#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. This data file is distributed with MrBayes, but Mark Holder added a simple nj (on pdistances) tree so that the file can be used with CIPRES services that require a starting tree. ] 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 trees; [Treefile saved Thu Sep 15 16:45:49 2005] [!>Neighbor-joining search settings: > Ties (if encountered) will be broken systematically > Distance measure = mean character difference > (Tree is unrooted) ] tree nj = [&U] (Struthio_camelus:0.06824,((Rhea_americana:0.00267,Pterocnemia_pennata:0.00983):0.03906,(Casuarius_casuarius:0.03428,Dromaius_novaehollandiae:0.01636):0.06520):0.01516,((((((Nothoprocta_cinerascens:0.10660,Eudromia_elegans:0.10119):0.14543,(((((Chauna_chavaria:0.04081,Anseranas_semipalmata:0.04058):0.03361,(((Dendrocygna_arcuata:0.00130,Dendrocygna_viduata:0.02251):0.01909,Dendrocygna_autumnalis:0.00458):0.00674,(Dendrocygna_eytoni_d:0.00668,Dendrocygna_eytoni_e:0.00495):0.05187):0.01300):0.00720,((Coscoroba_coscoroba:0.01389,Cereopsis_novaehollandiae:0.04635):0.01461,((Cygnus_atratus:0.00623,((Goose:0.00442,Anser_indicus:0.00721):0.00805,Branta_canadensis:0.01626):0.00529):0.00884,(Chloephaga_picta:0.00542,(Duck:0.00678,Anas_platyrhynchos:0.00484):0.00662):0.02682):0.00122):0.00448):0.02713,(((Ortalis_vetula:0.03860,Penelope_jacquacu:0.00140):0.02932,Penelope_superciliaris:0.00832):0.11855,(((((((((Bonasa_umbellus:0.05979,Arborophilia_torqueola:0.10021):0.01800,((Crossoptilon_auritum:0.00534,(Lophura_edwardsi:0.00689,Lophura_ignita:0.05058):0.00615):0.01037,(((Phasianus_colchicus:0.04163,Syrmaticus_reevesii:0.03883):0.02272,Syrmaticus_ellioti:0.01443):0.00747,Chrysolophus_amherstiae:0.03984):0.00396):0.00363):0.00689,((Tympanuchus_cupido:0.00498,(Tragopan_satyra:0.00927,Tragopan_temmincki:0.00264):0.00693):0.00291,Perdix_perdix:0.04174):0.00204):0.00190,(Lophophorus_impejanus:0.00393,(Numida_meleagris:0.00357,Acryllium_vulturinum:0.00908):0.02015):0.01014):0.00694,Meleagris_gallopavo:0.02047):0.00576,(Argusianus_argus_argus:0.08562,Pavo_cristatus:0.02026):0.02272):0.00080,((Alectoris_chukar:0.00793,Alectoris_rufa:0.00426):0.04785,(((Francolinus_francolinus_a:0.01121,Francolinus_francolinus_v:0.00083):0.14991,Bambusicola_thoracica:0.10626):0.02572,(Francolinus_pondicerianus:0.10320,(Gallus_gallus:0.00582,Grey_jungle_fowl:0.00568):0.09343):0.01028):0.02180):0.00895):0.00426,((((Francolinus_afer:0.02372,(Francolinus_coqui_v:0.00561,Francolinus_coqui_a:0.00658):0.01287):0.01991,Francolinus_erckelii:0.03604):0.05083,Polyplectron_bicalcaratum:0.16526):0.02414,(((Coturnix_delegorguei:0.01838,(Coturnix_coturnix_japonica_1:0.00704,Coturnix_coturnix_japonica_2:0.00445):0.00564):0.12900,Turnix_sylvatica:0.13390):0.02436,Afropavo_congensis:0.04490):0.00641):0.00406):0.00715,((((Oreortyx_pictus:0.02017,(Callipepla_squamata_n:1.677e-05,Callipepla_squamata_s:0.01175):0.01513):0.01171,Lophortyx_californicus:0.01154):0.01972,Colinus_virginianus:0.08193):0.01065,(Cyrtonyx_montezumae_l:0.00388,Cyrtonyx_montezumae_s:0.00847):0.06259):0.01267):0.04867):0.00867):0.00570,(Megapodius_freycinet:0.08218,Leipoa_ocellata:0.10701):0.03042):0.00290):0.01008,(Geococcyx_californianus:0.12853,Carpococcyx_renauldi:0.10039):0.07393):0.02086,Dacelo_novaeguineae:0.10711):0.00876,(((Grus_carunculatus:0.00053,Grus_vipio:0.01110):0.00277,Anthropoides_virgo:0.00886):0.03151,(Fulica_atra:0.03370,Gallirallus_australis:0.09883):0.07778):0.01687):0.00864,((((Pygoscelis_adeliae_f:0.00587,(Pygoscelis_adeliae_y:0.00615,(Spheniscus_humboldti:0.04200,Anhinga_novaehollandeae:0.02858):0.00534):0.00579):0.01305,(Phalacrocorax_sulcirostris:0.05696,Nycticorax_nycticorax:0.10583):0.01541):0.00881,(Vanellus_spinosus:0.02662,Larus_rudibundus:0.04314):0.03695):0.00720,Podargus_strigoides:0.10255):0.01435):0.03667); end;