Leading sequence. Asbu DFB-like

Transcription

1 Supplementary Figure 1: Amino acid alignment of cichlid, non-cichlid percomorph and Esox lucius (non-percomorph outgroup) MHC class IIB b sequences (exons 1-5). In the first column species names are abbreviated to a four letter code (first and second letter of both genus and species name). The second column presents GenBank accession numbers of the nucleotide sequences or the number of the scaffold on which the sequence is located. Enumeration of amino acid residues follows Klein et al. (1993). Cystein residues that evolved after diversification of cichlid Mhc class IIB b loci are shaded. Note that most newly evolved cystein residues are located in DBB-like (DBB5/hg 14), DDB-like and DCB-like sequences, the putative non-classical cichlid MHC genes. Synapomorphic amino acid residues of cichlid fishes are underlined. Leading sequence Auha L13222 MASSFLCLSL-LFI-SLSTADG Auha S63770?? Auha L13223??? Puny Puny Maze 466a DFB-like Maze 466b Puny Cyfr L13232???? Cyfr L13230?? G. Orni JN F Asbu DFB-like Orni JN G Puny 422a DBB-like Orni XM_ V.. Cyfr L13231?? G. Orni XM_ G. DEB-like Nebr 279b Cyfr L13233????????????????????.. Maze 486a DEB-like Auha L13224?????????????????????. Orni JN Orni JN Orni XM_ RFTF-...-.IHI... DEB-like Orni XM_ Orni JN Orni JN Nebr 375b Orni JN Orni JF Asbu DFB-like Maze 486b Orni JN Orni JN Nebr 279a DFB-like Orni XM_ I-...-.F... Nebr FTF-...-.IH... DCB-like Orni XM_ V.FT.-.L.-.IH... Orni XM_ Y-TF-...-.IH... Orni XM_ I Orni XM_ FT IHN... Asbu FT IR... Puny FT IR... Maze 530a...FT IR... Nebr FT IR... Orni XM_ D.FYF.F..-F..-I.CR... Orni XM_ D...F..-F..-I.CR... DDB-like Orni XM_ ??????????????????VS.. Puny 422b.D.Y...V..-F..-I.HR... Maze M...FT.-...-NIC... Orni XM_ M...T.-...-TIC.T.. Orni XM_ K...FT.-...-NIC... Asbu K...FT.-...-NIC.V.. Orla AB D..S L-T.CS..A Pore Z P.A.GWL.-VI.-TVHS.G. Ximu EU852868?????.GWL.-VI.-TVNA... Xipy EU852854?????.GWL.-VI.-TINA... Gaac AY P..ISV G.HA... Lacr EF ISF C... Mimi HM ISF Y... Epak EU SF Y... Epak EU SF Y... Epco GU SF Y... Pama AY SF CS... Pama AY SF CS... Dila DQ SF..LFI.-..Y... Mosa L SF..-...T..Y... Paol AY FI.SF..-F..-TVC... Veva GU F..SF..-F..-TVC... Cyse EU LIVSF..LFLL-TVH..E. Scma DQ SFA.-...-TVY... Savi AY SV Y... Eslu BT IQNIYIY.PG.LSISYRT.. noncichlid Percomorpha outgroup 1

2 Supplementary Figure 1 continued: Beta Auha L13222 FLSYSVDRCQFNSTELKDIEYIRSVYYNKLEIFRFSSSLGKFVGYTEYGVKQADYRNNDKAI LSSMKAQKETYCHNNIGVDYSAILSKS Auha S Auha L G...Y.Q...Y...V...K.F.DQP.V VAQRR.A...QH...IW..NP... Puny 2027.MY.M.E...DP...L.T.W...I.VN...K...YN.E.W.SGAFL NT.R.E..R..LH...WN.N... Puny 741.MN.V.S..D...Q..N.Y...MM.VV..D.NV.EY...DF...K.F.SIPGR A.DR...N... DFB-like Maze 466a.MN.RMA..V...QF.D.Y...MM.VV..D.NV.EY...DF...K.F.SIPGQ A.ER...L...V... Maze 