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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doi:10.1038/nature21072
Supplementary Table 1. List and measurements of the specimens of Saccorhytus
Specimen
number
number of
cones
photos of specimens
length(μm)
width(μm)
right
left
XX23-248
1011.81
629.92
0
0
XX25-62
557.78
513.33
0
2
XX26-170
1210.74
537.19
XX27-168
987.8
788.62
XX34-298
1078.51
752.07
diameter of
oral
nodular
cone
protuber
rugae
aperture(μm)
ances
diameter of
cones (μm)
?3 ?4
?
number of spines
right
left
chevron width of
circular
length of
pattern(μ chevron(μ
pores
spines(μm)
m)
m)
rectangle
pore
?
Y
Y
-
-
-
5.15
2.06
-
N
77.78 74.86 51.11 36.00
Y
Y
-
-
-
3.43
2.29
11.92
N
Y
Y
-
-
-
11.72
4.69
30.39
N
26.47
N
15.15
Y
-
-
2
2 195.65 177.03
65.22 62.5
Y
Y
2
2
>52.66
>86.41
>81.30
-
4
109.09 33.06
153.72 56.20
79.34 71.07
3 264.46 181.82
250.00
328.13 195.31
101.56
N
Y
1
1
168.67
>46.88
11.05
-
4.07
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XX35-228
XX36-22
XX42-83
XX42-323
116.3
N
？
-
-
>96.77
-
-
-
N
160.19 247.30 47.57 74.32
147.24
79.75
Y
Y
1
1
>63.73
>50.00
-
-
18.33
N
54.14 27.45
103.66 35.53
76.42 31.25
78.32 73.68
Y
N
1
1
55.74 57.84
-
N
84.21
N
N
-
-
-
-
-
16.91
N
N
Y
-
-
-
-
-
42.66
N
39.20 90.82
64.44
150.19
N
？
-
-
-
84.2
8.93
-
N
1164.44
637.04
1
0
920
500
2
1
4
82.71 83.33
284.15 78.95
4
178.86 78.13
174.83 360.66
147.37
929.69
722.66
800
793.89
223.91
XX44-273
1198.29
695.8
4
37.92 83.53
132.09 193.46
52.73 40.73
330.92 140.35
4
34.46
71.74 366.87
245.09 38.89
72.64 88.72
41.16
XX44-301
1064.16
823.02
2
2
164.35 187.57
130.30 212.03
5.63
3.52
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XX45-1
XX45-20
1071.43
991.47
1010.21
753.55
3
66.96
93.75 187.5
119.64
126.83 50
3
91.06 28.34
107.90
84.64
151.93
105.45
Y
Y
-
-
3
32.48
83.06 133.9
101.92
4 244.46 63.51
210.07
118.81 225.64 33.48 97.95
186.54
Y
Y
-
1
27.21
125.56
223.65
37.42
117.63
196.52
152.84
Y
Y
-
-
72.54 73.52
215.75
143.21
Y
Y
-
54.25 70.32
77.70 116.39
156.64 91.07
3 213.66 112.15
148.71
203.66 362.06
281.20
Y
Y
-
XX45-56
1156.51
861.55
3
60.13 207.54
323.27 65.63
4
194.25 319.62
224.06
XX46-27
760.66
686.36
4
91.03 94.13
238.03 179.75
XX47-498
1107.28
949.18
3
-
11.27
2.38 22 55.6
N
9.92
4.51
29.2
N
-
13.21
6.19
27.53
N
-
-
14.45
8.64
-
N
-
-
-
22.46
N
22.97
-
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XX47-558
731.46
564.89
XX48-64
985.73
778.58
3
XX48-288
960.4
518.92
3？
XX48-399
949.87
722.34
XX49-183
798.42
672.12
XX50-360
548.94
425.9
XX51-326
969.38
729.59
72.89
105.04
198.37
185.16
Y
Y
-
-
-
11.19
6.8
18.76
N
90.77 142.99 48.08 90.90
206.34 71.37 152.00 40.96
92.54
113.94
Y
Y
-
-
-
8.28
4.14
24.32
N
42.50 53.18 26.31 32.99
108.95
71.35
N
Y
-
-
-
-
-
22.67
N
37.71
84.80 266.91
176.06
3 345.08 116.69
267.99
134.02 336.20 61.16 93.48
248.08
Y
Y
-
-
-
-
-
20.06
N
-
23.18
N
-
N
-
N
4
3
3? ？
1
3？
3
94.45 130.46
259.48 205.25
188.66
130.33
Y
Y
-
-
-
-
1 144.47 171.17
119.48
74.78
N
Y
-
-
-
11.74
106.98 212.54 47.42 59.86
75.18
35.90
N
N
-
-
-
-
7.03
-
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RESEARCH SUPPLEMENTARY INFORMATION
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XX51-334
1005.1
785.71
-
-
-
-
Y
N
-
-
-
-
-
20.46
32.26
N
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
XX54-249
829.31
645.97
3? ？
?128.77
223.89
?118.36
?90.27
149.03
?76.29
Y
N
-
-
-
-
-
-
N
XX54-354
898.35
857.44
2？
157.87 182.13
121.68
130.09
Y
N
2
-
152.34
184.18
-
-
XX54-387
934.7
567.48
3？
71.50 214.28 36.26 64.49
140.21
23.13
Y
N
-
-
-
20.03
10.62
?48.66
-
N
N
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RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
XX55-43
1084.58
856.23
2？
210.08 261.00 179.35 82.45
Y
N
-
-
-
12.34
8.03
-
N
XX55-310
1024.35
906.88
2？
281.17 181.92
189.31
118.57
Y
Y
-
-
-
-
-
23.71
N
XX55-338
951.72
570.98
3？
50.52 125.22 17.09 70.10
95.46
58.39
Y
Y
1
113.19
-
-
9.12
N
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
Y
N
-
-
-
8.35
6.25
-
N
-
-
1？
-
-
135.89
52.05
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XX57-351
848.92
492.98
2？
57.16 162.40 30.70 66.29
Y
N
1
XX57-371
1152.72
745.52
2？
188.62 77.75 94.95 58.69
Y
N
-
-
XX57-473
847.29
658.12
-
N
N
-
-
xx58-118
1160
830
180
Y
?
