SUPPLEMENTARY MATERIAL
TABLES S2 – S4
TABLE S2. Tree notation, scores, permutation tail probability tests, source tree fit, and related data for
each of the molecular supertrees analyses.
TABLE S3. Tree notation, scores, permutation tail probability tests, source tree fit, and related data for
each of the morphological supertrees analyses.
TABLE S4. Symmetric distances between supertrees. Partition: Morph = morphology, Molec = molecular.
TABLE S2. Tree notation, scores, permutation tail probability tests, source tree fit, and related data for
each of the molecular supertrees analyses.
CLANN
Dfit Alltrees (Fig. 3d):
(out,(Polyplacophora,Monoplacophora),((Bivalvia,Gastropoda),(Solenogastres,(Scaphopoda,(Caudofove
ata,Cephalopoda)))));
Tree score = 14.39
YAPTP (Permutation Tail Probability) nreps=1000 (Creevey et al. 2004)
14.39 - 14.94
14.95 - 15.50
15.51 - 16.06
16.07 - 16.63
16.64 - 17.19
17.20 - 17.75
17.76 - 18.31
18.32 - 18.88
18.89 - 19.44
19.45 - 20.00
| (3)
|= (9)
|==== (31)
|================ (116)
|============================== (214)
|======================================== (277)
|=============================== (221)
|================ (114)
|= (13)
| (3)
Sfit Alltrees (Fig. 3d):
(out,(Polyplacophora,Monoplacophora),((Bivalvia,Gastropoda),(Solenogastres,(Scaphopoda,(Caudofove
ata,Cephalopoda)))));
Tree score = 14.39
YAPTP (Permutation Tail Probability) nreps=1000 (Creevey et al. 2004)
14.39 - 14.97
14.98 - 15.56
15.57 - 16.15
16.16 - 16.74
16.75 - 17.33
17.34 - 17.92
17.93 - 18.51
18.52 - 19.10
19.11 - 19.69
19.70 - 20.28
| (3)
|= (7)
|======== (57)
|====================== (147)
|======================================== (264)
|======================================= (263)
|=========================== (183)
|========= (64)
|= (12)
| (1)
Qfit Alltrees (Fig. 3d):
(out,(Polyplacophora,Monoplacophora),((Bivalvia,Gastropoda),(Solenogastres,(Scaphopoda,(Caudofove
ata,Cephalopoda)))));
Tree score = 5.54
YAPTP (Permutation Tail Probability) nreps=1000 (Creevey et al. 2004)
5.54 - 5.87
5.88 - 6.21
6.22 - 6.54
| (1)
| (0)
| (1)
6.55 - 6.88
6.89 - 7.22
7.23 - 7.56
7.57 - 7.89
7.90 - 8.23
8.24 - 8.57
8.58 - 8.91
| (8)
|== (25)
|============= (126)
|=========================== (255)
|======================================== (377)
|================== (176)
|=== (32)
AVCON (Fig. 3a):
(out:1.908811, ((((Polyplacophora:1.757746, ((Scaphopoda:1.557579,
Caudofoveata:1.593821):0.125162, Monoplacophora:2.113314):0.180332):0.113584,
Gastropoda:1.694391):0.128061, Bivalvia:1.685532):0.185222, Solenogastres:1.845121):0.249671,
Cephalopoda:1.759105);
RF-S [38 trees] (Figs. 3b & 3d):
[RF distance: 79]
(out,((((Scaphopoda,(Cephalopoda,Caudofoveata)),Solenogastres),Gastropoda),(Bivalvia,(Polyplacophor