466b.MN.RMA..V...QF.D.Y...MM.VV..D.NV.EY...DF...K.F.SIPGQ A.ER...L...V... Puny 1050.MN.V.S..D...Q..N.Y...MM.VV..D.NV.EY...DF...K.F.SIPGR A.DR...N... Cyfr L13232.MN.M.S..D...QF...Y...MM.VV..D..V.EY...DF...K.F.SQP.N AA.R...G...QH...I...N... Cyfr L M...A..D...T..S...MM.VV..D..V.E...KL...N..RF.K.QGR AA.R...G...LH...NWNKG... Orni JN MY.A..H.D...P...A..Q.Y...MM.YL..D..V...F.QL..NN..RL.K.QGM AA...V.VP...LW..NV... Asbu 900.MN.M.TG.V...TF...Y...MM.VV..D..V..Y...DF...N.ADW.K.QGD AA.R...G...VH...WN..V... DFB-like Orni JN MN.V.G..D...DP...QF.N.Y...MM.VV..D.NV.EY...F...N.EAW.K.QGR AT.R...V.VP...WN.N... Puny 422a.MT.RLS..D...RFTD.Y...MI..I..D.NV.T...F.DF...T.EAW..IP.R AT.R...G...KP..D.R.HNLM... DBB-like Orni XM_ MT.RLS..D...QFTD.Y...MI..I..D.NV...F.DF...T.ETW..IP.R A..R...G...KS..D.R.HKLT... Cyfr L13231.MM...N...Q...F...Y.FR.V.FT..D..V..Y...RN.EEW.K..GN AA.N...G...LH...WN.N... Orni XM_ MH...N...S.PQ...Y.FR.V.FT..D..V..Y...N.EEW.K..GN AA.N...V..QKK.DNR.N...P.. DEB-like Nebr 279b.MM.W.S..K...PQ...F...Y.FR.V.FT..D..V..Y...RN.EAW.K.QGD AA.N.K...QH...IW..N... Cyfr L13233.MH.W.S..N...S..Q...Y.FR.V.FT..D..V..Y...RN.EEW..RPGE AR...E..R...QVA.T.. Maze 486a.EM.MMS..N...Q...Y.FR.V.FT..D..V..Y...N.EAW..QPGQ AR.R.K...QVA.T.. DEB-like Auha L13224.KM.W.N..N...V.Y.F..I.YT..D..V.HY...N.E.W..LPGE ARWR.A...QH...NW..NP... Orni JN KM.MMN..V...P...K..V.Y...I.VN..D.DV...F...LRN.ETW.SGA-Y TQ...E.-.I.QQHTSSL..GF... Orni JN KM.MMNH.V...MV.Y...I.VT..D.DV...RT.E.W..QPGY TQL..E...V.QH...Y..N... Orni XM_ E.I...E...EM...Y.H...I.YI...V..Y..V.DF..NL.KRW..NT.L N.TRSKIA...LS...IHDR..IA.. DEB-like Orni XM_ KM.VLS..D...MK...Y...I.VT..D.DVR...K.ETW...Q.H MAAFRVE..R..YT...IW.RN... Orni JN E.N.W..A.T..D...FYF.YN...IKYIE...N.V...EAW...P.E ATRR.D..R..QH...IWN.N... Orni JN E.N.W..A.T..D...FYF.YN...IKYIE...N.V...EAW...P.E ATRR.D..R..QH...IWN.N... Nebr 375b..E.N.W..A.T.PD...FYL.YN...IKYVE...N.V...EAW...Q.Q AVW.T...A..KH...IW..GF.P.. Orni JN E.N.W..A.T..D...FYF.YN...IKYIE...L...N.EAW.K-QGD A.WR...V..KP..D...RSA.T.. Orni JF ME.Y.W..D...DFTA.S...IKYTQ...V...F..F...W.K.Q.Q MAGWR...QH...IW..NP... Asbu 698.ME.Y.G..D...FTL.Y...I.YA...V.EY..F.KF..YN..IW.K..GQ MAAWR...QH...IW..NP... DFB-like Maze 486b.ME.Y.YH.D...DP...FTF.L...I.YA...V.EY..F.KF..YN..IW.K.Q.Q MAAWR...QH...IW..NP... Orni JN ME.Y.S..D...S...TF.Y...I.YA...V.EY..F..F..HN..IW.K...R MATWR...QP...I..NNV... Orni JN ME.Y.S..D...S...TF.Y...I.YA...V.EY..F..F..HN..IW.K...R MATWR...QP...I..NNV... Nebr 279a.ME.Y.W..D...F.Y.M...I.YA...V.E...F.K...NN..IW.S..GQ VAAWR...V.LQH..NF..NP... DFB-like Orni XM_ ME.H...N...D...Y.C...I.YA...V...F.KH..YN..KW...P.E NNRR...R...??????????? Nebr 102..E.M.N..D...