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

Crab-eating macaque (Macaca fascicularis)

Macaque (Macaca mulatta)

Pig-tailed macaque (Macaca nemestrina)

Drill (Mandrillus leucophaeus)

Olive baboon (Papio anubis)

Sooty mangabey (Cercocebus atys)

Vervet-AGM (Chlorocebus sabaeus)

Black snub-nosed monkey (Rhinopithecus bieti)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Bonobo (Pan paniscus)

Chimpanzee (Pan troglodytes)

Gorilla (Gorilla gorilla gorilla)

Human (Homo sapiens)

Sumatran orangutan (Pongo abelii)

Gibbon (Nomascus leucogenys)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Panamanian white-faced capuchin (Cebus imitator)

White-tufted-ear marmoset (Callithrix jacchus)

Ma's night monkey (Aotus nancymaae)

Tarsier (Carlito syrichta)

Coquerel's sifaka (Propithecus coquereli)

Greater bamboo lemur (Prolemur simus)

Mouse Lemur (Microcebus murinus)

Bushbaby (Otolemur garnettii)

Mouse (Mus musculus reference (CL57BL6) strain)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Steppe mouse (Mus spicilegus)

Western wild mouse (Mus spretus reference strain)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Norway rat - BN/NHsdMcwi (Rattus norvegicus reference strain)

Chinese hamster PICR (Cricetulus griseus strain 17A/GY)

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)

Alpine marmot (Marmota marmota marmota)

Arctic ground squirrel (Urocitellus parryii)

Squirrel (Ictidomys tridecemlineatus)

Eurasian red squirrel (Sciurus vulgaris)

Degu (Octodon degus)

Guinea Pig (Cavia porcellus)

Long-tailed chinchilla (Chinchilla lanigera)

Naked mole-rat female (Heterocephalus glaber reference strain)

Kangaroo rat (Dipodomys ordii)

Pika (Ochotona princeps)

Rabbit (Oryctolagus cuniculus)

Tree Shrew (Tupaia belangeri)

Cattle (Bos taurus reference breed)

Domestic yak (Bos grunniens)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Wild yak (Bos mutus)

American bison (Bison bison bison)

Goat (Capra hircus reference breed)

Sheep (Ovis aries reference breed)

Siberian musk deer (Moschus moschiferus)

Yarkand deer (Cervus hanglu yarkandensis)

Beluga whale (Delphinapterus leucas)

Narwhal (Monodon monoceros)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter macrocephalus)

Vaquita (Phocoena sinus)

Blue whale (Balaenoptera musculus)

Alpaca (Vicugna pacos)

Arabian camel (Camelus dromedarius)

Chacoan peccary (Catagonus wagneri)

Pig (Sus scrofa reference breed)

American black bear (Ursus americanus)

Polar bear (Ursus maritimus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Dingo (Canis lupus dingo)

Dog (Canis lupus familiaris reference breed)

Red fox (Vulpes vulpes)

American mink (Neogale vison)

Ferret (Mustela putorius furo)

Leopard (Panthera pardus)

Lion (Panthera leo)

Tiger (Panthera tigris altaica)

Domestic cat (Felis catus reference breed)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Megabat (Pteropus vampyrus)

Microbat (Myotis lucifugus)

Donkey (Equus asinus reference breed)

Horse (Equus caballus breed thoroughbred)

Hedgehog (Erinaceus europaeus)

Shrew (Sorex araneus)

Elephant (Loxodonta africana)

Hyrax (Procavia capensis)

Lesser hedgehog tenrec (Echinops telfairi)

Armadillo (Dasypus novemcinctus)

Sloth (Choloepus hoffmanni)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Platypus (Ornithorhynchus anatinus)

Common canary (Serinus canaria)

Zebra finch (Taeniopygia guttata)

Collared flycatcher (Ficedula albicollis)

Great Tit (Parus major)

Medium ground-finch (Geospiza fortis)

Kakapo (Strigops habroptila)

Golden eagle (Aquila chrysaetos chrysaetos)

Chicken (Gallus gallus reference breed)

Japanese quail (Coturnix japonica)

Turkey (Meleagris gallopavo reference strain)

Duck (Anas platyrhynchos platyrhynchos)

Pink-footed goose (Anser brachyrhynchus)

African ostrich (Struthio camelus australis)

Australian saltwater crocodile (Crocodylus porosus)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Goodes thornscrub tortoise (Gopherus evgoodei)

Painted turtle (Chrysemys picta bellii)

Three-toed box turtle (Terrapene triunguis)

Chinese softshell turtle (Pelodiscus sinensis)

Eastern brown snake (Pseudonaja textilis)

Mainland tiger snake (Notechis scutatus)

Blue-ringed sea krait (Laticauda laticaudata)

Indian cobra (Naja naja)

Green anole (Anolis carolinensis reference strain)

Argentine black and white tegu (Salvator merianae)

Common wall lizard (Podarcis muralis)

Tuatara (Sphenodon punctatus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Coelacanth (Latimeria chalumnae)

Amazon molly (Poecilia formosa)

Guppy (Poecilia reticulata)

Sailfin molly (Poecilia latipinna)

Monterrey platyfish (Xiphophorus couchianus)

Platyfish (Xiphophorus maculatus)

Mummichog (Fundulus heteroclitus)

Sheepshead minnow (Cyprinodon variegatus)

Mangrove rivulus (Kryptolebias marmoratus)

Turquoise killifish (Nothobranchius furzeri)

Chinese medaka (Oryzias sinensis)

Indian medaka (Oryzias melastigma)

Japanese medaka HdrR (Oryzias latipes)

Javanese ricefish (Oryzias javanicus)

Burton's mouthbrooder (Haplochromis burtoni)

Eastern happy (Astatotilapia calliptera reference strain)

Makobe Island cichlid (Pundamilia nyererei)

Zebra mbuna (Maylandia zebra)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Midas cichlid (Amphilophus citrinellus)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Orange clownfish (Amphiprion percula)

Bicolor damselfish (Stegastes partitus)

Spiny chromis (Acanthochromis polyacanthus)

Lumpfish (Cyclopterus lumpus)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

Channel bull blenny (Cottoperca gobio)

Pike-perch (Sander lucioperca)

European seabass (Dicentrarchus labrax)

Large yellow croaker (Larimichthys crocea)

Fugu (Takifugu rubripes)

Tetraodon (Tetraodon nigroviridis)

Ballan wrasse (Labrus bergylta)

Gilthead seabream (Sparus aurata)

Greater amberjack (Seriola dumerili)

Yellowtail amberjack (Seriola lalandi dorsalis)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Barramundi perch (Lates calcarifer)

Climbing perch (Anabas testudineus reference strain)

Siamese fighting fish (Betta splendens)

Zig-zag eel (Mastacembelus armatus)

Tiger tail seahorse (Hippocampus comes)

Pinecone soldierfish (Myripristis murdjan)

Atlantic cod (Gadus morhua)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Coho salmon (Oncorhynchus kisutch)

Rainbow trout (Oncorhynchus mykiss)

Atlantic salmon (Salmo salar)

Brown trout (Salmo trutta)

Huchen (Hucho hucho)

Northern pike (Esox lucius reference strain)

Mexican tetra (Astyanax mexicanus)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Electric eel (Electrophorus electricus reference strain)

Common carp (Cyprinus carpio carpio)

Goldfish (Carassius auratus)

Zebrafish (Danio rerio)

Atlantic herring (Clupea harengus reference strain)

Denticle herring (Denticeps clupeoides reference strain)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

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

Drosophila melanogaster - (Fruit fly) (Drosophila melanogaster)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)