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Table 2 List of the species used in this study

From: Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

Order/suborder/superfamilya

Family

Speciesb

Accession No.c

Outgroup

   

   Coelacanthiformes

Latimeriidae

Latimeria menadoensis

AP006858

   Ceratodontiformes

Ceratodontidae

Neoceratodus forsteri

AJ584642

   Polypteriformes

Polypteridae

Polypterus ornatipinnis

AP004351

  

Polypterus senegalus

AP004352

  

Erpetoichthys calabaricus

AP004350

   Acipenseriformes

Acipenseridae

Acipenser transmontanus

AB042837

  

Scaphirhynchus cf. albus

AP004354

 

Polyodontidae

Polyodon spathula

AP004353

   Lepisosteiformes

Lepisosteidae

Lepisosteus oculatus

AB042861

  

Atractosteus spatula

AP004355

   Amiiformes

Amiidae

Amia calva

AB042952

   Hiodontiformes

Hiodontidae

Hiodon alosoides

AP004356

   Osteoglossiformes

Osteoglossidae

Osteoglossum bicirrhosum

AB043025

  

Pantodon buchholzi

AB043068

   Albuliformes

Notacanthidae

Notacanthus chemnitzi

AP002975

   Anguillformes

Anguillidae

Anguilla japonica

AB038556

 

Muraenidae

Gymnothorax kidako

AP002976

 

Congridae

Conger myriaster

AB038381

   Clupeiformes

Denticipitidae

Denticeps clupeoides

AP007276

 

Engraulidae

Engraulis japonicus

AB040676

 

Clupeidae

Sardinops melanostictus

AB032554

   Gonorynchiformes

Chanidae

Chanos chaos

AB054133

 

Gonorynchidae

Gonorynchus greyi

AB054134

 

Kneriidae

Kneria sp.

AF007278

 

Phractolaemidae

Phractolaemus ansorgii

AB070243

   Alepocephaliformes

Platytroctidae

Platytroctes apus

AP004107

 

Bathylaconidae

Herwigia kreffti

AP009582

 

Alepocephalidae

Alepocephalus tenebrosus

AP004100

   Salmoniformes

Salmonidae

Salmo salar

U12143

   Esociformes

Esocidae

Esox lucius

AP004103

   Polymixiiformes

Polymixiidae

Polymixia japonica

AB034826

   Gadiformes

Gadidae

Gadus morhua

X99772

   Perciformes

Cichlidae

Oreochromis sp.

AP009126

  

Neolamprologus brichardi

AP006014

  

Tropheus duboisi

AP006015

  

Astronotus ocellatus

AP009127

  

Paretroplus maculatus

AP009504

  

Etroplus maculatus

AP009505

  

Hypselecara temporalis

AP009506

  

Ptychochromoides katria

AP009507

  

Paratilapia polleni

AP009508

  

Tylochromis polylepis

AP009509

   Tetraodontiformes

Tetraodontidae

Takifugu rubripes

AJ421455

  

Tetraodon nigroviridis

AP006046

Ingroup

   

   Cypriniformes

   

Cyprinoidea

Cyprinidae

Cyprinus carpio

X61010

  

Danio rerio

AC024175

 

Psilorhynchidae

Psilorhynchus homaloptera

DQ026436

Cobitoidea

Gyrinocheilidae

Gyrinocheilus aymonieri

AB242164

 

Catostomidae

Catostomus commersonii

AB127394

 

Cobitidae

Cobitis striata

AB054125

 

Balitoridae

Formosania lacustre

M91245

   Characiformes

   

Citharinoidei

Distichodontidae

Distichodus sexfasciatus

AB070242**

  

Ichthyborus sp.

