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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

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

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Gilthead seabream (Sparus aurata)

Nile tilapia (Oreochromis niloticus)

Spiny chromis (Acanthochromis polyacanthus)

Bicolor damselfish (Stegastes partitus)

Goldfish (Carassius auratus)

Zig-zag eel (Mastacembelus armatus)

Tongue sole (Cynoglossus semilaevis)

Guppy (Poecilia reticulata)

Electric eel (Electrophorus electricus reference strain)

Channel bull blenny (Cottoperca gobio)

Javanese ricefish (Oryzias javanicus)

Siamese fighting fish (Betta splendens)

Greater amberjack (Seriola dumerili)

Rainbow trout (Oncorhynchus mykiss)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Brown trout (Salmo trutta)

Zebra mbuna (Maylandia zebra)

Mangrove rivulus (Kryptolebias marmoratus)

Monterrey platyfish (Xiphophorus couchianus)

Lyretail cichlid (Neolamprologus brichardi)

Tiger tail seahorse (Hippocampus comes)

Sailfin molly (Poecilia latipinna)

Common carp (Cyprinus carpio carpio)

Turquoise killifish (Nothobranchius furzeri)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Lumpfish (Cyclopterus lumpus)

Barramundi perch (Lates calcarifer)

Huchen (Hucho hucho)

Platyfish (Xiphophorus maculatus)

Eastern happy (Astatotilapia calliptera reference strain)

Yellowtail amberjack (Seriola lalandi dorsalis)

Japanese medaka HdrR (Oryzias latipes)

Zebrafish (Danio rerio)

Coho salmon (Oncorhynchus kisutch)

Mummichog (Fundulus heteroclitus)

Indian medaka (Oryzias melastigma)

Burton's mouthbrooder (Haplochromis burtoni)

Makobe Island cichlid (Pundamilia nyererei)

Amazon molly (Poecilia formosa)

Orange clownfish (Amphiprion percula)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

Sheepshead minnow (Cyprinodon variegatus)

Atlantic herring (Clupea harengus reference strain)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Northern pike (Esox lucius reference strain)

Atlantic cod (Gadus morhua)

Pinecone soldierfish (Myripristis murdjan)

Climbing perch (Anabas testudineus reference strain)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

European seabass (Dicentrarchus labrax)

Turbot (Scophthalmus maximus)

Pike-perch (Sander lucioperca)

Fugu (Takifugu rubripes)

Mexican tetra (Astyanax mexicanus)

Atlantic salmon (Salmo salar)

Tetraodon (Tetraodon nigroviridis)

Midas cichlid (Amphilophus citrinellus)

Chinese medaka (Oryzias sinensis)

Denticle herring (Denticeps clupeoides reference strain)

Ballan wrasse (Labrus bergylta)

Large yellow croaker (Larimichthys crocea)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Tropical clawed frog (Xenopus tropicalis)

Leishan spiny toad (Leptobrachium leishanense)

Common wombat (Vombatus ursinus)

Wallaby (Notamacropus eugenii)

Koala (Phascolarctos cinereus)

Tasmanian devil (Sarcophilus harrisii)

Opossum (Monodelphis domestica)

Panamanian white-faced capuchin (Cebus imitator)

Dog (Canis lupus familiaris reference breed)

White-tufted-ear marmoset (Callithrix jacchus)

Chacoan peccary (Catagonus wagneri)

Gorilla (Gorilla gorilla gorilla)

Yarkand deer (Cervus hanglu yarkandensis)

Ferret (Mustela putorius furo)

Ma's night monkey (Aotus nancymaae)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Crab-eating macaque (Macaca fascicularis)

Tree Shrew (Tupaia belangeri)

Mouse (Mus musculus reference (CL57BL6) strain)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Horse (Equus caballus breed thoroughbred)

Alpine marmot (Marmota marmota marmota)

Naked mole-rat female (Heterocephalus glaber reference strain)

Beluga whale (Delphinapterus leucas)

Donkey (Equus asinus reference breed)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Red fox (Vulpes vulpes)

Cat (Felis catus)

Golden Hamster (Mesocricetus auratus)