*...M...Y.R...I.YI...V.EY..V..F.ENL.EIW...TEE NLIRLKIA...QH..CSVLTRCGRDL DCB-like Orni XM_ E.M.E..K...M...Y.H...I.YI...V..Y..V..F.ENL.KHW...TEE N.TRSKIV...L...DIHDR...A.. Orni XM_ E.I...E...M...Y.H...I.YI...VEQY..F...ML.EIL..NT.L N.SRQMITE..YH..D.HDQ..IA.. Orni XM_ KM.V.S..D...K...Y...I.VT..D.DVR...F.GF...KHF.SQPGR ATL..E..R..QH...IW..NV.P.. Orni XM_ E.I...D...ENM...Y.H...M.YI...NV.QY..F.DF..RL.EVW...T.D NL.RLKIA...H..DINDR...T.. Asbu E.R.E..E...A..H...Y.R..K.I.YI...V..Y..F..H..EL.MLW..NT.R N..RQMVTE..YH..D.HDR.V.A.. Puny 749..E.R.E..E...A..H...Y.R..K.I.YI...V..Y..F..H..EL.MLW...T.R NL.RRMVTE..YH..D.HDR.V.A.. Maze 530a..E.R.E..E...A..H...Y.R..K.I.YI...E..Y..F..H...L.MLW..NT.R N..RQMVVQ..YH..D.HDR.V.A.. Nebr 286..E.R...E...A..H...Y.R..K.I.YI...V.EY..F..H...L.TLW...T.R N..RRMITA..YQ..N.HDR.V.A.. Orni XM_ YEY.TSS..L...R...Y...T.YV...V...RE..QW.K.QGQGSWTRKGQ.AA.R...KPK.DFW.QSV.T.A DDB-like Orni XM_ YEY.TSS..L...R...Y...T.YV...V...RE..QW.K.QGQGSWTRKGQ.AA.R...KPK.DFW.QSV.T.A Orni XM_ YEY.TSS..L...R...Y...RI.YV...V.M...E.E.F...PGQ AA.R...TP..DLW.RSV.T.. Puny 422b YEY.TSS..L...R..A...Y...RI.YV..D..V.T...RE.E.F.K.P.Q AA.R...TP..DLW.RSV.T.. Maze 340 YEC..ST..L...Q...F...Y...I.HV...DV.R...F.I.E.E.W.K.Q AQ.R...QH.TDLW.ANV... Orni XM_ YEL.NS...L...Q.V.F...C...I.FV...DV...DF.M.N.EMW.K.QGY AA.R...KH..DLW.TNV... Orni XM_ YEC..ST..L...F.T.Y...I.YV...DV...N.E.W.KNQ.L AQ.R...QP...IW.ADV... Asbu 1137 YEC..ST..L...R...F.T.Y...I.FV...DV..Y...F.M.N.EMW..NPGQ AA.R...QP.V.IW.ANV... Orla AB ME.A.N..E...SD.T...Y.M...RK.YA...Y...F...N.ERF.K.TSE VRR...KH..DI..QTA... Pore Z54077.REFA...V.S.P...QF...YC...FI..D.N...Y...L...N.ERW.K.TSL IAA...R...L..V.N..QNA.D.. Ximu EU MEFR.T..V...D.N..Q..D.YC...K.YA..D.N..RY...N.ERW.K.QS IAA...QH...IW.QTK.T.. Xipy EU RETL.G..V...D.N..QL...YI...K..L..D.NV..W...L...N.EQW.K.QS IAA...V.LQHVDI..Q.A.T.. Gaac AY MEFRTF..V...D.YFF...LT...V...F...RN.E.W..NPSY A...V..L.HVP.Y..NA.T.. Lacr EF MEFRLA..V...D..N...D.Y...M.YS...V..Y..F...N.E.W..NPSL ARERGE..R..L..VQA..QSA.D.. Mimi HM MESVLG..V...D...F.M.W...M.YT...V...F..R...N.ENW..NPSY AQARGE..R..L...KI..QTA.D.. Epak EU ME.VTTS.V...D...F...Y.F...FT...V..H...N.EFW.S.PSF AQ.R.E..R..V...I..Q.A.T.. Epak EU NFVTA..V...DP...L.Y.Y...YT...V...F...E.F...PS AQWRGD..RV.V..V.N..RNAVT.. Epco GU RC..LF..D...DP...Y.A...T...F...EAW..NPSY AQARGE..R..V.HVEAF.PHG.T.. Pama AY WYFATQ..D...S...M...E.Y.F..V.FA...V.E...L.L...QGW.K..S AVKR.E..R..KT.V.NE.AYA.TQ. Pama AY WYFATQ..D...S...M...E.Y.F..V.FA...V.E...L.L...QGW.K..S AVKR.E..R..KT.V.NE.AYA.TQ. Dila DQ N...D...DP.N...Y...LL...V.EY...L...N.ERL.K.PSE AA.R...LTTVNI..Q.V.D.. Mosa L N.A.G..V...DP.N...Y.E...A...V.E...L...K.W.S.PSE AQ.R.A..R..QH..NI..Q.A.D.. Paol AY H.T.TD.E...SK.N...TQ.Y...V...V..Y...F.I.N.ERW..GP-E VI.RRGE..S..FH.V.IFTESA.T.. Veva GU RY.VISN.EL...N...F.Q.YN...YVT.R..V..Y..TNA..E.N.EKW.SGP-E EQRR...QA..FP...IATENA.T.. Cyse EU EE.T.N..V...KPD..Q..Y.H...R.YV..D.RV.EY...SN.KAW.E.P-E VIQRRNE..R..VY.V.I..N.A.T.. Scma DQ YEFVESS.V...K.D...F.K.Y...YT...V..Y...RN??NKDTG--D AA.R...L..V.KT?E.A.T.. Savi AY Y.E.AL...V...SD...Y.T.F..I.DV...Y...P.L.Y.ENW...PSV AQRR...KY.VDIR.QNA.T.. Eslu BT YYEQR.VQ.R.T.KD.Q.A.L.D.YVF..V.YI..N.TV.EY...H..FN.KRW.S.T.Q AAERSELDRF.KP.A.I...N..D.T noncichlid Percomorpha outgroup 2