a,Monoplacophora))));
(out,((((Scaphopoda,(Cephalopoda,Caudofoveata)),Solenogastres),(Gastropoda,Bivalvia)),(Polyplacophor
a,Monoplacophora)));
(out,((Monoplacophora,Polyplacophora),((Solenogastres,(Scaphopoda,(Cephalopoda,Caudofoveata))),(G
astropoda,Bivalvia))));
(out,((Monoplacophora,Polyplacophora),((Solenogastres,(Scaphopoda,(Cephalopoda,Caudofoveata))),(G
astropoda,Bivalvia))));
(out,((Solenogastres,(Scaphopoda,(Cephalopoda,Caudofoveata))),((Monoplacophora,Polyplacophora),(G
astropoda,Bivalvia))));
(out,(((Solenogastres,(Scaphopoda,(Cephalopoda,Caudofoveata))),(Gastropoda,Bivalvia)),(Monoplacoph
ora,Polyplacophora)));
(out,(((Gastropoda,Bivalvia),(Monoplacophora,Polyplacophora)),(Solenogastres,(Scaphopoda,(Cephalop
oda,Caudofoveata)))));
(out,((Monoplacophora,Polyplacophora),((Gastropoda,Bivalvia),(Solenogastres,((Cephalopoda,Caudofov
eata),Scaphopoda)))));
(out,((Monoplacophora,Polyplacophora),((Gastropoda,Bivalvia),(Solenogastres,((Caudofoveata,Cephalo
poda),Scaphopoda)))));
(out,(((Gastropoda,Bivalvia),(Monoplacophora,Polyplacophora)),(Solenogastres,((Caudofoveata,Cephalo
poda),Scaphopoda))));
(out,((Monoplacophora,Polyplacophora),((Gastropoda,Bivalvia),(Solenogastres,((Caudofoveata,Cephalo
poda),Scaphopoda)))));
(out,((Gastropoda,(Solenogastres,((Caudofoveata,Cephalopoda),Scaphopoda))),((Monoplacophora,Poly
placophora),Bivalvia)));
(out,((Monoplacophora,Polyplacophora),((Gastropoda,Bivalvia),(Solenogastres,((Caudofoveata,Cephalo
poda),Scaphopoda)))));
(out,(((Gastropoda,Bivalvia),(Solenogastres,((Caudofoveata,Cephalopoda),Scaphopoda))),(Monoplacoph
ora,Polyplacophora)));
(out,(((Gastropoda,Bivalvia),(Solenogastres,((Caudofoveata,Cephalopoda),Scaphopoda))),(Monoplacoph
ora,Polyplacophora)));
(out,((Gastropoda,(Solenogastres,((Caudofoveata,Cephalopoda),Scaphopoda))),(Bivalvia,(Monoplacoph
ora,Polyplacophora))));
(out,((Gastropoda,(Solenogastres,((Caudofoveata,Cephalopoda),Scaphopoda))),(Bivalvia,(Monoplacoph
ora,Polyplacophora))));
(out,((Solenogastres,(Scaphopoda,(Caudofoveata,Cephalopoda))),((Gastropoda,Bivalvia),(Monoplacoph
ora,Polyplacophora))));
(out,(((Solenogastres,(Scaphopoda,(Caudofoveata,Cephalopoda))),Gastropoda),(Bivalvia,(Monoplacoph
ora,Polyplacophora))));
(out,(((Gastropoda,Bivalvia),(Solenogastres,(Scaphopoda,(Caudofoveata,Cephalopoda)))),(Monoplacoph
ora,Polyplacophora)));
(out,(((Gastropoda,Bivalvia),(Solenogastres,(Scaphopoda,(Caudofoveata,Cephalopoda)))),(Monoplacoph
ora,Polyplacophora)));
(out,((Gastropoda,(Solenogastres,(Scaphopoda,(Caudofoveata,Cephalopoda)))),(Bivalvia,(Monoplacoph
ora,Polyplacophora))));
(out,((Gastropoda,((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres)),(Bivalvia,(Monoplacoph
