Supporting Information
Appendix SA. Details on trees including fossil and extant species and supertree analyses.
Input trees for Supertree analyses were based on 30 morphological phylogenetic studies that
examined fossil and extant taxa. These are: Taverne (1997), Schultze and Cumbaa (2001),
Friedman and Blom (2006), Gardiner et al. (2005), Long et al. (2008), Swartz (2009), Choo
(2011), Xu and Gao (2011), Xu and Wu (2012) (early-branching actinopterygian and
neopterygian lineages); Grande and Hilton (2006) and Hilton and Forey (2009) (Chondrostei);
Grande and Bemis (1998) and Forey and Patterson (2006) (Amiiformes); Arratia (1999) and
Arratia (2008) (early teleosts); Taverne (1998), Li and Wilson (1999), Hilton (2003), Zhang
(2006), Wilson and Murray (2008) (Osteoglossomorpha); Forey (2004) (clupeomorphs; based on
previous studies cited therein); Poyato-Ariza et al. (2010) and Davis et al. (2013)
(Gonorynchiformes); (Borden et al. 2013) (paracanthopterygians); Tyler and Santini (2005)
(Zeiformes); Otero (2004) (Latinae); Friedman (2008) (Pleuronectiformes); Tyler et al. (1989)
(Luvaridae); Tyler and Bannikov (1997) (Siganidae); Santini and Tyler (2003)
(Tetraodontiformes).
A total of 240 fossil taxa were placed on the molecular phylogeny using a backbone
supertree approach; i.e., incongruent clades of extant taxa in the input trees were constrained to
conform to the molecular topology. To the best of our knowledge there are no algorithms
formally implementing backbone supertrees. This issue was circumvented by up-weighting
(“pseudoreplicating”) the molecular topology in the input trees. In many cases, outgroup taxa in
the input morphological trees were either added or removed to avoid spurious placements. In
some cases, non-disputed monophyletic taxa were not resolved as such in preliminary supertree
1
analyses due to non-overlapping sampling across datasets. Their monophyly was thus enforced
on the basis of previous studies. For merging purposes, extant taxa examined by the
morphological studies that belong in the same genera as those in the molecular tree were treated
as the same taxonomic unit. Other extant taxa present in the morphological trees but not in the
molecular phylogeny were removed.
Fossil and extant osteoglossomorph relationships hypothesized by several previous
studies (i.e., Taverne 1998; Li & Wilson 1999; Hilton 2003; Zhang 2006; Wilson & Murray
2008) are highly incongruent and preliminary supertree analyzes yielded spurious results (i.e.,
resulted in novel clades not found in any of the input trees). All previous hypotheses were thus
reconciled into a single osteoglossomorph supertree prior to the final supertree analysis. Several
adjustments were made to both the individual input trees and the osteoglossomorph supertree. (1)
Many unstable taxa were excluded from the corresponding input trees, including Jinanichthys,
Singida, Kuntulunia, Niierkunia, Huashia, and Joffrichthys. (2) The hypotheses by Li and
Wilson (1999) and Wilson and Murray (2008) were combined into a single input tree using the
latter topology as a backbone. (3) The relationships of arapaimids, osteoglossids, and
pantondontids in the molecular tree were incongruent with most morphological trees. The
molecular phylogeny as well as Wilson and Murray’s (2008) tree place arapaimids sister to
osteoglossids, whereas the remaining hypotheses indicate as sister-group relationship between
pantodontids and osteoglossids. Thus, the three lineages (including stem fossil taxa) were
collapsed into a polytomy in all trees that included a Pantodontidae + Osteoglossidae clade. (4)
Many marine osteoglossomorphs (i.e., Furichthys fieldsoei, Brychaetoides greenwoodi,
Xosteoglossid rebeccae, osteoglossiform indet., Brychaetus sp., and Heterosteoglossum foreyi)
were added onto Taverne’s (1998) tree, following the assessment presented by Bonde (2008).
2
While Bonde chose not to conduct a formal phylogenetic analysis, placement of these taxa in
clades is supported by synapomorphies. (5) The position of Kipalaichthys, Chanopsis,
Laeliichthys, and Paradercites in Taverne’s (1998) cladogram was questioned by Bonde (2008)
and thus they were excluded from the tree. (6) Foreyichthys was moved from the stem
Osteoglossidae/Arapaimidae + Pantodontidae clade in Taverne’s tree to the crown group, based
on the Bonde’s reassessment of the anatomical evidence. (7) The osteoglossomorph supertree
estimated after these modifications also resulted in several novel clades that were collapsed into
polytomies.
The dataset of amiid taxa compiled by Grande and Bemis (1998) and modified Forey and
Patterson (2006) (available from
http://paleodb.org/bridge.pl?a=getNexusFile&nexusfile_no=159) was reanalyzed in TNT. The
strict consensus of 8282 trees with 174 steps is reported. Finally, in order to obtain an adequate
placement of flatfish fossils following Friedman (2008), the monophyly of extant
Pleuronectiformes was enforced (see also Betancur-R. et al. 2013b; Betancur-R. & Orti 2014).
Details on time-calibration of the supertree cladogram are given in the main text. The complete
time tree with fossil and extant species is shown in Fig. S1.
Appendix SB. Fossils and branch-length scaling of fossil-based trees.
Table SB1. List of 240 fossils placed onto the global phylogeny using a supertree approach.
Individual trees were obtained from the aforementioned studies (Appendix SA). Habitat and
minimum age information was obtained from the corresponding references, the Paleobiology
3
Database (www.paleodb.org), and other sources. In many cases, the absolute minimum age is
based on the corresponding stratigraphic horizon (http://www.geosociety.org/science/timescale/).
Species with unknown habitat information are coded as either marine or freshwater to assess
sensitivity of analyses to coding ambiguity (see main text).
#
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
Fossil
Dialipina
Cheirolepis trailli
Cheirolepis schultzei
Cheirolepis canadensis
Osorioichthys marginis
Tegeolepis clarki
Howqualepis rostridens
Donnrosenia schaefferi
Gogosardina coatesi
Mimipiscis bartrami
Mimipiscis toombsi
Moythomasia n. sp.
