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

C.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Common wombat (Vombatus ursinus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Hedgehog (Erinaceus europaeus)

Blue whale (Balaenoptera musculus)

Shrew (Sorex araneus)

Dingo (Canis lupus dingo)

Chacoan peccary (Catagonus wagneri)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Beluga whale (Delphinapterus leucas)

American black bear (Ursus americanus)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Armadillo (Dasypus novemcinctus)

Vervet-AGM (Chlorocebus sabaeus)

Mouse Lemur (Microcebus murinus)

Giant panda (Ailuropoda melanoleuca reference isolate)

Panamanian white-faced capuchin (Cebus imitator)

Sooty mangabey (Cercocebus atys)

Dolphin (Tursiops truncatus)

Arctic ground squirrel (Urocitellus parryii)

Degu (Octodon degus)

Tree Shrew (Tupaia belangeri)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Red fox (Vulpes vulpes)

Lesser Egyptian jerboa (Jaculus jaculus)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Polar bear (Ursus maritimus)

American bison (Bison bison bison)

Gorilla (Gorilla gorilla gorilla)

Goat (Capra hircus reference breed)

Rabbit (Oryctolagus cuniculus)

Macaque (Macaca mulatta)

Gibbon (Nomascus leucogenys)

Lion (Panthera leo)

Golden Hamster (Mesocricetus auratus)

Pig (Sus scrofa reference breed)

Sperm whale (Physeter catodon)

Arabian camel (Camelus dromedarius)

Elephant (Loxodonta africana)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Drill (Mandrillus leucophaeus)

Sumatran orangutan (Pongo abelii)

Ma's night monkey (Aotus nancymaae)

Guinea Pig (Cavia porcellus)

Chimpanzee (Pan troglodytes)

Dog (Canis lupus familiaris reference breed)

Alpine marmot (Marmota marmota marmota)

Donkey (Equus asinus reference breed)

Siberian musk deer (Moschus moschiferus)

Alpaca (Vicugna pacos)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Prairie vole (Microtus ochrogaster)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Human (Homo sapiens)

Narwhal (Monodon monoceros)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Squirrel (Ictidomys tridecemlineatus)

Greater bamboo lemur (Prolemur simus)

Hyrax (Procavia capensis)

Microbat (Myotis lucifugus)

Bushbaby (Otolemur garnettii)

Eurasian red squirrel (Sciurus vulgaris)

Wild yak (Bos mutus)

White-tufted-ear marmoset (Callithrix jacchus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Naked mole-rat female (Heterocephalus glaber reference strain)

Coquerel's sifaka (Propithecus coquereli)

Bonobo (Pan paniscus)

Ferret (Mustela putorius furo)

Megabat (Pteropus vampyrus)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Lesser hedgehog tenrec (Echinops telfairi)

Sloth (Choloepus hoffmanni)

Olive baboon (Papio anubis)

Tiger (Panthera tigris altaica)

Kangaroo rat (Dipodomys ordii)

Domestic yak (Bos grunniens)

Sheep (Ovis aries reference breed)

Horse (Equus caballus breed thoroughbred)

Crab-eating macaque (Macaca fascicularis)

Steppe mouse (Mus spicilegus)

Yarkand deer (Cervus hanglu yarkandensis)

Leopard (Panthera pardus)

Pika (Ochotona princeps)

Cat (Felis catus)

Cow (Bos taurus reference breed)

Pig-tailed macaque (Macaca nemestrina)

Tarsier (Carlito syrichta)

American mink (Neogale vison)

Vaquita (Phocoena sinus)

Black snub-nosed monkey (Rhinopithecus bieti)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Mouse (Mus musculus reference (CL57BL6) strain)

Long-tailed chinchilla (Chinchilla lanigera)

Platypus (Ornithorhynchus anatinus)

Goodes thornscrub tortoise (Gopherus evgoodei)

Tuatara (Sphenodon punctatus)

Medium ground-finch (Geospiza fortis)

Indian cobra (Naja naja)

Australian saltwater crocodile (Crocodylus porosus)

Turkey (Meleagris gallopavo reference strain)

