Supp Data Table 1. Sequences analyzed in this study and their GenBank Accession Numbers

Name used on trees / Taxa 18S / Accession n. 18S / Taxa 28S / Accession n. 28S
CNIDARIA1 / Actinia equina / AJ133552.1 / Atolla vanhoeffeni / AY026368.1
CNIDARIA2 / Alcyonium gracillimum / Z92902.1 / Hydra circumcincta / AY026371.1
CNIDARIA3 / Anemonia sulcata / X53498.1 / Montastraea franksi / AY026375.1
CNIDARIA4 / Aurelia aurita / AY039208.1 / Nectopyramis sp / AY026377.1
CNIDARIA5 / Coryne pusilla / Z86107.1 / Podocoryne carnea / AY920802.1
CNIDARIA6 / Nematostella vectensis / AF254382.1 / Moerisia sp / AY920801.1
CNIDARIA7 / Parazoanthus axinellae / U42453.1 / Antipathes galapagensis / AY026365.1
CATENULIDA1 / Suomina sp. / AJ012532.1 / Suomina sp. / AY157152.1
CATENULIDA2 / Stenostomum leucops / D85095.1 / Stenostomum leucops / AY157151.1
RHABDITOPHORA1 / Macrostomum hystricinum / AF051329.1 / Paromalostomum fusculum / AY157155.1
RHABDITOPHORA2 / Discocelis tigrina / U70078. / Monocelis lineata / AY157159.1
RHABDITOPHORA3 / Thysanozoon brocchii / D85096.1 / Plicastoma cuticulata / AY157158.1
RHABDITOPHORA4 / Notoplana australis / AJ228786.1 / Geocentrophora wagini / AY157156.1
RHABDITOPHORA5 / Notoplana koreana / D85097.1 / Nematoplana sp. / AY157160.1
RHABDITOPHORA6 / Planocera multitentaculata / D83383.1 / Notoplana australis / AY157153.1
RHABDITOPHORA7 / Pseudoceros tritriatus / AJ228794.1 / Pterastericola australis / AY157161.1
RHABDITOPHORA8 / Haplopharynx rostratus / AJ012511.1 / Stylochus zebra / AF342800.1
ANNELIDA1 / Acanthobdella peledina / AY040680.1 / Nereis succinea / AY210464.1
ANNELIDA2 / Erpobdella octoculata / AF099949.1 / Eisenia fetida / AF212166.1
ANNELIDA3 / Glossiphonia complanata / AF099943.1 / Chaetopterus variopedatus / AY145399.1
ANNELIDA4 / Dero digitata / DQ459984.1 / Proceraea cornuta / AF212165.1
MOLLUSCA1 / Lima lima / AF120533.1 / Argopecten irradians / AY145391.1
MOLLUSCA2 / Nuculana minuta / DQ279938.1 / Nuculana pernula / AY145419.1
MOLLUSCA3 / Pteria hirundo / AF120532.1 / Mytilus galloprovincialis / AB103129.1
MOLLUSCA4 / Rhabdus rectius / AF120523.1 / Placopecten magellanicus / AF342798.1
MOLLUSCA5 / Yoldia myalis / AF207643.1 / Yoldia limatula / AY145424.1
SIPUNCULIDA1 / Aspidosiphon misakiensis / AF119090 / Apionsoma misakianum / AY210454.1
SIPUNCULIDA2 / Phascolosoma granulatum / X79874.1 / Phascolion strombi / AY210468.1
ECHIURA1 / Ochetostoma erythrogrammon / X79875.1 / Arhinchite pugettensis / AY210455.1
ECHIURA2 / Urechis caupo / AF119076.1 / Urechis caupo / AF519268
ECHIURA3 / Urechis caupo / AF342805.1 / Urechis caupo / AF342804.1
NEMERTEA1 / Amphiporus ochraceus / AY039668.1 / Amphiporus sp / AF342786.1
NEMERTEA2 / Cerebratulus lacteus / AY145368.1 / Cerebratulus lacteus / AY145396.1
NEMERTEA3 / Lineus ruber / AY039672.1 / Oerstedia dorsalis / AY210465.1
NEMERTEA4 / Lineus sp. / X79878.1 / Tubulanus annulatus / AY210473.1
BRACHIOPODA1 / Glottidia palmeri / AF201744.2 / Glottidia pyramidata / AY210459.1
BRACHIOPODA2 / Glottidia pyramidata / U12647.1 / Laqueus californianus / AY210460.1
BRACHIOPODA3 / Lingula anatina / X81631.1 / Terebratalia transversa / AF342802.1
PHORONIDA1 / Phoronis australis / AF119079.1 / Phoronis vancouverensis / AF342797.1
PHORONIDA2 / Phoronis psammophila / U36271.1 / Phoronis hippocrepia / AY839251.1
ROTIFERA1 / Brachionus patulus / AF154568.1 / Brachionus patulus / AY829084.1
ROTIFERA2 / Brachionus plicatilis / U49911.1 / Lecane bulla / AY829083.1
ROTIFERA3 / Lecane bulla / AF154566.1 / Epiphanes senta / DQ089742.
