Statistics on protein trees

The protein tree pipeline is described at the following page.

• Overview
• Gene tree coverage and Gene QC 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
	Gene QC	Validated genes	Short genes	Long genes	Split genes

Echinococcus granulosus (Dog tapeworm) (Echinococcus granulosus)

Schistosoma mansoni (Flatworm) (Schistosoma mansoni)

Owenia fusiformis (Segmented worms) (Owenia fusiformis)

Dimorphilus gyrociliatus (Segmented worms) (Dimorphilus gyrociliatus)

Helobdella robusta (Freshwater leech) (Helobdella robusta)

Crassostrea gigas (Pacific oyster) (Crassostrea gigas)

Mizuhopecten yessoensis (Yesso scallop, PY_sf001) (Mizuhopecten yessoensis strain PY_sf001)

Haliotis rufescens (Red abalone, VD_foot) (Haliotis rufescens strain VD_foot)

Haliotis rubra (Blacklip abalone, DU_JTF1) (Haliotis rubra strain DU_JTF1)

Lottia gigantea (Owl limpet) (Lottia gigantea)

Gigantopelta aegis (Deep sea snail, Gae_Host) (Gigantopelta aegis strain Gae_Host)

Biomphalaria glabrata (Bloodfluke planorb, BB02) (Biomphalaria glabrata strain BB02)

Octopus bimaculoides (California two-spot octopus, UCB-OBI-ISO-001) (Octopus bimaculoides strain UCB-OBI-ISO-001)

Pomphorhynchus laevis (Thorny-headed worm, GPI110) (Pomphorhynchus laevis strain GPI110)

Lingula anatina (Lamp shell, Amm_Jpn) (Lingula anatina strain Amm_Jpn)

Adineta vaga (Rotifer) (Adineta vaga)

Hypsibius exemplaris (Water bear tardigrade, Z151) (Hypsibius exemplaris strain Z151)

Paramacrobiotus metropolitanus (Water bear tardigrade, TYO) (Paramacrobiotus metropolitanus strain TYO)

Daphnia magna (Fresh water planktonic, NIES) (Daphnia magna strain NIES)

Daphnia pulex (Common water flea, KAP4) (Daphnia pulex strain KAP4)

Daphnia pulicaria (Water flea, SC F1-1A) (Daphnia pulicaria strain SC F1-1A)

Pollicipes pollicipes (Goose neck barnacle, AB1234) (Pollicipes pollicipes strain AB1234)

Amphibalanus amphitrite (Acorn barnacle, SeventyFive) (Amphibalanus amphitrite strain SeventyFive)

Homarus americanus (American lobster, GMGI-L3) (Homarus americanus strain GMGI-L3)

Homarus gammarus (European lobster, reference) (Homarus gammarus reference strain)

Procambarus clarkii (Red swamp crayfish, Jiangsu) (Procambarus clarkii strain Jiangsu)

Portunus trituberculatus (Swimming crab, SZX2019) (Portunus trituberculatus strain SZX2019)

Penaeus chinensis (Fleshy prawn) (Penaeus chinensis)

Penaeus vannamei (Pacific white shrimp) (Penaeus vannamei)

Penaeus japonicus (Kuruma shrimp, Ginoza2017) (Penaeus japonicus strain Ginoza2017)

Penaeus monodon (Black tiger shrimp, SGIC_2016) (Penaeus monodon strain SGIC_2016)

Hyalella azteca (Amphipod, HAZT.00-mixed) (Hyalella azteca strain HAZT.00-mixed)

Tigriopus californicus (Copepod, San Diego) (Tigriopus californicus strain San Diego)

Lepeophtheirus salmonis (Salmon louse, Lsal2020) (Lepeophtheirus salmonis strain Lsal2020)

Eurytemora affinis (Calanoid copepod, Atlantic clade) (Eurytemora affinis strain Atlantic clade)

Schistocerca americana (American grasshopper, TAMUIC-IGC-003095) (Schistocerca americana strain TAMUIC-IGC-003095)

Zootermopsis nevadensis (Nevada dampwood termite) (Zootermopsis nevadensis)

Acyrthosiphon pisum (Pea aphid, AL4f) (Acyrthosiphon pisum strain AL4f)

Cimex lectularius (Bed bug, Harlan) (Cimex lectularius strain Harlan)

Bombus terrestris (Buff-tailed bumblebee) (Bombus terrestris Bter_1.0)

Bombus terrestris (buff-tailed bumblebee, reference) (Bombus terrestris reference strain)

Apis mellifera (Honey bee, DH4) (Apis mellifera strain DH4)

Drosophila melanogaster (Fruit fly) (Drosophila melanogaster)

Anopheles gambiae (African malaria mosquito, PEST) (Anopheles gambiae strain PEST)

Bombyx mori (Domestic silkworm, p50T) (Bombyx mori strain p50T)

Tribolium castaneum (Red flour beetle, Georgia GA2) (Tribolium castaneum strain Georgia GA2)

Strigamia maritima (Soil centipede) (Strigamia maritima)

Limulus polyphemus (Atlantic horseshoe crab) (Limulus polyphemus)

Ixodes scapularis (Black-legged tick, PalLabHiFi) (Ixodes scapularis strain PalLabHiFi)

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

Loa loa (Eye worm, Cameroon SouthWest Province isolate) (Loa loa strain Cameroon SouthWest Province isolate)

Priapulus caudatus (Penis worm) (Priapulus caudatus)

Lytechinus variegatus (Green sea urchin, NC3) (Lytechinus variegatus strain NC3)

Lytechinus pictus (Painted urchin, DCL-2020) (Lytechinus pictus strain DCL-2020)

Strongylocentrotus purpuratus (Purple sea urchin, Spur 01) (Strongylocentrotus purpuratus strain Spur 01)

Asterias rubens (European starfish) (Asterias rubens)

Acanthaster planci (Crown-of-thorns starfish) (Acanthaster planci)

Anneissia japonica (Sea lily, Jap-2015-1) (Anneissia japonica strain Jap-2015-1)

Branchiostoma lanceolatum (Amphioxus) (Branchiostoma lanceolatum)

Saccoglossus kowalevskii (Acorn worm) (Saccoglossus kowalevskii)

Hofstenia miamia (Panther worm, MS-H3) (Hofstenia miamia strain MS-H3)

Hydra vulgaris (Swiftwater hydra, 105) (Hydra vulgaris strain 105)

Clytia hemisphaerica (Jellyfish, Z4C2) (Clytia hemisphaerica strain Z4C2)

Stylophora pistillata (Hood coral, CSM Monaco) (Stylophora pistillata strain CSM Monaco)

Acropora millepora (Stony coral, JS-1) (Acropora millepora strain JS-1)

Orbicella faveolata (Mountainous star coral, FL) (Orbicella faveolata strain FL)

Exaiptasia diaphana (Sea anemone, CC7) (Exaiptasia diaphana strain CC7)

Nematostella vectensis (Starlet sea anemone, CH2 x CH6) (Nematostella vectensis strain CH2 x CH6)

Actinia equina (Beadlet anemone, AE1) (Actinia equina strain AE1)

Dendronephthya gigantea (Carnation coral, DGI-Jeju-01) (Dendronephthya gigantea strain DGI-Jeju-01)

Thelohanellus kitauei (Myxozoan endoparasite) (Thelohanellus kitauei)

Mnemiopsis leidyi (Warty comb jelly) (Mnemiopsis leidyi)

Trichoplax adhaerens (Placozoa, Grell-BS-1999) (Trichoplax adhaerens strain Grell-BS-1999)

Amphimedon queenslandica (Demosponge) (Amphimedon queenslandica)