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

Alpaca (Vicugna pacos)

Alpine marmot (Marmota marmota marmota)

American bison (Bison bison bison)

American black bear (Ursus americanus)

American mink (Neogale vison)

Arabian camel (Camelus dromedarius)

Arctic ground squirrel (Urocitellus parryii)

Armadillo (Dasypus novemcinctus)

Beluga whale (Delphinapterus leucas)

Black snub-nosed monkey (Rhinopithecus bieti)

Blue whale (Balaenoptera musculus)

Bolivian squirrel monkey (Saimiri boliviensis boliviensis)

Bonobo (Pan paniscus)

Bushbaby (Otolemur garnettii)

Cattle (Bos taurus reference breed)

Chacoan peccary (Catagonus wagneri)

Chimpanzee (Pan troglodytes)

Chinese hamster CHOK1GS (Cricetulus griseus CHOK1GS_HDv1)

Coquerel's sifaka (Propithecus coquereli)

Crab-eating macaque (Macaca fascicularis)

Degu (Octodon degus)

Dingo (Canis lupus dingo)

Dog (Canis lupus familiaris reference breed)

Dolphin (Tursiops truncatus)

Domestic cat (Felis catus reference strain)

Domestic yak (Bos grunniens)

Donkey (Equus asinus reference breed)

Drill (Mandrillus leucophaeus)

Elephant (Loxodonta africana)

Eurasian red squirrel (Sciurus vulgaris)

Ferret (Mustela putorius furo)

Giant panda (Ailuropoda melanoleuca reference isolate)

Gibbon (Nomascus leucogenys)

Goat (Capra hircus reference breed)

Golden Hamster (Mesocricetus auratus)

Golden snub-nosed monkey (Rhinopithecus roxellana)

Gorilla (Gorilla gorilla gorilla)

Greater bamboo lemur (Prolemur simus)

Greater horseshoe bat (Rhinolophus ferrumequinum)

Guinea Pig (Cavia porcellus)

Hedgehog (Erinaceus europaeus)

Horse (Equus caballus breed thoroughbred)

Human (Homo sapiens)

Hybrid - Bos Indicus (Bos indicus x Bos taurus)

Hyrax (Procavia capensis)

Kangaroo rat (Dipodomys ordii)

Leopard (Panthera pardus)

Lesser Egyptian jerboa (Jaculus jaculus)

Lesser hedgehog tenrec (Echinops telfairi)

Lion (Panthera leo)

Long-tailed chinchilla (Chinchilla lanigera)

Ma's night monkey (Aotus nancymaae)

Macaque (Macaca mulatta)

Megabat (Pteropus vampyrus)

Microbat (Myotis lucifugus)

Mouse (Mus musculus reference (CL57BL6) strain)

Mouse Lemur (Microcebus murinus)

Naked mole-rat female (Heterocephalus glaber reference strain)

Narwhal (Monodon monoceros)

Northern American deer mouse (Peromyscus maniculatus bairdii)

Norway rat - BN/NHsdMcwi (Rattus norvegicus reference strain)

Olive baboon (Papio anubis)

Panamanian white-faced capuchin (Cebus imitator)

Pig (Sus scrofa reference breed)

Pig-tailed macaque (Macaca nemestrina)

Pika (Ochotona princeps)

Polar bear (Ursus maritimus)

Prairie vole (Microtus ochrogaster)

Rabbit (Oryctolagus cuniculus)

Red fox (Vulpes vulpes)

Ryukyu mouse (Mus caroli strain CAROLI_EIJ)

Sheep (Ovis aries reference breed)

Shrew (Sorex araneus)

Shrew mouse (Mus pahari strain PAHARI_EIJ)

Siberian musk deer (Moschus moschiferus)

Sloth (Choloepus hoffmanni)

Sooty mangabey (Cercocebus atys)

Sperm whale (Physeter catodon)

Squirrel (Ictidomys tridecemlineatus)

Steppe mouse (Mus spicilegus)

Sumatran orangutan (Pongo abelii)

Tarsier (Carlito syrichta)

Tiger (Panthera tigris altaica)

Tree Shrew (Tupaia belangeri)

Upper Galilee mountains blind mole rat (Nannospalax galili)

Vaquita (Phocoena sinus)

Vervet-AGM (Chlorocebus sabaeus)

Western wild mouse (Mus spretus reference strain)

White-tufted-ear marmoset (Callithrix jacchus)

Wild yak (Bos mutus)

Yarkand deer (Cervus hanglu yarkandensis)

Common wombat (Vombatus ursinus)

Koala (Phascolarctos cinereus)

Wallaby (Notamacropus eugenii)

Opossum (Monodelphis domestica)

Tasmanian devil (Sarcophilus harrisii)

Platypus (Ornithorhynchus anatinus)

Abingdon island giant tortoise (Chelonoidis abingdonii)

African ostrich (Struthio camelus australis)

Argentine black and white tegu (Salvator merianae)

Australian saltwater crocodile (Crocodylus porosus)