Moythomasia nitida
Moythomasia durgaringa
Stegotrachelus finlayi
Krasnoyarichthys jesseni
Novagonatodus kasantsevae
Limnomis delaneyi
Cuneognathus gardineri
Mansfieldiscus sweeti
Melanecta anneae
Woodicthys bearsdeni
Wendyichthys dicksoni
Kentuckia hlavini
Mesopoma
Pteronisculus
Birgeria
Saurichthys
Chondrosteus acipenseroides
Peipiaosteus
Protopsephurus liui
Psammorhynchus longipinnis
Boreosomus
Min. Age (MA)
398
390
372
372
368
361
383
383
372
372
372
372
372
372
383
359
347
359
359
347
318
318
318
359
338
247
251
241
191
125
125
71
251
4
Habitat
F
F
M
FM
M
M
F
F
M
M
M
M
M
M
F
M
F
F
F
F
M
M
M
M
M
M
M
M
M
F
F
F
M
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
Australosomus
Beishanichthys
Fukangichthys
Scanilepis
Evenkia
Perleidus
Felberia
Luganoia lepidosteoides
Macrosemius
Kyphosichthys
Semionotus
Watsonulus eugnathoides
Ionoscopus cyprinoides
Oshunia brevis
Ophiopsis procera
Macrepistius arenatus
Liodesmus gracilis
Liodesmus sprattiformis
Caturus furcatus
Amblysemius pachyurus
Sinamia zdanskyi
Ikechaoamia orientalis
Ikechaoamia meridionalis
Amiopsis woodwardi
Amiopsis dolloi
Amiopsis prisca
Amiopsis lepidota
Amiopsis damoni
Solnhofenamia elongata
Nipponamia satoi
Calamopleurus cylindricus
Calamopleurus mawsoni
Melvius thomasi
Melvius chauliodous
Vidalamia catalunica
Pachyamia latimaxillaris
Pachyamia mexicana
Maliamia gigas
Tomognathus mordax
Amia hesperia
Amia pattersoni
Amia scutata
Cyclurus ignotus
251
247
202
196
251
239
237
235
151
242
199
246
146
109
146
100
146
146
146
146
112
134
134
137
124
92
146
137
146
126
110
128
66
74
136
98
100
48
90
48
50
36
37
5
M
F
F
FM
F
M
M
M
M
M
FM
M
M
M
M
FM
M
M
M
M
F
F
F
FM
F
FM
M
FM
M
F
FM
F
FM
FM
FM
M
M
FM
M
F
F
F
FM
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
Cyclurus fragosus
Cyclurus oligocenicus
Cyclurus gurleyi
Cyclurus kehreri
Cyclurus macrocephalus
Cyclurus valenciennesi
Cyclurus efremovi
Pseudamiatus heintzi
Dapedium
Hypsocormus
Pachycormus
Mesturus
Vinctifer
Aspidorhynchus
Belonostomus
Pholidophorus macrocephalus
Pholidophorus bechei
Leptolepis coryphaenoides
Tharsis
Domeykos
Varasichthys
Luisichthys
Protoclupea
Chongichthys
Notelops
Apsopelix
Crossognathus
Goulmimichthys
Rhacolepis
Ascalabos
Pachythrissops
Allothrissops
Thrissops
Anaethalion zapporum
Anaethalion angustus
Anaethalion knorri
Tongxinichthys microdus
Jiuquanichthys liui
Kuyangichthys microdus
Lycoptera davidi
Tanolepis ningjiagouensis
Paralycoptera wui
Xixiaichthys
66
33
50
48
38
66
59
62
191
146
176
161
100
140
65.5
146
191
176
146
157
157
157
157
156
100
80
106
89
113
146
146
151
146
151
151
146
126
100
100
130
113
110
126
6
F
F
F
F
F
F
F
FM
M
M
M
M
FM
M
M
M
M
M
M
M
M
M
M
M
FM
M
M
M
FM
M
M
M
M
M
M
M
M
F
F
F
F
F
F
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
Plesiolycoptera daqingensis
Yanbiania wangqingica
Eohiodon woodruffi
Jiaohichthys
Eohiodon rosei
Hiodon consteniorum
Thaumaturus
Ostariostoma
Furichthys fieldsoei
Palaeonotopterus
Brychaetoides greenwoodi
Musperia radiata
Phaerodusichthys tavernei
Monopterus gigas
Heterosteoglossum foreyi
Chauliopareion
Xosteoglossid rebeccae
Opsithrissops osseus
osteoglossiform indet
Foreyichthys bolcensis
Ridewoodichthys caheni
Thrissopterus catullii
Sinoglossus lushanensis
Cretophareodus
Brychaetus sp
Brychaetus muelleri
Phareodus testis
Phareodus queenslandicus
Phareodus encaustus
Paraclupea
Ellimmichthys
Armigatus
Diplomystus
Triplomystus
Sorbinichthys
Spratticeps
Santanaclupea
Tischlingerichthys
Notogoneus
Charitopsis
Charitomosus
Judeichthys
Hakeliosomus
66
130
49
130
49
34
34
66
55
94
55
34
62
49
55
40
55
55
55
49
56
49
40
71
55
49
50
35
50
145
145
94
50
94
94
100
113
146
83
100
83
100
100
7
F
F
F
F
F
F
F
F
M
F
M
F
F
M
M
F
M
M
M
M
M
M
F
F
M
M
F
F
F
F
FM
M
F
M
M
M
FM
M
F
M
M
M
M
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
Ramallichthys
Mahengichthys
Gordichthys
Rubiesichthys
Aethalionopsis
Parachanos
Dastilbe
Tharrias
Humbertia
Erichalcis
Leptolepides haerteisi
Leptolepides sprattiformis
Orthogonikleithrus hoelli
Orthogonikleithrus leichi
Sphenocephalus
Mcconichthys
Trichophanes
Libotonius
Amphiplaga
Erismatopterus
Lateopisciculus
Massamoricthys
Archaeozeus skamolensis
Protozeus kuehnei
Cretazeus rinaldii
Palaeogadus
Eolates gracilis
Eolates aquensis
Heteronectes
Amphistium
Joleaudichthys
Numidopleura
Eobothus
Kushlukia permira
Kushlukia sp.