xx58-125
1326
697 ？
xx58-331
1108
897
-
-
-
2？
175
4
4？
278
150
89.2
12.33
8.31
-
N
-
9.33
6.13
-
N
-
-
-
16.3
N
-
-
20
N
3
?
N
3
25
N
1
150
318
151
N
?
-
-
-
231
166
N
?
-
-
-
10
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xx59-235
1050
451 ？
xx61-27
1251
968
2
3?
110
88
Y
Y
-
-
-
10
3
?
N
330
245
Y
Y
-
-
-
-
-
-
N
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RESEARCH SUPPLEMENTA
072
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
RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
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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RESEARCH SUPPLEMENTARY INFORMATION
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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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^`
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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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(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).
3
Bilateral symmetry
Absent (0), present (1). Absent in cnidarians. Echinoderms were originally bilateral in symmetry (see ref. 36).
See ref. 33.
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
5
Coelom formation
Schizocoely (0), enterocoely (1). Develop of coelom by schizocoely in Arthropoda, Onychophora, and Annelida; the coelom of Echinodermata,
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)
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).
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.
9
Position of mouth
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).
All vetulicolians have terminal mouth. The mouth of urochordates is coded as "?" (See ref.
43
anterior-posterior, dorsal-ventral) between cnidarians and bilaterians remains unresolved (see ref.
cnidarians as (?).
46
). The correlation of body axis (i.e. the
), thus we coded the position of mouth in
10
Mouth surrounded by oral Absent (0), present (1). Mouth surrounded by oral folds are present in acoelomorphs, scalidophorans, extant onychophorans and Saccorhytus,
folds or plates
Pomatrum, Xidazoon, Didazoon, and Banffia, hence coded as (1).
11
Multi-circlets of oral
folds
Absent (0), present (1), valved (2). Pomatrum, Xidazoon and Saccorhytus are coded as (1).
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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.
15
Position of anus
16
Segmentation or
metamerism
17
Body divided into 13
segments
coded as (0).
18
Terminal addition during
ontogeny
Absent (0), present (1). Addition of posterior segments during ontogeny along the anterior-posterior body axis is seen in arthropods, priapulids,
annelids, mollusks, but no evidence in cnidarians, acoelomorphs, kinorhynchs, vetulicolians, vetulocystids, and Saccorhytus.
Anterior to the tail (0). Terminal anus (1). Hemichordates, echinoderms and vetulicolians and vetulocystids were coded as (1). Chordates
(urochordates, cephalochordates and vertebrates coded as (0)). Not applicable in cnidarian, acoelomorphs and Saccorhytus.
Absent (0), present (1). Some aplacophoran postlarva showing distinct metamerism (see ref. 47), we coded it as {01}.
Absent (0), present (1). Most vetulicolians have 13 body segments (see ref. 31). Kinorhyncha has 13 segments but not homologous (see ref. 43),
Anterior segments fused
19
and condensed into a
head region with sensory
or feeding organs
Absent (0), present (1). The heads of arthropods and stem-group onychophorans are formed by fusion of anterior segments.
Anterior body with fused
20
dorsal and ventral
marginal zones
Absent (0), present (1). Dorsal and ventral marginal of the anterior body in vetulicolians are fused together forming a longitudinal narrow zone.
21
Shape of anterior body
region
Ovoid (0), subquadrate present (1). This character is from Aldridge et al. and only applicable for vetulicolians
22
Shape of pharyngeal
region
Doliform (0); globular (1). This character is only appliable for vetulicolians, vetulocystids and Saccorhytus
Posterior body with
23
numerous narrow
segments/annulations
Absent (0), present (1). In Banffia and Heteromorphus, there are many fine annulations between the anterior and the posterior body. Such
annulations are absent in other genera of vetulicolians.
24
Endoskeleton
mesodermally derived
Absent (0), present (1). The hard tissue under the surface membrane of vetulicolians is interpreted as endoskeleton homologous with crown-group
deuterostomes (see ref. 8).
25
Surface membrane
(epidermis)
Absent (0), present (1). The soft, labile (decay-prone) surface membrane can be observed in most specimens of various vetulicolian taxa, which
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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RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
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
27
Cuticle mainly made of
Į-chitin
Absent (0), present (1). Į-chitin cuticle is present in arthropods and onychophorans.
28
Growth by ecdysis
(molting)
Absent (0), present (1). No evidence of moulting in vetulicolians, vetulocystids and Saccorhytus.
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).
34
Longitudinal ventral
nerve cord(s)
35
Longitudinal dorsal nerve
cord(s)
36
Longitudinal lateral
grooves (median zone).
37
Pharyngeal gill slits.
38
Body cones
Absent (0), present (1).
39
Body cones with radial
folds
Absent (0), present (1).
