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)

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

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)

Beluga whale (Delphinapterus leucas)

Armadillo (Dasypus novemcinctus)

Kangaroo rat (Dipodomys ordii)

Macaque (Macaca mulatta)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Ma's night monkey (Aotus nancymaae)

Gibbon (Nomascus leucogenys)

Dingo (Canis lupus dingo)

Lesser Egyptian jerboa (Jaculus jaculus)

Sperm whale (Physeter catodon)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Panamanian white-faced capuchin (Cebus imitator)

Alpaca (Vicugna pacos)

Vaquita (Phocoena sinus)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Crab-eating macaque (Macaca fascicularis)

Eurasian red squirrel (Sciurus vulgaris)

Polar bear (Ursus maritimus)

Ferret (Mustela putorius furo)

Goat (Capra hircus reference breed)

Shrew (Sorex araneus)

Mouse (Mus musculus reference (CL57BL6) strain)

Pika (Ochotona princeps)

White-tufted-ear marmoset (Callithrix jacchus)

Pig-tailed macaque (Macaca nemestrina)

Domestic yak (Bos grunniens)

Prairie vole (Microtus ochrogaster)

Steppe mouse (Mus spicilegus)

Sooty mangabey (Cercocebus atys)

Hedgehog (Erinaceus europaeus)

Bushbaby (Otolemur garnettii)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Guinea Pig (Cavia porcellus)

Lesser hedgehog tenrec (Echinops telfairi)

Dolphin (Tursiops truncatus)

Vervet-AGM (Chlorocebus sabaeus)

Sloth (Choloepus hoffmanni)

Coquerel's sifaka (Propithecus coquereli)

Siberian musk deer (Moschus moschiferus)

Gorilla (Gorilla gorilla gorilla)

American bison (Bison bison bison)

Elephant (Loxodonta africana)

Chacoan peccary (Catagonus wagneri)

Horse (Equus caballus breed thoroughbred)

Giant panda (Ailuropoda melanoleuca reference isolate)

Chimpanzee (Pan troglodytes)

Microbat (Myotis lucifugus)

Golden Hamster (Mesocricetus auratus)

Hyrax (Procavia capensis)

Dog (Canis lupus familiaris reference breed)

Wild yak (Bos mutus)

Olive baboon (Papio anubis)

Pig (Sus scrofa reference breed)

American mink (Neogale vison)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Red fox (Vulpes vulpes)

American black bear (Ursus americanus)

Sumatran orangutan (Pongo abelii)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Human (Homo sapiens)

Drill (Mandrillus leucophaeus)

Megabat (Pteropus vampyrus)

Tiger (Panthera tigris altaica)

Alpine marmot (Marmota marmota marmota)

Squirrel (Ictidomys tridecemlineatus)

Blue whale (Balaenoptera musculus)

Tarsier (Carlito syrichta)

Leopard (Panthera pardus)

Cow (Bos taurus reference breed)

Rabbit (Oryctolagus cuniculus)

Arctic ground squirrel (Urocitellus parryii)

Degu (Octodon degus)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Yarkand deer (Cervus hanglu yarkandensis)

Sheep (Ovis aries reference breed)

Black snub-nosed monkey (Rhinopithecus bieti)

Arabian camel (Camelus dromedarius)

Mouse Lemur (Microcebus murinus)

Bonobo (Pan paniscus)

Tree Shrew (Tupaia belangeri)

Long-tailed chinchilla (Chinchilla lanigera)

Greater bamboo lemur (Prolemur simus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Narwhal (Monodon monoceros)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Cat (Felis catus)

Naked mole-rat female (Heterocephalus glaber reference strain)

Lion (Panthera leo)

Donkey (Equus asinus reference breed)

Platypus (Ornithorhynchus anatinus)

Three-toed box turtle (Terrapene carolina triunguis)

Tuatara (Sphenodon punctatus)

Common wall lizard (Podarcis muralis)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Eastern brown snake (Pseudonaja textilis)

Zebra finch (Taeniopygia guttata)

Indian cobra (Naja naja)

Great Tit (Parus major)

