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 122 123 124 125 126 127 128 129 130 131 132 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 133 134 135 136 137 138 139 140 141 142 143 Length 96 96 96 96 96 96 96 96 96 96 96 CI 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 RI 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 RC 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 HI 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323

Tree # 144 Length 96 CI 0.677 RI 0.839 RC 0.568 HI 0.323

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50% Majority-rule consensus of 144 trees

Bipartitions found in one or more trees and frequency of occurrence:

1 2 2 1234567890123456789012345 Freq % ------...... *********... 144 100.0% ...... *******..... 144 100.0% ..******...... 144 100.0% ..****...... 144 100.0% ..**...... 144 100.0% ....**...... 144 100.0% ...... **...... 144 100.0% ...... **... 144 100.0% ...... **. 144 100.0% ...... **...... 144 100.0% ...... ***...... 144 100.0%

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...... *.*...... 144 100.0% ...... **...... 144 100.0% ..*********************** 141 97.9% ...... ***************** 141 97.9% ...... **...... 126 87.5% ...... ************ 99 68.8% ...... ***...... 90 62.5% ...... ***...... 78 54.2% ...... ****..... 78 54.2% ...... ***...*..... 66 45.8% ...... *****...... 63 43.8% ...... ***********. 54 37.5% ...... *************** 42 29.2% ...... *** 33 22.9% ...... ****************. 33 22.9% ...... **...************ 33 22.9% ...... *********..* 33 22.9% ...... ***..**..... 27 18.8% ...... *****..... 18 12.5% ...... **.****..... 18 12.5% ...... **************. 15 10.4% ...... **.*..... 12 8.3% ...... *****.*..... 12 8.3% ...... ***.***..... 9 6.3% ...... *****...... **. 9 6.3% ...... **************... 9 6.3% ...... **...... * 3 2.1% ...... ***...... **. 3 2.1% ...... ************... 3 2.1% .*...... * 3 2.1% ..**********************. 3 2.1%

Consensus tree(s) written to treefile: F:\deuterostomes\OneDrive\phylogeny\final 18 1004\MajorityConTree.tre

Bootstrap method with heuristic search: Number of bootstrap replicates = 1000 Starting seed = 912710971 Optimality criterion = parsimony Character-status summary: Of 61 total characters: All characters are of type 'unord' All characters have equal weight 1 character is constant 1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59 Gaps are treated as "missing" Multistate taxa interpreted as uncertainty Starting tree(s) obtained via stepwise addition Addition sequence: simple (reference taxon = Cnidaria) Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect 'MaxTrees' setting = 1000 (will not be increased) Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted

1000 bootstrap replicates completed Note: Effectiveness of search may have been diminished due to tree-buffer overflow. Time used = 00:11:22.9

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Bootstrap 50% majority-rule consensus tree

Bipartitions found in one or more trees and frequency of occurrence (bootstrap support values):

1 2 2 1234567890123456789012345 Freq % ------..****...... 973.96 97.4% ....**...... 899.74 90.0% ...... **...... 849.59 85.0%

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...... **. 840.79 84.1% ...... **... 831.87 83.2% ..******...... 830.12 83.0% ...... *********... 811.32 81.1% ..*********************** 747.78 74.8% ..**...... 714.57 71.5% ...... ***************** 667.25 66.7% ...... ***...... 649.32 64.9% ...... **...... 583.91 58.4% ...... ***********. 568.45 56.8% ...... **...... 564.36 56.4% ...... *******..... 551.03 55.1% ...... **...... 545.11 54.5% ...... ****..... 486.31 48.6% ...... *.*...... 454.69 45.5% ...... ***...... 366.38 36.6% ...... ************ 364.65 36.5% ...... *****...... 299.32 29.9% ..**********************. 297.56 29.8% ...... ****************. 276.86 27.7% ...... **...... 237.77 23.8% ...***...... 230.01 23.0% .*...... * 203.83 20.4% ...... ****...... 159.84 16.0% ...... **...************ 155.70 15.6% ...... **...... 153.00 15.3% ...... ***...*..... 147.15 14.7% ..****.*...... 139.25 13.9% ...... **************** 128.09 12.8% ...... **...***********. 117.02 11.7% ...... ***.**... 115.37 11.5% ...... ***..****... 99.87 10.0% ...... **.************** 93.20 9.3% ...... *** 92.44 9.2% ..******.....***********. 89.82 9.0% ...... ****.************ 84.40 8.4% ...... **************. 83.81 8.4% ...... ****. 82.13 8.2% ...... *******... 81.61 8.2% ...... ****.***********. 76.36 7.6% ...... *************** 75.32 7.5% ...... *....************ 72.54 7.3% ...... ******... 70.88 7.1% ...... ***...... 68.80 6.9% ...... **...... * 65.17 6.5% ...... *....***********. 62.97 6.3% ...... *****..... 61.33 6.1% ...... ***************. 57.43 5.7% ...... **.****..... 57.13 5.7% ...... *********..* 56.21 5.6%