ora,Polyplacophora))));
(out,((((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres),(Bivalvia,Gastropoda)),(Monoplacoph
ora,Polyplacophora)));
(out,(((Bivalvia,Gastropoda),((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres)),(Monoplacoph
ora,Polyplacophora)));
(out,(((Bivalvia,Gastropoda),((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres)),(Monoplacoph
ora,Polyplacophora)));
(out,(((Bivalvia,Gastropoda),(Monoplacophora,Polyplacophora)),((Scaphopoda,(Caudofoveata,Cephalop
oda)),Solenogastres)));
(out,((Monoplacophora,Polyplacophora),((Bivalvia,Gastropoda),((Scaphopoda,(Caudofoveata,Cephalopo
da)),Solenogastres))));
(out,((Monoplacophora,Polyplacophora),((Bivalvia,Gastropoda),((Scaphopoda,(Caudofoveata,Cephalopo
da)),Solenogastres))));
(out,((Monoplacophora,Polyplacophora),((Bivalvia,Gastropoda),((Scaphopoda,(Caudofoveata,Cephalopo
da)),Solenogastres))));
(out,((Monoplacophora,Polyplacophora),((Bivalvia,Gastropoda),((Scaphopoda,(Caudofoveata,Cephalopo
da)),Solenogastres))));
(out,((Monoplacophora,Polyplacophora),(((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres),(B
ivalvia,Gastropoda))));
(out,((Monoplacophora,Polyplacophora),(((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres),(B
ivalvia,Gastropoda))));
(out,((Monoplacophora,Polyplacophora),(((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres),(B
ivalvia,Gastropoda))));
(out,((Monoplacophora,Polyplacophora),(((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres),(B
ivalvia,Gastropoda))));
(out,((Monoplacophora,Polyplacophora),(((Scaphopoda,(Caudofoveata,Cephalopoda)),Solenogastres),(B
ivalvia,Gastropoda))));
(out,((Monoplacophora,Polyplacophora),((Gastropoda,Bivalvia),((Scaphopoda,(Caudofoveata,Cephalopo
da)),Solenogastres))));
(out,((Gastropoda,(((Caudofoveata,Cephalopoda),Scaphopoda),Solenogastres)),((Monoplacophora,Poly
placophora),Bivalvia)));
Strict (Fig. 3b):
(out,((Scaphopoda,(Cephalopoda,Caudofoveata)1.00)1.00,Solenogastres)1.00,Gastropoda,Bivalvia,(Poly
placophora,Monoplacophora)1.00);
MajRule (Fig. 3d):
(out,(((Scaphopoda,(Cephalopoda,Caudofoveata)1.00)1.00,Solenogastres)1.00,(Gastropoda,Bivalvia)0.7
9)0.66,(Polyplacophora,Monoplacophora)1.00);
RAINBOW
MRP (Figs 3e & 3f):
MPR_1 (Fig. 3e):
(out,((Polyplacophora,Monoplacophora),((Bivalvia,Gastropoda),(((Solenogastres,Caudofoveata),Cephalo
poda),Scaphopoda))));
140 steps
MRP_2 (Fig. 3f):
(out,((Polyplacophora,Monoplacophora),(Bivalvia,((((Solenogastres,Caudofoveata),Cephalopoda),Scaph
opoda),Gastropoda))));
140 steps
MRP_1 supertree triple-fit statics:
Tree weight leaves
n
d
s
r1
r2
fit
--------------------------------------------------------------------1