Chinese softshell turtle (Pelodiscus sinensis)

African ostrich (Struthio camelus australis)

Collared flycatcher (Ficedula albicollis)

Golden eagle (Aquila chrysaetos chrysaetos)

Australian saltwater crocodile (Crocodylus porosus)

Pink-footed goose (Anser brachyrhynchus)

Kakapo (Strigops habroptila)

Mainland tiger snake (Notechis scutatus)

Medium ground-finch (Geospiza fortis)

Argentine black and white tegu (Salvator merianae)

Blue-ringed sea krait (Laticauda laticaudata)

Duck (Anas platyrhynchos platyrhynchos)

Green anole (Anolis carolinensis reference strain)

Turkey (Meleagris gallopavo reference strain)

Japanese quail (Coturnix japonica)

Common canary (Serinus canaria)

Goodes thornscrub tortoise (Gopherus evgoodei)

Painted turtle (Chrysemys picta bellii)

Chicken (Gallus gallus reference breed)

Coelacanth (Latimeria chalumnae)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Asian bonytongue (Scleropages formosus)

Makobe Island cichlid (Pundamilia nyererei)

Sailfin molly (Poecilia latipinna)

Monterrey platyfish (Xiphophorus couchianus)

Yellowtail amberjack (Seriola lalandi dorsalis)

European seabass (Dicentrarchus labrax)

Zebrafish (Danio rerio)

Goldfish (Carassius auratus)

Tetraodon (Tetraodon nigroviridis)

Climbing perch (Anabas testudineus)

Denticle herring (Denticeps clupeoides)

Channel catfish (Ictalurus punctatus)

Atlantic herring (Clupea harengus)

Coho salmon (Oncorhynchus kisutch)

Tiger tail seahorse (Hippocampus comes)

Platyfish (Xiphophorus maculatus)

Spiny chromis (Acanthochromis polyacanthus)

Channel bull blenny (Cottoperca gobio)

Sheepshead minnow (Cyprinodon variegatus)

Siamese fighting fish (Betta splendens)

Mexican tetra (Astyanax mexicanus)

Electric eel (Electrophorus electricus)

Ballan wrasse (Labrus bergylta)

Huchen (Hucho hucho)

Eastern happy (Astatotilapia calliptera)

Atlantic cod (Gadus morhua)

Javanese ricefish (Oryzias javanicus)

Turquoise killifish (Nothobranchius furzeri)

Red-bellied piranha (Pygocentrus nattereri)

Chinese medaka (Oryzias sinensis)

Gilthead seabream (Sparus aurata)

Greater amberjack (Seriola dumerili)

Bicolor damselfish (Stegastes partitus)

Atlantic salmon (Salmo salar)

Fugu (Takifugu rubripes)

Clown anemonefish (Amphiprion ocellaris)

Mangrove rivulus (Kryptolebias marmoratus)

Chinook salmon (Oncorhynchus tshawytscha)

Midas cichlid (Amphilophus citrinellus)

Zebra mbuna (Maylandia zebra)

Pinecone soldierfish (Myripristis murdjan)

Turbot (Scophthalmus maximus)

Pike-perch (Sander lucioperca)

Indian medaka (Oryzias melastigma)

Burton's mouthbrooder (Haplochromis burtoni)

Stickleback (Gasterosteus aculeatus)

Amazon molly (Poecilia formosa)

Large yellow croaker (Larimichthys crocea)

Rainbow trout (Oncorhynchus mykiss)

Zig-zag eel (Mastacembelus armatus)

Guppy (Poecilia reticulata)

Northern pike (Esox lucius)

Common carp (Cyprinus carpio carpio)

Orange clownfish (Amphiprion percula)

Japanese medaka HdrR (Oryzias latipes)

Lumpfish (Cyclopterus lumpus)

Mummichog (Fundulus heteroclitus)

Brown trout (Salmo trutta)

Tongue sole (Cynoglossus semilaevis)

Barramundi perch (Lates calcarifer)

Lyretail cichlid (Neolamprologus brichardi)

Nile tilapia (Oreochromis niloticus)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)