40
Orientation of body cones Perpendicular to the body surface(0); anteriorly directed (1)
41
Number of body cones
Absent (0), present (1). Arthropods, onychophorans, priapulids, kinorhychs, annelids and mollusks are coded as (1). Hemichordates have dorsal
and ventral nerve cords, coded as (1). Longitudinal ventral nerve cord is seen Xidazoon 40. Saccorhytus has a relatively large ventral mouth, but
somewhat shorter than the body length, thus assumed no space for the ventral nerve cord, we code it as (0).
Absent (0), present (1). Unique in chordates. Hemichordates have both ventral and dorsal nerve cords. Saccorhytus is coded as (?).
Absent (0), present (1). Two longitudinal lateral grooves where the gill pouches situated are present in Vetulicola, Beidazoon, and Ooedigera.
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
pharyngeal gill slits (see ref. 1). The body cones in Saccorhytus are attested as pecursors of pharyngeal gill slits (see main text).
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
44
accomplished within
pharynx
Absent (0), present (1). Vetulicolians have been demonstrated as filtering feeders using their pharynx (see ref. 45). The body cones of Saccorhytus
indicate a filtering feeding habit although a predatory potential cannot be excluded.
Endostyle, epibranchial
45
ridge, or thyroid that
accumulates iodine and
secretes mucus
Absent (0), present (1). Present in all major groups of deuterostomes except echinoderms. The stomochord of enteropneust hemichordates taken
to be homologous to the pharyngeal endostyle (see ref. 48).
46
Absent (0), present (1). Pharyngeal food-transport grooves are present in ventral side of hemichordates, dorsal side of urochordates and
Pharyngeal food-transport
cephalochordates. Vetulicolians proposed to have food-transport grooves on both the dorsal and ventral sides of the pharyngeal region (see ref.
groove
48
).
47
Peripharyngeal atrium.
Absent (0), present (1). Crown-group hemichordates, cephalochordates and urochordates have peripharyngeal atrium. The 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
junction
Absent (0), present (1). In Banffia and Heteromorphus, there is an X-type torsion between the anterior and the posterior body.
50
?Lenticulate respiratory
organ
Absent (0), present (1). In Vetulocystis and Dianchicystis, there is a lenticulate structure between the anterior and the posterior body that has been
interpreted as a respiratory organ (see ref. 10)
51
V- or W-shaped
myomeres
V- or W-shaped myomeres. Absent (0), present (1). Such myomeres are unique to cephalochordates and vertebrates. No such myomeres are
visible in vetulicolians, vetulicystids and Saccorhytus.
52
Neural crest cells
Absent (0), present (1). Neural crest cells have been considered unique to vertebrates, but recently this feature has been reportedly developed also
in urochordate embryos (see ref. 50)
53
Neurogenic placodes
Absent (0), present (1). Neurogenic placodes was traditionally considered as a innovation of vertebrates, but recently this feature has been
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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RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
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).
WWW.NATURE.COM/NATURE | 18
RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
(C) References cited in Description of characters.
31. Aldridge, R. J., Hou, X. G., Siveter, D. J., Siveter, D. J. & Gabbott, S. E. The systematics and
phylogenetic relationships of vetulicolians. Palaeontology 50, 131–168 (2007)
32. García–Bellido, D. C. et al. A new vetulicolian from Australia and its bearing on the chordate
affinities of an enigmatic Cambrian group. BMC Evol. Biol. 14, 214 (2014).
33. Peterson, K. J. & Eernisse, D. J. Animal phylogeny and the ancestry of bilaterians; inferences
from morphology and 18S rDNA gene sequences. Evol. Dev. 3, 170–205 (2001).
34. Swofford, D. L. PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods).
Version 4.
(Sinauer Associates, 2003).
35. Goloboff, P. A., Farris, J. S. & Nixon, K. C. TNT, a free program for phylogenetic analysis.
Cladistics 24, 774–786 (2008).
36. Zamora S., Rahman I. A. Deciphering the early evolution of echinoderms with Cambrian
fossils. Palaeontology 57, 1105–1119 (2014).
37. Hou X-G: Early Cambrian large bivalved arthropods from Chengjiang. Acta Palaeontol. Sin.
26, 286–298 (1987).
38. Shu, D-G. On the phylum Vetulicolia. Chinese Sci. Bull. 50, 2342–2354(2005).
39. Luo, H. et al.
Early Cambrian Chengjiang fauna from Kunming Region, China. Kunming:
Yunnan. Sci. & Tech. Press (1999).
40. Shu, D-G. et al. A pipiscid–like fossil from the Lower Cambrian of south China. Nature
400,746–749 (1999).
41. Chen, A-L. et al. A new vetulicolian from the Early Cambrian Chengjiang fauna in Yunnan of
China. Acta Geol. Sinica 77, 281–287(2003).
42. Walcott CD: Middle Cambrian annelids. Cambrian Geology and Paleontology II. Smithson.
Misc. Coll. 57, 109–144 (1911).
43. Schmidt–Rhaesa, A. The Evolution of Organ Systems. p383 (Oxford Univ. Press, 2007).
44. Liu, J. et al. An armoured Cambrian lobopodian from China with arthropod-like appendages.
Nature 470, 526–530 (2011).
45. Ou Q., Shu D., & Mayer, G. Cambrian lobopodians and extant onychophorans provide new
insights into early cephalization in Panarthropoda. Nature Commun. 3, 1261. (2012)
WWW.NATURE.COM/NATURE | 19
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
46. Martindale, M., Finnerty, J. & Henry, J. The Radiata and the evolutionary origins of the
bilaterian body plan. Mol. Phylogenet Evol. 24, 358–365 (2002).
47. Scheltema, A. H. and Ivanov, D. L. An aplacophoran postlarva with iterated dorsal groups of
spicules and skeletal similarities to Paleozoic fossils. Invert. Biol. 121, 1–10 (2002).