1
8
56
10
46
0
0
0.821
2
1
8
56
21
34
1
0
0.618
3
1
8
56
12
44
0
0
0.786
4
1
9
84
19
65
0
0
0.774
5
1
8
56
20
36
0
0
0.643
6
1
9
84
38
46
0
0
0.548
7
1
6
20
4
16
0
0
0.8
8
1
6
20
5
15
0
0
0.75
9
1
8
56
17
39
0
0
0.696
10
1
7
35
1
34
0
0
0.971
11
1
7
35
14
20
1
0
0.588
12
1
9
84
19
65
0
0
0.774
13
1
6
20
8
12
0
0
0.6
14
1
8
56
3
53
0
0
0.946
15
1
6
20
1
15
4
0
0.938
Average fit: 0.75
MRP_2 supertree triple-fit statics:
tree weight leaves
n
d
s
r1
r2
fit
----------------------------------------------------------------------------1
1
8
56
6
50
0
0
0.893
2
1
8
56
18
37
1
0
0.673
3
1
8
56
8
48
0
0
0.857
4
1
9
84
23
61
0
0
0.726
5
1
8
56
24
32
0
0
0.571
6
1
9
84
40
44
0
0
0.524
7
1
6
20
6
14
0
0
0.7
8
1
6
20
7
13
0
0
0.65
9
1
8
56
21
35
0
0
0.625
10
1
7
35
4
31
0
0
0.886
11
1
7
35
17
17
1
0
0.5
12
1
9
84
23
61
0
0
0.726
13
1
6
20
10
10
0
0
0.5
14
1
8
56
0
56
0
0
1
15
1
6
20
0
16
4
0
1
Average fit: 0.722
------------------------------------------------------------------------------weight: weight of tree i (note that tree weights were not used)
leaves: number of leaves in tree i
n: total number of triplets
d: triplets resolved differently in supertree and tree i
s: triplets resolved identically in supertree and tree i
r1: triplets resolved in supertree but not in tree i
r2: triplets resolved in tree i but not in supertree
fit: 1 - (d + r2)/(d + s + r2)
MRF (Fig. 3c):
((((Scaphopoda,(Cephalopoda,Caudofoveata)),Solenogastres),((Bivalvia,Gastropoda),(Monoplacophora,P
olyplacophora))),out);
47 flips
MRF supertree triple-fit statics:
tree
weight leaves
n
d
s
r1
r2
fit
----------------------------------------------------------------------------1
1
8
56
15
41
0
0
0.732
2
1
8
56
18
37
1
0
0.673
3
1
8
56
9
47
0
0
0.839
4
1
9
84
4
80
0
0
0.952
5
1
8
56
25
31
0
0
0.554
6
1
9
84
41
43
0
0
0.512
7
1
6
20
4
16
0
0
0.8
8
1
6
20
5
15
0
0
0.75
9
1
8
56
22
34
0
0
0.607
10
1
7
35
6
29
0
0
0.829
11
1
7
35
11
23
1
0
0.676
12
1
9
84
5
79
0
0
0.94
13
1
6
20
4
16
0
0
0.8
14
1
8
56
15
41
0
0
0.732
15
1
6
20
3
13
4
0
0.813
Average fit: 0.747
------------------------------------------------------------------------------weight: weight of tree i (note that tree weights were not used)
leaves: number of leaves in tree i
n: total number of triplets
d: triplets resolved differently in supertree and tree i
s: triplets resolved identically in supertree and tree i
r1: triplets resolved in supertree but not in tree i
r2: triplets resolved in tree i but not in supertree
fit: 1 - (d + r2)/(d + s + r2)
TABLE S3. Tree notation, scores, permutation tail probability tests, source tree fit, and related data for
each of the morphological supertrees analyses.
