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

Hydra vulgaris (Swiftwater hydra, 105) - GCA_022113875.1 (Hydra vulgaris strain 105)

Clytia hemisphaerica (Z4C2) (Clytia hemisphaerica strain Z4C2)

Pocillopora damicornis (RSMAS) - GCA_003704095.1 (Pocillopora damicornis strain RSMAS)

Stylophora pistillata (CSM Monaco) - GCA_002571385.1 (Stylophora pistillata strain CSM Monaco)

Acropora millepora (Stony coral, JS-1) - GCA_013753865.1 (Acropora millepora strain JS-1)

Orbicella faveolata (Mountainous star coral, FL) - GCA_002042975.1 (Orbicella faveolata strain FL)

Actinia tenebrosa (Australian red waratah sea anemone) - GCA_009602425.1 (Actinia tenebrosa)

Actinia equina (AE1) - GCA_011057435.1 (Actinia equina strain AE1)

Exaiptasia diaphana (Sea anemone, CC7) - GCA_001417965.1 (Exaiptasia diaphana strain CC7)

Nematostella vectensis (Nematostella vectensis strain CH2 x CH6)

Thelohanellus kitauei (Thelohanellus kitauei)

Lingula anatina (Lamp shell (Brachiopod), Amm_Jpn) - GCA_001039355.2 (Lingula anatina strain Amm_Jpn)

Lingula anatina (Lingula anatina LinAna1.0)

Owenia fusiformis (Segmented worms) - GCA_903813345.1 (Owenia fusiformis)

Capitella teleta (Capitella teleta)

Dimorphilus gyrociliatus (Segmented worms) - GCA_904063045.1 (Dimorphilus gyrociliatus)

Helobdella robusta (Helobdella robusta)

Schistosoma mansoni (PRJEA36577) (Schistosoma mansoni)

Hymenolepis microstoma (PRJEB124) (Hymenolepis microstoma)

Crassostrea gigas (Pacific oyster) - GCA_902806645.1 (Crassostrea gigas)

Crassostrea virginica (RU13XGHG1-28) - GCA_002022765.4 (Crassostrea virginica strain RU13XGHG1-28)

Mizuhopecten yessoensis (Yesso scallop, PY_sf001) - GCA_002113885.2 (Mizuhopecten yessoensis strain PY_sf001)

Mercenaria mercenaria (Hard clam (quahog), YKG-2019) - GCA_014805675.2 (Mercenaria mercenaria strain YKG-2019)

Octopus bimaculoides (Octopus bimaculoides PRJNA270931)

Octopus bimaculoides (Octopus, UCB-OBI-ISO-001) - GCA_001194135.1 (Octopus bimaculoides strain UCB-OBI-ISO-001)

Octopus sinensis (East Asian common octopus) - GCA_006345805.1 (Octopus sinensis)

Aplysia californica (California sea hare, F4 #8) - GCA_000002075.2 (Aplysia californica strain F4 #8)

Biomphalaria glabrata (Biomphalaria glabrata strain BB02)

Pomacea canaliculata (SZHN2017) - GCA_003073045.1 (Pomacea canaliculata strain SZHN2017)

Gigantopelta aegis (Deep sea snail, Gae_Host) - GCA_016097555.1 (Gigantopelta aegis strain Gae_Host)

Lottia gigantea (Lottia gigantea)

Adineta vaga (Adineta vaga)

Folsomia candida str. VU population (Folsomia candida)

Orchesella cincta (Orchesella cincta)

Acyrthosiphon pisum (AL4f) (Acyrthosiphon pisum strain AL4f)

Diuraphis noxia (RWA2) - GCA_001186385.1 (Diuraphis noxia strain RWA2)

Rhopalosiphum maidis (BTI-1) - GCA_003676215.3 (Rhopalosiphum maidis strain BTI-1)

Sipha flava (LNK) - GCA_003268045.1 (Sipha flava strain LNK)

Trialeurodes vaporariorum (IVF) (Trialeurodes vaporariorum strain IVF)

Rhodnius prolixus (Rhodnius prolixus strain CDC)

Cimex lectularius (Harlan) (Cimex lectularius strain Harlan)

