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.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

Lamprey (Petromyzon marinus)

Hagfish (Eptatretus burgeri)

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)

Domestic yak (Bos grunniens)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Pika (Ochotona princeps)

Naked mole-rat female (Heterocephalus glaber reference strain)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Degu (Octodon degus)

Alpine marmot (Marmota marmota marmota)

Gibbon (Nomascus leucogenys)

Panamanian white-faced capuchin (Cebus imitator)

Mouse Lemur (Microcebus murinus)

Ma's night monkey (Aotus nancymaae)

Golden Hamster (Mesocricetus auratus)

American bison (Bison bison bison)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Sheep (Ovis aries reference breed)

Narwhal (Monodon monoceros)

Armadillo (Dasypus novemcinctus)

Pig (Sus scrofa reference breed)

Tree Shrew (Tupaia belangeri)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Hyrax (Procavia capensis)

Pig-tailed macaque (Macaca nemestrina)

Coquerel's sifaka (Propithecus coquereli)

Cow (Bos taurus reference breed)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Human (Homo sapiens)

Sooty mangabey (Cercocebus atys)

Steppe mouse (Mus spicilegus)

American black bear (Ursus americanus)

Vaquita (Phocoena sinus)

Tiger (Panthera tigris altaica)

White-tufted-ear marmoset (Callithrix jacchus)

Yarkand deer (Cervus hanglu yarkandensis)

Horse (Equus caballus breed thoroughbred)

Dolphin (Tursiops truncatus)

Sperm whale (Physeter catodon)

Mouse (Mus musculus reference (CL57BL6) strain)

Chacoan peccary (Catagonus wagneri)

Polar bear (Ursus maritimus)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Tarsier (Carlito syrichta)

Sumatran orangutan (Pongo abelii)

Crab-eating macaque (Macaca fascicularis)

American mink (Neogale vison)

Lesser Egyptian jerboa (Jaculus jaculus)

Dingo (Canis lupus dingo)

Wild yak (Bos mutus)

Elephant (Loxodonta africana)

Guinea Pig (Cavia porcellus)

Gorilla (Gorilla gorilla gorilla)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Hedgehog (Erinaceus europaeus)

Chimpanzee (Pan troglodytes)

Cat (Felis catus)

Kangaroo rat (Dipodomys ordii)

Vervet-AGM (Chlorocebus sabaeus)

Sloth (Choloepus hoffmanni)

Eurasian red squirrel (Sciurus vulgaris)

Shrew (Sorex araneus)

Lion (Panthera leo)

Arabian camel (Camelus dromedarius)

Rabbit (Oryctolagus cuniculus)

Drill (Mandrillus leucophaeus)

Bushbaby (Otolemur garnettii)

Greater bamboo lemur (Prolemur simus)

Prairie vole (Microtus ochrogaster)

Alpaca (Vicugna pacos)

Lesser hedgehog tenrec (Echinops telfairi)

Olive baboon (Papio anubis)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Long-tailed chinchilla (Chinchilla lanigera)

Beluga whale (Delphinapterus leucas)

Dog (Canis lupus familiaris reference breed)

Black snub-nosed monkey (Rhinopithecus bieti)

Blue whale (Balaenoptera musculus)

Leopard (Panthera pardus)

Squirrel (Ictidomys tridecemlineatus)

Bonobo (Pan paniscus)

Goat (Capra hircus reference breed)

Donkey (Equus asinus reference breed)

Microbat (Myotis lucifugus)

Siberian musk deer (Moschus moschiferus)

Macaque (Macaca mulatta)

Red fox (Vulpes vulpes)

Arctic ground squirrel (Urocitellus parryii)

Giant panda (Ailuropoda melanoleuca reference isolate)

Megabat (Pteropus vampyrus)

Ferret (Mustela putorius furo)

Platypus (Ornithorhynchus anatinus)

Great Tit (Parus major)

Collared flycatcher (Ficedula albicollis)

Australian saltwater crocodile (Crocodylus porosus)

Green anole (Anolis carolinensis reference strain)

Kakapo (Strigops habroptila)