Avitoluvarus dianae
Avitoluvarus mariannae
Luvarus necopinatus
Ruffoichthys
Eosiganus
Siganopygaeus
Protosiganus
Cretatriacanthus guidottii
100
45
130
139
113
83
112
112
100
105
146
146
146
146
72
56
34
34
50
50
56
56
58
58
72
28
49
28
49
49
41
41
49
56
48
56
56
56
49
38
56
28
70
8
M
F
F
F
F
FM
FM
FM
M
M
M
M
M
M
M
F
F
F
F
F
F
F
M
M
M
M
M
F
M
M
M
M
M
M
M
M
M
M
M
M
M
M
M
206 Plectocretacicus clarae
95
M
207 Protriacanthus gortanii
90
M
208 Prohollardia avita
23
M
209 Carpathospinosus propheticus
23
M
210 Bolcabalistes varii
49
M
211 Eospinus daniltshenkoi
49
M
212 Spinacanthus cuneiformis
49
M
213 Protobalistum imperialis
49
M
214 Proaracana dubia
49
M
215 Eolactoria sorbinii
49
M
216 Oligolactoria bubiki
28
M
217 Prodiodon tenuispinus
49
M
218 Prodiodon erinaceus
49
M
219 Zignodon fornasieroae
49
M
220 Pshekhadiodon parini
41
M
221 Heptadiodon echinus
49
M
222 Archaeotetraodon jamestyleri
5
M
223 Sphoeroides hyperostosus
4
M
224 Archaeotetraodon winterbottomi
23
M
225 Protacanthodes ombonii
49
M
226 Protacanthodes nimesensis
49
M
227 Acanthopleurus trispinosus
23
M
228 Cryptobalistes brevis
28
M
229 Acanthopleurus collettei
28
M
230 Acanthopleurus serratus
28
M
231 Eoplectus bloti
49
M
232 Eotetraodon pygmaeus
49
M
233 Zignoichthys oblongus
49
M
234 Triodon antiquus
34
M
235 Eomola bimaxillaria
41
M
236 Moclaybalistes danekrus
59
M
237 Oligobalistes robustus
28
M
238 Balistomorphus ovalis
28
M
239 Balistomorphus orbiculatus
28
M
240 Balistomorphus spinosus
28
M
M: Marine.
F: Freshwater
FM: Unknown habitat or found in both marine and freshwater habitats.
Table SB2. Comparisons of the root age for extant ray-finned fishes (MRCA of Polypterus and
Danio) obtained with the fossil-based tree under different values of the “vartime” variable in
9
Paleotree (timePaleoPhy routine). Compare these ages with the divergence time estimated using
the extant only molecular tree, based and node-age calibrations (383 Ma). Values of vartime
above 1.0 impact the age of the root and were not included in downstream analyses.
Vartime
0.1
0.5
1.0
2.0
5.0
10.0
Root age (Ma)
395
395
395
403
438
740
Appendix SC. Ancestral state reconstructions.
Assessment of sensitivity of ancestral state (habitat) reconstructions: (i) default analyses (BiSSE
using trees with extant taxa; stochastic mapping [SIMMAP-MK2] using trees with fossil and
extant taxa) reported in the main text but depicting complete trees (Fig. SC1); (ii) alternative
analyses using ML-MK2 reconstructions (Fig. SC2); (iii) linear plots and regressions comparing
ML-MK1 vs. ML-MK2 reconstructions (Fig. SC3); (iv) linear plots comparing SIMMAP-MK2
reconstructions for alternative trees with fossil and extant taxa, scaled under different values of
the Vartime parameter (0.1, 0.5, 1.0) in Paleotree (Fig. SC4); and (v) SIMMAP-MK2 analyses
using alternative tree topologies (six additional trees obtained with RAxML search replicates;
Fig. SC5). The rationale for choosing MK2 (instead of the simpler MK1) as the default model is
explained with detail in Appendix SG.
10
Figure SC1. Ancestral state (habitat) reconstructions (ASR) under different models (BiSSE and
SIMMAP), coding scenarios (BEAM - brackish and euryhaline as marine; BEAF - brackish and
euryhaline as freshwater), and using different trees (including or excluding fossils). Ovals
highlight major differences in ancestral habitat reconstructions among early-branching linages.
11
12
Figure SC2. Ancestral state (habitat) reconstructions (ASR) under ML (Ape’s function Ace)
under different models (MK1 and MK2) and coding scenarios (BEAM - brackish and euryhaline
as marine; BEAF - brackish and euryhaline as freshwater). Ovals highlight major differences in
ancestral habitat reconstructions among early-branching linages.
Figure SC3. Linear plots of state probability (freshwater probability) at each node for ML-MK1
vs. ML-MK2 using Ape’s function Ace (see also Fig. SC2). BEAM: brackish and euryhaline
taxa coded as marine; BEAF: brackish and euryhaline taxa coded as freshwater.
13
Figure SC4. Linear plots of state probability (freshwater probability) at each node
obtained with SIMMAP for alternative trees with fossil and extant taxa. The alternative
trees used different values of the Vartime parameter for scaling of fossil branches in
Paleotree. State probabilities among alternative reconstructions are highly similar.
BEAM: brackish and euryhaline taxa coded as marine; BEAF: brackish and euryhaline
taxa coded as freshwater.
14
Figure SC5. Ancestral state (habitat) reconstructions (ASR) under SIMMAP using six alternative topologies obtained with the
RAxML tree searches and under alternative coding scenarios (BEAM - brackish and euryhaline as marine; BEAF - brackish and
euryhaline as freshwater). In all cases, early branching lineages are reconstructed with a high probability of freshwater occupancy,
indicating that the ASRs are robust to topological variations.
15
Appendix SD. State-dependent diversification (SSE).
Table SD1. Sampling fractions defined across 50 (mostly nested) clades to account for
sampling biases in the BiSSE analyses (uneven sampling). We also attempted to define
sampling fractions across 57 non-nested clades, but there were two situations that
violated the method’s assumptions: (1) one of the sates is absent in some clades, which
results in an undefined sampling fraction (a/0); and (2) the two states exist in the clade
but all the sampled taxa belong to one state only, which results in sampling fractions of 0
that cannot be handled by the method. As per recommendation of R. Fitzjohn (pers.
comm.), we thus defined sampling fractions across 50 clades that included all habitat
states (both sampled and unsampled species). Clades are shown in reverse phylogenetic
order; clade names follow our current classification scheme for bony fishes (Betancur-R.
et al. 2013a; Betancur-R. et al. 2014).
Clade
Cottioidei
Notothenioidei
Perciformes
Centrarchiformes s.l.