Pediculus humanus (Pediculus humanus corporis strain USDA)

Diabrotica virgifera virgifera (Ped12-6-A-3) - GCA_003013835.2 (Diabrotica virgifera virgifera strain Ped12-6-A-3)

Leptinotarsa decemlineata (Colorado potato beetle, Imidocloprid resistant) - GCA_000500325.2 (Leptinotarsa decemlineata strain Imidocloprid resistant)

Anoplophora glabripennis (ALB-LARVAE) (Anoplophora glabripennis strain ALB-LARVAE)

Dendroctonus ponderosae (Mountain pine beetle) - GCA_000355655.1 (Dendroctonus ponderosae)

Tribolium castaneum (Tribolium castaneum strain Georgia GA2)

Agrilus planipennis (Emerald ash borer, EAB-ADULT) - GCA_000699045.2 (Agrilus planipennis strain EAB-ADULT)

Bactrocera tryoni (Queensland fruitfly, S06) - GCA_016617805.2 (Bactrocera tryoni strain S06)

Bactrocera dorsalis (Oriental fruit fly, Punador) - GCA_000789215.2 (Bactrocera dorsalis strain Punador)

Ceratitis capitata (Mediterranean fruit fly) - GCA_000347755.4 (Ceratitis capitata)

Rhagoletis pomonella (Grant_MI) - GCA_013731165.1 (Rhagoletis pomonella strain Grant_MI)

Teleopsis dalmanni (2A) (Teleopsis dalmanni strain 2A)

Drosophila melanogaster (Drosophila melanogaster)

Musca domestica (Musca domestica strain aabys)

Stomoxys calcitrans (Stomoxys calcitrans strain USDA)

Glossina fuscipes (IAEA_lab_2018) (Glossina fuscipes strain IAEA_lab_2018)

Glossina palpalis (Glossina palpalis gambiensis strain IAEA)

Glossina pallidipes (Glossina pallidipes strain IAEA)

Glossina austeni (Glossina austeni strain TTRI)

Glossina morsitans (Glossina morsitans morsitans strain Yale)

Glossina brevipalpis (Glossina brevipalpis strain IAEA)

Lucilia cuprina (Lucilia cuprina strain LS)

Megaselia scalaris (Megaselia scalaris)

Hermetia illucens (Black soldier fly) - GCA_905115235.1 (Hermetia illucens)

Phlebotomus papatasi (Phlebotomus papatasi strain Israel)

Phlebotomus perniciosus (Murcia) - GCA_918844115.1 (Phlebotomus perniciosus strain Murcia)

Lutzomyia longipalpis (Lutzomyia longipalpis strain Jacobina)

Culicoides sonorensis (Culicoides sonorensis)

Belgica antarctica (Belgica antarctica)

Culex quinquefasciatus (Culex quinquefasciatus strain Johannesburg)

Culex quinquefasciatus (JHB) (Culex quinquefasciatus strain JHB)

Aedes albopictus (Aedes albopictus strain Foshan)

Aedes aegypti (LVP_AGWG) (Aedes aegypti strain LVP_AGWG)

Anopheles darlingi (Anopheles darlingi strain Coari)

Anopheles albimanus (Anopheles albimanus strain STECLA)

Anopheles sinensis (China) (Anopheles sinensis strain China)

Anopheles sinensis (Anopheles sinensis strain SINENSIS)

Anopheles atroparvus (EBRE) - GCA_914969975.1 (Anopheles atroparvus strain Infravec2 EBRE)

Anopheles stephensi (Anopheles stephensi strain SDA-500)

Anopheles stephensi (Indian) (Anopheles stephensi strain Indian)

Anopheles maculatus (Anopheles maculatus strain maculatus3)

Anopheles dirus (Anopheles dirus strain WRAIR2)

Anopheles farauti (Anopheles farauti strain FAR1)

Anopheles coluzzii (Ngousso) (Anopheles coluzzii strain Ngousso)

Anopheles coluzzii (Anopheles coluzzii strain Mali-NIH)

Anopheles gambiae (Anopheles gambiae strain PEST)

Anopheles melas (Anopheles melas strain CM1001059_A)

