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.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

Lamprey (Petromyzon marinus)

Hagfish (Eptatretus burgeri)

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)

Duck (Anas platyrhynchos platyrhynchos)

Pink-footed goose (Anser brachyrhynchus)

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)

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)

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)

Tuatara (Sphenodon punctatus)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Rabbit (Oryctolagus cuniculus)

Pika (Ochotona princeps)

Alpine marmot (Marmota marmota marmota)

Arctic ground squirrel (Urocitellus parryii)

Squirrel (Ictidomys tridecemlineatus)

Eurasian red squirrel (Sciurus vulgaris)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Mouse (Mus musculus reference (CL57BL6) strain)

Steppe mouse (Mus spicilegus)

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)

Naked mole-rat female (Heterocephalus glaber reference strain)

Guinea Pig (Cavia porcellus)

Degu (Octodon degus)

Long-tailed chinchilla (Chinchilla lanigera)

Kangaroo rat (Dipodomys ordii)

Mouse Lemur (Microcebus murinus)

Greater bamboo lemur (Prolemur simus)

Coquerel's sifaka (Propithecus coquereli)

Bushbaby (Otolemur garnettii)

Bonobo (Pan paniscus)

Chimpanzee (Pan troglodytes)

Gorilla (Gorilla gorilla gorilla)

Human (Homo sapiens)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Black snub-nosed monkey (Rhinopithecus bieti)

Pig-tailed macaque (Macaca nemestrina)

Crab-eating macaque (Macaca fascicularis)

Macaque (Macaca mulatta)

Sooty mangabey (Cercocebus atys)

Olive baboon (Papio anubis)

Drill (Mandrillus leucophaeus)

Vervet-AGM (Chlorocebus sabaeus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Panamanian white-faced capuchin (Cebus imitator)

White-tufted-ear marmoset (Callithrix jacchus)

Ma's night monkey (Aotus nancymaae)

Tarsier (Carlito syrichta)

Tree Shrew (Tupaia belangeri)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Microbat (Myotis lucifugus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Lion (Panthera leo)

Tiger (Panthera tigris altaica)

Leopard (Panthera pardus)

Cat (Felis catus)

Polar bear (Ursus maritimus)

American black bear (Ursus americanus)

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)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Vaquita (Phocoena sinus)

Sperm whale (Physeter catodon)

Dolphin (Tursiops truncatus)

Blue whale (Balaenoptera musculus)

Domestic yak (Bos grunniens)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Cow (Bos taurus reference breed)

Wild yak (Bos mutus)

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)

Hyrax (Procavia capensis)

Elephant (Loxodonta africana)

Lesser hedgehog tenrec (Echinops telfairi)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Tasmanian devil (Sarcophilus harrisii)

Opossum (Monodelphis domestica)

Platypus (Ornithorhynchus anatinus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Coelacanth (Latimeria chalumnae)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Asian bonytongue (Scleropages formosus)

Brown trout (Salmo trutta)

Atlantic salmon (Salmo salar)

Rainbow trout (Oncorhynchus mykiss)

Chinook salmon (Oncorhynchus tshawytscha)

Coho salmon (Oncorhynchus kisutch)

Huchen (Hucho hucho)

Northern pike (Esox lucius)

Siamese fighting fish (Betta splendens)

Climbing perch (Anabas testudineus)

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)

Mangrove rivulus (Kryptolebias marmoratus)

Turquoise killifish (Nothobranchius furzeri)

Platyfish (Xiphophorus maculatus)

Monterrey platyfish (Xiphophorus couchianus)

Sailfin molly (Poecilia latipinna)

Guppy (Poecilia reticulata)

Amazon molly (Poecilia formosa)

Sheepshead minnow (Cyprinodon variegatus)

Mummichog (Fundulus heteroclitus)

Indian medaka (Oryzias melastigma)

Japanese medaka HdrR (Oryzias latipes)

Javanese ricefish (Oryzias javanicus)

Chinese medaka (Oryzias sinensis)

Zebra mbuna (Maylandia zebra)

Burton's mouthbrooder (Haplochromis burtoni)

Makobe Island cichlid (Pundamilia nyererei)

Eastern happy (Astatotilapia calliptera)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Orange clownfish (Amphiprion percula)

Clown anemonefish (Amphiprion ocellaris)

Bicolor damselfish (Stegastes partitus)

Spiny chromis (Acanthochromis polyacanthus)

Tetraodon (Tetraodon nigroviridis)

Fugu (Takifugu rubripes)

European seabass (Dicentrarchus labrax)

Large yellow croaker (Larimichthys crocea)

Stickleback (Gasterosteus aculeatus)

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)

Goldfish (Carassius auratus)

Common carp (Cyprinus carpio carpio)

Zebrafish (Danio rerio)

Mexican tetra (Astyanax mexicanus)

Red-bellied piranha (Pygocentrus nattereri)

Electric eel (Electrophorus electricus)

Channel catfish (Ictalurus punctatus)

Denticle herring (Denticeps clupeoides)

Atlantic herring (Clupea harengus)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)