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)

Burton's mouthbrooder (Haplochromis burtoni)

Zebra mbuna (Maylandia zebra)

Eastern happy (Astatotilapia calliptera reference strain)

Makobe Island cichlid (Pundamilia nyererei)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Turquoise killifish (Nothobranchius furzeri)

Mangrove rivulus (Kryptolebias marmoratus)

Platyfish (Xiphophorus maculatus)

Monterrey platyfish (Xiphophorus couchianus)

Guppy (Poecilia reticulata)

Sailfin molly (Poecilia latipinna)

Amazon molly (Poecilia formosa)

Sheepshead minnow (Cyprinodon variegatus)

Mummichog (Fundulus heteroclitus)

Japanese medaka HdrR (Oryzias latipes)

Indian medaka (Oryzias melastigma)

Chinese medaka (Oryzias sinensis)

Javanese ricefish (Oryzias javanicus)

Orange clownfish (Amphiprion percula)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

Greater amberjack (Seriola dumerili)

Yellowtail amberjack (Seriola lalandi dorsalis)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Barramundi perch (Lates calcarifer)

European seabass (Dicentrarchus labrax)

Large yellow croaker (Larimichthys crocea)

Fugu (Takifugu rubripes)

Tetraodon (Tetraodon nigroviridis)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

Lumpfish (Cyclopterus lumpus)

Channel bull blenny (Cottoperca gobio)

Pike-perch (Sander lucioperca)

Ballan wrasse (Labrus bergylta)

Gilthead seabream (Sparus aurata)

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)

Coho salmon (Oncorhynchus kisutch)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Huchen (Hucho hucho)

Northern pike (Esox lucius reference strain)

Atlantic herring (Clupea harengus reference strain)

Denticle herring (Denticeps clupeoides reference strain)

Goldfish (Carassius auratus)

Common carp (Cyprinus carpio carpio)

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)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Rabbit (Oryctolagus cuniculus)

Pika (Ochotona princeps)

Mouse (Mus musculus reference (CL57BL6) strain)

Steppe mouse (Mus spicilegus)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Golden Hamster (Mesocricetus auratus)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Prairie vole (Microtus ochrogaster)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Lesser Egyptian jerboa (Jaculus jaculus)

Alpine marmot (Marmota marmota marmota)

Arctic ground squirrel (Urocitellus parryii)

Squirrel (Ictidomys tridecemlineatus)

Eurasian red squirrel (Sciurus vulgaris)

Guinea Pig (Cavia porcellus)

Degu (Octodon degus)

Naked mole-rat female (Heterocephalus glaber reference strain)

Long-tailed chinchilla (Chinchilla lanigera)

Kangaroo rat (Dipodomys ordii)

Greater bamboo lemur (Prolemur simus)

Coquerel's sifaka (Propithecus coquereli)

Mouse Lemur (Microcebus murinus)

Bushbaby (Otolemur garnettii)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Black snub-nosed monkey (Rhinopithecus bieti)

Macaque (Macaca mulatta)

Pig-tailed macaque (Macaca nemestrina)

Crab-eating macaque (Macaca fascicularis)

Olive baboon (Papio anubis)

Vervet-AGM (Chlorocebus sabaeus)

Sooty mangabey (Cercocebus atys)

Drill (Mandrillus leucophaeus)

Bonobo (Pan paniscus)

Chimpanzee (Pan troglodytes)

Human (Homo sapiens)

Gorilla (Gorilla gorilla gorilla)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Panamanian white-faced capuchin (Cebus imitator)

White-tufted-ear marmoset (Callithrix jacchus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Ma's night monkey (Aotus nancymaae)

Tarsier (Carlito syrichta)

Tree Shrew (Tupaia belangeri)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Microbat (Myotis lucifugus)

Megabat (Pteropus vampyrus)

Shrew (Sorex araneus)

Hedgehog (Erinaceus europaeus)

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)

American mink (Neogale vison)

Ferret (Mustela putorius furo)

Polar bear (Ursus maritimus)

American black bear (Ursus americanus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Sperm whale (Physeter catodon)

Dolphin (Tursiops truncatus)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Arabian camel (Camelus dromedarius)

Alpaca (Vicugna pacos)

Sheep (Ovis aries reference breed)

Goat (Capra hircus reference breed)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Domestic yak (Bos grunniens)

Wild yak (Bos mutus)

Cow (Bos taurus reference breed)

American bison (Bison bison bison)

Siberian musk deer (Moschus moschiferus)

Yarkand deer (Cervus hanglu yarkandensis)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Hyrax (Procavia capensis)

Elephant (Loxodonta africana)

Lesser hedgehog tenrec (Echinops telfairi)

Platypus (Ornithorhynchus anatinus)

Pink-footed goose (Anser brachyrhynchus)

Duck (Anas platyrhynchos platyrhynchos)

Chicken (Gallus gallus reference breed)

Turkey (Meleagris gallopavo reference strain)

Japanese quail (Coturnix japonica)

Zebra finch (Taeniopygia guttata)

Common canary (Serinus canaria)

Medium ground-finch (Geospiza fortis)

Great Tit (Parus major)

Collared flycatcher (Ficedula albicollis)

Kakapo (Strigops habroptila)

Golden eagle (Aquila chrysaetos chrysaetos)

African ostrich (Struthio camelus australis)

Australian saltwater crocodile (Crocodylus porosus)

Goodes thornscrub tortoise (Gopherus evgoodei)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Painted turtle (Chrysemys picta bellii)

Three-toed box turtle (Terrapene carolina triunguis)

Chinese softshell turtle (Pelodiscus sinensis)

Mainland tiger snake (Notechis scutatus)

Eastern brown snake (Pseudonaja textilis)

Indian cobra (Naja naja)

Blue-ringed sea krait (Laticauda laticaudata)

Green anole (Anolis carolinensis reference strain)

Argentine black and white tegu (Salvator merianae)

Common wall lizard (Podarcis muralis)

Tuatara (Sphenodon punctatus)

Tropical clawed frog (Xenopus tropicalis)

Leishan spiny toad (Leptobrachium leishanense)

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)