AP011993**

 

Citharinidae

Citharinus congicus*

AP011985**

Characoidei

Parodontidae

Parodon affinis

AP011998**

 

Curimatidae

Curimatopsis evelynae

AP011988**

 

Anostomidae

Leporinus affinis

AP011994**

 

Chilodontidae

Chilodus punctatus

AP011984**

 

Crenuchidae

Crenuchus spilurus

AP011986**

 

Hemiodontidae

Hemiodopsis gracilis

AP011990**

 

Alestidae

Micralestes sp.

AP011996**

  

Phenacogrammus interruptus

AB054129

 

Gasteropelecidae

Carnegiella strigata

AP011983**

 

Characidae

Astyanax mexicanus

AP011982**

  

Chalceus macrolepidotus

AB054130

  

Myleus sp.

AP011997**

  

Paracheirodon innesi

AP011999**

  

Pygocentrus nattereri

AP012000**

 

Acestrorhynchidae

Acestrorhynchus sp.

AP011981**

 

Cynodontidae

Hydrolycus scomberoides

AP011989**

 

Erythrinidae

Hoplias malabaricus

AP011992**

 

Lebiasinidae

Lebiasina astrigata

AP011995**

 

Ctenoluciidae

Boulengerella maculata

AB070207

  

Ctenolucius hujeta*

AP011987**

 

Hepsetidae

Hepsetus odoe

AP011991**

   Siluriformes

   

Diplomystoidea

Diplomystidae

Diplomystes nahuelbutaensis

AP012011**

Cetopsoidea

Cetopsidae

Cetopsidium sp.

AP012007**

  

Helogenes marmoratus*

AP012014**

Loricaroidea

Amphiliidae

Amphilius sp.

AP012002**

 

Tricomycteridae

Trichomycterus areolatus

AP012026**

 

Callichthyidae

Corydoras rabauti

AB054128

 

Astroblepidae

Astroblepus sp.

AP012004**

 

Loricariidae

Pterygoplichthys disjunctivus

AP012021**

Sisoroidea

Amblycipitidae

Liobagrus reinii

AP012015**

 

Erethistidae

Hara jerdoni

AP012012**

 

Aspredinidae

Bunocephalus coracoideus

AP012006**

Cranoglanoidea

Cranoglanididae

Cranoglanis bouderius

AY898626

Ictaluroidea

Ictaluridae

Ictalurus punctatus

AF482987

Doradoidea

Mochokidae

Synodontis schoutedeni

AP012023**

 

Doradidae

Amblydoras gonzalezi

AP012001**

 

Auchenipteridae

Tatia pergiae

AP012024**

  

Tetranematichthys quadrifilis

AP012025**

Siluroidea

Siluridae

Silurus asotus

AP012022**

 

Malapteruridae

Malapterurus electricus

AP012016**

 

Auchenoglanididae

Auchenoglanis occidentalis

AP012005**

 

Chacidae

Chaca bankanensis

AP012008**

 

Plotosidae

Plotosus japonicus

AP012020**

 

Clariidae

Clarias sp.

AP012010**

 

Heteropneustidae

Heteropneustes fossilis

AP012013**

Bagroidea

Claroteidae

Chrysichthys sp.

AP012009**

 

Ariidae

Sciades seemanni

AP012003**

 

Schilbeidae

Pareutropius debauwi

AP012017**

 

Pangasiidae

Pangasius larnaudii

AP012018**

 

Bagridae

Pseudobagrus tokiensis

AB054132

 

Pimelodidae

Pimelodus pictus

AP012019**

   Gymnotiformes

   

Gymnotoidei

Gymnotidae

Electrophorus electricus

AP011978**

  

Gymnotus carapo*

AP011979**

Sternopygoidei

Rhamphichthyidae

Gymnorhamphichthys sp.

AP011980**

 

Sternopygidae

Eigenmannia sp.

AB054131

 

Apteronotidae

Apteronotus albifrons

AB054132

  1. a Classifications follow [3] except for the recognition of Alepocephaliformes [5, 7].
  2. b Those species with single asterisks were also used for nuclear DNA sequence analysis.
  3. c Those sequences with double asterisks were newly determined during this study.