Blue-ringed sea krait (Laticauda laticaudata)

Chicken (Gallus gallus reference breed)

Chinese softshell turtle (Pelodiscus sinensis)

Collared flycatcher (Ficedula albicollis)

Common canary (Serinus canaria)

Common wall lizard (Podarcis muralis)

Duck (Anas platyrhynchos platyrhynchos)

Eastern brown snake (Pseudonaja textilis)

Golden eagle (Aquila chrysaetos chrysaetos)

Goodes thornscrub tortoise (Gopherus evgoodei)

Great Tit (Parus major)

Green anole (Anolis carolinensis reference strain)

Indian cobra (Naja naja)

Japanese quail (Coturnix japonica)

Kakapo (Strigops habroptila)

Mainland tiger snake (Notechis scutatus)

Medium ground-finch (Geospiza fortis)

Painted turtle (Chrysemys picta bellii)

Pink-footed goose (Anser brachyrhynchus)

Three-toed box turtle (Terrapene triunguis)

Tuatara (Sphenodon punctatus)

Turkey (Meleagris gallopavo reference strain)

Zebra finch (Taeniopygia guttata)

Leishan spiny toad (Leptobrachium leishanense)

Tropical clawed frog (Xenopus tropicalis)

Coelacanth (Latimeria chalumnae)

Amazon molly (Poecilia formosa)

Atlantic cod (Gadus morhua)

Atlantic herring (Clupea harengus reference strain)

Atlantic salmon (Salmo salar)

Ballan wrasse (Labrus bergylta)

Barramundi perch (Lates calcarifer)

Bicolor damselfish (Stegastes partitus)

Brown trout (Salmo trutta)

Burton's mouthbrooder (Haplochromis burtoni)

Channel bull blenny (Cottoperca gobio)

Channel catfish (Ictalurus punctatus strain USDA103-YYmale1)

Chinese medaka (Oryzias sinensis)

Chinook salmon (Oncorhynchus tshawytscha reference strain)

Climbing perch (Anabas testudineus reference strain)

Clown anemonefish (Amphiprion ocellaris ecotype Okinawa)

Coho salmon (Oncorhynchus kisutch)

Common carp (Cyprinus carpio carpio)

Denticle herring (Denticeps clupeoides reference strain)

Eastern happy (Astatotilapia calliptera reference strain)

Electric eel (Electrophorus electricus reference strain)

European seabass (Dicentrarchus labrax)

Fugu (Takifugu rubripes)

Gilthead seabream (Sparus aurata)

Goldfish (Carassius auratus)

Greater amberjack (Seriola dumerili)

Guppy (Poecilia reticulata)

Huchen (Hucho hucho)

Indian medaka (Oryzias melastigma)

Japanese medaka HdrR (Oryzias latipes)

Javanese ricefish (Oryzias javanicus)

Large yellow croaker (Larimichthys crocea)

Lumpfish (Cyclopterus lumpus)

Lyretail cichlid (Neolamprologus brichardi)

Makobe Island cichlid (Pundamilia nyererei)

Mangrove rivulus (Kryptolebias marmoratus)

Mexican tetra (Astyanax mexicanus)

Midas cichlid (Amphilophus citrinellus)

Monterrey platyfish (Xiphophorus couchianus)

Mummichog (Fundulus heteroclitus)

Nile tilapia (Oreochromis niloticus)

Northern pike (Esox lucius reference strain)

Orange clownfish (Amphiprion percula)

Pike-perch (Sander lucioperca)

Pinecone soldierfish (Myripristis murdjan)

Platyfish (Xiphophorus maculatus)

Rainbow trout (Oncorhynchus mykiss)

Red-bellied piranha (Pygocentrus nattereri reference strain)

Sailfin molly (Poecilia latipinna)

Sheepshead minnow (Cyprinodon variegatus)

Siamese fighting fish (Betta splendens)

Spiny chromis (Acanthochromis polyacanthus)

Stickleback (Gasterosteus aculeatus aculeatus reference strain)

Tetraodon (Tetraodon nigroviridis)

Tiger tail seahorse (Hippocampus comes)

Tongue sole (Cynoglossus semilaevis)

Turbot (Scophthalmus maximus)

Turquoise killifish (Nothobranchius furzeri)

Yellowtail amberjack (Seriola lalandi dorsalis)

Zebra mbuna (Maylandia zebra)

Zebrafish (Danio rerio)

Zig-zag eel (Mastacembelus armatus)

Asian bonytongue (Scleropages formosus)

Paramormyrops kingsleyae (Paramormyrops kingsleyae)

Spotted gar (Lepisosteus oculatus)

Reedfish (Erpetoichthys calabaricus)

Elephant shark (Callorhinchus milii)

Hagfish (Eptatretus burgeri)

Lamprey (Petromyzon marinus)

C.intestinalis (Ciona intestinalis)

C.savignyi (Ciona savignyi)

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

Drosophila melanogaster (Fruit fly) - GCA_000001215.4 [FlyBase annotation] (Drosophila melanogaster)

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288C)