CLANN
Dfit Alltrees (Fig 3g):
(((out,(Caudofoveata,Solenogastres)),Polyplacophora),Monoplacophora,((Cephalopoda,Gastropoda),(Biv
alvia,Scaphopoda)));
Tree score = 21.52
YAPTP (Permutation Tail Probability) nreps=1000 (Creevey et al. 2004)
21.52 - 23.30
23.31 - 25.09
25.10 - 26.88
26.89 - 28.67
28.68 - 30.46
30.47 - 32.25
32.26 - 34.04
34.05 - 35.83
35.84 - 37.62
37.63 - 39.41
| (1)
| (0)
| (0)
| (0)
| (0)
| (3)
|========= (155)
|======================================== (637)
|============ (202)
| (3)
Sfit Alltrees (Fig 3g):
(((out,(Caudofoveata,Solenogastres)),Polyplacophora),Monoplacophora,((Cephalopoda,Gastropoda),(Biv
alvia,Scaphopoda)));
Tree score = 20.25
YAPTP (Permutation Tail Probability) nreps=1000 (Creevey et al. 2004)
20.25 - 22.73
22.74 - 25.23
25.24 - 27.72
27.73 - 30.21
30.22 - 32.71
32.72 - 35.20
35.21 - 37.69
37.70 - 40.19
40.20 - 42.68
42.69 - 45.17
| (1)
| (0)
| (0)
|= (12)
|============= (116)
|====================================== (325)
|======================================== (338)
|==================== (169)
|==== (38)
| (2)
Qfit Alltrees (Fig 3g):
(((out,(Caudofoveata,Solenogastres)),Polyplacophora),Monoplacophora,((Cephalopoda,Gastropoda),(Biv
alvia,Scaphopoda)));
Tree score = 4.90
YAPTP (Permutation Tail Probability) nreps=1000 (Creevey et al. 2004)
4.90 - 6.08
6.09 - 7.28
7.29 - 8.47
| (1)
| (0)
| (0)
8.48 - 9.66
9.67 - 10.85
10.86 - 12.04
12.05 - 13.23
13.24 - 14.42
14.43 - 15.61
15.62 - 16.80
| (0)
| (0)
| (0)
| (0)
| (13)
|======================================== (541)
|================================ (446)
AVCON (Fig. 3h):
(out:1.538969, ((Polyplacophora:1.054711, Monoplacophora:1.345289):0.753527,
Bivalvia:1.342878):0.212714, ((Solenogastres:1.700037, (Scaphopoda:1.299488,
(Caudofoveata:1.426712, Cephalopoda:1.342519):0.540407):0.280618):0.484693,
Gastropoda:1.341589):0.204895);
RF-S [51 trees] (Fig. 3g):
[RF distance: 103]
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Scaphopoda,Bivalvia)))),(Caudofov
eata,Solenogastres)));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Sca
phopoda,Bivalvia))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda),(Sca
phopoda,Bivalvia))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Scaphopoda,Bivalvia),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Scaphopoda,Bivalvia),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Scaphopoda,Bivalvia),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Scaphopoda,Bivalvia),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Gastropoda,Cephalopoda),(Biv
alvia,Scaphopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Gastropoda,Cephalopoda),(Biv
alvia,Scaphopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Gastropoda,Cephalopoda),(Biv
alvia,Scaphopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
(out,((Caudofoveata,Solenogastres),(Polyplacophora,(Monoplacophora,((Bivalvia,Scaphopoda),(Gastrop
oda,Cephalopoda))))));
Strict & MajRule (Fig. 3g):
(out,(Polyplacophora,(Monoplacophora,((Cephalopoda,Gastropoda)1.00,(Scaphopoda,Bivalvia)1.00)1.00
)1.00)1.00,(Caudofoveata,Solenogastres)1.00)
