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)

Atlantic herring (Clupea harengus reference strain)

Denticle herring (Denticeps clupeoides reference strain)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Mexican tetra (Astyanax mexicanus)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Electric eel (Electrophorus electricus reference strain)

Brown trout (Salmo trutta)

Atlantic salmon (Salmo salar)

Rainbow trout (Oncorhynchus mykiss)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Coho salmon (Oncorhynchus kisutch)

Huchen (Hucho hucho)

Northern pike (Esox lucius reference strain)

Climbing perch (Anabas testudineus reference strain)

Siamese fighting fish (Betta splendens)

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)

Amazon molly (Poecilia formosa)

Guppy (Poecilia reticulata)

Sailfin molly (Poecilia latipinna)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Japanese medaka HdrR (Oryzias latipes)

Javanese ricefish (Oryzias javanicus)

Chinese medaka (Oryzias sinensis)

Indian medaka (Oryzias melastigma)

Makobe Island cichlid (Pundamilia nyererei)

Burton's mouthbrooder (Haplochromis burtoni)

Zebra mbuna (Maylandia zebra)

Eastern happy (Astatotilapia calliptera reference strain)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Orange clownfish (Amphiprion percula)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Bicolor damselfish (Stegastes partitus)

Spiny chromis (Acanthochromis polyacanthus)

Tetraodon (Tetraodon nigroviridis)

Fugu (Takifugu rubripes)

Large yellow croaker (Larimichthys crocea)

European seabass (Dicentrarchus labrax)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

Lumpfish (Cyclopterus lumpus)

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)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Asian bonytongue (Scleropages formosus)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Tropical clawed frog (Xenopus tropicalis)

Leishan spiny toad (Leptobrachium leishanense)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Greater bamboo lemur (Prolemur simus)

Coquerel's sifaka (Propithecus coquereli)

Mouse Lemur (Microcebus murinus)

Bushbaby (Otolemur garnettii)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Black snub-nosed monkey (Rhinopithecus bieti)

Crab-eating macaque (Macaca fascicularis)

Pig-tailed macaque (Macaca nemestrina)

Macaque (Macaca mulatta)

Sooty mangabey (Cercocebus atys)

Olive baboon (Papio anubis)

Vervet-AGM (Chlorocebus sabaeus)

Drill (Mandrillus leucophaeus)

Bonobo (Pan paniscus)

Chimpanzee (Pan troglodytes)

Gorilla (Gorilla gorilla gorilla)

Human (Homo sapiens)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Panamanian white-faced capuchin (Cebus imitator)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

White-tufted-ear marmoset (Callithrix jacchus)

Ma's night monkey (Aotus nancymaae)

Tarsier (Carlito syrichta)

Rabbit (Oryctolagus cuniculus)

Pika (Ochotona princeps)

Steppe mouse (Mus spicilegus)

Mouse (Mus musculus reference (CL57BL6) strain)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Ryukyu mouse (Mus caroli strain CAROLI_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)

Arctic ground squirrel (Urocitellus parryii)

Squirrel (Ictidomys tridecemlineatus)

Alpine marmot (Marmota marmota marmota)

Eurasian red squirrel (Sciurus vulgaris)

Guinea Pig (Cavia porcellus)

Naked mole-rat female (Heterocephalus glaber reference strain)

Degu (Octodon degus)

Long-tailed chinchilla (Chinchilla lanigera)

Kangaroo rat (Dipodomys ordii)

Tree Shrew (Tupaia belangeri)

Donkey (Equus asinus reference breed)

Horse (Equus caballus breed thoroughbred)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Microbat (Myotis lucifugus)

Megabat (Pteropus vampyrus)

Tiger (Panthera tigris altaica)

Leopard (Panthera pardus)

Lion (Panthera leo)

Cat (Felis catus)

Ferret (Mustela putorius furo)

American mink (Neogale vison)

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)

Shrew (Sorex araneus)

Hedgehog (Erinaceus europaeus)

Arabian camel (Camelus dromedarius)

Alpaca (Vicugna pacos)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter catodon)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Goat (Capra hircus reference breed)

Sheep (Ovis aries reference breed)

Wild yak (Bos mutus)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Domestic yak (Bos grunniens)

Cow (Bos taurus reference breed)

American bison (Bison bison bison)

Yarkand deer (Cervus hanglu yarkandensis)

Siberian musk deer (Moschus moschiferus)

Elephant (Loxodonta africana)

Hyrax (Procavia capensis)

Lesser hedgehog tenrec (Echinops telfairi)

Platypus (Ornithorhynchus anatinus)

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)

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)

Collared flycatcher (Ficedula albicollis)

Medium ground-finch (Geospiza fortis)

Great Tit (Parus major)

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)

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)