Terapontiformes
Terapontiformes + Centrarchiformes s.l.
Tetraodontiformes
Tetraodontiformes + Lophiiformes
Sciaenidae
Eupercaria
Beloniformes
Cyprinodontiformes
Atheriniformes
Atherinomorphae
Cichlomorphae
Ovalentaria
BEAM Freshwater
0.0294
1.0000
0.0698
0.2763
0.0455
0.1917
0.0769
0.0769
0.0385
0.1005
0.0404
0.0067
0.0551
0.0163
0.0110
0.0148
16
BEAM Marine
0.0670
0.1032
0.0660
0.1746
0.1235
0.1458
0.1301
0.1043
0.0755
0.0884
0.1195
0.2593
0.1101
0.1288
0.1429
0.0809
BEAF Freshwater
0.0442
1.0000
0.0748
0.2763
0.0877
0.1955
0.0625
0.0625
0.0588
0.1162
0.0696
0.0115
0.0687
0.0251
0.0110
0.0220
BEAF Marine
0.0659
0.0974
0.0653
0.1746
0.1029
0.1374
0.1332
0.1055
0.0750
0.0863
0.1049
0.1111
0.0843
0.0979
0.2500
0.0731
Pleuronectiformes
Carangiaria
Carangiaria + Anabantaria
Carangiaria + Anabantaria + Ovalentaria
Syngnathiformes + Scombriformes
Gobiiformes
Kurtiformes
Gobiaria
Percomorpha
Polymixiiformes + Euacanthomorphacea
Zeiogadaria
Paracanthomorphacea
Acanthomorphata
Neoteleostei
Osmeriformes
Stomiatii
Protacanthopterygii
Euteleostei
Diplomystoidei + Siluroidei
Siluriformes
Siluriformes + Characiformes
Characiphysae
Otophysi
Gonorynchiformes
Ostariophysi
Alepocephaliformes + Ostariophysi
Clupeiformes
Otomorpha
Clupeocephala
Osteoglossocephalai
Elopomorpha
Teleostei
Neopterygii
Actinopteri
ROOT
BEAM: brackish and euryhaline as marine
BEAF: brackish and euryhaline as
freshwater
0.0238
0.0606
0.0640
0.0205
0.0286
0.0058
0.1333
0.0094
0.0284
0.0284
0.2500
0.7000
0.0298
0.0298
0.2857
0.2857
0.0365
0.0309
0.0140
0.0104
0.0115
0.0124
0.0099
0.0938
0.0102
0.0102
0.0200
0.0103
0.0172
0.0177
0.1250
0.0177
0.0181
0.0183
1.00000
0.1027
0.1357
0.1357
0.0983
0.0954
0.0386
0.0569
0.0419
0.0833
0.0851
0.0718
0.0714
0.0849
0.0865
0.2647
0.0846
0.0805
0.0864
0.0187
0.0187
0.0185
0.0185
0.0175
0.6667
0.0500
0.0615
0.0235
0.0412
0.0847
0.0847
0.0164
0.0806
0.0806
0.0806
1.00000
0.0533
0.1290
0.0813
0.0294
0.0357
0.0120
0.1579
0.0156
0.0387
0.0387
1.0000
0.5385
0.0399
0.0399
0.2571
0.2500
0.0538
0.0422
0.0143
0.0106
0.0117
0.0125
0.0099
0.1471
0.0104
0.0104
0.0292
0.0107
0.0222
0.0226
0.0652
0.0227
0.0230
0.0233
1.00000
0.1032
0.1314
0.1314
0.0915
0.0966
0.0409
0.0545
0.0438
0.0813
0.0832
0.0714
0.0718
0.0831
0.0849
0.3333
0.0741
0.0562
0.0843
0.0125
0.0125
0.0125
0.0125
0.0123
0.5000
0.0353
0.0578
0.0176
0.0376
0.0829
0.0829
0.0149
0.0787
0.0787
0.0787
1.00000
Table SD2. Assessments of best-fit models and preliminary rates obtained using a
maximum likelihood framework. The ten GeoSSE models tested were the full (λM, λF,
17
λMF, μM, μF, qMF, and qFM), no intermediate speciation (no λMF), equal speciation
(λM~λF), equal extinction (μM~μF), equal speciation and equal extinction (λM~λF and
μM~μF), equal speciation and dispersal (λM~λF and qMF~qFM), equal extinction and
dispersal (μM~μF and qMF~qFM), and all-equal rates (no sMF, λM~λF, μM~μF, and
qMF~qFM). The nine BiSSE models tested were similar except that the full model has
only six parameters (λM, λF, μM, μF, qMF, and qFM) and thus does not account for
intermediate speciation (λMF).
Method
BiSSE
BiSSE
GeoSSE
GeoSSE
BiSSE
BiSSE
Sampling
Even
Even
Even
Even
Uneven (50 clades)
Uneven (50 clades)
Coding
scenarios
BEAF
BEAM
BAF
BAM
BEAF
BEAM
Best-fit
model
Full
Full
Full
No λMF
λM~λF
Full
Net. Div.
ratio
2.4
2.8
2.6
2.7
1.6
1.8
Turnover
ratio
0.91
0.89
0.89
0.88
0.96
0.93
Net diversification rates ratio: net diversification rates marine/net diversification rates freshwater
Turnover rates ratio: turnover rates marine/turnover rates freshwater
BAM: brackish as marine (GeoSSE)
BAF: brackish as freshwater (GeoSSE)
BEAM: brackish and euryhaline as marine (BiSSE)
BEAF: brackish and euryhaline as freshwater (BiSSE)
18
Figure SD1. MCMC plots of net diversification (speciation minus extinction) and turnover (extinction/speciation) rates across habitats
based on the Clupeocepahala subtree. BAM: brackish as marine (GeoSSE); BAF: brackish as freshwater (GeoSSE); BEAM: brackish
and euryhaline as marine (BiSSE); BEAF: brackish and euryhaline as freshwater (BiSSE).
19
Appendix SE. Transition rates.
Table SE1. Estimates of transition rates obtained with alternative methods (SIMMAP,
SSE) coding scenarios (BEAM, BEAF, BAM, BAF), sampling fraction schemes (even,
uneven), and trees (extant or extant + fossils).