RAINBOW
MRP (Fig. 3g):
(out,(((Monoplacophora,((Cephalopoda,Gastropoda),(Bivalvia,Scaphopoda))),Polyplacophora),(Caudofov
eata,Solenogastres)));
207 steps
MRP supertree triple-fit statics:
tree weight leaves
n
d
s
r1
r2
fit
--------------------------------------------------------------------------1
1
6
20
0
16
4
0
1
2
1
7
35
2
29
4
0
0.935
3
1
9
84
8
76
0
0
0.905
4
1
9
84
10
70
4
0
0.875
5
1
9
84
6
74
4
0
0.925
6
1
9
84
4
80
0
0
0.952
7
1
9
84
5
79
0
0
0.94
8
1
9
84
6
78
0
0
0.929
9
1
9
84
13
71
0
0
0.845
10
1
9
84
8
76
0
0
0.905
11
1
9
84
8
76
0
0
0.905
12
1
9
84
3
81
0
0
0.964
13
1
6
20
3
17
0
0
0.85
14
1
9
84
0
78
6
0
1
15
1
8
56
2
50
4
0
0.962
16
1
6
20
5
9
6
0
0.643
17
1
7
35
9
15
11
0
0.625
18
1
7
35
0
33
2
0
1
19
1
9
84
13
67
4
0
0.838
20
1
9
84
0
74
10
0
1
21
1
9
84
7
77
0
0
0.917
22
1
6
20
4
16
0
0
0.8
23
1
7
35
7
28
0
0
0.8
24
1
7
35
2
32
1
0
0.941
25
1
7
35
2
31
2
0
0.939
26
27
1
1
7
9
35
84
6
2
28
68
1
14
0
0
0.824
0.971
Average fit: 0.896
weight: weight of tree i (note that tree weights were not used)
leaves: number of leaves in tree i
n: total number of triplets
d: triplets resolved differently in supertree and tree i
s: triplets resolved identically in supertree and tree i
r1: triplets resolved in supertree but not in tree i
r2: triplets resolved in tree i but not in supertree
fit: 1 - (d + r2)/(d + s + r2)
MRF (Fig. 3g)
(((Solenogastres,Caudofoveata),((Monoplacophora,((Gastropoda,Cephalopoda),(Bivalvia,Scaphopoda))),
Polyplacophora)),out);
41 flips
MRF supertree triple-fit statics:
tree weight leaves
n
d
s
r1
r2
fit
----------------------------------------------------------------------------1
1
6
20
0
16
4
0
1
2
1
7
35
2
29
4
0
0.935
3
1
9
84
8
76
0
0
0.905
4
1
9
84
10
70
4
0
0.875
5
1
9
84
6
74
4
0
0.925
6
1
9
84
4
80
0
0
0.952
7
1
9
84
5
79
0
0
0.94
8
1
9
84
6
78
0
0
0.929
9
1
9
84
13
71
0
0
0.845
10
1
9
84
8
76
0
0
0.905
11
1
9
84
8
76
0
0
0.905
12
1
9
84
3
81
0
0
0.964
13
1
6
20
3
17
0
0
0.85
14
1
9
84
0
78
6
0
1
15
1
8
56
2
50
4
0
0.962
16
1
6
20
5
9
6
0
0.643
17
1
7
35
9
15
11
0
0.625
18
1
7
35
0
33
2
0
1
19
1
9
84
13
67
4
0
0.838
20
1
9
84
0
74
10
0
1
21
1
9
84
7
77
0
0
0.917
22
1
6
20
4
16
0
0
0.8
23
1
7
35
7
28
0
0
0.8
24
1
7
35
2
32
1
0
0.941
25
1
7
35
2
31
2
0
0.939
26
1
7
35
6
28
1
0
0.824
27
1
9
84
2
68
14
0
0.971
Average fit: 0.896
------------------------------------------------------------------------------weight: weight of tree i (note that tree weights were not used)
leaves: number of leaves in tree i
n: total number of triplets
d: triplets resolved differently in supertree and tree i
s: triplets resolved identically in supertree and tree i
r1: triplets resolved in supertree but not in tree i
r2: triplets resolved in tree i but not in supertree
fit: 1 - (d + r2)/(d + s + r2)
TABLE S4. Symmetric distances between supertrees. Partition: Morph = morphology, Molec = molecular.
Fig. 3d
Fig. 3b
Fig. 3e
Molec Fig. 3f
Fig. 3c
Fig. 3a
Morph Fig. 3g
Fig. 3h
Fig. 3d
Fig. 3b
Fig. 3e
2
5
7
3
12
12
4
7
7
3
10
10
2
2
6
13
11
9
Fig. 3f
Molec
8
13
11
7
Fig. 3c
Fig 3a
13
13
5
12
12
Fig. 3g Fig. 3h
Morph
12