Kakapo (Strigops habroptila)

Golden eagle (Aquila chrysaetos chrysaetos)

Eastern brown snake (Pseudonaja textilis)

Japanese quail (Coturnix japonica)

Mainland tiger snake (Notechis scutatus)

Argentine black and white tegu (Salvator merianae)

Common canary (Serinus canaria)

Common wall lizard (Podarcis muralis)

Great Tit (Parus major)

Collared flycatcher (Ficedula albicollis)

Pink-footed goose (Anser brachyrhynchus)

Blue-ringed sea krait (Laticauda laticaudata)

Green anole (Anolis carolinensis reference strain)

African ostrich (Struthio camelus australis)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Three-toed box turtle (Terrapene carolina triunguis)

Zebra finch (Taeniopygia guttata)

Chicken (Gallus gallus reference breed)

Chinese softshell turtle (Pelodiscus sinensis)

Duck (Anas platyrhynchos platyrhynchos)

Painted turtle (Chrysemys picta bellii)

Coelacanth (Latimeria chalumnae)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Pinecone soldierfish (Myripristis murdjan)

Zebrafish (Danio rerio)

Pike-perch (Sander lucioperca)

Mummichog (Fundulus heteroclitus)

Lyretail cichlid (Neolamprologus brichardi)

Zig-zag eel (Mastacembelus armatus)

Guppy (Poecilia reticulata)

Coho salmon (Oncorhynchus kisutch)

Mexican tetra (Astyanax mexicanus)

European seabass (Dicentrarchus labrax)

Lumpfish (Cyclopterus lumpus)

Siamese fighting fish (Betta splendens)

Yellowtail amberjack (Seriola lalandi dorsalis)

Large yellow croaker (Larimichthys crocea)

Monterrey platyfish (Xiphophorus couchianus)

Climbing perch (Anabas testudineus)

Channel bull blenny (Cottoperca gobio)

Tetraodon (Tetraodon nigroviridis)

Orange clownfish (Amphiprion percula)

Red-bellied piranha (Pygocentrus nattereri)

Atlantic herring (Clupea harengus)

Gilthead seabream (Sparus aurata)

Bicolor damselfish (Stegastes partitus)

Makobe Island cichlid (Pundamilia nyererei)

Mangrove rivulus (Kryptolebias marmoratus)

Spiny chromis (Acanthochromis polyacanthus)

Amazon molly (Poecilia formosa)

Barramundi perch (Lates calcarifer)

Huchen (Hucho hucho)

Tongue sole (Cynoglossus semilaevis)

Denticle herring (Denticeps clupeoides)

Stickleback (Gasterosteus aculeatus)

Midas cichlid (Amphilophus citrinellus)

Ballan wrasse (Labrus bergylta)

Clown anemonefish (Amphiprion ocellaris)

Zebra mbuna (Maylandia zebra)

Brown trout (Salmo trutta)

Goldfish (Carassius auratus)

Japanese medaka HdrR (Oryzias latipes)

Electric eel (Electrophorus electricus)

Tiger tail seahorse (Hippocampus comes)

Rainbow trout (Oncorhynchus mykiss)

Atlantic cod (Gadus morhua)

Sheepshead minnow (Cyprinodon variegatus)

Platyfish (Xiphophorus maculatus)

Atlantic salmon (Salmo salar)

Indian medaka (Oryzias melastigma)

Common carp (Cyprinus carpio carpio)

Turbot (Scophthalmus maximus)

Chinook salmon (Oncorhynchus tshawytscha)

Javanese ricefish (Oryzias javanicus)

Sailfin molly (Poecilia latipinna)

Turquoise killifish (Nothobranchius furzeri)

Greater amberjack (Seriola dumerili)

Burton's mouthbrooder (Haplochromis burtoni)

Northern pike (Esox lucius)

Fugu (Takifugu rubripes)

Eastern happy (Astatotilapia calliptera)

Channel catfish (Ictalurus punctatus)

Nile tilapia (Oreochromis niloticus)

Chinese medaka (Oryzias sinensis)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

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

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)