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

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Zig-zag eel (Mastacembelus armatus)

Tiger tail seahorse (Hippocampus comes)

Brown trout (Salmo trutta)

Makobe Island cichlid (Pundamilia nyererei)

Denticle herring (Denticeps clupeoides)

Barramundi perch (Lates calcarifer)

Channel bull blenny (Cottoperca gobio)

Lumpfish (Cyclopterus lumpus)

Yellowtail amberjack (Seriola lalandi dorsalis)

Lyretail cichlid (Neolamprologus brichardi)

Indian medaka (Oryzias melastigma)

Mexican tetra (Astyanax mexicanus)

Monterrey platyfish (Xiphophorus couchianus)

Tetraodon (Tetraodon nigroviridis)

Amazon molly (Poecilia formosa)

Huchen (Hucho hucho)

Fugu (Takifugu rubripes)

Greater amberjack (Seriola dumerili)

Turbot (Scophthalmus maximus)

Nile tilapia (Oreochromis niloticus)

Zebra mbuna (Maylandia zebra)

Japanese medaka HdrR (Oryzias latipes)

Midas cichlid (Amphilophus citrinellus)

Mangrove rivulus (Kryptolebias marmoratus)

Clown anemonefish (Amphiprion ocellaris)

Mummichog (Fundulus heteroclitus)

Orange clownfish (Amphiprion percula)

Atlantic herring (Clupea harengus)

Tongue sole (Cynoglossus semilaevis)

Spiny chromis (Acanthochromis polyacanthus)

Atlantic cod (Gadus morhua)

Pike-perch (Sander lucioperca)

Bicolor damselfish (Stegastes partitus)

Sailfin molly (Poecilia latipinna)

Large yellow croaker (Larimichthys crocea)

Red-bellied piranha (Pygocentrus nattereri)

Chinese medaka (Oryzias sinensis)

Electric eel (Electrophorus electricus)

Goldfish (Carassius auratus)

Common carp (Cyprinus carpio carpio)

Pinecone soldierfish (Myripristis murdjan)

European seabass (Dicentrarchus labrax)

Stickleback (Gasterosteus aculeatus)

Gilthead seabream (Sparus aurata)

Northern pike (Esox lucius)

Eastern happy (Astatotilapia calliptera)

Rainbow trout (Oncorhynchus mykiss)

Channel catfish (Ictalurus punctatus)

Atlantic salmon (Salmo salar)

Climbing perch (Anabas testudineus)

Sheepshead minnow (Cyprinodon variegatus)

Coho salmon (Oncorhynchus kisutch)

Chinook salmon (Oncorhynchus tshawytscha)

Siamese fighting fish (Betta splendens)

Ballan wrasse (Labrus bergylta)

Platyfish (Xiphophorus maculatus)

Turquoise killifish (Nothobranchius furzeri)

Guppy (Poecilia reticulata)

Zebrafish (Danio rerio)

Burton's mouthbrooder (Haplochromis burtoni)

Javanese ricefish (Oryzias javanicus)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Wallaby (Notamacropus eugenii)

Koala (Phascolarctos cinereus)

Common wombat (Vombatus ursinus)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Rabbit (Oryctolagus cuniculus)

Golden Hamster (Mesocricetus auratus)

Blue whale (Balaenoptera musculus)

Armadillo (Dasypus novemcinctus)

Macaque (Macaca mulatta)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Wild yak (Bos mutus)

Vervet-AGM (Chlorocebus sabaeus)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Red fox (Vulpes vulpes)

Dolphin (Tursiops truncatus)

Pig (Sus scrofa reference breed)

Elephant (Loxodonta africana)

Domestic yak (Bos grunniens)

Mouse Lemur (Microcebus murinus)

Pig-tailed macaque (Macaca nemestrina)

Shrew (Sorex araneus)

Sumatran orangutan (Pongo abelii)

White-tufted-ear marmoset (Callithrix jacchus)

Panamanian white-faced capuchin (Cebus imitator)

Narwhal (Monodon monoceros)

Bushbaby (Otolemur garnettii)

Olive baboon (Papio anubis)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Siberian musk deer (Moschus moschiferus)

Lesser hedgehog tenrec (Echinops telfairi)

Sheep (Ovis aries reference breed)

Ferret (Mustela putorius furo)

Degu (Octodon degus)

Mouse (Mus musculus reference (CL57BL6) strain)