3 Supplementary Figure 1 continued: Beta Auha L13222 VQPSVKLHSMKPASSHHPAMLVCSVYDFYPSEIKVSWLRDGKEITSDVTSTEEMADGDWYYQTHSHLEYTPRSGEKISCVVEHASLKEPLKTDW Auha S Auha L T...TT.L..Q...I...Q...I... Puny 2027 AP.T...TT...V...Q.V... Puny 741 AK.YI...T.L..Q...I...F...N.Q...K...DK..I... DFB-like Maze 466a AT.Y.R...ST.P.GI.Q...KN...Q.VSA...K...EK..I... Maze 466b AT.Y.R...ST.P.GI.Q...KN...Q.VSA...K...EK..I... Puny 1050 AK.Y.R...ST.P.GI.Q...KY...Q.VSA...K...DK..I... Cyfr L13232 AE.Y.R...ST.P.GN.Q...KY...EKVSA...I... Cyfr L13230 AK.Y.R...ST.P.G..Q...KY...EKVSA...E... Orni JN AK.Y.R...ST.P.GN.Q...F.KN...EKVSA...K...I... Asbu 900 AK.Y.R...ST.P.GI.Q...KY...Q.VSA...K...I... DFB-like Orni JN AP.T...T..L...K.R...H.N.E.V...K...K...EK..I... Puny 422a AP.T...TT.L...F..K...H...Q.V...E...S.CY...ER..I... DBB-like Orni XM_ A..T...TT.L...F..K...H...Q.V...E...CY...EK..I.N. Cyfr L13231 AK.Y...TIT...Q...F..K...Q.V...I... Orni XM_ AK.Y...TM.L...F...Q...Q.V...EK..I... DEB-like Nebr 279b AK...T...Q...F...H...E.V...K...EK..I... Cyfr L13233 AK.Y.R...T...F..K...H.N.Q.V... Maze 486a.K.Y...T...K...Q.V... DEB-like Auha L13224.K.Y...T..Y.Q...K...Q.V...K...EK..I... Orni JN K.Y.R...TT...Q...K...Q.V...K...EK..I... Orni JN AK.Y.R...TT...Q...F..K...Q.V...F...K...EK..I... Orni XM_ R...RIK.KT.L.GQ...N.F.RK...QKV...Q..PN...N...I... DEB-like Orni XM_ AK.Y...TT.DY...F..K...Q.V...K...EK..I... Orni JN S.T.RIQ.SAAS.G...KY...Q.V...K...EK..I... Orni JN S.T.RIQ.SAAS.G...KY...E.V...I...K...I... Nebr 375b.HLT.RIQ.SAAS.G...F..K...V...K...K...I... Orni JN AS.T...M.V..Q...F...R...L...K...EK..I... Orni JF K.Y.R...TA.L...R...K...Q.V...DK..I... Asbu 698.K.Y.R...T.L..Q...R...K...Q.V...K...EK..I... DFB-like Maze 486b.K.Y...T...K...Q.V...K...EK..I... Orni JN AK.Y.R...TT.L..Q...R...K...Q.V...K...EK..I... Orni JN AK.Y.R...TT.L..Q...R...K...Q.V...K...DK..I... Nebr 279a AK.Y.R...T..L...Q.VS...K...EK..I... DFB-like Orni XM_ ?K.Y...T...F..K...Q.VS...K...EK..I... Nebr RIK.KT.L.G*N...S...F...N.R...Q.V...GK.SN..*...Y...P...V...I... DCB-like Orni XM_ R.RIK.KT.L.GQ...F.TK...Q.VY...V.PN...K...V..S...I... Orni XM_ R.R.RIK.KT.L.GQ...F.NK...R...EQ.V...V.PN...Y...V..S...I... Orni XM_ ??????????????????????????????????????????????????????...I...K...EK..I... Orni XM_ RIK..T.P.GQ...F..K...QAVS..I...PN...Q...I... Asbu RIK.KT.L.GQ...F...Q.V...K...N...Y...N...I... Puny RIK.KT.L.GQ...F...Q.V...K...N...Y...N...I... Maze 530a...RIN.KT.L.G...F...Q.V...K...N...Y...N...I... Nebr RIK.KT.L.G...F...Q.V...N...Y...N...I... Orni XM_ K...R..