Method
Sampling fractions Tree/coding
BiSSE
Even
Extant/BEAF
BiSSE
Even
Extant/BEAM
GeoSSE
Even
Extant/BAF
GeoSSE
Even
Extant/BAM
BiSSE
Uneven (50 clades)
Extant/BEAF
BiSSE
Uneven (50 clades)
Extant/BEAM
SIMMAP-MK2 _
Extant/BEAM
SIMMAP-MK2 _
Extant/BEAF
SIMMAP-MK2 _
Extant + fossils/BEAM
SIMMAP-MK2 _
Extant + fossils/BEAF
qFM: freshwater-to-marine transition rate
qMF: marine-to-freshwater transition rate
BEAM: brackish and euryhaline as marine (BiSSE, SIMMAP)
BEAF: brackish and euryhaline as freshwater (BiSSE, SIMMAP)
BAM: brackish as marine (GeoSSE)
BAF: brackish as freshwater (GeoSSE)
Transition rate ratio
(qMF/qFM)
11.6
21.5
31.6
36.2
2.0
2.1
4.9
1.6
1.4
1.2
Appendix SF. Clade-based analyses.
Table SF1. List of 67 non-nested target clades and their estimates of stem and crown
ages, species richness, mean habitat state (freshwater) probability, and discretized habitat
state. Clade state probabilities were estimated by averaging the results obtained with
different models (BiSSE, SIMMAP, ML) and coding strategies (BEAM and BEAF).
20
Habitat discretization resulted in 20 freshwater (freshwater probability >0.9) and 35
marine clades (freshwater probability < 0.1); 12 remaining clades had ambiguous state
probabilities (>0.1 and <0.9) and were thus excluded from consideration (listed as “?”).
Taxa denoted with asterisk have a crown age of 80–50 Ma (9 freshwater, 19 marine
clades, and 5 ambiguous that were excluded), which were selected for reduced cladebased comparisons (see main text).
Clade
Stem Age
(Ma)
Crown
Age (Ma)
Polypteriformes
Acipenseriformes
Holostei
Elopiformes
Albuliformes
Notacanthiformes*
Anguilliformes*
Hiodontiformes
Osteoglossiformes
Clupeiformes
Alepocephaliformes*
Gonorynchoidei
Chanoidei + Knerioidei
Cobitoidea*
Cyprinoidea*
Gymnotiformes*
Characiformes
Loricaroidei
Diplomystoidei + Siluroidei
Lepidogalaxiiformes
Argentiniformes*
Galaxiiformes*
Esociformes*
Salmoniformes
Retropinnidae
Osmeriformes (in part)
Stomiatiformes
Ateleopodiformes
Aulopiformes
Neoscopelidae
Myctophidae*
Lampridiformes
382.6
350.1
322.5
196.2
150.8
101.0
101.0
227.1
227.1
230.2
219.7
175.9
175.9
99.3
99.3
147.8
137.0
115.8
115.8
231.8
159.6
145.6
104.5
55.8
73.7
73.7
129.4
192.3
182.8
73.6
73.6
150.3
29.2
138.9
267.9
133.6
40.5
50.7
79.4
9.5
163.1
188.9
53.3
18.2
147.1
78.8
63.3
69.0
114.8
110.6
106.2
3.5
70.5
50.0
79.4
35.3
22.5
34.3
83.8
8.1
113.9
42.4
51.7
81.7
21
Mean state
Clade
(freshwater)
richness
probability
12
0.999
28
0.988
8
0.962
9
0.439
13
0.011
27
0.000
934
0.000
2
1.000
228
0.998
398
0.820
140
0.006
5
0.065
33
0.867
1143
1.000
2916
1.000
204
1.000
2004
1.000
1385
1.000
2183
1.000
2
1.000
89
0.033
50
0.814
13
0.984
216
0.536
6
0.546
35
0.495
427
0.001
13
0.000
262
0.000
7
0.000
252
0.000
24
0.001
Discretized
clade
habitat
Freshwater
Freshwater
Freshwater
?
?
Marine
Marine
Freshwater
Freshwater
?
Marine
Marine
?
Freshwater
Freshwater
Freshwater
Freshwater
Freshwater
Freshwater
Freshwater
Marine
?
Freshwater
?
?
?
Marine
Marine
Marine
Marine
Marine
Marine
Percopsiformes*
Zeiformes*
Gadariae*
Polymixiiformes
Beryciformes
Holocentriformes*
Ophidiiformes*
Batrachoidiformes
Kurtiformes*
Gobiiformes*
Syngnathiformes*
Scombriformes*
Synbranchiformes*
Anabantoidei*
Channoidei*
Carangiaria*
Polycentridae
Cichllidae*
Atheriniformes*
Cyprinodontiformes*
Beloniformes*
Pomacentridae + Mugilidae +
Blenniiformes + others
Labriformes*
Moronidae + Ephippiformes
Lobotiformes + Sciaenidae
Acanthuriformes +
Pomacanthidae +
Chaetodontidae + Haemulidae
+ Lutjanidae + others
Spariformes*
Lophiiformes +
Tetraodontiformes*
Uranoscopiformes
Pempheriformes
Terapontiformes +
Centrarchiformes
Serranidae*
Percidae
Notothenioidei*
Cottioidei*
135.0
107.1
107.1
154.8
146.5
145.0
132.8
126.8
102.3
102.3
94.6
94.6
80.7
70.7
70.7
96.4
94.2
88.7
77.4
76.4
76.4
63.2
66.5
78.8
13.7
125.3
52.5
75.4
39.8
80.3
72.8
74.3
50.3
73.7
62.8
67.4
69.4
46.1
76.4
70.9
66.9
71.9
9
33
612
10
182
84
531
84
349
1996
662
274
124
69
163
1068
4
1642
345
1227
258
0.980
0.000
0.001
0.000
0.000
0.001
0.000
0.000
0.052
0.202
0.000
0.000
0.999
1.000
1.000
0.000
0.989
0.988
0.500
0.512
0.502
Freshwater
Marine
Marine
Marine
Marine
Marine
Marine
Marine
Marine
?
Marine
Marine
Freshwater
Freshwater
Freshwater
Marine
Freshwater
Freshwater
?
?
?
