Phylogenetic summary of ncRNA families

• Overview
• Gene tree coverage 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
	Species-specific duplications	Single-copy genes	Multi-copy genes

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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Asian bonytongue (Scleropages formosus)

Atlantic cod (Gadus morhua)

Chinook salmon (Oncorhynchus tshawytscha)

Red-bellied piranha (Pygocentrus nattereri)

Orange clownfish (Amphiprion percula)

Ballan wrasse (Labrus bergylta)

Makobe Island cichlid (Pundamilia nyererei)

Goldfish (Carassius auratus)

Zig-zag eel (Mastacembelus armatus)

Lyretail cichlid (Neolamprologus brichardi)

Climbing perch (Anabas testudineus)

Siamese fighting fish (Betta splendens)

Turquoise killifish (Nothobranchius furzeri)

Javanese ricefish (Oryzias javanicus)

Electric eel (Electrophorus electricus)

Large yellow croaker (Larimichthys crocea)

European seabass (Dicentrarchus labrax)

Lumpfish (Cyclopterus lumpus)

Zebrafish (Danio rerio)

Sheepshead minnow (Cyprinodon variegatus)

Brown trout (Salmo trutta)

Northern pike (Esox lucius)

Barramundi perch (Lates calcarifer)

Eastern happy (Astatotilapia calliptera)

Atlantic salmon (Salmo salar)

Midas cichlid (Amphilophus citrinellus)

Atlantic herring (Clupea harengus)

Channel catfish (Ictalurus punctatus)

Mummichog (Fundulus heteroclitus)

Tongue sole (Cynoglossus semilaevis)

Common carp (Cyprinus carpio carpio)

Greater amberjack (Seriola dumerili)

Tiger tail seahorse (Hippocampus comes)

Fugu (Takifugu rubripes)

Sailfin molly (Poecilia latipinna)

Denticle herring (Denticeps clupeoides)

Stickleback (Gasterosteus aculeatus)

Huchen (Hucho hucho)

Turbot (Scophthalmus maximus)

Burton's mouthbrooder (Haplochromis burtoni)

Guppy (Poecilia reticulata)

Platyfish (Xiphophorus maculatus)

Mangrove rivulus (Kryptolebias marmoratus)

Amazon molly (Poecilia formosa)

Gilthead seabream (Sparus aurata)

Japanese medaka HdrR (Oryzias latipes)

Channel bull blenny (Cottoperca gobio)

Rainbow trout (Oncorhynchus mykiss)

Yellowtail amberjack (Seriola lalandi dorsalis)

Pinecone soldierfish (Myripristis murdjan)

Pike-perch (Sander lucioperca)

Spiny chromis (Acanthochromis polyacanthus)

Chinese medaka (Oryzias sinensis)

Tetraodon (Tetraodon nigroviridis)

Indian medaka (Oryzias melastigma)

Coho salmon (Oncorhynchus kisutch)

Mexican tetra (Astyanax mexicanus)

Bicolor damselfish (Stegastes partitus)

Clown anemonefish (Amphiprion ocellaris)

Zebra mbuna (Maylandia zebra)

Monterrey platyfish (Xiphophorus couchianus)

Nile tilapia (Oreochromis niloticus)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Steppe mouse (Mus spicilegus)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Siberian musk deer (Moschus moschiferus)

Ma's night monkey (Aotus nancymaae)

Degu (Octodon degus)

Gibbon (Nomascus leucogenys)

Beluga whale (Delphinapterus leucas)

Hedgehog (Erinaceus europaeus)

Cow (Bos taurus reference breed)

Mouse Lemur (Microcebus murinus)

Bushbaby (Otolemur garnettii)

American mink (Neogale vison)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Narwhal (Monodon monoceros)

Pig (Sus scrofa reference breed)

Leopard (Panthera pardus)

Polar bear (Ursus maritimus)

Rabbit (Oryctolagus cuniculus)

Lesser Egyptian jerboa (Jaculus jaculus)

Greater bamboo lemur (Prolemur simus)

Drill (Mandrillus leucophaeus)

Eurasian red squirrel (Sciurus vulgaris)

Guinea Pig (Cavia porcellus)

