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

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

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

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)

Clytia hemisphaerica (Z4C2) (Clytia hemisphaerica strain Z4C2)

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

Thelohanellus kitauei (Thelohanellus kitauei)

Lingula anatina (Lingula anatina LinAna1.0)

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

Capitella teleta (Capitella teleta)

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

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

Octopus bimaculoides (Octopus bimaculoides PRJNA270931)

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)

Stegodyphus mimosarum (Stegodyphus mimosarum)

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

Ixodes scapularis (Ixodes scapularis strain Wikel)

Ixodes scapularis (PalLabHiFi) (Ixodes scapularis strain PalLabHiFi)

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

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

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

Varroa destructor (Varroa destructor)

Leptotrombidium deliense (Leptotrombidium deliense strain UoL-UT)

Dinothrombium tinctorium (Dinothrombium tinctorium strain UoL-WK)

Tetranychus urticae (Tetranychus urticae)

Sarcoptes scabiei (SSS_KF_BRIS2020) (Sarcoptes scabiei strain SSS_KF_BRIS2020)

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

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

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

Orchesella cincta (Orchesella cincta)

Folsomia candida str. VU population (Folsomia candida)

Rhodnius prolixus (Rhodnius prolixus strain CDC)

Cimex lectularius (Harlan) (Cimex lectularius strain Harlan)

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

Acyrthosiphon pisum (AL4f) (Acyrthosiphon pisum strain AL4f)

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)

Pediculus humanus (Pediculus humanus corporis strain USDA)

Musca domestica (Musca domestica strain aabys)

Stomoxys calcitrans (Stomoxys calcitrans strain USDA)

Glossina palpalis (Glossina palpalis gambiensis strain IAEA)

Glossina fuscipes (IAEA_lab_2018) (Glossina fuscipes strain IAEA_lab_2018)

Glossina pallidipes (Glossina pallidipes strain IAEA)

Glossina morsitans (Glossina morsitans morsitans strain Yale)

Glossina austeni (Glossina austeni strain TTRI)

Glossina brevipalpis (Glossina brevipalpis strain IAEA)

Lucilia cuprina (Lucilia cuprina strain LS)

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)

Drosophila melanogaster (Drosophila melanogaster)

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

Megaselia scalaris (Megaselia scalaris)

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

Culex quinquefasciatus (JHB) (Culex quinquefasciatus strain JHB)

Culex quinquefasciatus (Culex quinquefasciatus strain Johannesburg)

Aedes aegypti (LVP_AGWG) (Aedes aegypti strain LVP_AGWG)

Aedes albopictus (Aedes albopictus strain Foshan)

Anopheles albimanus (Anopheles albimanus strain STECLA)

Anopheles darlingi (Anopheles darlingi strain Coari)

Anopheles sinensis (Anopheles sinensis strain SINENSIS)

Anopheles sinensis (China) (Anopheles sinensis strain China)

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

Anopheles farauti (Anopheles farauti strain FAR1)

Anopheles dirus (Anopheles dirus strain WRAIR2)

Anopheles stephensi (Indian) (Anopheles stephensi strain Indian)

Anopheles stephensi (Anopheles stephensi strain SDA-500)

Anopheles maculatus (Anopheles maculatus strain maculatus3)

Anopheles funestus (Anopheles funestus strain FUMOZ)

Anopheles culicifacies (Anopheles culicifacies strain A-37)

Anopheles minimus (Anopheles minimus strain MINIMUS1)

Anopheles coluzzii (Ngousso) (Anopheles coluzzii strain Ngousso)

Anopheles coluzzii (Anopheles coluzzii strain Mali-NIH)

Anopheles quadriannulatus (Anopheles quadriannulatus strain SANGWE)

Anopheles arabiensis (Anopheles arabiensis strain Dongola)

Anopheles merus (Anopheles merus strain MAF)

Anopheles melas (Anopheles melas strain CM1001059_A)

Anopheles gambiae (Anopheles gambiae strain PEST)

Anopheles epiroticus (Anopheles epiroticus strain Epiroticus2)

Anopheles christyi (Anopheles christyi strain ACHKN1017)

Culicoides sonorensis (Culicoides sonorensis)

Belgica antarctica (Belgica antarctica)

Phlebotomus papatasi (Phlebotomus papatasi strain Israel)

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

Lutzomyia longipalpis (Lutzomyia longipalpis strain Jacobina)

Mayetiola destructor (Mayetiola destructor strain Kansas Great Plain)

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)

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

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

Nasonia vitripennis (AsymCx) (Nasonia vitripennis strain AsymCx)

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

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

Bombus terrestris (Bombus terrestris)

Bombus impatiens (Bombus impatiens)

Apis mellifera (DH4) (Apis mellifera strain DH4)

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)

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

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

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

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)

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)

Lepeophtheirus salmonis (Lepeophtheirus salmonis)

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

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

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

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

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

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

Strigamia maritima (Strigamia maritima)

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

Caenorhabditis japonica (PRJNA12591) (Caenorhabditis japonica)

Caenorhabditis brenneri (PRJNA20035) (Caenorhabditis brenneri)

Caenorhabditis briggsae (PRJNA10731) (Caenorhabditis briggsae)

Caenorhabditis elegans (PRJNA13758) (Caenorhabditis elegans strain N2)

Caenorhabditis remanei (PRJNA53967) (Caenorhabditis remanei)

Pristionchus pacificus (PRJNA12644) (Pristionchus pacificus strain PS312)

Brugia malayi (PRJNA10729) (Brugia malayi strain FR3)

Loa loa (Loa loa strain Cameroon SouthWest Province isolate)

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

Ascaris suum (PRJNA62057) (Ascaris suum strain AG01)

Strongyloides ratti (PRJEB125) (Strongyloides ratti)

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

Trichinella spiralis (Trichinella spiralis strain ISS_195)

Trichuris muris (PRJEB126) (Trichuris muris)

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)

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

Branchiostoma lanceolatum (Branchiostoma lanceolatum)

Hofstenia miamia (Hofstenia miamia strain MS-H3)

Mnemiopsis leidyi (Mnemiopsis leidyi)

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

Amphimedon queenslandica (Amphimedon queenslandica)