Human (Homo sapiens)

Pig (Sus scrofa reference breed)

Black snub-nosed monkey (Rhinopithecus bieti)

Olive baboon (Papio anubis)

Drill (Mandrillus leucophaeus)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Narwhal (Monodon monoceros)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Pig-tailed macaque (Macaca nemestrina)

Arctic ground squirrel (Urocitellus parryii)

Tarsier (Carlito syrichta)

American bison (Bison bison bison)

Coquerel's sifaka (Propithecus coquereli)

Sloth (Choloepus hoffmanni)

Prairie vole (Microtus ochrogaster)

Hyrax (Procavia capensis)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Gibbon (Nomascus leucogenys)

Siberian musk deer (Moschus moschiferus)

Sheep (Ovis aries reference breed)

Squirrel (Ictidomys tridecemlineatus)

Eurasian red squirrel (Sciurus vulgaris)

Vaquita (Phocoena sinus)

Sperm whale (Physeter catodon)

Mouse Lemur (Microcebus murinus)

Sumatran orangutan (Pongo abelii)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Cow (Bos taurus reference breed)

Rabbit (Oryctolagus cuniculus)

Degu (Octodon degus)

Arabian camel (Camelus dromedarius)

Bushbaby (Otolemur garnettii)

Sooty mangabey (Cercocebus atys)

Bonobo (Pan paniscus)

Armadillo (Dasypus novemcinctus)

Megabat (Pteropus vampyrus)

American black bear (Ursus americanus)

Wild yak (Bos mutus)

Hedgehog (Erinaceus europaeus)

Guinea Pig (Cavia porcellus)

Long-tailed chinchilla (Chinchilla lanigera)

Giant panda (Ailuropoda melanoleuca reference isolate)

Blue whale (Balaenoptera musculus)

Elephant (Loxodonta africana)

Leopard (Panthera pardus)

Kangaroo rat (Dipodomys ordii)

Lesser Egyptian jerboa (Jaculus jaculus)

Chimpanzee (Pan troglodytes)

Alpaca (Vicugna pacos)

Greater bamboo lemur (Prolemur simus)

Lion (Panthera leo)

Dolphin (Tursiops truncatus)

Microbat (Myotis lucifugus)

Goat (Capra hircus reference breed)

Tiger (Panthera tigris altaica)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Vervet-AGM (Chlorocebus sabaeus)

Lesser hedgehog tenrec (Echinops telfairi)

Shrew (Sorex araneus)

Pika (Ochotona princeps)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Steppe mouse (Mus spicilegus)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Dingo (Canis lupus dingo)

Macaque (Macaca mulatta)

Polar bear (Ursus maritimus)

Domestic yak (Bos grunniens)

American mink (Neogale vison)

Platypus (Ornithorhynchus anatinus)

Green anole (Anolis carolinensis reference strain)

Pink-footed goose (Anser brachyrhynchus)

Goodes thornscrub tortoise (Gopherus evgoodei)

Kakapo (Strigops habroptila)

Painted turtle (Chrysemys picta bellii)

Australian saltwater crocodile (Crocodylus porosus)

Zebra finch (Taeniopygia guttata)

Medium ground-finch (Geospiza fortis)

Chicken (Gallus gallus reference breed)

Golden eagle (Aquila chrysaetos chrysaetos)

Common wall lizard (Podarcis muralis)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Turkey (Meleagris gallopavo reference strain)

Mainland tiger snake (Notechis scutatus)

African ostrich (Struthio camelus australis)

Collared flycatcher (Ficedula albicollis)

Argentine black and white tegu (Salvator merianae)

Indian cobra (Naja naja)

Blue-ringed sea krait (Laticauda laticaudata)

Great Tit (Parus major)

Tuatara (Sphenodon punctatus)

Duck (Anas platyrhynchos platyrhynchos)

Japanese quail (Coturnix japonica)

Chinese softshell turtle (Pelodiscus sinensis)

Eastern brown snake (Pseudonaja textilis)

Three-toed box turtle (Terrapene carolina triunguis)

Common canary (Serinus canaria)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)