97.2
93.6
93.8
92.2
94.6
76.7
88.6
86.4
1920
625
24
298
0.085
0.000
0.007
0.001
Marine
Marine
Marine
Marine
92.2
85.9
85.7
80.3
691
253
0.000
0.000
Marine
Marine
80.8
95.3
93.2
80.4
89.0
89.6
787
165
195
0.000
0.000
0.000
Marine
Marine
Marine
93.2
80.2
66.0
76.0
73.1
84.7
80.1
40.3
63.0
70.8
282
535
233
156
1266
0.060
0.000
0.994
0.004
0.000
Marine
Marine
Freshwater
Marine
Marine
Table SF2. Estimates of net diversification rates for the 55 target clades (35 marine and
20 freshwater) using both crown and stem equations implemented in the method-of-
22
moments (Magallon & Sanderson 2001). Rates were calculated based on the mean values
of ε
0.30) habitats and confidence limits were assessed
all cases, net diversification rates are higher for
marine (MA) vs. freshwater (FW) clades, although only two comparisons (crown-based)
are significant (*P< 0.05).
Extinction
(ε)
0.0
FW= 0.53;
MA= 0.30
0.9
Mean net
div. rates
FW - Crown
0.0504
Mean net div.
rates MA Crown
0.0705
U test P
value
0.043*
Mean net
div. rates
FW - Stem
0.0419
Mean net
div. rates
MA - Stem
0.0503
U test
P
value
0.326
0.0468
0.0330
0.0689
0.0433
0.019*
0.082
0.0360
0.0249
0.0470
0.0296
0.110
0.362
Table SF3. Estimates of net diversification rates for a subset of the clades in Table SF1
(9 freshwater and 19 marine clades) whose crown age is 80–50 Ma. Both crown and stem
equations implemented in the method-of-moments are compared (Magallon & Sanderson
2001). Rates were calculated based on the mean values of ε (extinction) estimated with
fractions. In all cases, net diversification rates are higher for marine (MA) vs. freshwater
(FW) clades, although only one comparison (crown-based) is marginally significant (*P
= 0.068) presumably due to reduced statistical power.
Extinction
(ε)
Mean net
div. rates
FW - Crown
Mean net div.
rates MA Crown
23
U test P
value
Mean net
div. rates
FW - Stem
Mean net
div. rates
MA - Stem
U test
P
value
0.0
FW= 0.53;
MA= 0.30
0.9
0.0266
0.0436
0.06813
0.0476
0.0522
0.7355
0.0596
0.0426
0.0716
0.0490
0.2051
0.3568
0.0481
0.0330
0.0550
0.0357
0.4982
0.7355
Table SF4. Estimates of net diversification rates for a subset of the clades in Table SF1
(9 freshwater and 19 marine clades) whose crown age is 80–50 Ma. Both crown and stem
equations implemented in the method-of-moments are compared (Magallon & Sanderson
2001). Rates were calculated based on the mean values of ε (extinction) estimated with
BiSSE/GeoSSE for freshwater (= 0.53) and marine (= 0.30) habitats and confidence
limits were assessed under arbitrarily high (= 0.90) and low (= 0.0) extinction fractions.
Most rate estimates based on crown equations are significantly higher than those based
on stem equations for marine (MA) clades, whereas all crown vs. stem comparisons for
freshwater (FW) clades are non-significant. Note that these results may suffer from
limited statistical power.
Extinction
(ε)
0.0
FW= 0.53;
MA= 0.30
0.9
Mean net
div. rates
FW - Crown
0.0266
Mean net
div. rates
FW - Stem
0.0476
U test P
value
0.297
Mean net
div. rates
MA - Crown
0.0436
Mean net
div. rates
MA - Stem
0.0522
U test P
value
0.284
0.0596
0.0426
0.0481
0.0330
0.340
0.340
0.0716
0.0490
0.0550
0.0357
0.099**
0.008**
**P< 0.01
24
Figure SF1. Correlations of (log) species richness against crown and stem ages, for 19
marine and 9 freshwater clades. Note that these results may suffer from limited statistical
power.
Appendix SG. Comparisons of model fitting using Markov models that assume fixed
diversification parameters but allow transition rates to be either symmetric (MK1) or
asymmetric (MK2).
25
One of the reviewers of the paper (Graham Slater) commented: “What would be
useful, straightforward and clearer for this manuscript would be to first compare the fit of
different flavors of MK models to the extant only and extant plus extinct datasets using
ML. This could be done, for instance, by fitting equal rates, symmetric (meaning
transition rates within, but not among pairs of states, are equal), and all rates different
models using fitDiscrete in Geiger.”
We followed his suggestion and tested the fit of both datasets (extant only and
fossil-based) to the MK1 (equal rates) and MK2 (all-rates-different) models using the
fitDiscrete function in Geiger as well as the Ace function in Ape. In all cases the tests
failed to reject the null MK1 model (ΔAIC <4; Table SG1), although those using the
fossil-based dataset were marginally below significance.
Table SG1. Results of model fitting using Markov models that assume fixed
diversification parameters but allow transition rates to be symmetric (MK1; qMF~qFM)
or asymmetric (MK2; qMF≠qFM).
ΔAIC fitDiscrete
(Geiger)
ML
Extant/BEAM
2.00
ML
Extant/BEAF
1.50
ML
Extant + fossils/BEAM 3.56
ML
Extant + fossils/BEAF 3.79
BEAM: brackish and euryhaline as marine
BEAF: brackish and euryhaline as freshwater
Method
Tree/coding
ΔAIC Ace
(Ape)
0.67
1.54
3.55
3.79
These results were surprising (particularly for the extant-only dataset) given that
model fitting using SSE strongly indicated asymmetrical transition rates in most cases
26
(ΔAIC values of up to 74; results of Table 2 summarized on Table SG2 for ease of
comparison).
Table SG2. Results of model fitting using SSE models (extant-only dataset) where
transition rates are fixed as equal (qMF~qFM) while speciation and extinction are free to
vary (λM≠λF; μM≠μF). Adapted from Table 2.
