Table 1.

List of Species Included in the Phylogenetic Analyses

Organismsource	Scientific Name	Class	Order	Reference
Ray-finned fish
Asian arowana*	Scleropages formosus	Actinopterygii	Osteoglossiformes	This study
European eelZ	Anguilla anguilla	Actinopterygii	Anguilliformes	Henkel et al. (2012)
MedakaE	Oryzias latipes	Actinopterygii	Beloniformes	Kasahara et al. (2007)
Blind cave fishE	Astyanax mexicanus	Actinopterygii	Characiformes	McGaugh et al. (2014)
Common carpC	Cyprinus carpio	Actinopterygii	Cypriniformes	Xu et al. (2014)
ZebrafishE	Danio rerio	Actinopterygii	Cypriniformes	Howe et al. (2013)
Amazon mollyE	Poecilia formosa	Actinopterygii	Cyprinodontiformes	Unpublished
Southern platyfishE	Xiphophorus maculatus	Actinopterygii	Cyprinodontiformes	Schartl et al. (2013)
Northern pikeV	Esox lucius	Actinopterygii	Esociformes	Rondeau et al. (2014)
Atlantic codE	Gadus morhua	Actinopterygii	Gadiformes	Star et al. (2011)
Three-spined sticklebackE	Gasterosteus aculeatus	Actinopterygii	Gasterosteiformes	Jones et al. (2012)
Electric eelF	Electrophorus electricus	Actinopterygii	Gymnotiformes	Gallant et al. (2014)
Spotted garE	Lepisosteus oculatus	Actinopterygii	Lepisosteiformes	Unpublished
Nile tilapiaE	Oreochromis niloticus	Actinopterygii	Perciformes	Brawand et al. (2014)
Atlantic salmonSA	Salmo salar	Actinopterygii	Salmoniformes	Davidson et al. (2010)
Rainbow troutG	Oncorhynchus mykiss	Actinopterygii	Salmoniformes	Berthelot et al. (2014)
Japanese pufferE	Takifugu rubripes	Actinopterygii	Tetraodontiformes	Aparicio et al. (2002)
Green spotted pufferE	Tetraodon nigroviridis	Actinopterygii	Tetraodontiformes	Jaillon et al. (2004)
Lobe-finned fish
African coelacanthE	Latimeria chalumnae	Sarcopterygii	Coelacanthiformes	Amemiya et al. (2013)
aLungfishSR	Protopterus annectens	Sarcopterygii	Lepidosireniformes	Amemiya et al. (2013)
Cartilaginous fish
Elephant sharkA	Callorhinchus milii	Chondrichthyes	Chimaeriformes	Venkatesh et al. (2014)
bSmall-spotted catsharkSK	Scyliorhinus canicula	Chondrichthyes	Carchariniformes	Wyffels et al. (2014)
bLittle skateSK	Leucoraja erinacea	Chondrichthyes	Rajiformes	Wang et al. (2012)
Tetrapods
Western clawed frogE	Xenopus tropicalis	Amphibia	Anura	Fuchs et al. (2006)
ChickenE	Gallus gallus	Aves	Galliformes	Hillier et al. (2004)
HumanE	Homo sapiens	Mammalia	Primates	Venter et al. (2001)
LizardE	Anolis carolinensis	Reptilia	Squamata	Alföldi et al. (2011)

Note.—Codes for source: A*STAR (A), CarpBase (C), Ensembl (E), efish genomics (F), Genoscope (G), SalmonDB (SA), SkateBase (SK), SRA (SR), UVic (V), ZF Genomics (Z), this study (*).

^aRaw transcriptome reads were used.

^bAssembled transcripts were used.