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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

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

Lamprey (Petromyzon marinus)

Hagfish (Eptatretus burgeri)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Goldfish (Carassius auratus)

Common carp (Cyprinus carpio carpio)

Zebrafish (Danio rerio)

Red-bellied piranha (Pygocentrus nattereri)

Mexican tetra (Astyanax mexicanus)

Channel catfish (Ictalurus punctatus)

Electric eel (Electrophorus electricus)

Denticle herring (Denticeps clupeoides)

Atlantic herring (Clupea harengus)

Siamese fighting fish (Betta splendens)

Climbing perch (Anabas testudineus)

Zig-zag eel (Mastacembelus armatus)

Yellowtail amberjack (Seriola lalandi dorsalis)

Greater amberjack (Seriola dumerili)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Barramundi perch (Lates calcarifer)

Mangrove rivulus (Kryptolebias marmoratus)

Turquoise killifish (Nothobranchius furzeri)

Monterrey platyfish (Xiphophorus couchianus)

Platyfish (Xiphophorus maculatus)

Sailfin molly (Poecilia latipinna)

Guppy (Poecilia reticulata)

Amazon molly (Poecilia formosa)

Sheepshead minnow (Cyprinodon variegatus)

Mummichog (Fundulus heteroclitus)

Japanese medaka HdrR (Oryzias latipes)

Javanese ricefish (Oryzias javanicus)

Chinese medaka (Oryzias sinensis)

Indian medaka (Oryzias melastigma)

Makobe Island cichlid (Pundamilia nyererei)

Zebra mbuna (Maylandia zebra)

Burton's mouthbrooder (Haplochromis burtoni)

Eastern happy (Astatotilapia calliptera)

Nile tilapia (Oreochromis niloticus)

Lyretail cichlid (Neolamprologus brichardi)

Midas cichlid (Amphilophus citrinellus)

Clown anemonefish (Amphiprion ocellaris)

Orange clownfish (Amphiprion percula)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

European seabass (Dicentrarchus labrax)

Large yellow croaker (Larimichthys crocea)

Fugu (Takifugu rubripes)

Tetraodon (Tetraodon nigroviridis)

Stickleback (Gasterosteus aculeatus)

Lumpfish (Cyclopterus lumpus)

Channel bull blenny (Cottoperca gobio)

Pike-perch (Sander lucioperca)

Gilthead seabream (Sparus aurata)

Ballan wrasse (Labrus bergylta)

Tiger tail seahorse (Hippocampus comes)

Pinecone soldierfish (Myripristis murdjan)

Atlantic cod (Gadus morhua)

Atlantic salmon (Salmo salar)

Brown trout (Salmo trutta)

Rainbow trout (Oncorhynchus mykiss)

Chinook salmon (Oncorhynchus tshawytscha)

Coho salmon (Oncorhynchus kisutch)

Huchen (Hucho hucho)

Northern pike (Esox lucius)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Tropical clawed frog (Xenopus tropicalis)

Leishan spiny toad (Leptobrachium leishanense)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Tasmanian devil (Sarcophilus harrisii)

Opossum (Monodelphis domestica)

Mouse Lemur (Microcebus murinus)

Coquerel's sifaka (Propithecus coquereli)

Greater bamboo lemur (Prolemur simus)

Bushbaby (Otolemur garnettii)

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)

Sooty mangabey (Cercocebus atys)

Olive baboon (Papio anubis)

Drill (Mandrillus leucophaeus)

Vervet-AGM (Chlorocebus sabaeus)

Chimpanzee (Pan troglodytes)

Bonobo (Pan paniscus)

Gorilla (Gorilla gorilla gorilla)

Human (Homo sapiens)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

White-tufted-ear marmoset (Callithrix jacchus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Panamanian white-faced capuchin (Cebus imitator)

Ma's night monkey (Aotus nancymaae)

Tarsier (Carlito syrichta)

Pika (Ochotona princeps)

Rabbit (Oryctolagus cuniculus)

Steppe mouse (Mus spicilegus)

Mouse (Mus musculus reference (CL57BL6) strain)

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)

Squirrel (Ictidomys tridecemlineatus)

Arctic ground squirrel (Urocitellus parryii)

Eurasian red squirrel (Sciurus vulgaris)

Naked mole-rat female (Heterocephalus glaber reference strain)

Guinea Pig (Cavia porcellus)

Long-tailed chinchilla (Chinchilla lanigera)

Degu (Octodon degus)

Kangaroo rat (Dipodomys ordii)

Tree Shrew (Tupaia belangeri)

Microbat (Myotis lucifugus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Leopard (Panthera pardus)

Lion (Panthera leo)

Tiger (Panthera tigris altaica)

Cat (Felis catus)

American black bear (Ursus americanus)

Polar bear (Ursus maritimus)

Giant panda (Ailuropoda melanoleuca reference isolate)

American mink (Neogale vison)

Ferret (Mustela putorius furo)

Dingo (Canis lupus dingo)

Dog (Canis lupus familiaris reference breed)

Red fox (Vulpes vulpes)

Donkey (Equus asinus reference breed)

Horse (Equus caballus breed thoroughbred)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Chacoan peccary (Catagonus wagneri)

Pig (Sus scrofa reference breed)

Arabian camel (Camelus dromedarius)

Alpaca (Vicugna pacos)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter catodon)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Wild yak (Bos mutus)

Domestic yak (Bos grunniens)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Cow (Bos taurus reference breed)

American bison (Bison bison bison)

Sheep (Ovis aries reference breed)

Goat (Capra hircus reference breed)

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)

Three-toed box turtle (Terrapene carolina triunguis)

Painted turtle (Chrysemys picta bellii)

Goodes thornscrub tortoise (Gopherus evgoodei)

Abingdon island giant tortoise (Chelonoidis abingdonii)

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)

Medium ground-finch (Geospiza fortis)

Great Tit (Parus major)

Golden eagle (Aquila chrysaetos chrysaetos)

Kakapo (Strigops habroptila)

African ostrich (Struthio camelus australis)

Australian saltwater crocodile (Crocodylus porosus)

Argentine black and white tegu (Salvator merianae)

Common wall lizard (Podarcis muralis)

Eastern brown snake (Pseudonaja textilis)

Mainland tiger snake (Notechis scutatus)

Indian cobra (Naja naja)

Blue-ringed sea krait (Laticauda laticaudata)

Green anole (Anolis carolinensis reference strain)

Tuatara (Sphenodon punctatus)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)