ROTIFERA4 / Asplanchna sieboldi / AF092434.1 / Asplanchna sieboldi / AY829085.1
ROTIFERA5 / Philodina roseola / AF154567.1 / Sinantherina socialis / AY210471.1
CYCLIOPHORA / Symbion pandora / AY218106.1 / Symbion sp. / AY210472.1
MICROGNATHOZOA / Limnognathia maerski / AJ487046.1 / Non Available
ENTOPROCTA / Barentsia benedeni / U36272.1 / Barentsia gracilis / AY210456.1
PRIAPULIDA1 / Halicryptus spinulosus / AF342790.1 / Halicryptus spinulosus / AF342789.1
PRIAPULIDA2 / Priapulus caudatus / Z38009.1 / Priapulus caudatus / AY210840.1
KINORHYNCHA / Pycnophyes kielensis / U67997.1 / Pycnophyes kielensis / AY863411.1
NEMATODA1 / Catanema sp / Y16912 / Xiphinema americanum / AY580056.1
NEMATODA2 / Desmodora ovigera / Y16913.1 / Ascaris lumbricoides / AY210806.1
NEMATODA3 / Enoplus brevis / U88336.1 / Labiostrongylus bipapillosus / AJ512837.1
NEMATOMORPHA1 / Gordius albopunctatus / U88337.1 / Gordius aquaticus / AY210817.1
NEMATOMORPHA2 / Neochordodes occidentalis / AF421768.1 / Gordius sp. / AY863410.1
NEMATOMORPHA3 / Paragordius tricuspidatus / AF421771.1 / Chordodes morgani / AF342787.1
TARDIGRADA / Milnesium tardigradum / U49909.1 / Milnesium sp / AY210826.1
ARTHROPODA1 / Callipallene sp. / AY210807 / Callipallene sp. / AY210807.1
ARTHROPODA2 / Colossendeis sp. / AF005440.1 / Colossendeis sp. / AY210809.1
ARTHROPODA3 / Limulus polyphemus / L81949.1 / Limulus polyphemus / AF212167.1
ARTHROPODA4 / Pandinus imperator / AY210831 / Pandinus imperator / AY210830.1
ARTHROPODA5 / Cormocephalus_monteithi / AF173249 / Cormocephalus_monteithi / AY210812.1
ARTHROPODA6 / Lithobius obscurus / AF334271 / Lithobius obscurus / AY210825.1
ARTHROPODA7 / Orthoporus sp. / AY210829.1 / Orthoporus sp. / AY210842.1
ARTHROPODA8 / Squilla empusa / L81946 / Squilla empusa / AY210842.1
ARTHROPODA9 / Triops longicaudatus / AF144219.1 / Triops longicaudatus / AY157606.1
ARTHROPODA10 / Gromphadorhina laevigata / AY210820 / Gromphadorhina laevigata / AY210819.1
ARTHROPODA11 / Ctenolepisma longicaudata / AY210811 / Ctenolepisma longicaudata / AY210810.1
ECHINODERMATA1 / Endoxocrinus parrae / Z80951.1 / Antedon serrata / D14357
ECHINODERMATA2 / Antedon serrata / D14357.1 / Asterias forbesii / AF212169.2
ECHINODERMATA3 / Astropecten latespinosus / AB084546 / Florometra serratissima / AF212168.2
ECHINODERMATA4 / Asterina coronata / AB084566 / Asterias forbesii / AF212169.2