Golden eagle (Aquila chrysaetos chrysaetos)

Zebra finch (Taeniopygia guttata)

Chinese softshell turtle (Pelodiscus sinensis)

Japanese quail (Coturnix japonica)

Blue-ringed sea krait (Laticauda laticaudata)

Common wall lizard (Podarcis muralis)

Goodes thornscrub tortoise (Gopherus evgoodei)

Indian cobra (Naja naja)

Pink-footed goose (Anser brachyrhynchus)

African ostrich (Struthio camelus australis)

Common canary (Serinus canaria)

Mainland tiger snake (Notechis scutatus)

Tuatara (Sphenodon punctatus)

Painted turtle (Chrysemys picta bellii)

Argentine black and white tegu (Salvator merianae)

Turkey (Meleagris gallopavo reference strain)

Chicken (Gallus gallus reference breed)

Eastern brown snake (Pseudonaja textilis)

Three-toed box turtle (Terrapene carolina triunguis)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Duck (Anas platyrhynchos platyrhynchos)

Medium ground-finch (Geospiza fortis)

Coelacanth (Latimeria chalumnae)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Red-bellied piranha (Pygocentrus nattereri)

Turbot (Scophthalmus maximus)

Spiny chromis (Acanthochromis polyacanthus)

Clown anemonefish (Amphiprion ocellaris)

Goldfish (Carassius auratus)

Lyretail cichlid (Neolamprologus brichardi)

Channel catfish (Ictalurus punctatus)

Midas cichlid (Amphilophus citrinellus)

Greater amberjack (Seriola dumerili)

Zebrafish (Danio rerio)

Mexican tetra (Astyanax mexicanus)

Guppy (Poecilia reticulata)

Indian medaka (Oryzias melastigma)

Japanese medaka HdrR (Oryzias latipes)

Bicolor damselfish (Stegastes partitus)

Orange clownfish (Amphiprion percula)

Nile tilapia (Oreochromis niloticus)

Tiger tail seahorse (Hippocampus comes)

Pinecone soldierfish (Myripristis murdjan)

Coho salmon (Oncorhynchus kisutch)

Turquoise killifish (Nothobranchius furzeri)

Makobe Island cichlid (Pundamilia nyererei)

Burton's mouthbrooder (Haplochromis burtoni)

Lumpfish (Cyclopterus lumpus)

Atlantic cod (Gadus morhua)

Amazon molly (Poecilia formosa)

Electric eel (Electrophorus electricus)

Tongue sole (Cynoglossus semilaevis)

European seabass (Dicentrarchus labrax)

Chinese medaka (Oryzias sinensis)

Atlantic salmon (Salmo salar)

Yellowtail amberjack (Seriola lalandi dorsalis)

Chinook salmon (Oncorhynchus tshawytscha)

Zebra mbuna (Maylandia zebra)

Stickleback (Gasterosteus aculeatus)

Ballan wrasse (Labrus bergylta)

Tetraodon (Tetraodon nigroviridis)

Brown trout (Salmo trutta)

Javanese ricefish (Oryzias javanicus)

Monterrey platyfish (Xiphophorus couchianus)

Large yellow croaker (Larimichthys crocea)

Huchen (Hucho hucho)

Northern pike (Esox lucius)

Rainbow trout (Oncorhynchus mykiss)

Zig-zag eel (Mastacembelus armatus)

Eastern happy (Astatotilapia calliptera)

Gilthead seabream (Sparus aurata)

Mummichog (Fundulus heteroclitus)

Sailfin molly (Poecilia latipinna)

Siamese fighting fish (Betta splendens)

Fugu (Takifugu rubripes)

Barramundi perch (Lates calcarifer)

Pike-perch (Sander lucioperca)

Common carp (Cyprinus carpio carpio)

Platyfish (Xiphophorus maculatus)

Channel bull blenny (Cottoperca gobio)

Denticle herring (Denticeps clupeoides)

Mangrove rivulus (Kryptolebias marmoratus)

Climbing perch (Anabas testudineus)

Atlantic herring (Clupea harengus)

Sheepshead minnow (Cyprinodon variegatus)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)