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)

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Wallaby (Notamacropus eugenii)

Koala (Phascolarctos cinereus)

Common wombat (Vombatus ursinus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Sloth (Choloepus hoffmanni)

Armadillo (Dasypus novemcinctus)

Mouse Lemur (Microcebus murinus)

Coquerel's sifaka (Propithecus coquereli)

Greater bamboo lemur (Prolemur simus)

Bushbaby (Otolemur garnettii)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Panamanian white-faced capuchin (Cebus imitator)

White-tufted-ear marmoset (Callithrix jacchus)

Ma's night monkey (Aotus nancymaae)

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)

Bonobo (Pan paniscus)

Chimpanzee (Pan troglodytes)

Human (Homo sapiens)

Gorilla (Gorilla gorilla gorilla)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Tarsier (Carlito syrichta)

Rabbit (Oryctolagus cuniculus)

Pika (Ochotona princeps)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Mouse (Mus musculus reference (CL57BL6) strain)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Steppe mouse (Mus spicilegus)

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)

Alpine marmot (Marmota marmota marmota)

Squirrel (Ictidomys tridecemlineatus)

Arctic ground squirrel (Urocitellus parryii)

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)

Tree Shrew (Tupaia belangeri)

Tiger (Panthera tigris altaica)

Lion (Panthera leo)

Leopard (Panthera pardus)

Cat (Felis catus)

Dog (Canis lupus familiaris reference breed)

Dingo (Canis lupus dingo)

Red fox (Vulpes vulpes)

Polar bear (Ursus maritimus)

American black bear (Ursus americanus)

Giant panda (Ailuropoda melanoleuca reference isolate)

American mink (Neogale vison)

Ferret (Mustela putorius furo)

Microbat (Myotis lucifugus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Narwhal (Monodon monoceros)

Beluga whale (Delphinapterus leucas)

Vaquita (Phocoena sinus)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter catodon)

Blue whale (Balaenoptera musculus)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Cow (Bos taurus reference breed)

Domestic yak (Bos grunniens)

Wild yak (Bos mutus)

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)

Elephant (Loxodonta africana)

Lesser hedgehog tenrec (Echinops telfairi)

Hyrax (Procavia capensis)

Platypus (Ornithorhynchus anatinus)

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)

Pink-footed goose (Anser brachyrhynchus)

Duck (Anas platyrhynchos platyrhynchos)

Chicken (Gallus gallus reference breed)

Japanese quail (Coturnix japonica)

Turkey (Meleagris gallopavo reference strain)

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)

Argentine black and white tegu (Salvator merianae)

Common wall lizard (Podarcis muralis)

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)

Tuatara (Sphenodon punctatus)

Coelacanth (Latimeria chalumnae)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Asian bonytongue (Scleropages formosus)

Siamese fighting fish (Betta splendens)

Climbing perch (Anabas testudineus)

Zig-zag eel (Mastacembelus armatus)

Greater amberjack (Seriola dumerili)

Yellowtail amberjack (Seriola lalandi dorsalis)

Turbot (Scophthalmus maximus)

Tongue sole (Cynoglossus semilaevis)

Barramundi perch (Lates calcarifer)

Burton's mouthbrooder (Haplochromis burtoni)

Eastern happy (Astatotilapia calliptera)

Zebra mbuna (Maylandia zebra)

Makobe Island cichlid (Pundamilia nyererei)

Nile tilapia (Oreochromis niloticus)

Lyretail cichlid (Neolamprologus brichardi)

Midas cichlid (Amphilophus citrinellus)

Turquoise killifish (Nothobranchius furzeri)

Mangrove rivulus (Kryptolebias marmoratus)

Platyfish (Xiphophorus maculatus)

Monterrey platyfish (Xiphophorus couchianus)

Amazon molly (Poecilia formosa)

Sailfin molly (Poecilia latipinna)

Guppy (Poecilia reticulata)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Japanese medaka HdrR (Oryzias latipes)

Chinese medaka (Oryzias sinensis)

Indian medaka (Oryzias melastigma)

Javanese ricefish (Oryzias javanicus)

Clown anemonefish (Amphiprion ocellaris)

Orange clownfish (Amphiprion percula)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

Large yellow croaker (Larimichthys crocea)

European seabass (Dicentrarchus labrax)

Tetraodon (Tetraodon nigroviridis)

Fugu (Takifugu rubripes)

Stickleback (Gasterosteus aculeatus)

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)

Coho salmon (Oncorhynchus kisutch)

Chinook salmon (Oncorhynchus tshawytscha)

Rainbow trout (Oncorhynchus mykiss)

Huchen (Hucho hucho)

Northern pike (Esox lucius)

Goldfish (Carassius auratus)

Common carp (Cyprinus carpio carpio)

Zebrafish (Danio rerio)

Red-bellied piranha (Pygocentrus nattereri)

Mexican tetra (Astyanax mexicanus)

Electric eel (Electrophorus electricus)

Channel catfish (Ictalurus punctatus)

Atlantic herring (Clupea harengus)

Denticle herring (Denticeps clupeoides)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)