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)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Siamese fighting fish (Betta splendens)

Climbing perch (Anabas testudineus reference strain)

Zig-zag eel (Mastacembelus armatus)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Greater amberjack (Seriola dumerili)

Yellowtail amberjack (Seriola lalandi dorsalis)

Barramundi perch (Lates calcarifer)

Makobe Island cichlid (Pundamilia nyererei)

Burton's mouthbrooder (Haplochromis burtoni)

Zebra mbuna (Maylandia zebra)

Eastern happy (Astatotilapia calliptera reference strain)

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)

Sailfin molly (Poecilia latipinna)

Guppy (Poecilia reticulata)

Amazon molly (Poecilia formosa)

Sheepshead minnow (Cyprinodon variegatus)

Mummichog (Fundulus heteroclitus)

Chinese medaka (Oryzias sinensis)

Indian medaka (Oryzias melastigma)

Javanese ricefish (Oryzias javanicus)

Japanese medaka HdrR (Oryzias latipes)

Orange clownfish (Amphiprion percula)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

Large yellow croaker (Larimichthys crocea)

European seabass (Dicentrarchus labrax)

Fugu (Takifugu rubripes)

Tetraodon (Tetraodon nigroviridis)

Lumpfish (Cyclopterus lumpus)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

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)

Coho salmon (Oncorhynchus kisutch)

Rainbow trout (Oncorhynchus mykiss)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Huchen (Hucho hucho)

Northern pike (Esox lucius reference strain)

Atlantic herring (Clupea harengus reference strain)

Denticle herring (Denticeps clupeoides reference strain)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Mexican tetra (Astyanax mexicanus)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Electric eel (Electrophorus electricus reference strain)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Argentine black and white tegu (Salvator merianae)

Common wall lizard (Podarcis muralis)

Mainland tiger snake (Notechis scutatus)

Eastern brown snake (Pseudonaja textilis)

Blue-ringed sea krait (Laticauda laticaudata)

Indian cobra (Naja naja)

Green anole (Anolis carolinensis reference strain)

Tuatara (Sphenodon punctatus)

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)

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)

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)

Sloth (Choloepus hoffmanni)

Armadillo (Dasypus novemcinctus)

Pika (Ochotona princeps)

Rabbit (Oryctolagus cuniculus)

Mouse (Mus musculus reference (CL57BL6) strain)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

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)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Prairie vole (Microtus ochrogaster)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Lesser Egyptian jerboa (Jaculus jaculus)

Arctic ground squirrel (Urocitellus parryii)

Squirrel (Ictidomys tridecemlineatus)

Alpine marmot (Marmota marmota marmota)

Eurasian red squirrel (Sciurus vulgaris)

Degu (Octodon degus)

Guinea Pig (Cavia porcellus)

Naked mole-rat female (Heterocephalus glaber reference strain)

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)

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)

Sooty mangabey (Cercocebus atys)

Olive baboon (Papio anubis)

Drill (Mandrillus leucophaeus)

Vervet-AGM (Chlorocebus sabaeus)

Bonobo (Pan paniscus)

Chimpanzee (Pan troglodytes)

Human (Homo sapiens)

Gorilla (Gorilla gorilla gorilla)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

White-tufted-ear marmoset (Callithrix jacchus)

Panamanian white-faced capuchin (Cebus imitator)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Ma's night monkey (Aotus nancymaae)

Tarsier (Carlito syrichta)

Tree Shrew (Tupaia belangeri)

Microbat (Myotis lucifugus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Shrew (Sorex araneus)

Hedgehog (Erinaceus europaeus)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Tiger (Panthera tigris altaica)

Lion (Panthera leo)

Leopard (Panthera pardus)

Cat (Felis catus)

American mink (Neogale vison)

Ferret (Mustela putorius furo)

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)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Narwhal (Monodon monoceros)

Beluga whale (Delphinapterus leucas)

Vaquita (Phocoena sinus)

Sperm whale (Physeter catodon)

Dolphin (Tursiops truncatus)

Blue whale (Balaenoptera musculus)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Wild yak (Bos mutus)

Cow (Bos taurus reference breed)

Domestic yak (Bos grunniens)

American bison (Bison bison bison)

Goat (Capra hircus reference breed)

Sheep (Ovis aries reference breed)

Yarkand deer (Cervus hanglu yarkandensis)

Siberian musk deer (Moschus moschiferus)

Lesser hedgehog tenrec (Echinops telfairi)

Hyrax (Procavia capensis)

Elephant (Loxodonta africana)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Platypus (Ornithorhynchus anatinus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

Lamprey (Petromyzon marinus)

Hagfish (Eptatretus burgeri)

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)