-SI.PVYLN..I...N...K...N.QQVSP.I...V.F.NA..L...YM...M...V... DDB-like Orni XM_ K...R..-SI.PVYLN..I...N...K...N.QQVSP.I...V.F.NA..L...YM...M...V... Orni XM_ K.F.R..WT..PVD...I.A..I...KY...T...N.QRV..NT.T...LP.A..F..???????????????????????????????? Puny 422b AK.F.R..WT..PID...I.A...KY...N.Q.V..NT.A.D.LP.A..F...Y...M...ER..V... Maze 340.K...R...TMAPGC...KL...N.Q.T...I...F.N...L..V...M...M...D...IIN. Orni XM_ T...R...TMAPGC...KL...N.Q...I...F.N...L..V...M.K...M...EK..IIN. Orni XM_ T...R...TMAPGC...KL...N.Q...I...F.N...L..V...M...EK..IIN. Asbu 1137.K...R...TMAPGR...KQ...N.Q.T...I...F.N...L..V...I...M...DK..IIN. Orla AB R.RVQ.LA.SGG...KT.R...GKE.VS...A..E...I...K...D..V... Pore Z54077.A.T...RT.PAG...S...R...KT...H...Q.V...T.D..E...V..T...R...R...PT...V... Ximu EU A.T.R.Y.TT.PAG...S...R...KT...Q...Q.V...T.D..E...V..Q...R...R...V...I... Xipy EU A.T.S...TT.PAG...S...R...KT...Q...Q.V...T.D..E...V..Q...R...R...V...I... Gaac AY AE.Y.R...ET.PGGGPLS...KK.I.R.T...RPE.TG...D.L...I..SK..V... Lacr EF AK.Y.R...VT.PGG...S...F...QH...I...Q.V...D.L..A...I...I... Mimi HM AE.Y.M...VT.PGG...S...F...KH...Q.V...D.L..A...I...A...Y...I..C Epak EU AE.Y.R...VT.SGGK.S...FN...KK...V...D.L...I...R...V... Epak EU AK.Y.I.S.TS.SGGK.S...F...KK...V...D.L...I...R...V... Epco GU AE.Y.R...VT.SGGK.S...F...KK...V...D.L..A...I...R...V... Pama AY AK.Y.R.Q.VT.SAGK.QS.S...F..F.KL...F...Q.V...D.L...F..I...V... Pama AY AK.Y.R.Q.VT.SAGK.QS.S...F..F.KL...F...Q.V...D.L...F..I...V... Dila DQ K.Y.R.R.VA.PAGK..S...F.KH.R...Q.V...D.L..A..F..I...R...V... Mosa L V...VA.PAGK..S...F.KH.R...Q.V...P.D.L..A..F..I...V... Paol AY AK.Y.R.N.VA.PAGK.-...F...KR...Q...Q.V...D.L...I...M.K...SK..I... Veva GU K...T...VA.PAGK...I...F.KR.R...Q...Q.V.H...D.L...F..I...SK..I... Cyse EU AE.Y.R...ET.PAGK..S...KQ.S...R...Q.VST...D.L...F..I...SK..V... Scma DQ K.Y.R...EEHHGGK..TV...F...KR.R...QI.E..V..G...D.L..S...I...V...V... Savi AY AE.Y.R.S.TASPGGK.S...KQ.R...T...Q.V...D.L...I...M...R...I... Eslu BT AK...RIS.VT.P.GI.T...M..A.E...KP.R.T.Q...H..K...I...L...I..Q...K...M...S..P..MVY.. noncichlid Percomorpha outgroup 3

4 Supplementary Figure 1 continued: Connecting peptide + transmembrane region + cytoplasmic tail Auha L13222 D----PSMPESERNNVAIGASGLILGLILSLAGFIYYKRKAR Auha S Auha L L...KL... Puny KL...R... Puny KL... DFB-like Maze 466a.PS--S...KL... Maze 466b.PS--S...KL... Puny 1050.PS--S...KL... Cyfr L13232.PS--S...KL... Cyfr L13230.PS--S...KL...R... Orni JN PS--S...KL...R... Asbu 900.PS--S...KL... DFB-like Orni JN KL... Puny 422a.PSSSSF..KT..DKL.V...L.C...L...RQR.. DBB-like Orni XM_ PSSSSF..KI..YKL...C...RQR.. Cyfr L Orni XM_ KL...V... DEB-like Nebr 279b.PS--S...KL...R... Cyfr L KL... Maze 486a KL... DEB-like Auha L13224 G----S...KL... Orni JN PSSDS...KL...R... Orni JN PSSES...KL...R... Orni XM_ PPSDK.T...TTL-I...I.T...L...FL.RW... DEB-like Orni XM_ PSSDS...KL...R...Q Orni JN PSSDS...KL...R... Orni JN KL... Nebr 375b KL... Orni JN PSSDS...KL...V... Orni JF PS--S...KL...R... Asbu 698.PSSDS...KL... DFB-like Maze 486b.PSSES...KL... Orni JN PSSDS...KL...R... Orni JN PS--S...KL...R... Nebr 279a.PS--S...KL...R... DFB-like Orni XM_ S...KL...R... Nebr 102 EPSSDK.TS.TTTM-I...I.T...L...F.RL..S DCB-like Orni XM_ PSSDK.TS..TPL-T...I.T...L.V.Y.F.RW... Orni XM_ ESSSDK.TS..TPL-T...I.T...V.L...F.RW... Orni XM_ PSSDS...KL...R... Orni XM_ PSSDK.TS..TTL-I...I.T...L...F.RWR.. Asbu 1034 EPSSDK.T...TML-I...I.T...L...CFL.RW..A Puny 749 EPSSDK.T...TML-I...I.T...L...CFL.RW..A Maze 530a EPSSDK.T...TTL-I...I.T...L...CFL.RW..P Nebr 286 EPSSDK.T...TTL-I...I.T...L...CFL.RW..P Orni XM_ V S..KKL-MIV..F...LFF...V..TRMCS. DDB-like Orni XM_ V S..KKL-MIV..F...LFF...V..IRMCS. Orni XM_ ?????????????????????????????????????????? Puny 422b V S..KKL-MIV..F...LFF...V..TRMCS. Maze 340 V----.P...T..L-IIV..I...FV..V..-R..SG Orni XM_ V----.P...T..L-IIV..V...F...V..-R..SG Orni XM_ V----.P...T..L-IIV.VV...F...V..-R.RSG Asbu 1137 V----.P...T..L-IIV..I...FV..V..-R..SG Orla AB K...V... Pore Z54077 E D.D..KL... Ximu EU L...KL...VK Xipy EU L...KL...VK Gaac AY N K...T... Lacr EF L...KI... Mimi HM S----R...KI... Epak EU KI...V... Epak EU KI...V... Epco GU KI...V... Pama AY KI...T... Pama AY KI...T... Dila DQ KI... Mosa L KI... Paol AY KI...T...T...Q Veva GU Q..KI...T...T...Q Cyse EU KI...R..V. Scma DQ KI...T...T. Savi AY KL...V... Eslu BT KI...V..A.IA...LV...K.SA noncichlid Percomorpha outgroup 4

5 Supplementary Figure 2: Recombination events detected using nucleotide alignment across cichlid MHC sequences. Nucleotide sequences were translated in amino acids for simpler visualization. Recombinant sequence is printed on the top of the alignment. Putative parental sequences are shaded. Note that recombination events are ancient and that mutations might have occurred after the recombination event. Some sequences could not yet be assigned to a region of the cichlid MHC. For the phylogenetic position of these sequences see figure 1 in the main article. Recombination event 1 (p-value: 0.001; mutations saved by introduction of recombination event: 21) Puny 2027 unknown MASSFLCLSLLFISLSTADGFMYYMVERCQFNSTDPKDIELITSWYYNKIEVNRFSSSLGKFVGYTKYGVYNAEYWNSGAFL-NTMRAEKERYCLHNIGVWNSNILSKSAPPTVKLHSTTPASSHHPAMLVCSVYDFYPSEIKVSWVRDGQEVTSDVTSTEEMA Orni JN unknown...g...n.v.g..d...qf.n.y...mm..v..d.nv.ey...ef..k...a..kdqgrla...q..tv.vp...k.l...k.r...h.n.e... Maze 486a DEB-like...EM..MS..N...ELQ...Y.R.Y.FR.V.FT..D..V..Y...E...K...A..NQPGQLAR...K..T..HN...DYQVA.T..VK.Y...M...K...L Puny 2027 unknown DGDWYYQTHSHLEYTPRSGEKISCVVEHASLKEPLKTDWDPSMPESERNKLAIGASGLILGLILSLAGFIYYRRKAR Orni JN unknown...k...k...ek..i...k... Maze 486a DEB-like...K... Recombination event 2 (p-value: 