48. Satoh, N. et al. On a possible evolutionary link of the stomochord of hemichordates to
pharyngeal organs of chordates. Genesis 52, 925–934(2014).
49. Vinther, J. et al. Vetulicolians from the Lower Cambrian Sirius Passet Lagerstätte, North
Greenland, and the polarity of morphological characters in basal deuterostomes.
Palaeontology 54, 711–719 (2011).
50. Abitua, P. B., Wagner, E., Navarrete, I. A., & Levine, M. Identification of a rudimentary
neural crest in a non–vertebrate chordate. Nature 492, 104–107 (2012).
51. Röttinger, E. & Martindale M.Q. Ventralization of an indirect developing hemichordate by
NiCl2 suggests a conserved mechanism of dorso-ventral (D/V) patterning in
Ambulacraria (hemichordates and echinoderms) Dev. Bio. 354, 173–190 (2011).
52. Henry, J.Q. et al. Deuterostome evolution: early development in the enteropneust
hemichordate, Ptychodera flava. Evo. Dev. 3, 375–390 (2001)
53. Decker, H., and van Holde K.E. Oxygen and the Evolution of Life. Springer (2001).
54. Haase, A., Stern, M., Wächtler, K. & Bicker, G. A tissue-specific marker of Ecdysozoa. Dev.
Genes Evol. 211, 428–433, doi:10.1007/s004270100173 (2001).
WWW.NATURE.COM/NATURE | 20
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doi:10.1038/nature21072
(d) PAUP commands
#NEXUS
Begin Data;
Dimensions nTax=25 nChar=61;
FORMAT
DATATYPE=STANDARD
INTERLEAVE=YES;
MISSING=?
GAP=-
SYMBOLS="0123"
Matrix
Cnidaria 1
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
-
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
Acoelomorpha 0
0
0
0
0
1
0
0
1
?
0
?
0
?
0
?
0
0
0
0
0
0
0
-
1
-
0
0
0
0
0
0
0
0
-
0
0
0
1
0
0
0
0
0
0
Arthropoda
1
0
0
1
0
0
1
0
1
1
?
1
0
0
0
0
0
1
1
0
1
2
1
0
2
1
-
0
1
-
0
1
0
0
1
0
0
0
-
1
1
0
1
0
0
1
1
0
0
0
0
Onychophora
1
0
0
1
0
0
1
0
1
1
?
1
0
0
0
0
0
1
1
0
1
0
1
0
{12} 1
1
1
-
0
1
0
0
1
0
0
0
-
1
1
0
1
0
0
1
1
0
0
0
0
Kinorhyncha
0
0
0
?
0
0
0
1
0
1
1
?
0
?
?
0
0
?
1
0
1
0
1
0
2
0
-
1
1
-
0
1
0
1
1
0
1
0
-
1
1
0
1
0
0
1
1
0
0
0
0
Priapulida
1
0
0
1
0
0
0
1
0
1
1
?
{01} 0
0
0
0
1
1
0
1
0
1
0
2
0
-
1
1
-
0
1
0
1
1
0
1
0
-
1
1
0
1
0
0
0
1
0
0
0
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RESEARCH SUPPLEMENTARY INFORMATION
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Mollusca 0
0
0
1
{01} 1
0
1
0
1
0
0
0
0
0
0
1
0
0
0
0
0
1
0
-
0
0
-
0
0
0
0
0
0
0
1
-
1
0
0
1
0
0
{01} 0
1
0
0
0
1
0
0
Annelida 0
0
0
1
{01} 1
0
1
0
1
0
0
0
0
0
0
1
0
0
0
1
0
1
0
-
0
0
-
0
0
0
0
0
0
0
1
-
1
0
0
1
0
0
1
1
0
0
0
0
1
0
0
Echinodermata
0
0
0
0
1
1
0
{01} 0
0
1
1
1
1
1
{01} 1
1
1
1
0
1
1
0
2
0
0
{02} 0
0
-
0
0
?
0
0
0
0
0
-
1
0
0
{01} 0
0
0
0
0
Enteropneusta 1
0
0
1
1
0
0
0
1
1
1
1
1
1
1
1
1
1
0
1
1
0
0
2
0
1
1
1
0
0
1
0
0
1
0
0
0
0
0
-
1
0
0
1
0
0
0
1
0
1
0
Urochordata
0
0
0
0
1
0
0
0
1
1
0
1
1
1
1
0
0
1
0
1
0
0
0
1
0
1
?
1
0
0
1
0
0
1
0
0
1
0
0
0
1
0
0
0
0
0
?
0
1
1
1
Cephalochordata
0
1
0
0
0
1
0
1
0
0
0
1
1
0
1
1
1
1
0
1
1
0
1
1
0
0
1
0
1
1
1
0
0
1
0
0
1
0
0
1
0
0
-
1
0
0
0
0
1
1
0
0
Vertebrata
0
0
0
1
0
1
0
0
0
1
1
0
1
1
1
1
0
1
1
0
1
1
0
0
0
0
0
1
1
0
0
0
0
0
0
0
0
1
0
0
-
1
0
0
0
0
1
1
0
1
1
1
Vetulicola
0
1
?
?
0
1
?
?
1
1
?
1
1
0
?
1
0
1
?
?
0
0
?
?
1
0
?
?
1
0
1
0
1
2
?
?
0
0
1
2
?
0
0
0
0
0
1
?
0
1
0
0
1
?
?
1
0
?
?
Beidazoon
0
1
?
?
0
1
?
?
1
1
?
