#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 18, 2025; 21:22 GMT TreeBASE (cc) 1994-2008 Study reference: Watanabe H., Schmidt H.A., Kuhn A., Höger S.K., Kocagöz Y., Laumann-lipp N., Özbek S., & Holstein T.W. 2014. Nodal signalling determines biradial asymmetry in Hydra. Nature, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16190] BEGIN TAXA; TITLE Untitled_Taxa_Block; DIMENSIONS NTAX=55; TAXLABELS 'Acropora digitifera Cer/NST-like1' Acropora_digitifera_Gremlin 'Acropora millepora Cer/NST-like1' 'Acropora millepora Cer/NST-like2a' 'Acropora millepora Cer/NST-like2b' Acropora_millepora_Gremlin Acropora_millepora_NST1 'Branchiostoma floridae Cerberus-like' Branchiostoma_floridae_Gremlin2 Ciona_intestinalis_Gremlin 'Cladonema pacificum Cerberus-like1' 'Cladonema pacificum Cerberus-like1/2' 'Cladonema pacificum Cerberus-like3' 'Cladonema pacificum Cerberus-like3/4' 'Cladonema pacificum Cerberus-like4a' 'Cladonema pacificum Cerberus-like4b' Cladonema_pacificum_DAND5 Danio_rerio_DAND5 Danio_rerio_Gremlin1 'Danio rerio Gremlin1-like' Danio_rerio_Gremlin2 'Danio rerio Gremlin2-like' Danio_rerio_NST1 Gallus_gallus_Cerberus1 Gallus_gallus_Gremlin1 Gallus_gallus_Gremlin2 Gallus_gallus_NST1a Gallus_gallus_NST1b 'Hydra magnipapillata Cerberus-like1' 'Hydra magnipapillata Cerberus-like2a' 'Hydra magnipapillata Cerberus-like2b' 'Hydra magnipapillata Cerberus-like3' 'Hydra magnipapillata Cerberus-like4' 'Hydra magnipapillata Gremlin-like' Hydra_magnipapillata_Noggin Lottia_gigantea_Gremlin Mus_musculus_Cerberus1 Mus_musculus_DAND5 Mus_musculus_Gremlin1 Mus_musculus_Gremlin2 Mus_musculus_NST1 Mus_musculus_Noggin Nematostella_vectensis_Gremlin 'Nematostella vectensis Gremlin-like' 'Saccoglossus kowalevskii Gremlin1-like' Saccoglossus_kowalevskii_Gremlin292 Saccoglossus_kowalevskii_NST1 Strongylocentrotus_purpuratus_Gremlin Tribolium_castaneum_Gremlin1 Tribolium_castaneum_NST1 Trichoplax_adhaerens_NST1 Xenopus_laevis_Cerberus Xenopus_laevis_DAND5 Xenopus_laevis_Gremlin1 Xenopus_laevis_NST1 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M23498] TITLE 'Cerberus/Dan/Gremlin gene family alignment'; LINK TAXA = Untitled_Taxa_Block; DIMENSIONS NCHAR=121; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 ] [ . . . . . . . . . . . . ] 'Acropora digitifera Cer/NST-like1' CRAYSFKEKIR--HRGCNNVTIENNMCYGQC--NS-FYIP-----------------------KRFVSCS-----YCAPSRME-IYEIRLECPGQN------PDFVLKKVPIVKECACKDC Acropora_digitifera_Gremlin CKTRAFKQTIK--IPGCLPVQVVNNFCYGQC--NS-MYIPNHASE-----------------KPLFESCT-----TCMPKRSF-TKTVTLRCPTLP------VKFRKHKYLHSKKCRCSTV 'Acropora millepora