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| author | nml |
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| date | Tue, 15 Dec 2015 14:26:53 -0500 |
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#NEXUS [ Data from: Laskowski, M., Jr., and W.M. Fitch. 1989. Evolution of avian ovomucoids and of birds. Pp. 371-387 in B. Fernholm, K. Bremer, and H. Jornvall (eds.), The Hierarchy of Life. Elsevier Press, Amsterdam. ] begin data; dimensions ntax=89 nchar=88; format datatype=protein missing=? gap=- matchchar=.; matrix [ 10 20 30 40 50 60 70 80 ] [ . . . . . . . . ] Struthio_camelus VKYPNTNEEGKEVVLPKILSPIGSDGVYSNELANIEYTNVSK??????FAT--VDDYKPVPLDYMLDSKTSNKNNVVESSGTLRHFGK Rhea_americana .............L..E..N.V.T................?.D?????...--...H...S.E..........D.....N...S.... Pterocnemia_pennata .............L..E..N.V.A..................DHD?EV...--...H...S.E..........D.....N...S.... Casuarius_casuarius ........D....L.....N.........DD......A....DHDKEV...--..E....SPE.......N..DS....N...G.... Dromaius_novaehollandiae ........D....L.....N..........D......A..??D?????...--.......S.E.......N..D.....N...G.... Nothoprocta_cinerascens .....A.D.....P...TP...A.NA.FGS....V....I..DHDK?????T-..G...AT.E.F..NQ.A..A....KNV....L.. Eudromia_elegans .R.....D.....P...TP..V.AN....S....V....I?.?????????S-I.G...AT.EFF..NQ....A.A..KNV..N.I.E Pygoscelis_adeliae_f .TF..........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S.... Pygoscelis_adeliae_y .T...........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S.... Spheniscus_humboldti .T.S.........LIT.......T..................D?DKEVI..--I......S.E..............D.N.I.S.... Phalacrocorax_sulcirostris .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S.... Anhinga_novaehollandeae .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S.... Nycticorax_nycticorax .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S.... Chauna_chavaria .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S.... Anseranas_semipalmata .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S.... Dendrocygna_arcuata .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S.... Dendrocygna_autumnalis .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S.... Dendrocygna_eytoni_d .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S.... Dendrocygna_eytoni_e .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S.... Dendrocygna_viduata .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S.... Coscoroba_coscoroba ..F..........L.T.D.I...T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S.... Cygnus_atratus .RF..........L.T.D.....T...............I..DHDKEAV..--......ATME....N..G......D.N...S.... Goose .RF..........L.T.D.....T...............I..DHDKEAV..--......ATVE....N..D......D.N...S.... Anser_indicus .RF..........L.T.D.A...T...............I..DHDKEAV..--......ATVE....N..D......D.N...S.... Branta_canadensis .RF.......R..L.T.D.....T...............I..DHD???V..--......ATVE....N..G......D.N...S.... Cereopsis_novaehollandiae ..F..........L...DVI.T.T...............I..D?D??AV..--......ARME....N..G......D.N...S.... Chloephaga_picta .RF..........L.T.E.....T...............I..D??KEAV..--..G...ATME....N..G......D.N...S...E Duck .RF..........L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E Anas_platyrhynchos .RF........D.L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E Megapodius_freycinet .R...........LVTQDV?...T....?....G...??I????????LV.--......ST.EDK..NQ....S...D.N...S.... Leipoa_ocellata IRH..........LVTEDS....T...............I..E?DK??VV.--..G.THAT.ELK..NQ....G..AQ.N...S.... Ortalis_vetula ...........D.LA.EDPNL.......T-.......???????????..PN-...H..ALQEQKI.N..D..S...D.N...S.... Penelope_jacquacu ...........D.LA.EDP.........T-.........I..ERDKEA..PN-...H..ALQEQK..N..D..S...D.N...S.... Penelope_superciliaris ...........D.LVAEDP....................I..E?DKEA..PN-...H..ALQEQK..N..D..S...D.N...S.... Bonasa_umbellus .RF........V.LV.EDPR...T.A.....M.......I..EHD???L.AS-..E...ATME.R..N..G........N.N.S...T Tympanuchus_cupido .RF........D.LVTED.H...T...............I..EHD???L.AS-..E...ATME.R..N..G........N...S.... Oreortyx_pictus .RF........D.LAT.E.H...T........S......I..EHDTEA..AS-..E...AT.E.R.....A........N...S.... Callipepla_squamata_n .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..A........N...S.... Callipepla_squamata_s .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..AS.......N...S.... Lophortyx_californicus .RF........D.LVT.E.Q...T........Y......I..EHD?EA..AS-..E...AT.E.R..N..A........N...S.... Colinus_virginianus .RF........D.LATEE.H...T....MS.MF......T..EHDTEA..AS-..E...AMSE.R..N..V........N...S.... Cyrtonyx_montezumae_l .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...AT.E.VI.N..G........N...S.... Cyrtonyx_montezumae_s .