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

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

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

Penaeus vannamei (Pacific white shrimp) (Penaeus vannamei)

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

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

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

Eurytemora carolleeae (Crustaceans) - GCF_000591075.1 [RefSeq annotation] (Eurytemora carolleeae)

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

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

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)

Anopheles darlingi (American malaria mosquito) - GCA_943734745.1 (Anopheles darlingi)

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

Cydia pomonella (The codling moth, Wapato2018A) - GCF_033807575.1 [RefSeq annotation] (Cydia pomonella isolate Wapato2018A)

Spodoptera frugiperda (Fall armyworm, SF20-4) (Spodoptera frugiperda strain SF20-4)

Apis dorsata (Giant honeybee) (Apis dorsata)

Tribolium madens (Black flour beetle, multiple individuals) (Tribolium madens strain multiple individuals)

Halyomorpha halys (Brown marmorated stink bug, HHAL.00) (Halyomorpha halys strain HHAL.00)

Strigamia maritima (Soil centipede) (Strigamia maritima)

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

Limulus polyphemus (Atlantic horseshoe crab) (Limulus polyphemus)

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

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

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

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

Gordionus sp. m RMFG-2023 (Horsehair worms) - GCF_954871325.1 [RefSeq annotation] (Gordionus sp. m RMFG-2023)

Priapulus caudatus (Penis worm) (Priapulus caudatus)

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

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

Biomphalaria glabrata (Bloodfluke planorb) - GCA_947242115.1 (Biomphalaria glabrata)

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

Lottia gigantea (Owl limpet) (Lottia gigantea)

Magallana gigas (Bivalves) - GCF_963853765.1 [RefSeq annotation] (Magallana gigas)

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

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

Dimorphilus gyrociliatus (Segmented worms) (Dimorphilus gyrociliatus)

Owenia fusiformis (Segmented worms) (Owenia fusiformis)

Helobdella robusta (Freshwater leech) (Helobdella robusta)

Echinococcus granulosus (Dog tapeworm) (Echinococcus granulosus)

Schistosoma mansoni (Flatworm) (Schistosoma mansoni)

Lineus longissimus (Bootlace worm, reference) (Lineus longissimus reference strain)

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

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

Adineta vaga (Rotifer) (Adineta vaga)

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

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

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

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

Asterias rubens (European starfish) (Asterias rubens)

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)

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

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

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

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

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

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

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

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

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

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)

Halichondria panicea (Sponges) - GCF_963675165.1 [RefSeq annotation] (Halichondria panicea)