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.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Asian bonytongue (Scleropages formosus)

Denticle herring (Denticeps clupeoides reference strain)

Atlantic herring (Clupea harengus reference strain)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Mexican tetra (Astyanax mexicanus)

Electric eel (Electrophorus electricus reference strain)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Atlantic salmon (Salmo salar)

Brown trout (Salmo trutta)

Coho salmon (Oncorhynchus kisutch)

Rainbow trout (Oncorhynchus mykiss)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

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)

Eastern happy (Astatotilapia calliptera reference strain)

Makobe Island cichlid (Pundamilia nyererei)

Burton's mouthbrooder (Haplochromis burtoni)

Zebra mbuna (Maylandia zebra)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Mangrove rivulus (Kryptolebias marmoratus)

Turquoise killifish (Nothobranchius furzeri)

Monterrey platyfish (Xiphophorus couchianus)

Platyfish (Xiphophorus maculatus)

Amazon molly (Poecilia formosa)

Guppy (Poecilia reticulata)

Sailfin molly (Poecilia latipinna)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Indian medaka (Oryzias melastigma)

Japanese medaka HdrR (Oryzias latipes)

Chinese medaka (Oryzias sinensis)

Javanese ricefish (Oryzias javanicus)

Orange clownfish (Amphiprion percula)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

Turbot (Scophthalmus maximus)

Tongue sole (Cynoglossus semilaevis)

Yellowtail amberjack (Seriola lalandi dorsalis)

Greater amberjack (Seriola dumerili)

Barramundi perch (Lates calcarifer)

Large yellow croaker (Larimichthys crocea)

European seabass (Dicentrarchus labrax)

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)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Duck (Anas platyrhynchos platyrhynchos)

Pink-footed goose (Anser brachyrhynchus)

Japanese quail (Coturnix japonica)

Chicken (Gallus gallus reference breed)

Turkey (Meleagris gallopavo reference strain)

Zebra finch (Taeniopygia guttata)

Common canary (Serinus canaria)

Great Tit (Parus major)

Collared flycatcher (Ficedula albicollis)

Medium ground-finch (Geospiza fortis)

Golden eagle (Aquila chrysaetos chrysaetos)

Kakapo (Strigops habroptila)

African ostrich (Struthio camelus australis)

Australian saltwater crocodile (Crocodylus porosus)

Painted turtle (Chrysemys picta bellii)

Three-toed box turtle (Terrapene carolina triunguis)

Goodes thornscrub tortoise (Gopherus evgoodei)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Chinese softshell turtle (Pelodiscus sinensis)

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)

Common wall lizard (Podarcis muralis)

Argentine black and white tegu (Salvator merianae)

Tuatara (Sphenodon punctatus)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

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)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Prairie vole (Microtus ochrogaster)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Lesser Egyptian jerboa (Jaculus jaculus)

Alpine marmot (Marmota marmota marmota)

Squirrel (Ictidomys tridecemlineatus)

Arctic ground squirrel (Urocitellus parryii)

Eurasian red squirrel (Sciurus vulgaris)

Naked mole-rat female (Heterocephalus glaber reference strain)

Long-tailed chinchilla (Chinchilla lanigera)

Degu (Octodon degus)

Guinea Pig (Cavia porcellus)

Kangaroo rat (Dipodomys ordii)

Coquerel's sifaka (Propithecus coquereli)

Greater bamboo lemur (Prolemur simus)

Mouse Lemur (Microcebus murinus)

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)

Vervet-AGM (Chlorocebus sabaeus)

Drill (Mandrillus leucophaeus)

Olive baboon (Papio anubis)

Sooty mangabey (Cercocebus atys)

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)

Tree Shrew (Tupaia belangeri)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Microbat (Myotis lucifugus)

Megabat (Pteropus vampyrus)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Horse (Equus caballus breed thoroughbred)

Donkey (Equus asinus reference breed)

Tiger (Panthera tigris altaica)

Leopard (Panthera pardus)

Lion (Panthera leo)

Cat (Felis catus)

Ferret (Mustela putorius furo)

American mink (Neogale vison)

Dingo (Canis lupus dingo)

Dog (Canis lupus familiaris reference breed)

Red fox (Vulpes vulpes)

Polar bear (Ursus maritimus)

American black bear (Ursus americanus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Pig (Sus scrofa reference breed)

Chacoan peccary (Catagonus wagneri)

Narwhal (Monodon monoceros)

Beluga whale (Delphinapterus leucas)

Sperm whale (Physeter catodon)

Dolphin (Tursiops truncatus)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Cow (Bos taurus reference breed)

Wild yak (Bos mutus)

Domestic yak (Bos grunniens)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

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)

Hyrax (Procavia capensis)

Lesser hedgehog tenrec (Echinops telfairi)

Elephant (Loxodonta africana)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Tasmanian devil (Sarcophilus harrisii)

Opossum (Monodelphis domestica)

Platypus (Ornithorhynchus anatinus)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)