Method
BiSSE
BiSSE
GeoSSE
GeoSSE
BiSSE
BiSSE
Sampling fractions
Even
Even
Even
Even
Unveven (50 clades)
Unveven (50 clades)
Tree/coding
Extant/BEAF
Extant/BEAM
Extant/BAF
Extant/BAM
Extant/BEAF
Extant/BEAM
qMF~qFM (ΔAIC)
62***
65***
74***
70***
4*
2
BEAM: brackish and euryhaline as marine (BiSSE, SIMMAP)
BEAF: brackish and euryhaline as freshwater (BiSSE, SIMMAP)
BAM: brackish as marine (GeoSSE)
BAF: brackish as freshwater (GeoSSE)
The fitDiscrete and Ace results are not only contrary to those using SSE, but also
challenge the biological notion that habitat transitions in fishes are asymmetric (see
Introduction). This bizarre result led us to hypothesize that these functions may lack
statistical power. To test this idea we first used the tree and habitat data from our
previous study with ariid catfishes (Betancur-R et al. 2012) where we show that transition
rates are highly asymmetric: there were 12 independent events of freshwater colonization
by marine ariid lineages vs. (possibly) a single event of freshwater-to-marine invasion in
recent times (Fig. 1). The ΔAIC score from this comparison was, again, not significant
(fitDiscrete = 1.91; Ace = 2.72).
27
We then simulated 10 birth-death trees (λ=0.1, μ=0.03) and binary characters for
1500 taxa using the tree.bd and sim.character functions in diversitree. Character states
were simulated under MK2 assuming highly asymmetrical rates, with state shifts being
more than an order of magnitude higher for one transition type than the other (q01 =
0.0003; q10= 0.006). These transition parameter values were based on our results using
BiSSE, BDAM coding, and even sampling – i.e., the BiSSE result with the highest ΔAIC
(65) in our model comparisons (see Table SG2). Once again, both fitDiscrete and Ace
failed to reject the null hypothesis of equal transition rates in all comparisons, although
one ΔAIC score was marginally below 4.0 (Table SG3)
Table SG3. Results of MK1 vs. MK2 model fitting using 10 datasets simulated with
highly asymmetrical transition rate parameters (q01 = 0.0003; q10= 0.006).
Simulation
1
2
3
4
5
6
7
8
9
10
ΔAIC fitDiscrete
(Geiger)
0.99
1.98
1.84
1.98
1.98
2.00
1.92
3.65
1.99
1.98
ΔAIC Ace
(Ape)
0.99
1.98
1.98
1.98
1.98
1.98
1.98
1.98
1.98
1.98
It is beyond the scope of this study to properly assess the power of fitDiscrete and
Ace, as that would require more exhaustive analyses. However, these preliminary results
show that these tests may suffer from high rates of type II error. We thus base our
28
conclusions on the asymmetry of habitat transition following the SSE result and conduct
all major ancestral state reconstructions using the MK2 model (asymmetric rates) under
SIMMAP and ML. It is noteworthy, however, that the ASRs using Ace are robust to
model choice (MK1 vs. MK2; Fig. SC2).
29
REFERENCES
1.
Arratia, G. (1999). The monophyly of Teleostei and stem-group teleosts. Consensus
and disagreements. In: Mesozoic Fishes 2 – Systematics and Fossil Record (eds.
Arratia, G & Schultze, HP). Verlag Dr. F. Pfeil München, pp. 265-334.
2.
Arratia, G. (2008). The varasichthyid and other crossognathiform fishes, and the
Break-up of Pangaea. Geological Society London Special Publications, 295, 7192.
3.
Betancur-R, R., Ortí, G., Stein, A.M., Marceniuk, A.P. & Alexander Pyron, R. (2012).
Apparent signal of competition limiting diversification after ecological
transitions from marine to freshwater habitats. Ecology Letters, 15, 822-830.
4.
Betancur-R., R., Broughton, R.E., Wiley, E.O., Carpenter, K., Lopez, J.A., Li, C. et al.
(2013a). The tree of life and a new classification of bony fishes. PLoS Currents
Tree of Life, 2013 Apr 18.
5.
Betancur-R., R., Li, C., Munroe, T.A., Ballesteros, J.A. & Orti, G. (2013b). Addressing
gene-tree discordance and non-stationarity to resolve a multi-locus
phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Systematic Biology,
62, 763–785.
6.
Betancur-R., R. & Orti, G. (2014). Molecular evidence for the monophyly of flatfishes
(Carangimorpharia: Pleuronectiformes). Molecular phylogenetics and
evolution, 73, 18-22.
7.
Betancur-R., R., Wiley, E.O., Miya, M., Lecointre, G. & Orti, G. (2014). Phylogenetic
Classification of Bony Fishes. Version 3. Available at:
http://www.deepfin.org/Classification_v3.htm Last accessed July 2014.
8.
Bonde, N. (2008). Osteoglossomorphs of the marine Lower Eocene of Denmark –
with remarks on other Eocene taxa and their importance for
palaeobiogeography. In: Fishes and the Break-up of Pangaea (eds. Cavin, L,
Longbottom, A & Richter, M). Geological Society, London, Special Publications
London, pp. 253–310.
9.
Borden, W.C., Grande, T. & Smith, W.L. (2013). Comparative osteology and myology
of the caudal fin in the Paracanthopterygii (Teleostei: Acanthomorpha). In:
Mesozoic Fishes 5 - Global Diversity and Evolution (eds. Arratia, G & Schultze,
H-P). Verlag F. Pfeil Muenchen.
10.
Choo, B. (2011). Revision of the actinopterygian genus Mimipiscis (=Mimia) from
the Upper Devonian Gogo Formation of Western Australia and the
30
interrelationships of the early Actinopterygii. Earth and Environmental
Science Transactions of the Royal Society of Edinburgh, 102, 77-104.
11.
Davis, A.M., Arratia, G. & Kaiser, T.M. (2013). The first fossil shellear and its
implications for the evolution and divergence of the Kneriidae (Teleostei:
Gonorynchiformes). In: Mesozoic Fishes 5 - Global Diversity and Evolution
(eds. Arratia, G, Schultze, H-P & Wilson, MVH). Verlag F. Pfeil Muenchen, pp.
325-362.
12.
Forey, P. (2004). Basal clupeomorphs and ellimmichthyiform phylogeny. In:
Mesozoic Fishes 3 – Systematics, Paleoenvironments and Biodiversity (eds.
Arratia, G & Tintori, A). Verlag Dr. F. Pfeil München, pp. 391-404.
13.
Forey, P.L. & Patterson, C. (2006). Description and systematic relationships of
†Tomognathus, an enigmatic fish from the English Chalk. Journal of
Systematic Palaeontology, 4, 157-184.
14.
Friedman, M. (2008). The evolutionary origin of flatfish asymmetry. Nature, 454,
209-212.
