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)

Pika (Ochotona princeps)

Rabbit (Oryctolagus cuniculus)

Squirrel (Ictidomys tridecemlineatus)

Alpine marmot (Marmota marmota marmota)

Arctic ground squirrel (Urocitellus parryii)

Eurasian red squirrel (Sciurus vulgaris)

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)

Degu (Octodon degus)

Naked mole-rat female (Heterocephalus glaber reference strain)

Long-tailed chinchilla (Chinchilla lanigera)

Guinea Pig (Cavia porcellus)

Kangaroo rat (Dipodomys ordii)

Chimpanzee (Pan troglodytes)

Bonobo (Pan paniscus)

Human (Homo sapiens)

Gorilla (Gorilla gorilla gorilla)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Black snub-nosed monkey (Rhinopithecus bieti)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Macaque (Macaca mulatta)

Pig-tailed macaque (Macaca nemestrina)

Crab-eating macaque (Macaca fascicularis)

Vervet-AGM (Chlorocebus sabaeus)

Drill (Mandrillus leucophaeus)

Sooty mangabey (Cercocebus atys)

Olive baboon (Papio anubis)

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)

Greater bamboo lemur (Prolemur simus)

Coquerel's sifaka (Propithecus coquereli)

Mouse Lemur (Microcebus murinus)

Bushbaby (Otolemur garnettii)

Tree Shrew (Tupaia belangeri)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Microbat (Myotis lucifugus)

Megabat (Pteropus vampyrus)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Leopard (Panthera pardus)

Tiger (Panthera tigris altaica)

Lion (Panthera leo)

Cat (Felis catus)

American black bear (Ursus americanus)

Polar bear (Ursus maritimus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Dog (Canis lupus familiaris reference breed)

Dingo (Canis lupus dingo)

Red fox (Vulpes vulpes)

Ferret (Mustela putorius furo)

American mink (Neogale vison)

Shrew (Sorex araneus)

Hedgehog (Erinaceus europaeus)

Chacoan peccary (Catagonus wagneri)

Pig (Sus scrofa reference breed)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Vaquita (Phocoena sinus)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter catodon)

Blue whale (Balaenoptera musculus)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Sheep (Ovis aries reference breed)

Goat (Capra hircus reference breed)

Cow (Bos taurus reference breed)

Domestic yak (Bos grunniens)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Wild yak (Bos mutus)

American bison (Bison bison bison)

Siberian musk deer (Moschus moschiferus)

Yarkand deer (Cervus hanglu yarkandensis)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Lesser hedgehog tenrec (Echinops telfairi)

Elephant (Loxodonta africana)

Hyrax (Procavia capensis)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Platypus (Ornithorhynchus anatinus)

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)

Common wall lizard (Podarcis muralis)

Argentine black and white tegu (Salvator merianae)

Tuatara (Sphenodon punctatus)

Three-toed box turtle (Terrapene carolina triunguis)

Painted turtle (Chrysemys picta bellii)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Goodes thornscrub tortoise (Gopherus evgoodei)

Chinese softshell turtle (Pelodiscus sinensis)

Pink-footed goose (Anser brachyrhynchus)

Duck (Anas platyrhynchos platyrhynchos)

Japanese quail (Coturnix japonica)

Chicken (Gallus gallus reference breed)

Turkey (Meleagris gallopavo reference strain)

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)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Coelacanth (Latimeria chalumnae)

Atlantic herring (Clupea harengus)

Denticle herring (Denticeps clupeoides)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Mexican tetra (Astyanax mexicanus)

Red-bellied piranha (Pygocentrus nattereri)

Electric eel (Electrophorus electricus)

Channel catfish (Ictalurus punctatus)

Siamese fighting fish (Betta splendens)

Climbing perch (Anabas testudineus)

Zig-zag eel (Mastacembelus armatus)

Yellowtail amberjack (Seriola lalandi dorsalis)

Greater amberjack (Seriola dumerili)

Turbot (Scophthalmus maximus)

Tongue sole (Cynoglossus semilaevis)

Barramundi perch (Lates calcarifer)

Mangrove rivulus (Kryptolebias marmoratus)

Turquoise killifish (Nothobranchius furzeri)

Platyfish (Xiphophorus maculatus)

Monterrey platyfish (Xiphophorus couchianus)

Guppy (Poecilia reticulata)

Sailfin molly (Poecilia latipinna)

Amazon molly (Poecilia formosa)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Indian medaka (Oryzias melastigma)

Chinese medaka (Oryzias sinensis)

Japanese medaka HdrR (Oryzias latipes)

Javanese ricefish (Oryzias javanicus)

Eastern happy (Astatotilapia calliptera)

Zebra mbuna (Maylandia zebra)

Makobe Island cichlid (Pundamilia nyererei)

Burton's mouthbrooder (Haplochromis burtoni)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Clown anemonefish (Amphiprion ocellaris)

Orange clownfish (Amphiprion percula)

Bicolor damselfish (Stegastes partitus)

Spiny chromis (Acanthochromis polyacanthus)

Fugu (Takifugu rubripes)

Tetraodon (Tetraodon nigroviridis)

Large yellow croaker (Larimichthys crocea)

European seabass (Dicentrarchus labrax)

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 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)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)