Anopheles merus (Anopheles merus strain MAF)

Anopheles quadriannulatus (Anopheles quadriannulatus strain SANGWE)

Anopheles arabiensis (Anopheles arabiensis strain Dongola)

Anopheles epiroticus (Anopheles epiroticus strain Epiroticus2)

Anopheles christyi (Anopheles christyi strain ACHKN1017)

Anopheles minimus (Anopheles minimus strain MINIMUS1)

Anopheles culicifacies (Anopheles culicifacies strain A-37)

Anopheles funestus (Anopheles funestus strain FUMOZ)

Mayetiola destructor (Mayetiola destructor strain Kansas Great Plain)

Monomorium pharaonis (Pharaoh ant, MP-MQ-018) - GCA_013373865.2 (Monomorium pharaonis strain MP-MQ-018)

Solenopsis invicta (M01_SB) (Solenopsis invicta strain M01_SB)

Atta cephalotes (Atta cephalotes)

Ooceraea biroi (Clonal raider ant, clonal line C1) - GCA_003672135.1 (Ooceraea biroi strain clonal line C1)

Bombus terrestris (Bombus terrestris)

Bombus impatiens (Bombus impatiens)

Apis mellifera (DH4) (Apis mellifera strain DH4)

Aphidius gifuensis (Parasitoid wasp, YNYX2018) - GCA_014905175.1 (Aphidius gifuensis strain YNYX2018)

Cotesia glomerata (CgM1) - GCA_020080835.1 (Cotesia glomerata strain CgM1)

Copidosoma floridanum (CFLO.00-Male) - GCA_000648655.2 (Copidosoma floridanum strain CFLO.00-Male)

Nasonia vitripennis (AsymCx) (Nasonia vitripennis strain AsymCx)

Trichogramma pretiosum (Unisexual culture from Peru) - GCA_000599845.3 (Trichogramma pretiosum strain Unisexual culture from Peru)

Orussus abietinus (Parasitic wood wasp, OABI.00-Male) - GCA_000612105.2 (Orussus abietinus strain OABI.00-Male)

Melitaea cinxia (Melitaea cinxia)

Heliconius melpomene (Heliconius melpomene)

Danaus plexippus plexippus (F-2) (Danaus plexippus plexippus strain F-2)

Bombyx mori (p50T) (Bombyx mori strain p50T)

Zootermopsis nevadensis (Zootermopsis nevadensis)

Daphnia magna (Fresh water planktonic, NIES) - GCA_020631705.2 (Daphnia magna strain NIES)

Daphnia pulex (Daphnia pulex)

Amphibalanus amphitrite (Acorn barnacle, SeventyFive) - GCA_019059575.1 (Amphibalanus amphitrite strain SeventyFive)

Pollicipes pollicipes (Goose neck barnacle, AB1234) - GCA_011947565.2 (Pollicipes pollicipes strain AB1234)

Homarus americanus (American lobster, GMGI-L3) - GCA_018991925.1 (Homarus americanus strain GMGI-L3)

Procambarus clarkii (Red swamp crayfish, Jiangsu) - GCA_020424385.2 (Procambarus clarkii strain Jiangsu)

Portunus trituberculatus (Swimming crab, SZX2019) - GCA_017591435.1 (Portunus trituberculatus strain SZX2019)

Penaeus japonicus (Kuruma shrimp, Ginoza2017) - GCA_017312705.1 (Penaeus japonicus strain Ginoza2017)

Penaeus monodon (SGIC_2016) - GCA_015228065.1 (Penaeus monodon strain SGIC_2016)

Penaeus vannamei (Pacific white shrimp) - GCA_003789085.1 (Penaeus vannamei)

Hyalella azteca (Amphipod, HAZT.00-mixed) - GCA_000764305.2 (Hyalella azteca strain HAZT.00-mixed)

Tigriopus californicus (San Diego) (Tigriopus californicus strain San Diego)

Lepeophtheirus salmonis (Lepeophtheirus salmonis)

Eurytemora affinis (Calanoid copepod, Atlantic clade) - GCA_000591075.2 (Eurytemora affinis strain Atlantic clade)