15.
Friedman, M. & Blom, H. (2006). A NEW ACTINOPTERYGIAN FROM THE
FAMENNIAN OF EAST GREENLAND AND THE INTERRELATIONSHIPS OF
DEVONIAN RAY-FINNED FISHES. Journal of Paleontology, 80, 1186-1204.
16.
Gardiner, B.G., Schaeffer, B. & Masserie, J.A. (2005). A review of the lower
actinopterygian phylogeny. Zoological Journal of the Linnean Society, 144,
511-525.
17.
Grande, L. & Bemis, W.E. (1998). A comprehensive phylogenetic study of amiid
fishes (Amiidae) based on comparative skeletal anatomy. An empirical
search for interconnected patterns of natural history. Journal of Vertebrate
Paleontology (Memoir 4, supplement) 18, 690.
18.
Grande, L. & Hilton, E.J. (2006). An Exquisitely Preserved Skeleton Representing a
Primitive Sturgeon from the Upper Cretaceous Judith River Formation of
Montana (Acipenseriformes: Acipenseridae: N. Gen. And Sp). Journal of
Paleontology, 80, 1-39.
19.
Hilton, E.J. (2003). Comparative osteology and phylogenetic systematics of fossil and
living bony-tongue fishes (Actinopterygii, Teleostei, Osteoglossomorpha).
Zoological Journal of the Linnean Society, 137, 1–100.
20.
Hilton, E.J. & Forey, P.L. (2009). Redescription of †Chondrosteus acipenseroides
Egerton, 1858 (Acipenseriformes, †Chondrosteidae) from the lower Lias of
Lyme Regis (Dorset, England), with comments on the early evolution of
sturgeons and paddlefishes. Journal of Systematic Palaeontology, 7, 427-453.
31
21.
Li, G.-Q. & Wilson, M.V.H. (1999). Early divergence of Hiodontiformes sensu stricto
in East Asia and phylogeny of some Late Mesozoic teleosts from China. In:
Mesozoic Fishes 2 – Systematics and Fossil Record (eds. Arratia, G & Schultze,
H-P). Verlag Dr. Friedrich Pfeil Mü nchen pp. 369-384.
22.
Long, J.A., Choo, B. & Young, G.C. (2008). A new basal actinopterygian fish from the
Middle Devonian Aztec Siltstone of Antarctica. Antarctic Science, 20.
23.
Magallon, S. & Sanderson, M.J. (2001). Absolute diversification rates in angiosperm
clades. Evolution, 55, 1762-1780.
24.
Otero, O. (2004). Anatomy, systematics and phylogeny of both Recent and fossil latid
fishes (Teleostei, Perciformes, Latidae). Zoological Journal of the Linnean
Society, 141, 81-133.
25.
Poyato-Ariza, F.J., Grande, T. & Diogo, R. (2010). Gonorynchiform Interrelationships:
Historic Overview, Analysis, and Revised Systematics of the Group. In:
Gonorynchiformes and Ostariophysan Relationships (eds. Grande, T, PoyatoAriza, FJ & Diogo, R). Science Publishers, pp. 227-338.
26.
Santini, F. & Tyler, J.C. (2003). A phylogeny of the families of fossil and extant
tetraodontiform fishes (Acanthomorpha, Tetraodontiformes), Upper
Cretaceous to Recent. Zoological Journal of the Linnean Society, 139, 565–617.
27.
Schultze, H.-P. & Cumbaa, S.L. (2001). Dialipina and the characters of basal
actinopterygians. In: Major events in Early Vertebrate Evolution, Paleontology,
Phylogeny, Genetics and Development (ed. Ahlberg, PE). Systematic
Association Special Volume - Taylor & Francis London and New York., pp.
315-332.
28.
Swartz, B.A. (2009). Devonian actinopterygian phylogeny and evolution based on a
redescription ofStegotrachelus finlayi. Zoological Journal of the Linnean
Society, 156, 750-784.
29.
Taverne, L. (1997). Osorioichthys marginis, ‘Paéonisciforme’ du famennien de
Belgique, et la phylogénie de Actinoptérygiens dévonians (Pisces). Bulletin de
l’institut Royal des Sciences Naturelles de Belgique, 67, 57–78.
30.
Taverne, L. (1998). Les ostéoglossomorphes marins de l’Éocène du Monte Bolca
(Italie): Monopteros Volta 1796, Thrissopterus Heckel, 1856 et Foreyichthys
Taverne, 1979. Considérations sur la phylogénie des téléostéens
ostéoglossomorphes. Studie e Ricerche sui Giacimenti Terziari di Bolca, 7, 67–
158.
31.
32
Tyler, J.C. & Bannikov, A.F. (1997). Relationships of the Fossil and Recent Genera of
Rabbitfishes (Acanthuroidei: Siganidae). Smithsonian Contributions to
Zoology, 84, 1-34.
32.
Tyler, J.C., Johnson, G.D., Nakamura, I. & Collette, B.B. (1989). Morphology of Luvarus
imperialis (Luvaridae), with a phylogenetic analysis of the Acanthuroidei.
Smithsonian Contributions to Zoology, 485, 1-78.
33.
Tyler, J.C. & Santini, F. (2005). A phylogeny of the fossil and extant zeiform-like
fishes, Upper Cretaceous to Recent, with comments on the putative
zeomorph clade (Acanthomorpha). Zoologica Scripta, 34, 157-175.
34.
Wilson, M.V.H. & Murray, A.M. (2008). Osteoglossomorpha: phylogeny,
biogeography, and fossil record and the significance of key African and
Chinese fossil taxa. Geological Society, London, Special Publications, 295, 185219.
35.
Xu, G.-H. & Gao, K.-Q. (2011). A new scanilepiform from the Lower Triassic of
northern Gansu Province, China, and phylogenetic relationships of nonteleostean Actinopterygii. Zoological Journal of the Linnean Society, 161, 595612.
36.
Xu, G.-H. & Wu, F.-X. (2012). A deep-bodied ginglymodian fish from the Middle
Triassic of eastern Yunnan Province, China, and the phylogeny of lower
neopterygians. Chinese Science Bulletin, 57, 111-118.
37.
Zhang, J.-Y. (2006). Phylogeny of Osteoglossomorpha. Vert. Pal. Asiat., 44, 43-59.
33