Crab-eating macaque (Macaca fascicularis)

Upper Galilee mountains blind mole rat (Nannospalax galili)

American mink (Neogale vison)

Arctic ground squirrel (Urocitellus parryii)

Cat (Felis catus)

Lesser Egyptian jerboa (Jaculus jaculus)

Sloth (Choloepus hoffmanni)

Giant panda (Ailuropoda melanoleuca reference isolate)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Tiger (Panthera tigris altaica)

Naked mole-rat female (Heterocephalus glaber reference strain)

Leopard (Panthera pardus)

Squirrel (Ictidomys tridecemlineatus)

Eurasian red squirrel (Sciurus vulgaris)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

American black bear (Ursus americanus)

Algerian mouse (Mus spretus strain SPRET/EiJ)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Hyrax (Procavia capensis)

Dingo (Canis lupus dingo)

Megabat (Pteropus vampyrus)

Human (Homo sapiens)

Black snub-nosed monkey (Rhinopithecus bieti)

Greater bamboo lemur (Prolemur simus)

Drill (Mandrillus leucophaeus)

Long-tailed chinchilla (Chinchilla lanigera)

Lion (Panthera leo)

Polar bear (Ursus maritimus)

Horse (Equus caballus breed thoroughbred)

Gibbon (Nomascus leucogenys)

Chimpanzee (Pan troglodytes)

Rat (Rattus norvegicus strain BN/NHsdMcwi)

Beluga whale (Delphinapterus leucas)

Chacoan peccary (Catagonus wagneri)

Sperm whale (Physeter catodon)

Pika (Ochotona princeps)

Coquerel's sifaka (Propithecus coquereli)

Vaquita (Phocoena sinus)

Donkey (Equus asinus reference breed)

Cow (Bos taurus reference breed)

Alpine marmot (Marmota marmota marmota)

Alpaca (Vicugna pacos)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Goat (Capra hircus reference breed)

Tarsier (Carlito syrichta)

Gorilla (Gorilla gorilla gorilla)

Arabian camel (Camelus dromedarius)

Hedgehog (Erinaceus europaeus)

Steppe mouse (Mus spicilegus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Tree Shrew (Tupaia belangeri)

Dog (Canis lupus familiaris reference breed)

Yarkand deer (Cervus hanglu yarkandensis)

Sooty mangabey (Cercocebus atys)

Guinea Pig (Cavia porcellus)

Prairie vole (Microtus ochrogaster)

Bonobo (Pan paniscus)

Ma's night monkey (Aotus nancymaae)

Microbat (Myotis lucifugus)

Kangaroo rat (Dipodomys ordii)

American bison (Bison bison bison)

Platypus (Ornithorhynchus anatinus)

Common canary (Serinus canaria)

Collared flycatcher (Ficedula albicollis)

Three-toed box turtle (Terrapene carolina triunguis)

Green anole (Anolis carolinensis reference strain)

Painted turtle (Chrysemys picta bellii)

Blue-ringed sea krait (Laticauda laticaudata)

Turkey (Meleagris gallopavo reference strain)

Chicken (Gallus gallus reference breed)

Mainland tiger snake (Notechis scutatus)

Australian saltwater crocodile (Crocodylus porosus)

Duck (Anas platyrhynchos platyrhynchos)

Zebra finch (Taeniopygia guttata)

Medium ground-finch (Geospiza fortis)

Goodes thornscrub tortoise (Gopherus evgoodei)

Great Tit (Parus major)

African ostrich (Struthio camelus australis)

Abingdon island giant tortoise (Chelonoidis abingdonii)

Common wall lizard (Podarcis muralis)

Indian cobra (Naja naja)

Argentine black and white tegu (Salvator merianae)

Japanese quail (Coturnix japonica)

Eastern brown snake (Pseudonaja textilis)

Pink-footed goose (Anser brachyrhynchus)

Tuatara (Sphenodon punctatus)

Kakapo (Strigops habroptila)

Chinese softshell turtle (Pelodiscus sinensis)

Golden eagle (Aquila chrysaetos chrysaetos)

Coelacanth (Latimeria chalumnae)

Elephant shark (Callorhinchus milii)

Lamprey (Petromyzon marinus)

Hagfish (Eptatretus burgeri)

C.savignyi (Ciona savignyi)

C.intestinalis (Ciona intestinalis)

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

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)