1364 groups at (relative) frequency less than 5% not shown

1 tree saved to file "F:\deuterostomes\OneDrive\phylogeny\final 18 1004\BootstrapMajorityConTree.tre"

Heuristic search settings: Optimality criterion = parsimony Character-status summary: Of 61 total characters: All characters are of type 'unord' All characters have equal weight 1 character is constant 1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59 Gaps are treated as "missing" Multistate taxa interpreted as uncertainty Starting tree(s) obtained via stepwise addition

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Addition sequence: simple (reference taxon = Cnidaria) Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect 'MaxTrees' setting = 1000 (will not be increased) Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted

Heuristic search completed Total number of rearrangements tried = 716437 Score of best tree(s) found = 96 Number of trees retained = 144 Time used = 0.15 sec

Characters reweighted by maximum value of rescaled consistency indices.

Heuristic search settings: Optimality criterion = parsimony Character-status summary: Of 61 total characters: All characters are of type 'unord' 43 characters have weight 1 18 characters have weights other than 1 1 character is constant 1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59 Gaps are treated as "missing" Multistate taxa interpreted as uncertainty Starting tree(s) obtained via stepwise addition Addition sequence: simple (reference taxon = Cnidaria) Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect 'MaxTrees' setting = 1000 (will not be increased) Branches collapsed (creating polytomies) if maximum branch length is zero 'MulTrees' option in effect Topological constraints not enforced Trees are unrooted

Heuristic search completed Total number of rearrangements tried = 222605 Score of best tree(s) found = 59.24444 Number of trees retained = 45 Time used = 0.07 sec

Characters reweighted by maximum value of rescaled consistency indices.

45 trees saved to file "F:\deuterostomes\OneDrive\phylogeny\final 18 1004\MPTrees_Weighted.tre"

Lengths and fit measures of trees in memory: Character-status summary: Of 61 total characters: All characters are of type 'unord' 42 characters have weight 1 19 characters have weights other than 1 1 character is constant 1 variable character is parsimony-uninformative Number of parsimony-informative characters = 59 Gaps are treated as "missing" Multistate taxa interpreted as uncertainty

Tree lengths written to file "F:\deuterostomes\OneDrive\phylogeny\final 18 1004\Score_MPTrees_Weighted.txt"

Sum of min. possible lengths = 48.99389

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Sum of max. possible lengths = 177.09389

Tree # 1 2 3 4 5 6 7 Length 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 CI 0.878 0.878 0.878 0.878 0.878 0.878 0.878 RI 0.947 0.947 0.947 0.947 0.947 0.947 0.947 RC 0.831 0.831 0.831 0.831 0.831 0.831 0.831 HI 0.122 0.122 0.122 0.122 0.122 0.122 0.122

Tree # 8 9 10 11 12 13 14 Length 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 CI 0.878 0.878 0.878 0.878 0.878 0.878 0.878 RI 0.947 0.947 0.947 0.947 0.947 0.947 0.947 RC 0.831 0.831 0.831 0.831 0.831 0.831 0.831 HI 0.122 0.122 0.122 0.122 0.122 0.122 0.122

Tree # 15 16 17 18 19 20 21 Length 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 CI 0.878 0.878 0.878 0.878 0.878 0.878 0.878 RI 0.947 0.947 0.947 0.947 0.947 0.947 0.947 RC 0.831 0.831 0.831 0.831 0.831 0.831 0.831 HI 0.122 0.122 0.122 0.122 0.122 0.122 0.122

Tree # 22 23 24 25 26 27 28 Length 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 CI 0.878 0.878 0.878 0.878 0.878 0.878 0.878 RI 0.947 0.947 0.947 0.947 0.947 0.947 0.947 RC 0.831 0.831 0.831 0.831 0.831 0.831 0.831 HI 0.122 0.122 0.122 0.122 0.122 0.122 0.122

Tree # 29 30 31 32 33 34 35 Length 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 CI 0.878 0.878 0.878 0.878 0.878 0.878 0.878 RI 0.947 0.947 0.947 0.947 0.947 0.947 0.947 RC 0.831 0.831 0.831 0.831 0.831 0.831 0.831 HI 0.122 0.122 0.122 0.122 0.122 0.122 0.122

Tree # 36 37 38 39 40 41 42 Length 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 CI 0.878 0.878 0.878 0.878 0.878 0.878 0.878 RI 0.947 0.947 0.947 0.947 0.947 0.947 0.947 RC 0.831 0.831 0.831 0.831 0.831 0.831 0.831 HI 0.122 0.122 0.122 0.122 0.122 0.122 0.122

Tree # 43 44 45 Length 55.82222 55.82222 55.82222 CI 0.878 0.878 0.878 RI 0.947 0.947 0.947 RC 0.831 0.831 0.831 HI 0.122 0.122 0.122

WWW.NATURE.COM/NATURE | 35 doi:10.1038/nature21072 RESEARCH SUPPLEMENTARY INFORMATION

Strict consensus of 45 trees:

Consensus tree(s) written to treefile: F:\deuterostomes\OneDrive\phylogeny\final 18 1004\StrictConTree_Weighted.tre