Cer/NST-like1' CRAYSFKEKIR--HRGCNNVTIENNMCYGQC--NS-FYIP-----------------------KRFVSCS-----YCAPSRME-IYEIRLECPGQN------PDFVLKKVPIVKECACKDC 'Acropora millepora Cer/NST-like2a' CKMQSFNLTIR--RRGCEPKTVTKNFCFGQC--RS-FYVPFRKK--------------------TFESCA-----YCTPVAFT-VKSVLLNCPGRS-----QHDRMAKSFKVVTACSCRVC 'Acropora millepora Cer/NST-like2b' CKIKPIRISFQ--PAGCEKRHLSQNLCIGTC--TS-FYIPTKAG--------------------PWENYN-----CCAPSAFV-TRSLSFTCPGKS-----PPGGVAVVARVASECKCTKC Acropora_millepora_Gremlin CKTRAFKQTIK--IPGCLPVQVVNNFCYGQC--NS-MYIPNHASE-----------------KPLFESCT-----TCMPKRSF-TKIVTLRCPTLP------VKFRKHRYIHSKKCRC--- Acropora_millepora_NST1 CRPVEIQHSLQ--EPGCETKVIENRACMGQC--FS-YYAPGTNPRKDLS-------------DKRTKYCD-----MGKPSLKS-WTKVSLDCPGT------NHGQVDKLVEIIYSCTCQKC 'Branchiostoma floridae Cerberus-like' CKAVAFDQEVT--SPGCETKLARNKFCYGQC--SS-FHIPRQHPG-------------------PFDSCA-----SCTPTRMR-NEKVVLNCQG--------NETKVRKVSIVEECACRPC Branchiostoma_floridae_Gremlin2 CKTQPLRQTVR--AKGCLSRTVINRFCYGQC--NS-FYIPKHVRKDA----------------ESFQSCA-----FCKPHRYS-MITVTLRCPSLT------PNFKRKRIQRVKKCKCMSV Ciona_intestinalis_Gremlin CKSQPVRQYIR--TADGCKGELINQFCYGQC--NS-FYIPKDIEIDERDGE---------IETDYFRFCA-----FCKPKTEE-WISVRLRCRRKG--RKKRGRYVIKRVKRVKGCTCISV 'Cladonema pacificum Cerberus-like1' CRKIKTIQTII--KPDCDNLFVENYICVGNC--VS-KSSPSFIVQVG-----------------NKKLCG-----TCVATVVK-QRK-QLNCPER------KKKRRFKDIDFVISCRC--- 'Cladonema pacificum Cerberus-like1/2' CHAVDFVQEST--HRKCTTKYIQNKLCTGTC--KS-VYTAR----------------------GELNICM-----ACRPDNTT-KVQIQLDCPKSR---KKRKRIRFRNIELVHTCRCKIE 'Cladonema pacificum Cerberus-like3' CYAKPYNQTIS--HRNCLPVIVPNKYCLGAC--AS-YALPGE-------------------NGNEIQKCR-----GCKLDEVE-MTIIKLECPRRK------KRFKLKKVFLVKSCKCQ-- 'Cladonema pacificum Cerberus-like3/4' CQAYRFNQSFH--EKGCKSLQIENNFCYGGC--IS-ITLPHVTGATQST-----------------KVSR------CFPYRYV-YKDIEFEC-ENG-------VKKARSIQIVESCRCSKK 'Cladonema pacificum Cerberus-like4a' CNRYAFVQNVT--IPGCESKLITNYYCQGFC--NS-FVWPN--------------------TGMDLTFVK-----SCLPDQKE-TKFIKLKCPGRR------KGYKLKALFYVKTCKC--- 'Cladonema pacificum Cerberus-like4b' CALMPFNQTIF--HDDCISKIIENNYCFGGC--SS-TTQPKFF--DDK----------------SETLCH-----YCWVDKKE-TVTVKLLCPGRK------KKFKMKMLHVVKSCQCR-- Cladonema_pacificum_DAND5 CRTIPFKQTIR--KKGCVSVTVMNNICYGQC--QS-TQAPLSLLKA-----------------NVKSKTH-----QCFPDLIV-KRKLLLFCPGRK------RLLRFKKVLMVHGCKC--- Danio_rerio_DAND5 CAAVPFTQRIT--EEGCETVTVHNNLCYGQC--SS-MFVPSSGGSH-----------------GQQAQCM-----RCGPSRA--RSVLLHLR--RG------SEVRERRVLIVEECKCETS Danio_rerio_Gremlin1 CKTQPLKLMIY--EDGCQPRAIINRFCYGQC--NS-FYIPRHIYQED----------------GAFQSCS-----VCKPKSFT-TVTYTLFCPGQT------PNTKKKRVRRVKQCRCTSV 'Danio rerio Gremlin1-like' CKTQPLKQTIH--EEGCISRTIINRFCYGQC--NS-FYIPRHVRREE----------------GAFQSCS-----FCKPKRFT-TMSFTLSCPDQQ------PPTRKKRVQRVKQCRCISI