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

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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Lamprey (Petromyzon marinus)

Hagfish (Eptatretus burgeri)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

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)

Eastern happy (Astatotilapia calliptera)

Zebra mbuna (Maylandia zebra)

Burton's mouthbrooder (Haplochromis burtoni)

Makobe Island cichlid (Pundamilia nyererei)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Turquoise killifish (Nothobranchius furzeri)

Mangrove rivulus (Kryptolebias marmoratus)

Platyfish (Xiphophorus maculatus)

Monterrey platyfish (Xiphophorus couchianus)

Amazon molly (Poecilia formosa)

Guppy (Poecilia reticulata)

Sailfin molly (Poecilia latipinna)

Sheepshead minnow (Cyprinodon variegatus)

Mummichog (Fundulus heteroclitus)

Chinese medaka (Oryzias sinensis)

Japanese medaka HdrR (Oryzias latipes)

Indian medaka (Oryzias melastigma)

Javanese ricefish (Oryzias javanicus)

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)

Tetraodon (Tetraodon nigroviridis)

Fugu (Takifugu rubripes)

Lumpfish (Cyclopterus lumpus)

Stickleback (Gasterosteus aculeatus)

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)

Brown trout (Salmo trutta)

Atlantic salmon (Salmo salar)

Chinook salmon (Oncorhynchus tshawytscha)

Rainbow trout (Oncorhynchus mykiss)

Coho salmon (Oncorhynchus kisutch)

Huchen (Hucho hucho)

Northern pike (Esox lucius)

Atlantic herring (Clupea harengus)

Denticle herring (Denticeps clupeoides)

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)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Tropical clawed frog (Xenopus tropicalis)

Leishan spiny toad (Leptobrachium leishanense)

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)

Turkey (Meleagris gallopavo reference strain)

Japanese quail (Coturnix japonica)

Chicken (Gallus gallus reference breed)

Zebra finch (Taeniopygia guttata)

Common canary (Serinus canaria)

Great Tit (Parus major)

Medium ground-finch (Geospiza fortis)

Collared flycatcher (Ficedula albicollis)

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)

Indian cobra (Naja naja)

Blue-ringed sea krait (Laticauda laticaudata)

Green anole (Anolis carolinensis reference strain)

Tuatara (Sphenodon punctatus)

Mouse Lemur (Microcebus murinus)

Coquerel's sifaka (Propithecus coquereli)

Greater bamboo lemur (Prolemur simus)

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)

Black snub-nosed monkey (Rhinopithecus bieti)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Macaque (Macaca mulatta)

Crab-eating macaque (Macaca fascicularis)

Pig-tailed macaque (Macaca nemestrina)

Vervet-AGM (Chlorocebus sabaeus)

Olive baboon (Papio anubis)

Sooty mangabey (Cercocebus atys)

Drill (Mandrillus leucophaeus)

Chimpanzee (Pan troglodytes)

Bonobo (Pan paniscus)

Human (Homo sapiens)

Gorilla (Gorilla gorilla gorilla)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Tarsier (Carlito syrichta)

Pika (Ochotona princeps)

Rabbit (Oryctolagus cuniculus)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Mouse (Mus musculus reference (CL57BL6) strain)

Steppe mouse (Mus spicilegus)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Golden Hamster (Mesocricetus auratus)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Prairie vole (Microtus ochrogaster)

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)

Tree Shrew (Tupaia belangeri)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Microbat (Myotis lucifugus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Tiger (Panthera tigris altaica)

Leopard (Panthera pardus)

Lion (Panthera leo)

Cat (Felis catus)

Ferret (Mustela putorius furo)

American mink (Neogale vison)

Dog (Canis lupus familiaris reference breed)

Dingo (Canis lupus dingo)

Red fox (Vulpes vulpes)

American black bear (Ursus americanus)

Polar bear (Ursus maritimus)

Giant panda (Ailuropoda melanoleuca reference isolate)

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)

Chacoan peccary (Catagonus wagneri)

Pig (Sus scrofa reference breed)

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)

Siberian musk deer (Moschus moschiferus)

Yarkand deer (Cervus hanglu yarkandensis)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Hyrax (Procavia capensis)

Lesser hedgehog tenrec (Echinops telfairi)

Elephant (Loxodonta africana)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Platypus (Ornithorhynchus anatinus)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)