1
1
0
?
1
0
1
?
?
0
0
?
?
1
0
?
?
1
0
1
0
1
2
?
?
0
0
1
2
?
0
0
0
0
0
1
?
0
1
0
0
1
?
?
1
0
?
?
Ooedigera
0
?
0
?
1
1
0
1
0
?
0
?
1
?
1
1
0
2
?
0
0
2
-
0
-
0
0
1
?
1
0
1
?
1
0
WWW.NATURE.COM/NATURE | 22
RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
1
?
1
?
1
?
0
?
1
?
0
?
0
?
0
1
?
1
?
0
0
0
0
?
?
?
Pomatrum
0
1
?
?
0
1
?
?
1
1
?
1
0
0
?
1
0
1
?
?
0
0
?
?
1
0
?
?
1
1
1
0
1
2
?
?
1
0
1
1
?
0
0
0
0
0
1
?
0
1
0
0
1
?
?
1
0
?
?
Xidazoon ?
0
1
?
?
1
1
?
1
0
0
?
1
0
1
?
?
0
0
?
?
1
0
?
?
1
1
1
0
1
2
?
?
1
0
1
1
?
0
0
0
0
0
1
?
0
1
0
0
1
1
?
1
0
?
0
1
?
?
Didazoon ?
0
1
?
?
1
1
?
1
0
0
?
1
0
1
?
?
0
0
?
?
1
0
?
?
1
1
1
0
1
2
?
1
1
0
1
2
?
0
0
0
0
0
1
?
0
1
0
0
1
?
?
1
0
?
0
1
?
?
Yuyuanozoon
0
1
?
?
0
1
?
?
1
1
?
1
0
0
?
1
0
1
?
?
0
0
?
?
1
0
?
?
1
1
1
0
1
2
?
?
0
0
1
2
?
0
0
0
0
0
1
?
0
1
0
0
1
?
?
1
0
?
?
Heteromorphus
0
0
0
1
?
?
?
0
1
?
?
1
1
?
1
0
0
?
1
0
1
?
?
1
0
?
?
1
0
?
?
1
0
1
0
1
2
?
?
1
0
1
2
?
0
0
0
0
1
1
?
0
1
0
0
1
?
?
?
Banffia ?
0
1
?
?
1
1
?
1
0
0
?
1
0
1
?
?
1
0
?
?
1
0
?
?
?
0
1
0
1
2
?
?
1
0
1
2
?
0
0
0
0
1
1
?
0
1
0
0
1
?
?
0
0
?
0
1
?
?
Vetulocystis
0
0
?
?
0
1
?
?
0
1
?
1
1
?
?
1
0
?
?
1
1
?
?
1
0
?
?
1
0
1
?
1
?
?
?
?
0
?
?
?
0
0
0
0
0
1
?
1
1
0
0
1
?
?
0
?
?
?
Dianchicystis
0
0
?
?
0
1
?
?
0
1
?
1
1
?
?
1
0
?
?
1
1
?
?
1
0
?
?
1
0
1
?
1
?
?
?
?
0
?
?
?
0
0
0
0
0
1
?
1
1
0
0
1
?
?
0
?
?
?
Saccorhytus
0
0
0
?
0
1
0
?
0
1
?
1
2
?
?
1
0
?
?
0
2
?
?
1
0
?
?
1
0
?
0
?
1
0
?
?
1
0
0
1
?
0
0
0
0
-
0
?
0
?
0
0
0
?
?
?
WWW.NATURE.COM/NATURE | 23
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RESEARCH SUPPLEMENTARY INFORMATION
;
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;
WWW.NATURE.COM/NATURE | 24
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
(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
WWW.NATURE.COM/NATURE | 25
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
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
WWW.NATURE.COM/NATURE | 26
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
HI excluding uninformative characters = 0.3263
Retention index (RI) = 0.8394
Rescaled consistency index (RC) = 0.5683
/-- Cnidaria
|
|
/ Acoelomorpha
+------26
|
\----------- Saccorhytus
|
|
/---- Arthropoda
|
/--27
|
|
\ Onychophora
|
/-------------29
|
|
|
/-- Kinorhyncha
|
|
\----28
48
/--31
\-- Priapulida
|
|
|
|
|
|
/-- Mollusca
|
|
\----30
|
|
\ Annelida
|
|
|
|
/------ Echinodermata
|
|
/-------32
|
|
|
\-- Enteropneusta
|
|
|
|
|
/----35
/------ Urochordata
\-----------------47
|
|
/-33
|
|
|
| \-------- Vertebrata
|
|
\----34
|
|
\ Cephalochordata
|
|
|
|
/ Vetulicola
|
|
/36
|
|
| \ Beidazoon
|
|
|
|
|
|
/ Pomatrum
\-----------------46
40
/37
|
|
| \ Xidazoon
|
/--41 /38
|
|
| | \ Didazoon
|
|
+39
|
|
| \ Yuyuanozoon
|
/-----43
|
|
|
|
\ Ooedigera
|
|
|
|
|
|
/ Heteromorphus
\----45
\--42
|
\ Banffia
|
|
/ Vetulocystis
\----44
\ Dianchicystis
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
WWW.NATURE.COM/NATURE | 27
RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
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 #
Length
CI
RI
RC
HI
1
96
0.677
0.839
0.568
0.323
2
96
0.677
0.839
0.568
0.323
3
96
0.677
0.839
0.568
0.323
4
96
0.677
0.839
0.568
0.323
5
96
0.677
0.839
0.568
0.323
6
96
0.677
0.839
0.568
0.323
7
96
0.677
0.839
0.568
0.323
8
96
0.677
0.839
0.568
0.323
9
96
0.677
0.839
0.568
0.323
10
96
0.677
0.839
0.568
0.323
11
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
12
96
0.677
0.839
0.568
0.323
13
96
0.677
0.839
0.568
0.323
14
96
0.677
0.839
0.568
0.323
15
96
0.677
0.839
0.568
0.323
16
96
0.677
0.839
0.568
0.323
17
96
0.677
0.839
0.568
0.323
18
96
0.677
0.839
0.568
0.323
19
96
0.677
0.839
0.568
0.323
20
96
0.677
0.839
0.568
0.323
21
96
0.677
0.839
0.568
0.323
22
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
23
96
0.677
0.839
0.568
0.323
24
96
0.677
0.839
0.568
0.323
25
96
0.677
0.839
0.568
0.323
26
96
0.677
0.839
0.568
0.323
27
96
0.677
0.839
0.568
0.323
28
96
0.677
0.839
0.568
0.323
29
96
0.677
0.839
0.568
0.323
30
96
0.677
0.839
0.568
0.323
31
96
0.677
0.839
0.568
0.323
32
96
0.677
0.839
0.568
0.323
33
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
34
96
0.677
0.839
0.568
0.323
35
96
0.677
0.839
0.568
0.323
36
96
0.677
0.839
0.568
0.323
37
96
0.677
0.839
0.568
0.323
38
96
0.677
0.839
0.568
0.323
39
96
0.677