Strigamia maritima (Strigamia maritima)

Parasteatoda tepidariorum (Goettingen) - GCA_000365465.3 (Parasteatoda tepidariorum strain Goettingen)

Stegodyphus mimosarum (Stegodyphus mimosarum)

Ixodes scapularis (Ixodes scapularis strain Wikel)

Ixodes scapularis (PalLabHiFi) (Ixodes scapularis strain PalLabHiFi)

Rhipicephalus microplus (Rmic-2018) (Rhipicephalus microplus strain Rmic-2018)

Rhipicephalus sanguineus (Rsan-2018) (Rhipicephalus sanguineus strain Rsan-2018)

Dermacentor silvarum (Dsil-2018) (Dermacentor silvarum strain Dsil-2018)

Varroa destructor (Varroa destructor)

Dermatophagoides pteronyssinus (airmid) - GCA_001901225.2 (Dermatophagoides pteronyssinus strain airmid)

Sarcoptes scabiei (SSS_KF_BRIS2020) (Sarcoptes scabiei strain SSS_KF_BRIS2020)

Leptotrombidium deliense (Leptotrombidium deliense strain UoL-UT)

Dinothrombium tinctorium (Dinothrombium tinctorium strain UoL-WK)

Tetranychus urticae (Tetranychus urticae)

Centruroides sculpturatus (CEXI.00-Female) - GCA_000671375.2 (Centruroides sculpturatus strain CEXI.00-Female)

Limulus polyphemus (Atlantic horseshoe crab) - GCA_000517525.1 (Limulus polyphemus)

Hypsibius exemplaris (Water bear tardigrade, Z151) - GCA_002082055.1 (Hypsibius exemplaris strain Z151)

Caenorhabditis remanei (PRJNA53967) (Caenorhabditis remanei)

Caenorhabditis brenneri (PRJNA20035) (Caenorhabditis brenneri)

Caenorhabditis briggsae (PRJNA10731) (Caenorhabditis briggsae)

Caenorhabditis japonica (PRJNA12591) (Caenorhabditis japonica)

Caenorhabditis elegans (PRJNA13758) (Caenorhabditis elegans strain N2)

Pristionchus pacificus (PRJNA12644) (Pristionchus pacificus strain PS312)

Loa loa (Loa loa strain Cameroon SouthWest Province isolate)

Onchocerca volvulus (PRJEB513) (Onchocerca volvulus strain O. volvulus Cameroon isolate)

Brugia malayi (PRJNA10729) (Brugia malayi strain FR3)

Ascaris suum (PRJNA62057) (Ascaris suum strain AG01)

Strongyloides ratti (PRJEB125) (Strongyloides ratti)

Necator americanus (PRJNA72135) (Necator americanus strain N. amaericanus Hunan isolate)

Trichuris muris (PRJEB126) (Trichuris muris)

Trichinella spiralis (Trichinella spiralis strain ISS_195)

Priapulus caudatus (Penis worm) - GCA_000485595.2 (Priapulus caudatus)

Strongylocentrotus purpuratus (Spur 01) (Strongylocentrotus purpuratus strain Spur 01)

Lytechinus variegatus (Green sea urchin, NC3) - GCA_018143015.1 (Lytechinus variegatus strain NC3)

Acanthaster planci (Crown-of-thorns starfish) - GCA_001949145.1 (Acanthaster planci)

Patiria miniata (Bat star starfish, m_02_andy) - GCA_015706575.1 (Patiria miniata strain m_02_andy)

Asterias rubens (European starfish) - GCA_902459465.3 (Asterias rubens)

Anneissia japonica (Sea lily, Jap-2015-1) - GCA_011630105.1 (Anneissia japonica strain Jap-2015-1)

Branchiostoma lanceolatum (Branchiostoma lanceolatum)

Saccoglossus kowalevskii (Acorn worm) - GCA_000003605.1 (Saccoglossus kowalevskii)

Hofstenia miamia (Hofstenia miamia strain MS-H3)

Mnemiopsis leidyi (Mnemiopsis leidyi)

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

Amphimedon queenslandica (Amphimedon queenslandica)