ECHINODERMATA5 / Asthenosoma owstoni / Z37118.1 / Arbacia punctulata / AY026367.1
ECHINODERMATA6 / Strongylocentrotus purpuratus / L28055.1 / Strongylocentrotus purpuratus / AF212171.1
HEMICHORDATA1 / Saccoglossus pusillus / AF236800 / Saccoglossus pusillus / AF212174.2
HEMICHORDATA2 / Balanoglossus carnosus / D14359.1 / Harrimania planktophilus / AF212173.1
HEMICHORDATA3 / Glossobalanus minutus / AF119089.1 / Cephalodiscus gracilis / AF212172.1
HEMICHORDATA4 / Ptychodera flava / AF278681.1 / Ptychodera flava / AF212176.1
UROCHORDATA / Ciona intestinalis / AB013017.1 / Ciona intestinalis / AF212177.1
CEPHALOCHORDATA / Branchiostoma floridae / M97571.1 / Branchiostoma floridae / AF061796.1
VERTEBRATA1 / Mitsukurina owstoni / AY049840.1 / Petromyzon marinus / AF061798.1
VERTEBRATA2 / Alligator mississippiensis / AF173605.1 / Oncorhynchus mykiss / U34341.1
VERTEBRATA3 / Gallus gallus / AF173612.1 / Latimeria chalumnae / U34336.1
VERTEBRATA4 / Mus musculus / NR_003278.1 / Squalus acanthias / AF061800
VERTEBRATA5 / Xenopus borealis / X59733.1 / Xenopus borealis / X59733.1
VERTEBRATA6 / Urobatis jamaicensis / AY049861 / Ambystoma macrodactylum / AF212178.1
VERTEBRATA7 / Homo sapiens / NR_003286.1 / Homo sapiens / NR_003287.1
Acoel-set
ACOELA1 / Paratomella rubra / AF102892 / Paratomella rubra / AY157604
ACOELA2 / Paratomella unichaeta / AY078379 / Childia groenlandica / AY157603
ACOELA3 / Myopea sp / AY078380 / Anaperus biculeatus / AY157602
NEMERTODERMATIDA / Meara stichopi / AF119085 / Meara stichopi / AY157605
Gnat-set
GNATHOSTOMULIDA1 / Gnathostomula paradoxa / Z81325 / Non Available
GNATHOSTOMULIDA2 / Gnathostomula sp / AF119083 / Non Available
GNATHOSTOMULIDA3 / Haplognathia sp / AF119084 / Non Available
ACANTOCEPHALA1 / Oncicola sp / AF064818 / Oncicola sp / AY210467
ACANTOCEPHALA2 / Koronacantha pectinaria / AF092433 / Koronacantha pectinaria / AY829094
ACANTOCEPHALA3 / Neoechinorhynchus saginata / AY830150 / Neoechinorhynchus saginata / AY829091
Bryo-set
BRYOZOA / Caberea boryi / AF119082 / Watersipora subtorquata / DQ333341
Gast-set
GASTROTRICHA1 / Paraturbanella teissieri / AY228138 / Non Available
GASTROTRICHA2 / Chaetonotus sp / AJ001735 / Non Available
GASTROTRICHA3 / Turbanella cornuta / AF157007 / Non Available
Chae-set
CHAETOGNATHA1 / Sagitta crassa / D14363 / Sagitta elegans / AF342799.1
CHAETOGNATHA2 / Sagitta elegans / Z19551 / Sagitta elegans / AF342799.1