0.839
0.568
0.323
40
96
0.677
0.839
0.568
0.323
41
96
0.677
0.839
0.568
0.323
42
96
0.677
0.839
0.568
0.323
43
96
0.677
0.839
0.568
0.323
44
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
45
96
0.677
0.839
0.568
0.323
46
96
0.677
0.839
0.568
0.323
47
96
0.677
0.839
0.568
0.323
48
96
0.677
0.839
0.568
0.323
49
96
0.677
0.839
0.568
0.323
50
96
0.677
0.839
0.568
0.323
51
96
0.677
0.839
0.568
0.323
52
96
0.677
0.839
0.568
0.323
53
96
0.677
0.839
0.568
0.323
54
96
0.677
0.839
0.568
0.323
55
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
56
96
0.677
0.839
0.568
0.323
57
96
0.677
0.839
0.568
0.323
58
96
0.677
0.839
0.568
0.323
59
96
0.677
0.839
0.568
0.323
60
96
0.677
0.839
0.568
0.323
61
96
0.677
0.839
0.568
0.323
62
96
0.677
0.839
0.568
0.323
63
96
0.677
0.839
0.568
0.323
64
96
0.677
0.839
0.568
0.323
65
96
0.677
0.839
0.568
0.323
66
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
67
96
0.677
0.839
0.568
0.323
68
96
0.677
0.839
0.568
0.323
69
96
0.677
0.839
0.568
0.323
70
96
0.677
0.839
0.568
0.323
71
96
0.677
0.839
0.568
0.323
72
96
0.677
0.839
0.568
0.323
73
96
0.677
0.839
0.568
0.323
74
96
0.677
0.839
0.568
0.323
75
96
0.677
0.839
0.568
0.323
76
96
0.677
0.839
0.568
0.323
77
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
78
96
0.677
0.839
0.568
0.323
79
96
0.677
0.839
0.568
0.323
80
96
0.677
0.839
0.568
0.323
81
96
0.677
0.839
0.568
0.323
82
96
0.677
0.839
0.568
0.323
83
96
0.677
0.839
0.568
0.323
84
96
0.677
0.839
0.568
0.323
85
96
0.677
0.839
0.568
0.323
86
96
0.677
0.839
0.568
0.323
87
96
0.677
0.839
0.568
0.323
88
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
89
90
91
92
93
94
95
96
97
98
99
96
96
96
96
96
96
96
96
96
96
96
0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677 0.677
0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839 0.839
0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568 0.568
WWW.NATURE.COM/NATURE | 28
RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
HI
0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323 0.323
Tree #
Length
CI
RI
RC
HI
100
96
0.677
0.839
0.568
0.323
101
96
0.677
0.839
0.568
0.323
102
96
0.677
0.839
0.568
0.323
103
96
0.677
0.839
0.568
0.323
104
96
0.677
0.839
0.568
0.323
105
96
0.677
0.839
0.568
0.323
106
96
0.677
0.839
0.568
0.323
107
96
0.677
0.839
0.568
0.323
108
96
0.677
0.839
0.568
0.323
109
96
0.677
0.839
0.568
0.323
110
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
111
96
0.677
0.839
0.568
0.323
112
96
0.677
0.839
0.568
0.323
113
96
0.677
0.839
0.568
0.323
114
96
0.677
0.839
0.568
0.323
115
96
0.677
0.839
0.568
0.323
116
96
0.677
0.839
0.568
0.323
117
96
0.677
0.839
0.568
0.323
118
96
0.677
0.839
0.568
0.323
119
96
0.677
0.839
0.568
0.323
120
96
0.677
0.839
0.568
0.323
121
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
122
96
0.677
0.839
0.568
0.323
123
96
0.677
0.839
0.568
0.323
124
96
0.677
0.839
0.568
0.323
125
96
0.677
0.839
0.568
0.323
126
96
0.677
0.839
0.568
0.323
127
96
0.677
0.839
0.568
0.323
128
96
0.677
0.839
0.568
0.323
129
96
0.677
0.839
0.568
0.323
130
96
0.677
0.839
0.568
0.323
131
96
0.677
0.839
0.568
0.323
132
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
133
96
0.677
0.839
0.568
0.323
134
96
0.677
0.839
0.568
0.323
135
96
0.677
0.839
0.568
0.323
136
96
0.677
0.839
0.568
0.323
137
96
0.677
0.839
0.568
0.323
138
96
0.677
0.839
0.568
0.323
139
96
0.677
0.839
0.568
0.323
140
96
0.677
0.839
0.568
0.323
141
96
0.677
0.839
0.568
0.323
142
96
0.677
0.839
0.568
0.323
143
96
0.677
0.839
0.568
0.323
Tree #
Length
CI
RI
RC
HI
144
96
0.677
0.839
0.568
0.323
WWW.NATURE.COM/NATURE | 29
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
50% Majority-rule consensus of 144 trees
/--------------------------------------------------------|
+--------------------------------------------------------|
|
/-----|
/-100--+
|
|
\-----|
/-100-+
|
|
|
/-----|
|
\-100--+
|
/--------------100--------------+
\-----|
|
|
|
|
|
/-----|
|
\----100-----+
|
|
\-----|
|
|
|
/-----|
|
/-----------------100-----------------+
|
|
|
\-----|
|
|
\-98--+
|
/-----|
|
/-100--+
|
|
|
\-----|
+-------------100--------------+
|
|
\------------|
|
|
|
/-----|
|
/-100--+
|
|
|
\-----|
|
/----63-----+
\--98--+
|
\------------|
|
|
|
/-----|
/-100--+
/--88--+
|
|
|
|
\-----|
|
|
/-54--+
|
|
|
|
\------------|
