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

C.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

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)

Duck (Anas platyrhynchos platyrhynchos)

Pink-footed goose (Anser brachyrhynchus)

Japanese quail (Coturnix japonica)

Chicken (Gallus gallus reference breed)

Turkey (Meleagris gallopavo reference strain)

Common canary (Serinus canaria)

Zebra finch (Taeniopygia guttata)

Great Tit (Parus major)

Collared flycatcher (Ficedula albicollis)

Medium ground-finch (Geospiza fortis)

Golden eagle (Aquila chrysaetos chrysaetos)

Kakapo (Strigops habroptila)

African ostrich (Struthio camelus australis)

Australian saltwater crocodile (Crocodylus porosus)

Goodes thornscrub tortoise (Gopherus evgoodei)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Three-toed box turtle (Terrapene carolina triunguis)

Painted turtle (Chrysemys picta bellii)

Chinese softshell turtle (Pelodiscus sinensis)

Sloth (Choloepus hoffmanni)

Armadillo (Dasypus novemcinctus)

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)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Golden Hamster (Mesocricetus auratus)

Prairie vole (Microtus ochrogaster)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Lesser Egyptian jerboa (Jaculus jaculus)

Squirrel (Ictidomys tridecemlineatus)

Alpine marmot (Marmota marmota marmota)

Arctic ground squirrel (Urocitellus parryii)

Eurasian red squirrel (Sciurus vulgaris)

Degu (Octodon degus)

Long-tailed chinchilla (Chinchilla lanigera)

Naked mole-rat female (Heterocephalus glaber reference strain)

Guinea Pig (Cavia porcellus)

Kangaroo rat (Dipodomys ordii)

Mouse Lemur (Microcebus murinus)

Greater bamboo lemur (Prolemur simus)

Coquerel's sifaka (Propithecus coquereli)

Bushbaby (Otolemur garnettii)

White-tufted-ear marmoset (Callithrix jacchus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Panamanian white-faced capuchin (Cebus imitator)

Ma's night monkey (Aotus nancymaae)

Bonobo (Pan paniscus)

Chimpanzee (Pan troglodytes)

Human (Homo sapiens)

Gorilla (Gorilla gorilla gorilla)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Black snub-nosed monkey (Rhinopithecus bieti)

Crab-eating macaque (Macaca fascicularis)

Pig-tailed macaque (Macaca nemestrina)

Macaque (Macaca mulatta)

Drill (Mandrillus leucophaeus)

Sooty mangabey (Cercocebus atys)

Olive baboon (Papio anubis)

Vervet-AGM (Chlorocebus sabaeus)

Tarsier (Carlito syrichta)

Tree Shrew (Tupaia belangeri)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Microbat (Myotis lucifugus)

Megabat (Pteropus vampyrus)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Leopard (Panthera pardus)

Lion (Panthera leo)

Tiger (Panthera tigris altaica)

Cat (Felis catus)

American mink (Neogale vison)

Ferret (Mustela putorius furo)

Polar bear (Ursus maritimus)

American black bear (Ursus americanus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Dog (Canis lupus familiaris reference breed)

Dingo (Canis lupus dingo)

Red fox (Vulpes vulpes)

Narwhal (Monodon monoceros)

Beluga whale (Delphinapterus leucas)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter catodon)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Domestic yak (Bos grunniens)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Wild yak (Bos mutus)

Cow (Bos taurus reference breed)

American bison (Bison bison bison)

Sheep (Ovis aries reference breed)

Goat (Capra hircus reference breed)

Yarkand deer (Cervus hanglu yarkandensis)

Siberian musk deer (Moschus moschiferus)

Elephant (Loxodonta africana)

Hyrax (Procavia capensis)

Lesser hedgehog tenrec (Echinops telfairi)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Tasmanian devil (Sarcophilus harrisii)

Opossum (Monodelphis domestica)

Platypus (Ornithorhynchus anatinus)

Tropical clawed frog (Xenopus tropicalis)

Leishan spiny toad (Leptobrachium leishanense)

Coelacanth (Latimeria chalumnae)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Atlantic herring (Clupea harengus reference strain)

Denticle herring (Denticeps clupeoides reference strain)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Mexican tetra (Astyanax mexicanus)

Electric eel (Electrophorus electricus reference strain)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Climbing perch (Anabas testudineus reference strain)

Siamese fighting fish (Betta splendens)

Zig-zag eel (Mastacembelus armatus)

Greater amberjack (Seriola dumerili)

Yellowtail amberjack (Seriola lalandi dorsalis)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Barramundi perch (Lates calcarifer)

Turquoise killifish (Nothobranchius furzeri)

Mangrove rivulus (Kryptolebias marmoratus)

Monterrey platyfish (Xiphophorus couchianus)

Platyfish (Xiphophorus maculatus)

Amazon molly (Poecilia formosa)

Guppy (Poecilia reticulata)

Sailfin molly (Poecilia latipinna)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Japanese medaka HdrR (Oryzias latipes)

Chinese medaka (Oryzias sinensis)

Javanese ricefish (Oryzias javanicus)

Indian medaka (Oryzias melastigma)

Burton's mouthbrooder (Haplochromis burtoni)

Eastern happy (Astatotilapia calliptera reference strain)

Zebra mbuna (Maylandia zebra)

Makobe Island cichlid (Pundamilia nyererei)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Orange clownfish (Amphiprion percula)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

Tetraodon (Tetraodon nigroviridis)

Fugu (Takifugu rubripes)

European seabass (Dicentrarchus labrax)

Large yellow croaker (Larimichthys crocea)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

Lumpfish (Cyclopterus lumpus)

Pike-perch (Sander lucioperca)

Channel bull blenny (Cottoperca gobio)

Ballan wrasse (Labrus bergylta)

Gilthead seabream (Sparus aurata)

Tiger tail seahorse (Hippocampus comes)

Pinecone soldierfish (Myripristis murdjan)

Atlantic cod (Gadus morhua)

Atlantic salmon (Salmo salar)

Brown trout (Salmo trutta)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Rainbow trout (Oncorhynchus mykiss)

Coho salmon (Oncorhynchus kisutch)

Huchen (Hucho hucho)

Northern pike (Esox lucius reference strain)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

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

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)