0.001; mutations saved by introduction of recombination event: 20) Orni XM_ DCB-like MASSFVCFTLLLISIHTADGFLEYMVERCKFNSTELKDMEYIYSHYYNKIEYIRFSSSVGKYVGVTEFGENLAKHWNNDTEELNSTRSKIVTYCLNNIDIHDRAILAKSVQPRVRIKSKTPLSGQHPAMLVCSVYDFFPTKIKVSWLRDGQEVYSDVTSTEVMP Orni XM_ DCB-like...LR..F.F...I...I.D..E...E...D..V...R...N.AL...A...S..G...I...R.S...N...R... K.T...QE. Orni XM_ DCB-like...LY-.F.F...I.D..E...EQ...F..Y.VM..EIL..N.AL...S.QM.TE..YH...V..Q..I...R...N....R...E...T... Orni XM_ DCB-like NGDWYYQTHSHLEYKPRSGEKISCVVEHVSLSEPLITDWDPSSDKSTSESTPL-TAIGASILTLGLILLLVGYIFYRWKAR Orni XM_ DCB-like...T...N...A..K...P...P...T.-I...A.FFL... Orni XM_ DCB-like...Y...T...ES V...A.F... Recombination event 3 (p-value: 0.002; mutations saved by introduction of recombination event: 19) Orni JN unknown MASSFLCLSLLFISLSTADGFLEYNVWRCAFTSTDLKDIEFYFSYNYNKIKYIEFSSSLGKFVGYTELGVKNAEAWNK-QGDLASWRAQKEVYCKPNIDVDYRSALTKSASPTVKLHSMMPVSSQHPAMLVCSVYDFFPSEIRVSWLRDGKELTSDVTSTEEMA Orni JN unknown...n.v...q...ndpae..tr..d..r..qh..giwnsni.s..v...riq.saas.gh...y.ky.k...e.v... Orni JN DFB-like...M..Y.S..D.N.SE...YT...Y...E.AR...V.EY..F..F..H..DI...DKARM.T...T..Q...GI..NNV.S...K.Y.R...TT.L...R...Y..K.K...Q.V... Orni JN unknown DGDWYYQTHSHLEYTPRSGEKISCKVEHASLEKPLITDWDPSSDSSMPESERNKLAIGASGLILGLILSLAGFVYYKRKAR Orni JN unknown...i...ke p...i... Orni JN DFB-like...I..R... 5

6 Supplementary Figure 2 continued: Recombination event 4 (p-value: 0.002; mutations saved by introduction of recombination event: 18.2) Puny 1050 DFB-like MASSFLCLSLLFISLSTADGFMNYVVSRCDFNSTELKDIQYINSYYYNMMEVVRFDSNVGEYVGYTDFGVKQAKYFNSIPGRLASDRAQKETYCHNNIGVDYSNILSKSAKPYVRLHSSTPPSGIHQAMLVCSVYDFYPKYIKVSWLRDGQEVSADVTSTEEMA Puny 741 DFB-like...IK...M..L.SQ.P...I...F.SE...N...ITS... Asbu 900 DFB-like...M.TG.V...TF.R...S..K...N.ADW.KDQ.D..AM...G...VH...WN.AV... Maze 466a Maze 466b Puny 1050 Puny 741 Asbu 900 Maze 466a Maze 466b DFB-like...RMA..V...F.D...Q...E...L...AV...T...N... DFB-like...RMA..V...F.D...Q...E...L...AV...T...N.... DFB-like DGDWYYQTHSHLEYTPRSGEKISCKVEHASLDKPLITDWDPSSSMPESERNKLAIGASGLILGLILSLAGFIYYKRKAR DFB-like...--P... DFB-like...KE... DFB-like...E... DFB-like...E... Recombination event 5 (p-value: 0.001; mutations saved by introduction of recombination event: 16) Orni JN unknown MASSFLCLGLLFISLSTADGFMNYVVGRCDFNSTDPKDIQFINSYYYNMMEVVRFDSNVGEYVGYTEFGVKNAEAWNKDQGRLATMRAQKETVCVPNIGVWNSNILSKSAPPTVKLHSTKPLSSHHPAMLVCSVYDFYPSKIRVSWHRNGEEVTSDVTSTEEMA Puny 741 DFB-like...S...S...EL...Y...D...Q.KYF.SIP...SD...Y.HN...DY...K.YI...MT...Q...I...F..E.K...L...Q.I... Puny 1050 DFB-like...S...S...EL...Y...D...Q.KYF.SIP...SD...Y.HN...DY...K.Y.R...ST.P.GI.Q...KY.K...L.D.Q..SA... Nebr 279a DFB-like...S...E.Y.W...EL...E..Y.M...KI.YA..S.S...F..F.KY..N..DI..S.K.QV. AW...LQH..NFY..P...K.Y.R...E.K...L.D.Q..S... Orni JN unknown