/-100-+
\-54--+
|
|
|
\------------------|
|
|
|
|
|
/-----|
|
\-----------100-----------+
|
|
\-----\-69--+
|
/-----+--------------100--------------+
|
\-----|
\--------------------------------------
Cnidaria(1)
Acoelomorpha(2)
Arthropoda(3)
Onychophora(4)
Kinorhyncha(5)
Priapulida(6)
Mollusca(7)
Annelida(8)
Echinodermata(9)
Enteropneusta(10)
Urochordata(11)
Vertebrata(13)
Cephalochordata(12)
Vetulicola(14)
Beidazoon(15)
Ooedigera(16)
Pomatrum(17)
Xidazoon(18)
Didazoon(19)
Yuyuanozoon(20)
Heteromorphus(21)
Banffia(22)
Vetulocystis(23)
Dianchicystis(24)
Saccorhytus(25)
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%
WWW.NATURE.COM/NATURE | 30
RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
..........*.*............
.............**..........
..***********************
........*****************
................**.......
.............************
.............***.........
................***......
................****.....
.............***...*.....
........*****............
.............***********.
..........***************
......................***
........****************.
........**...************
.............*********..*
.............***..**.....
...............*****.....
.............**.****.....
..........**************.
................**.*.....
.............*****.*.....
.............***.***.....
........*****.........**.
........**************...
........**..............*
..........***.........**.
..........************...
.*......................*
..**********************.
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
WWW.NATURE.COM/NATURE | 31
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
Bootstrap 50% majority-rule consensus tree
/--------------------------------------------------------|
+--------------------------------------------------------|
|
/-------|
/--71---+
|
|
\-------|
/--97---+
|
|
|
/-------|
|
\--90---+
|
/-----------83-----------+
\-------|
|
|
|
|
|
/-------|
|
\------85-------+
|
|
\-------|
|
|
|
/-------|
|
/---------------56---------------+
|
|
|
\-------|
|
|
|
|
|
/-------|
|
|
|
\--75---+
+---------------65---------------+-------|
|
|
|
|
\-------|
|
|
|
/-------|
|
/--55---+
|
|
|
\-------|
|
|
|
|
+---------------|
|
|
|
|
|
/-------\--67---+
/--55---+--58---+
|
|
|
\-------|
|
|
|
|
+---------------|
/---81---+
|
|
|
|
\---------------|
|
|
|
|
|
/-------+--57---+
\------83-------+
|
|
\-------|
|
|
|
/-------|
\-----------84-----------+
|
\-------|
\-----------------------------------------
Cnidaria(1)
Acoelomorpha(2)
Arthropoda(3)
Onychophora(4)
Kinorhyncha(5)
Priapulida(6)
Mollusca(7)
Annelida(8)
Echinodermata(9)
Enteropneusta(10)
Urochordata(11)
Cephalochordata(12)
Vertebrata(13)
Vetulicola(14)
Beidazoon(15)
Ooedigera(16)
Pomatrum(17)
Xidazoon(18)
Didazoon(19)
Yuyuanozoon(20)
Heteromorphus(21)
Banffia(22)
Vetulocystis(23)
Dianchicystis(24)
Saccorhytus(25)
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%
WWW.NATURE.COM/NATURE | 32
RESEARCH SUPPLEMENTARY INFORMATION
doi:10.1038/nature21072
......................**.
....................**...
..******.................
.............*********...
..***********************
..**.....................
........*****************
..........***............
................**.......
.............***********.
........**...............
.............*******.....
.............**..........
................****.....
..........*.*............
................***......
.............************
........*****............
..**********************.
........****************.
...........**............
...***...................
.*......................*
.........****............
........**...************
..........**.............
.............***...*.....
..****.*.................
.........****************
........**...***********.
................***.**...
.............***..****...
........**.**************
......................***
..******.....***********.
........****.************
..........**************.
....................****.
...............*******...
........****.***********.
..........***************
........*....************
................******...
.............***.........
........**..............*
........*....***********.
...............*****.....
.........***************.
.............**.****.....
