Phylogenetic summary of protein families

• Overview
• Gene tree coverage and Gene QC for each species
• Size of gene trees (split by their root taxon)
• Gene tree nodes, and the inference of speciation / duplication events

Overall Summary

Legend
Internal nodes (ancestral taxa)	Node types	Speciations	Duplications	Dubious nodes
Leaves (extant species)	Gene tree coverage	Genes in multi-species trees	Genes in single-species trees	Orphaned genes
	Gene QC	Validated genes	Short genes	Long genes	Split genes

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Climbing perch (Anabas testudineus reference strain)

Siamese fighting fish (Betta splendens)

Zig-zag eel (Mastacembelus armatus)

Turquoise killifish (Nothobranchius furzeri)

Mangrove rivulus (Kryptolebias marmoratus)

Monterrey platyfish (Xiphophorus couchianus)

Platyfish (Xiphophorus maculatus)

Amazon molly (Poecilia formosa)

Sailfin molly (Poecilia latipinna)

Guppy (Poecilia reticulata)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Chinese medaka (Oryzias sinensis)

Javanese ricefish (Oryzias javanicus)

Japanese medaka HdrR (Oryzias latipes)

Indian medaka (Oryzias melastigma)

Eastern happy (Astatotilapia calliptera reference strain)

Burton's mouthbrooder (Haplochromis burtoni)

Makobe Island cichlid (Pundamilia nyererei)

Zebra mbuna (Maylandia zebra)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Orange clownfish (Amphiprion percula)

Bicolor damselfish (Stegastes partitus)

Spiny chromis (Acanthochromis polyacanthus)

Turbot (Scophthalmus maximus)

Tongue sole (Cynoglossus semilaevis)

Greater amberjack (Seriola dumerili)

Yellowtail amberjack (Seriola lalandi dorsalis)

Barramundi perch (Lates calcarifer)

Tetraodon (Tetraodon nigroviridis)

Fugu (Takifugu rubripes)

Large yellow croaker (Larimichthys crocea)

European seabass (Dicentrarchus labrax)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

Lumpfish (Cyclopterus lumpus)

Pike-perch (Sander lucioperca)

Channel bull blenny (Cottoperca gobio)

Gilthead seabream (Sparus aurata)

Ballan wrasse (Labrus bergylta)

Tiger tail seahorse (Hippocampus comes)

Pinecone soldierfish (Myripristis murdjan)

Atlantic cod (Gadus morhua)

Brown trout (Salmo trutta)

Atlantic salmon (Salmo salar)

Rainbow trout (Oncorhynchus mykiss)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Coho salmon (Oncorhynchus kisutch)

Huchen (Hucho hucho)

Northern pike (Esox lucius reference strain)

Atlantic herring (Clupea harengus reference strain)

Denticle herring (Denticeps clupeoides reference strain)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Mexican tetra (Astyanax mexicanus)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Electric eel (Electrophorus electricus reference strain)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Sloth (Choloepus hoffmanni)

Armadillo (Dasypus novemcinctus)

Rabbit (Oryctolagus cuniculus)

Pika (Ochotona princeps)

Steppe mouse (Mus spicilegus)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Mouse (Mus musculus reference (CL57BL6) strain)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Golden Hamster (Mesocricetus auratus)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Prairie vole (Microtus ochrogaster)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Lesser Egyptian jerboa (Jaculus jaculus)

Arctic ground squirrel (Urocitellus parryii)

Alpine marmot (Marmota marmota marmota)

Squirrel (Ictidomys tridecemlineatus)

Eurasian red squirrel (Sciurus vulgaris)

Guinea Pig (Cavia porcellus)

Degu (Octodon degus)

Long-tailed chinchilla (Chinchilla lanigera)

Naked mole-rat female (Heterocephalus glaber reference strain)

Kangaroo rat (Dipodomys ordii)

Panamanian white-faced capuchin (Cebus imitator)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

White-tufted-ear marmoset (Callithrix jacchus)

Ma's night monkey (Aotus nancymaae)

Chimpanzee (Pan troglodytes)

Bonobo (Pan paniscus)

Gorilla (Gorilla gorilla gorilla)

Human (Homo sapiens)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Black snub-nosed monkey (Rhinopithecus bieti)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Pig-tailed macaque (Macaca nemestrina)

Crab-eating macaque (Macaca fascicularis)

Macaque (Macaca mulatta)

Sooty mangabey (Cercocebus atys)

Vervet-AGM (Chlorocebus sabaeus)

Olive baboon (Papio anubis)

Drill (Mandrillus leucophaeus)

Tarsier (Carlito syrichta)

Greater bamboo lemur (Prolemur simus)

Coquerel's sifaka (Propithecus coquereli)

Mouse Lemur (Microcebus murinus)

Bushbaby (Otolemur garnettii)

Tree Shrew (Tupaia belangeri)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Microbat (Myotis lucifugus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Tiger (Panthera tigris altaica)

Leopard (Panthera pardus)

Lion (Panthera leo)

Cat (Felis catus)

Dingo (Canis lupus dingo)

Dog (Canis lupus familiaris reference breed)

Red fox (Vulpes vulpes)

Ferret (Mustela putorius furo)

American mink (Neogale vison)

Polar bear (Ursus maritimus)

American black bear (Ursus americanus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Donkey (Equus asinus reference breed)

Horse (Equus caballus breed thoroughbred)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter catodon)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Arabian camel (Camelus dromedarius)

Alpaca (Vicugna pacos)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Domestic yak (Bos grunniens)

Wild yak (Bos mutus)

Cow (Bos taurus reference breed)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

American bison (Bison bison bison)

Goat (Capra hircus reference breed)

Sheep (Ovis aries reference breed)

Siberian musk deer (Moschus moschiferus)

Yarkand deer (Cervus hanglu yarkandensis)

Hyrax (Procavia capensis)

Lesser hedgehog tenrec (Echinops telfairi)

Elephant (Loxodonta africana)

Wallaby (Notamacropus eugenii)

Koala (Phascolarctos cinereus)

Common wombat (Vombatus ursinus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Platypus (Ornithorhynchus anatinus)

Eastern brown snake (Pseudonaja textilis)

Mainland tiger snake (Notechis scutatus)

Blue-ringed sea krait (Laticauda laticaudata)

Indian cobra (Naja naja)

Green anole (Anolis carolinensis reference strain)

Argentine black and white tegu (Salvator merianae)

Common wall lizard (Podarcis muralis)

Tuatara (Sphenodon punctatus)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Goodes thornscrub tortoise (Gopherus evgoodei)

Painted turtle (Chrysemys picta bellii)

Three-toed box turtle (Terrapene carolina triunguis)

Chinese softshell turtle (Pelodiscus sinensis)

Pink-footed goose (Anser brachyrhynchus)

Duck (Anas platyrhynchos platyrhynchos)

Turkey (Meleagris gallopavo reference strain)

Chicken (Gallus gallus reference breed)

Japanese quail (Coturnix japonica)

Common canary (Serinus canaria)

Zebra finch (Taeniopygia guttata)

Collared flycatcher (Ficedula albicollis)

Great Tit (Parus major)

Medium ground-finch (Geospiza fortis)

Kakapo (Strigops habroptila)

Golden eagle (Aquila chrysaetos chrysaetos)

African ostrich (Struthio camelus australis)

Australian saltwater crocodile (Crocodylus porosus)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

C.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Caenorhabditis elegans (Nematode, N2) (Caenorhabditis elegans strain N2)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)