DGDWYYQTHSHLEYTPKSGEKISCKVEHASLEKPLITDWD--PSMPESERNKLAIGASGLILGLILSLAGFIYYKRKAR Puny 741 DFB-like...R...D Puny 1050 DFB-like...R...D...PSS... Nebr 279a DFB-like...R...PSS...R... Recombination event 6 (p-value: 0.001; mutations saved by introduction of recombination event: 14.4) Orni JN unknown MASSFLCLSLLFISLSTADGFLEYNVWRCAFTSTDLKDIEFYFSYNYNKIKYIEFSSSLGKFVGYNEVGVKQAEAWNNDPAELATRRADKERYCQHNIGIWNSNILSKSVSPTVRIQSSAASSGHHPAMLVCSVYDFYPKYIKVSWLRDGQEVTSDVTSTEEMA Orni JN DFB-like......E... Orni JN DFB-like...M..Y.S..D.N.SE...YT...Y...E.AR...V.EY..FT.F..HN.DI..K.K.RM..W..Q..T...P...DYN.V...AK.Y..LH.TTPL.SQ...R...SK... Orni JN unknown DGDWYYQTHSHLEYTPRSGEKISCKVEHASLEKPLITDWDPSSDSSMPESERNKLAIGASGLILGLILSLAGFIYYRRKAR Orni JN DFB-like...I...KE P...K... Orni JN DFB-like... Recombination event 7 (p-value: 0.001; mutations saved by introduction of recombination event: 13.2) Nebr 279b DEB-like MASSFLCLSLLFISLSTADGFMMYWVSRCKFNSTEPQDIEFIRSYYFRKVEFTRFDSSVGKYVGYTEYGVRNAEAWNKDQGDLAAMNAKKETYCQHNIGIWYSNILSKSAKPSVKLHSMTPASSQHPAMLVCSVYDFFPSEIKVSWHRDGEEVTSDVTSTEEMA Cyfr L13231 DEB-like...G...S.D..N...L...E...K.N...Q.G...L...V.N...Y...TIT...K...L...Q... Nebr 279a Maze 486a DFB-like...E.Y.W..D...LK...Y.M.YN.I.YA..S...EF..F.K...N..DI..S.K.QV..WR.Q...V.LQH..NF...P...Y.R...TK.L..H...Y...L...Q..S... DEB-like...E..MM...N...L...Y...K...NQP.Q..R.R...HN...VD.QVA.T..V..Y...H...Y..K...L...Q... Nebr 279b DEB-like DGDWYYQTHSHLEYTPRSGEKISCKVEHASLEKPLITDWDPSSSMPESERNKLAIGASGLILGLILSLAGFIYYRRKAR Cyfr L13231 DEB-like...I...V...KE..K...--P...NV...K... Nebr 279a DFB-like... Maze 486a DEB-like...V...KE..K...--P...K... 6

7 Supplementary Figure 2 continued: Recombination event 8 (p-value: 0.005; mutations saved by introduction of recombination event: 13.0) Orni XM_ DCB-like MASSFLY-TFLFISIHTADGFLEYIVDRCEFNSTELKDMEYIYSHYYNKIEYIRFSSSVEQYVGFTEYGVMLAEILNNNTALLNSSRQMITEYCYHNIDVHDQAIIAKSVRPRVRIKSKTPLSGQHPAMLVCSVYDFFPNKIKVRWLRDEQEVTSDVTSTEVMP Asbu 1034 DCB-like...CF.L...R...R.E...A..HI...R..K...GK...H..E..MLW...R...M...V...R.VL...Q.S...SE...S...G...KE.A Nebr 286 DCB-like...CF.L...R...R...A..HI...R..K...GE...H..K..TLW..D..R...M.R...A...Q..N...R.VL...Q.S...H...SE...S...G...E.A Orni XM_ DCB-like.L.L...M.E..K...GK...V..F.EN..KHW..D.EE T.SK.VT..LN...I..R..L...Q...T...S...G...Y... Orni XM_ DCB-like NGDWYYQTHSYLEYTPRSGEKISCVVEHVSLSEPLITDWESSSDKSTSESTPL-TAIGASILTLGLVLLLAGFIFYRWKAR Asbu 1034 DCB-like...N...A..K...P...P...M.-I...I...CFL...A Nebr 286 DCB-like...N...A..K...P...P...T.-I...I...CFL...P Orni XM_ DCB-like...H...K...DP I...V.Y... 7

8 Supplementary Figure 3: Maximum likelyhood cladogram based of 293 perciform MHC class IIB b sequences from GenBank. Support values are based on 100 bootstrap replicates. Numbers in brackets indicate the number of sequences of a particular perciform family used in this analysis. 8