.............*********..*
840.79
831.87
830.12
811.32
747.78
714.57
667.25
649.32
583.91
568.45
564.36
551.03
545.11
486.31
454.69
366.38
364.65
299.32
297.56
276.86
237.77
230.01
203.83
159.84
155.70
153.00
147.15
139.25
128.09
117.02
115.37
99.87
93.20
92.44
89.82
84.40
83.81
82.13
81.61
76.36
75.32
72.54
70.88
68.80
65.17
62.97
61.33
57.43
57.13
56.21
84.1%
83.2%
83.0%
81.1%
74.8%
71.5%
66.7%
64.9%
58.4%
56.8%
56.4%
55.1%
54.5%
48.6%
45.5%
36.6%
36.5%
29.9%
29.8%
27.7%
23.8%
23.0%
20.4%
16.0%
15.6%
15.3%
14.7%
13.9%
12.8%
11.7%
11.5%
10.0%
9.3%
9.2%
9.0%
8.4%
8.4%
8.2%
8.2%
7.6%
7.5%
7.3%
7.1%
6.9%
6.5%
6.3%
6.1%
5.7%
5.7%
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
WWW.NATURE.COM/NATURE | 33
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
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
WWW.NATURE.COM/NATURE | 34
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
Sum of max. possible lengths = 177.09389
Tree #
Length
CI
RI
RC
HI
1
2
3
4
5
6
7
55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222
0.878
0.878
0.878
0.878
0.878
0.878
0.878
0.947
0.947
0.947
0.947
0.947
0.947
0.947
0.831
0.831
0.831
0.831
0.831
0.831
0.831
0.122
0.122
0.122
0.122
0.122
0.122
0.122
Tree #
Length
CI
RI
RC
HI
8
9
10
11
12
13
14
55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222
0.878
0.878
0.878
0.878
0.878
0.878
0.878
0.947
0.947
0.947
0.947
0.947
0.947
0.947
0.831
0.831
0.831
0.831
0.831
0.831
0.831
0.122
0.122
0.122
0.122
0.122
0.122
0.122
Tree #
Length
CI
RI
RC
HI
15
16
17
18
19
20
21
55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222
0.878
0.878
0.878
0.878
0.878
0.878
0.878
0.947
0.947
0.947
0.947
0.947
0.947
0.947
0.831
0.831
0.831
0.831
0.831
0.831
0.831
0.122
0.122
0.122
0.122
0.122
0.122
0.122
Tree #
Length
CI
RI
RC
HI
22
23
24
25
26
27
28
55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222
0.878
0.878
0.878
0.878
0.878
0.878
0.878
0.947
0.947
0.947
0.947
0.947
0.947
0.947
0.831
0.831
0.831
0.831
0.831
0.831
0.831
0.122
0.122
0.122
0.122
0.122
0.122
0.122
Tree #
Length
CI
RI
RC
HI
29
30
31
32
33
34
35
55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222
0.878
0.878
0.878
0.878
0.878
0.878
0.878
0.947
0.947
0.947
0.947
0.947
0.947
0.947
0.831
0.831
0.831
0.831
0.831
0.831
0.831
0.122
0.122
0.122
0.122
0.122
0.122
0.122
Tree #
Length
CI
RI
RC
HI
36
37
38
39
40
41
42
55.82222 55.82222 55.82222 55.82222 55.82222 55.82222 55.82222
0.878
0.878
0.878
0.878
0.878
0.878
0.878
0.947
0.947
0.947
0.947
0.947
0.947
0.947
0.831
0.831
0.831
0.831
0.831
0.831
0.831
0.122
0.122
0.122
0.122
0.122
0.122
0.122
Tree #
Length
CI
RI
RC
HI
43
44
45
55.82222 55.82222 55.82222
0.878
0.878
0.878
0.947
0.947
0.947
0.831
0.831
0.831
0.122
0.122
0.122
WWW.NATURE.COM/NATURE | 35
doi:10.1038/nature21072
RESEARCH SUPPLEMENTARY INFORMATION
Strict consensus of 45 trees:
/------------------------------------------------------------|
+------------------------------------------------------------|
|
/-------|
/------+
|
|
\-------|
/-------+
|
|
|
/-------|
|
\------+
|
/-----------------------------+
\-------|
|
|
|
|
|
/-------|
|
\--------------+
|
|
\-------|
|
|
|
/-------|
|
/-------------------------------------+
|
|
|
\-------|
|
|
\-------+
|
/-------|
|
/------+
|
|
|
\-------|
+------------------------------+
|
|
\--------------|
|
|
|
/-------|
|
/--------------+
|
|
|
\-------|
|
|
\------+
+----------------------|
|
|
/-------+
/-------|
|
|
/------+
|
|
|
|
\-------|
|
|
|
|
|
\-------+--------------|
/------+
|
|
|
|
\--------------|
|
|
|
|
|
/-------|
|
\----------------------+
|
|
\-------\-------+
|
/-------+-----------------------------+
|
\-------|
\--------------------------------------
Cnidaria
Acoelomorpha
Arthropoda
Onychophora
Kinorhyncha
Priapulida
Mollusca
Annelida
Echinodermata
Enteropneusta
Urochordata
Vertebrata
Cephalochordata
Vetulicola
Beidazoon
Ooedigera
Pomatrum
Xidazoon
Didazoon
Yuyuanozoon
Heteromorphus
Banffia
Vetulocystis
Dianchicystis
Saccorhytus
Consensus tree(s) written to treefile:
F:\deuterostomes\OneDrive\phylogeny\final 18 1004\StrictConTree_Weighted.tre
WWW.NATURE.COM/NATURE | 36