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

Lamprey (Petromyzon marinus)

Hagfish (Eptatretus burgeri)

Atlantic salmon (Salmo salar)

Brown trout (Salmo trutta)

Rainbow trout (Oncorhynchus mykiss)

Coho salmon (Oncorhynchus kisutch)

Chinook salmon (Oncorhynchus tshawytscha)

Huchen (Hucho hucho)

Northern pike (Esox lucius)

Climbing perch (Anabas testudineus)

Siamese fighting fish (Betta splendens)

Zig-zag eel (Mastacembelus armatus)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Yellowtail amberjack (Seriola lalandi dorsalis)

Greater amberjack (Seriola dumerili)

Barramundi perch (Lates calcarifer)

Eastern happy (Astatotilapia calliptera)

Makobe Island cichlid (Pundamilia nyererei)

Burton's mouthbrooder (Haplochromis burtoni)

Zebra mbuna (Maylandia zebra)

Nile tilapia (Oreochromis niloticus)

Lyretail cichlid (Neolamprologus brichardi)

Midas cichlid (Amphilophus citrinellus)

Turquoise killifish (Nothobranchius furzeri)

Mangrove rivulus (Kryptolebias marmoratus)

Monterrey platyfish (Xiphophorus couchianus)

Platyfish (Xiphophorus maculatus)

Guppy (Poecilia reticulata)

Amazon molly (Poecilia formosa)

Sailfin molly (Poecilia latipinna)

Sheepshead minnow (Cyprinodon variegatus)

Mummichog (Fundulus heteroclitus)

Indian medaka (Oryzias melastigma)

Chinese medaka (Oryzias sinensis)

Javanese ricefish (Oryzias javanicus)

Japanese medaka HdrR (Oryzias latipes)

Orange clownfish (Amphiprion percula)

Clown anemonefish (Amphiprion ocellaris)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

European seabass (Dicentrarchus labrax)

Large yellow croaker (Larimichthys crocea)

Fugu (Takifugu rubripes)

Tetraodon (Tetraodon nigroviridis)

Lumpfish (Cyclopterus lumpus)

Stickleback (Gasterosteus aculeatus)

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)

Atlantic herring (Clupea harengus)

Denticle herring (Denticeps clupeoides)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Red-bellied piranha (Pygocentrus nattereri)

Mexican tetra (Astyanax mexicanus)

Electric eel (Electrophorus electricus)

Channel catfish (Ictalurus punctatus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Asian bonytongue (Scleropages formosus)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Pika (Ochotona princeps)

Rabbit (Oryctolagus cuniculus)

Steppe mouse (Mus spicilegus)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Mouse (Mus musculus reference (CL57BL6) strain)

Ryukyu mouse (Mus caroli strain CAROLI_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)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Prairie vole (Microtus ochrogaster)

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)

Long-tailed chinchilla (Chinchilla lanigera)

Naked mole-rat female (Heterocephalus glaber reference strain)

Kangaroo rat (Dipodomys ordii)

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)

Macaque (Macaca mulatta)

Crab-eating macaque (Macaca fascicularis)

Vervet-AGM (Chlorocebus sabaeus)

Sooty mangabey (Cercocebus atys)

Olive baboon (Papio anubis)

Drill (Mandrillus leucophaeus)

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)

Coquerel's sifaka (Propithecus coquereli)

Greater bamboo lemur (Prolemur simus)

Mouse Lemur (Microcebus murinus)

Bushbaby (Otolemur garnettii)

Tree Shrew (Tupaia belangeri)

Microbat (Myotis lucifugus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Donkey (Equus asinus reference breed)

Horse (Equus caballus breed thoroughbred)

Lion (Panthera leo)

Leopard (Panthera pardus)

Tiger (Panthera tigris altaica)

Cat (Felis catus)

Dog (Canis lupus familiaris reference breed)

Dingo (Canis lupus dingo)

Red fox (Vulpes vulpes)

American black bear (Ursus americanus)

Polar bear (Ursus maritimus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Ferret (Mustela putorius furo)

American mink (Neogale vison)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Sperm whale (Physeter catodon)

Vaquita (Phocoena sinus)

Dolphin (Tursiops truncatus)

Blue whale (Balaenoptera musculus)

Chacoan peccary (Catagonus wagneri)

Pig (Sus scrofa reference breed)

Goat (Capra hircus reference breed)

Sheep (Ovis aries reference breed)

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)

Yarkand deer (Cervus hanglu yarkandensis)

Siberian musk deer (Moschus moschiferus)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Hyrax (Procavia capensis)

Lesser hedgehog tenrec (Echinops telfairi)

Elephant (Loxodonta africana)

Koala (Phascolarctos cinereus)

Common wombat (Vombatus ursinus)

Wallaby (Notamacropus eugenii)

Tasmanian devil (Sarcophilus harrisii)

Opossum (Monodelphis domestica)

Platypus (Ornithorhynchus anatinus)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Goodes thornscrub tortoise (Gopherus evgoodei)

Three-toed box turtle (Terrapene carolina triunguis)

Painted turtle (Chrysemys picta bellii)

Chinese softshell turtle (Pelodiscus sinensis)

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)

Collared flycatcher (Ficedula albicollis)

Great Tit (Parus major)

Kakapo (Strigops habroptila)

Golden eagle (Aquila chrysaetos chrysaetos)

African ostrich (Struthio camelus australis)

Australian saltwater crocodile (Crocodylus porosus)

Common wall lizard (Podarcis muralis)

Argentine black and white tegu (Salvator merianae)

Mainland tiger snake (Notechis scutatus)

Eastern brown snake (Pseudonaja textilis)

Blue-ringed sea krait (Laticauda laticaudata)

Indian cobra (Naja naja)

Green anole (Anolis carolinensis reference strain)

Tuatara (Sphenodon punctatus)

Tropical clawed frog (Xenopus tropicalis)

Leishan spiny toad (Leptobrachium leishanense)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

C.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)