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...ATSE.VI.N..G........N...S.... Alectoris_chukar ARF..A.....D..VTED.R...T....T-.........I..EHDGETL.A--..E...AT.E.R.....G........N...S.... Alectoris_rufa ARF..A.....D..VTED.H...T....T-.........I..EHD???L.A--..E...AT.E.R.....G........N...S.... Francolinus_afer .RF..A....RD..VSEN.R...TH........SM....I..EHDREAP.AS-..E...ATME.RV.NI.G......K.N...S.... Francolinus_erckelii .RF..A.....D.AVSEN.R...T...N-.....M....I??EHD?EAP.AS-..E...ATME.RV.NI.G......K.N...S.K.. Francolinus_coqui_v .RF..A....RD..VSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S.... Francolinus_coqui_a .RF..A....RD.AVSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S.... Francolinus_francolinus_a ARF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........ Francolinus_francolinus_v .RF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........ Francolinus_pondicerianus ARFS.A.....D.LVIDDPR.M.T....DS..F.M....I..EHD???LPAS-..E...DTTEER..N..G........N...S.... Perdix_perdix .RF........D.LVTED.Q...T...............I..EHT???L.AS-..E...ATME.R..N..G..D.....N...N.... Coturnix_delegorguei .RF........DE.V.DE.RF..T....NH.MF.K....I..EQDGET???S-..E...A.K..RV.N..G........N...NR... Coturnix_coturnix_japonica_1 .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N...........N...N.... Coturnix_coturnix_japonica_2 .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N..G........N...N.... Arborophilia_torqueola .RF..S.....V..VKEDPR...T.........H..T??I?.?????????S-....M.ATME.RV.N..G........N...S.... Bambusicola_thoracica ARF..A.....V.LDTQE.R...T.......MS......I.IK?DKE?L.AS-..E...ETAEERI.N..G........N....N... Tragopan_satyra .RF........D.LVTED.H...T...............I..GHDREAL.AS-..E...ATME.R..N..G........N...S.... Tragopan_temmincki .RF........D.LVTED.R...T...............I..GHD???L.AS-..E...ATME.R..N..G........N...S.... Lophophorus_impejanus .RF..A.....D.LVTED.R...T...............I..EHDREAL.AS-..E...ATME.R..N..G........N...S.... Crossoptilon_auritum .RF........D.LVAED.R...T...............I..ERDGEAL.AS-..E...ATME.R..N..G........N...S.... Lophura_edwardsi .RF........D.LVAED.R...T.......M.......I..ERDGEAL.AS-..E...ATME.R..N..G........N...S.... Lophura_ignita .RF........D.LVGEDIR...T.......M.......N..ERDGEAL.AS-..E...ATME.R..N.SD........N...S.... Gallus_gallus ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTAEDR..N..G........N...S.... Grey_jungle_fowl ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTVEDR..N..G........N...S.... Phasianus_colchicus .RF..........LVAED.R.V.T.....S.........I..EHEGEAL.AS-..E...ATME.R..N..G........N...NR..Q Syrmaticus_ellioti .RF..K.....D.LVAED.H...T...............I..ER?G??L.AS-..E...ATME.R..N..G........N...S.... Syrmaticus_reevesii .RF..K.......LVAED.H...T.....S.........I..ERNGEAL.AS-..E...ATME.R..N..G........N...SR..E Chrysolophus_amherstiae .RFL.....S.D-LVAED.H...T...............I..EHDG?AL.AS-..E...ATME.R..N..G........N...N.... Polyplectron_bicalcaratum .RF....K...D.LA.EEVR...T.....D.S..RD...I..EHDR?????S-..E.Q.TTTEHRVNNE.G......K.N..VS.... Argusianus_argus_argus .RF........D.LVSEDRH...T.....H..T......I..EHD?EAL.A--..EH..AT.EDR..N.I...D..L..N...S.... Pavo_cristatus .RF..A.....D.LVSED.H...T.....H.........I..EHDREAL.AS-..E...AT.EHR..N..G........N...S.... Afropavo_congensis .RF........D.SAS.D.R...T.....H.........I..EHDGEAL.AS-..E...ATMEQR..N..G........N...S.... Numida_meleagris .RF..A.....D.LVTED.R...T......D........I.?????EAL.A--..E...ATME.R..N..D........N...S.... Acryllium_vulturinum .RF..A.....D.LVIED.R...T......D........I..EHD???L.A--..E...ATME.R..N..D........N...S.... Meleagris_gallopavo .RF........D.LVTED.R...T...H.-.........I..EHDREAL.AS-..E...AT.E.R..N..G........N...S.... Grus_carunculatus .T...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S.... Anthropoides_virgo .T...........LVT.......T..................DHDKEVT..--......AT.E..F...........D.N...S.... Grus_vipio IT...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S.... Fulica_atra .T...........LVT.....V.TN......S..........DYDKEVT..--..G.Q.AS.E.VF.N.....D..AD.N...S.... Vanellus_spinosus .T...........LVT.......T..........L.......DYDKEVI..--......AS................D.N...S..E. Larus_rudibundus .T...........LAT.A...V....................DYDKEDI..--......AS................D.N...S..E. Turnix_sylvatica .RF........DT.AD.D.P.........-.M.......I..EHD??T???S-..E...GMMERL..N..ND.......N...N...E Gallirallus_australis .T.........V.LVT.NI..V.TN...T..S.I...S....DYD???T..??..G.QSA.Q..VF.N........AD.N...S.... Geococcyx_californianus .A...A......ALVTTARLH..T....G.....L.H..I..DYNKEVI.S--.N.....S.L....N..G.....AD.N...S.... Dacelo_novaeguineae .......D.....LVTE......T.R................EHDKEAI..-Q..EH..AT...RI.......D..MD.N...S.... Carpococcyx_renauldi .R...S......GLATT.R....T....G.....L....I..DYD???I..--.......T.ED...NI.H..Y..AH.N..FS.... Podargus_strigoides .T.......S...LVDEV.....T..........L.-..I..DRDK??I..--....Q..MG...............D.N...N.... ; end; [ begin mrbayes; [The following line will let the mcmc chain integrate over the ten fixed amino-acid rate matrices. You can also fix the rates to those in one of the rate matrices.] prset aamodelpr=mixed; end; ]