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)

Climbing perch (Anabas testudineus reference strain)

Siamese fighting fish (Betta splendens)

Zig-zag eel (Mastacembelus armatus)

Mangrove rivulus (Kryptolebias marmoratus)

Turquoise killifish (Nothobranchius furzeri)

Monterrey platyfish (Xiphophorus couchianus)

Platyfish (Xiphophorus maculatus)

Sailfin molly (Poecilia latipinna)

Guppy (Poecilia reticulata)

Amazon molly (Poecilia formosa)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Indian medaka (Oryzias melastigma)

Japanese medaka HdrR (Oryzias latipes)

Chinese medaka (Oryzias sinensis)

Javanese ricefish (Oryzias javanicus)

Makobe Island cichlid (Pundamilia nyererei)

Eastern happy (Astatotilapia calliptera reference strain)

Zebra mbuna (Maylandia zebra)

Burton's mouthbrooder (Haplochromis burtoni)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Orange clownfish (Amphiprion percula)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

Yellowtail amberjack (Seriola lalandi dorsalis)

Greater amberjack (Seriola dumerili)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Barramundi perch (Lates calcarifer)

European seabass (Dicentrarchus labrax)

Large yellow croaker (Larimichthys crocea)

Tetraodon (Tetraodon nigroviridis)

Fugu (Takifugu rubripes)

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)

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)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Mexican tetra (Astyanax mexicanus)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Electric eel (Electrophorus electricus reference strain)

Atlantic herring (Clupea harengus reference strain)

Denticle herring (Denticeps clupeoides reference strain)

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)

Goodes thornscrub tortoise (Gopherus evgoodei)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Three-toed box turtle (Terrapene carolina triunguis)

Painted turtle (Chrysemys picta bellii)

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)

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)

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)

Argentine black and white tegu (Salvator merianae)

Common wall lizard (Podarcis muralis)

Tuatara (Sphenodon punctatus)

Wallaby (Notamacropus eugenii)

Koala (Phascolarctos cinereus)

Common wombat (Vombatus ursinus)

Tasmanian devil (Sarcophilus harrisii)

Opossum (Monodelphis domestica)

Greater bamboo lemur (Prolemur simus)

Mouse Lemur (Microcebus murinus)

Coquerel's sifaka (Propithecus coquereli)

Bushbaby (Otolemur garnettii)

Chimpanzee (Pan troglodytes)

Bonobo (Pan paniscus)

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)

Drill (Mandrillus leucophaeus)

Olive baboon (Papio anubis)

Vervet-AGM (Chlorocebus sabaeus)

Sooty mangabey (Cercocebus atys)

Panamanian white-faced capuchin (Cebus imitator)

White-tufted-ear marmoset (Callithrix jacchus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Ma's night monkey (Aotus nancymaae)

Tarsier (Carlito syrichta)

Pika (Ochotona princeps)

Rabbit (Oryctolagus cuniculus)

Squirrel (Ictidomys tridecemlineatus)

Arctic ground squirrel (Urocitellus parryii)

Alpine marmot (Marmota marmota marmota)

Eurasian red squirrel (Sciurus vulgaris)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Steppe mouse (Mus spicilegus)

Mouse (Mus musculus reference (CL57BL6) strain)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Golden Hamster (Mesocricetus auratus)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Prairie vole (Microtus ochrogaster)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Lesser Egyptian jerboa (Jaculus jaculus)

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)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Microbat (Myotis lucifugus)

Megabat (Pteropus vampyrus)

Leopard (Panthera pardus)

Lion (Panthera leo)

Tiger (Panthera tigris altaica)

Cat (Felis catus)

Dingo (Canis lupus dingo)

Dog (Canis lupus familiaris reference breed)

Red fox (Vulpes vulpes)

American black bear (Ursus americanus)

Polar bear (Ursus maritimus)

Giant panda (Ailuropoda melanoleuca reference isolate)

American mink (Neogale vison)

Ferret (Mustela putorius furo)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Shrew (Sorex araneus)

Hedgehog (Erinaceus europaeus)

Arabian camel (Camelus dromedarius)

Alpaca (Vicugna pacos)

Narwhal (Monodon monoceros)

Beluga whale (Delphinapterus leucas)

Sperm whale (Physeter catodon)

Dolphin (Tursiops truncatus)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Chacoan peccary (Catagonus wagneri)

Pig (Sus scrofa reference breed)

Sheep (Ovis aries reference breed)

Goat (Capra hircus reference breed)

Wild yak (Bos mutus)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Cow (Bos taurus reference breed)

Domestic yak (Bos grunniens)

American bison (Bison bison bison)

Siberian musk deer (Moschus moschiferus)

Yarkand deer (Cervus hanglu yarkandensis)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Elephant (Loxodonta africana)

Lesser hedgehog tenrec (Echinops telfairi)

Hyrax (Procavia capensis)

Platypus (Ornithorhynchus anatinus)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

C.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)