Danio_rerio_Gremlin2 CKTQPLRQTVS--QEGCRSRTVINRFCYGQC--NS-FYIPRHVKKEQ----------------ESFQSCA-----FCRPQRFT-SLTVELDCSDLQ------PPVRYRKIQRIKQCRCMSV 'Danio rerio Gremlin2-like' CKTQPLRQTVS--LEGCLSRTVINRFCYGQC--NS-FYIPRHLTSQSSHRSRKTASTP--DHTTSFQSCA-----FCRPSRIT-TVTVRLHCPGLQ------PPYRQRKVQRIKQCKCVSV Danio_rerio_NST1 CEAKNITQIVG--HTGCTPRSIQNRACLGQC--FS-YSVPNTFPQS----------------TESLVHCD-----SCMPAQTQ-WEVVTLDCSGSD-----EAPRVDKLVERILHCSCQSC Gallus_gallus_Cerberus1 CRTLPFSQSVA--HESCEKVIVQNNLCFGKC--SS-FHVPGPDDR-------------------LYTFCS-----KCLPTKFS-MKHLDLNC--TS------SVPVVKKVMIVEECNCETQ Gallus_gallus_Gremlin1 CKTQPLKQTIH--EEGCNSRTIINRFCYGQC--NS-FYIPRHVRKEE----------------GSFQSCS-----FCKPKKFT-TMTVTLNCPELQ------PPRKKKRITRVKECRCISI Gallus_gallus_Gremlin2 CKTQPLRQTVS--EEGCVSRTIINRFCYGQC--NS-FYIPRHVKKEE----------------ESFQSCA-----FCKPHKVT-SSTVQLECPELD------PPFRLKKIQKVKQCRCMSV Gallus_gallus_NST1a CEAKNITQIVG--HSGCESKSIQNRACLGQC--FS-YSVPNTFPQS----------------TESLVHCD-----SCMPAQSM-WEIVTLDCPGND-----EIPRVDKLVEKILHCSCQAC Gallus_gallus_NST1b CEAKNITQIVG--HSGCESKSIQNRACLGQC--FS-YSVPNTFPQS----------------TESLVHCD-----SCMPAQSM-WEIVTLDCPGND-----EIPRVDKLVEKILHCSCQAC 'Hydra magnipapillata Cerberus-like1' CKSITFIQPII--REGCDTIMVENSYCVGSC--KS-ITSISTDTN-----------------INPSNFSY-----YCDAAEIH-EEKFQLNCNSR------KKKNLTKIIAVVKSCKCKAQ 'Hydra magnipapillata Cerberus-like2a' CHAIPFIEYVE--HENCDKVSTQNLLCFGSCFVKSNHFINKKI--------------------SLENMFG-----SCKPIKRF-SRVLYLNCSNT-------NKKTFITHNITSSCSCAN- 'Hydra magnipapillata Cerberus-like2b' CQAIPFIEYIN--YEGCDKVSIQNLLCFGSCYVKPKYFVNEKL-------------------ASL-NIFG-----SCQPVKLF-PRLIYLNCSDG-------KKKKFITHNITSECSCAD- 'Hydra magnipapillata Cerberus-like3' CYTKEYKQTVF--KENCIPLVITNKMCYGSC--LS-ISIPSY-------------------NKGRTSECS-----SCSPNESE-IKEIRFKCPRQN------RKHKLKKQIIVHSCKCLKY 'Hydra magnipapillata Cerberus-like4' CGVFPFNQTVT--KNGCEGKYVANNFCFGQC--GS-FIIPYYNITNKK------------ISRLTLENCK-----QCVPEDFE-LTKIPIYCPERK------KKHQFAKVLLIKKCVCKKN 'Hydra magnipapillata Gremlin-like' CMVHGTKYQQVISERDCKAVTIDVPFCYGQC--NS-FFIPRYG--ED------------------FNSCN-----TCMPKKWN-ETKVQLNCKTDG-----EWRVVIKKVLLIGSCECQEV Hydra_magnipapillata_Noggin LSKCPVKYKWI---D-LGENIFPQYIKRGSC--SK-K-----------------------------KTCSFPAGMTCEESKWKSVDILLYTCLKEYNSVSLDCKWRPMPVNILTECSC-QC Lottia_gigantea_Gremlin CKTQPLKQVIR--EKGCLRTTVINSFCYGQC--NS-FFIPKSDKSDEN--------------PAAFMSCG-----FCKPRKYR-MIIVTLRCPGKK-----GMRFKRKRVMRIKKCRCMAV Mus_musculus_Cerberus1 CRTVPFNQTIA--HEDCQKVVVQNNLCFGKC--SS-IRFPGEGAD-------------------AHSFCS-----HCSPTKFT-TVHLMLNC--TS------PTPVVKMVMQVEECQCMVK Mus_musculus_DAND5 