Blue whale (Balaenoptera musculus)

Sumatran orangutan (Pongo abelii)

Chacoan peccary (Catagonus wagneri)

Lesser hedgehog tenrec (Echinops telfairi)

Dog (Canis lupus familiaris reference breed)

Dolphin (Tursiops truncatus)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Human (Homo sapiens)

Red fox (Vulpes vulpes)

Sperm whale (Physeter catodon)

Cat (Felis catus)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Squirrel (Ictidomys tridecemlineatus)

Hyrax (Procavia capensis)

Donkey (Equus asinus reference breed)

Gorilla (Gorilla gorilla gorilla)

Black snub-nosed monkey (Rhinopithecus bieti)

Lion (Panthera leo)

Long-tailed chinchilla (Chinchilla lanigera)

White-tufted-ear marmoset (Callithrix jacchus)

Macaque (Macaca mulatta)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Domestic yak (Bos grunniens)

Ferret (Mustela putorius furo)

Vervet-AGM (Chlorocebus sabaeus)

Elephant (Loxodonta africana)

Giant panda (Ailuropoda melanoleuca reference isolate)

Shrew (Sorex araneus)

Pig-tailed macaque (Macaca nemestrina)

American black bear (Ursus americanus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Alpaca (Vicugna pacos)

Tarsier (Carlito syrichta)

Pika (Ochotona princeps)

Armadillo (Dasypus novemcinctus)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Wild yak (Bos mutus)

Chimpanzee (Pan troglodytes)

Sloth (Choloepus hoffmanni)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Olive baboon (Papio anubis)

Goat (Capra hircus reference breed)

Mouse (Mus musculus reference (CL57BL6) strain)

Kangaroo rat (Dipodomys ordii)

Sheep (Ovis aries reference breed)

Megabat (Pteropus vampyrus)

Prairie vole (Microtus ochrogaster)

Coquerel's sifaka (Propithecus coquereli)

Arctic ground squirrel (Urocitellus parryii)

Crab-eating macaque (Macaca fascicularis)

Panamanian white-faced capuchin (Cebus imitator)

Sooty mangabey (Cercocebus atys)

Tree Shrew (Tupaia belangeri)

Yarkand deer (Cervus hanglu yarkandensis)

Bonobo (Pan paniscus)

Vaquita (Phocoena sinus)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Naked mole-rat female (Heterocephalus glaber reference strain)

Dingo (Canis lupus dingo)

Golden Hamster (Mesocricetus auratus)

American bison (Bison bison bison)

Horse (Equus caballus breed thoroughbred)

Microbat (Myotis lucifugus)

Arabian camel (Camelus dromedarius)

Tiger (Panthera tigris altaica)

Alpine marmot (Marmota marmota marmota)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Platypus (Ornithorhynchus anatinus)

Medium ground-finch (Geospiza fortis)

Zebra finch (Taeniopygia guttata)

Painted turtle (Chrysemys picta bellii)

Indian cobra (Naja naja)

Chicken (Gallus gallus reference breed)

Australian saltwater crocodile (Crocodylus porosus)

Duck (Anas platyrhynchos platyrhynchos)

Tuatara (Sphenodon punctatus)

Eastern brown snake (Pseudonaja textilis)

Mainland tiger snake (Notechis scutatus)

Abingdon island giant tortoise (Chelonoidis abingdonii)

African ostrich (Struthio camelus australis)

Argentine black and white tegu (Salvator merianae)

Japanese quail (Coturnix japonica)

Golden eagle (Aquila chrysaetos chrysaetos)

Pink-footed goose (Anser brachyrhynchus)

Great Tit (Parus major)

Collared flycatcher (Ficedula albicollis)

Three-toed box turtle (Terrapene carolina triunguis)

Kakapo (Strigops habroptila)

Blue-ringed sea krait (Laticauda laticaudata)

Common canary (Serinus canaria)

Turkey (Meleagris gallopavo reference strain)

Common wall lizard (Podarcis muralis)

Green anole (Anolis carolinensis reference strain)

Goodes thornscrub tortoise (Gopherus evgoodei)

Chinese softshell turtle (Pelodiscus sinensis)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

C.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)