CKALSFVQVIS--RPGCTSARVLNHLCFGRC--SS-FYIPSSDP-------------------TPVVFCN-----SCVPARKR-WTSVTLWCGAGQ---LASPRRVRISTVLVQKCQCRPK Mus_musculus_Gremlin1 CKTQPLKQTIH--EEGCNSRTIINRFCYGQC--NS-FYIPRHIRKEE----------------GSFQSCS-----FCKPKKFT-TMMVTLNCPELQ------PPTKKKRVTRVKQCRCISI Mus_musculus_Gremlin2 CKTQPLRQTVS--EEGCRSRTILNRFCYGQC--NS-FYIPRHVKKEE----------------DSFQSCA-----FCKPQRVT-SVIVELECPGLD------PPFRIKKIQKVKHCRCMSV Mus_musculus_NST1 CEAKNITQIVG--HSGCEAKSIQNRACLGQC--FS-YSVPNTFPQS----------------TESLVHCD-----SCMPAQSM-WEIVTLECPDHE-----EVPRVDKLVEKIVHCSCQAC Mus_musculus_Noggin QTFCPVLYAWN---D-LGSRFWPRYVKVGSC--FS-K-----------------------------RSCSVPEGMVCKPSKSVHLTVLRWRCQRRG---GQRCGWIPIQYPIISECKC-SC Nematostella_vectensis_Gremlin CKLRPVLQKLH--HPGCNSSFIMNNMCYGQC--MS-FFIPR-----------------------HFTSCA-----FCTPVSKN-VVSVHLKCAG--------DLKVVKKVSIIQSCSCRPC 'Nematostella vectensis Gremlin-like' CKTKPVKQIIR--IEGCEPAEIVNNFCYGQC--NS-LYIPHYNRQ-----------------TPAFESCA-----TCIPVRVH-RRSVYLNCPNAK------QKRKRHRYTYVKRCRCVTF 'Saccoglossus kowalevskii Gremlin1-like' CKTQPLKQTIY--ADGCISRTIINRFCYGQC--NS-FFIPKQELRQH---------------VSAFQSCS-----FCKPYRFN-WITVTLRCPGQK------PRLQRKRVQRIKECRCMAV Saccoglossus_kowalevskii_Gremlin292 CLGAVFEQEIK--HDGCKSVFVKNKLCYGQC--GS-FFVPRAKHG-------------------HFESCS-----YCTPVRSR-VEIISLTCPG--------RANRVKKVEIVESCGCRPC Saccoglossus_kowalevskii_NST1 CEAQEIEQIIG--HDQCTSKPISNRVCVGQC--FS-YRIPRTVPPTPN--------------KEDLHYCD-----CCRPSVVT-WEKITLDCNSD------EMPQVDKMVEMIQECTCKAC Strongylocentrotus_purpuratus_Gremlin CKTQPLKQRIE--EPGCIPRTIANRFCYGQC--NS-FFIPKQAASYN----------------EAFKSCS-----FCKPFRVN-HITVTLRCPGQN------PPIKRKRVPRVKRCRCMAV Tribolium_castaneum_Gremlin1 CKTEPLIQKVK--EEGCLTRTVINRFCYGQC--NS-FYIPKNPKKRHRHIPVSEETEDEDQNGPAFKACA-----FCRPSKFT-WISVTLKCPSLM------PPFRKKRIQRIKQCKCIAA Tribolium_castaneum_NST1 CQTTPIQQVVA--SPGYESVTIHNNVCVGAC--YS-YSIPSTQPAEPG--------------ELLGPYCD-----SCQPVETK-CYHVTLHADGKN---TEGPKTFQKRVQIILKCSCMSC Trichoplax_adhaerens_NST1 CKLAKIEQVLS--HPGCISKTISNHICVGQC--YS-YRIPKSYPPEAG--------------QENLQHCE-----CCHVVDHT-WNTVELKCP-T------LKNNVDKLVQYIRSCDCRRC Xenopus_laevis_Cerberus CKTLPFTQNIV--HENCDRMVIQNNLCFGKC--IS-LHVPNQQDRR--------------------NTCS-----HCLPSKFT-LNHLTLNC--TG------SKNVVKVVMMVEECTCEAH Xenopus_laevis_DAND5 CHALPFIQNVF--RKNCFPVRLPNKFCFGQC--NS-FYVPGWPA-------------------GLSQPCT-----SCAPSRSR-RISLPLRC--RS------GHLAWQEVELVEECECETR Xenopus_laevis_Gremlin1 CKTQPLKQTIH--EDGCNSRTIINRFCYGQC--NS-FYIPRHIRREE----------------GSFQSCS-----FCKPKKFT-TMVVTLNCPELQ------PPTKKKRITRVKQCRCISI Xenopus_laevis_NST1 CEAKNITQIVG--HSGCESKSIQNRACLGQC--FS-YSVPNTFPQS----------------TESLVHCD-----SCMPIDSV-WDVVTLECPGNE-----EFPRVDKLVEKILQCSCQAC ; END;