| blob | 85d599f3f471be18e974f31afc0604fa59080ddb |
1 #NEXUS
4 BEGIN DATA;
5 DIMENSIONS NTAX=89 NCHAR=88;
7 [!Data from:
9 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. Jšrnvall (eds.), The Hierarchy of Life. Elsevier Press, Amsterdam.
11 Thanks to Walter Fitch for supplying the data matrix, March 1990.]
12 FORMAT DATATYPE=PROTEIN SYMBOLS = " 1 2 3 4" MISSING=? GAP=- MATCHCHAR=. ;
13 MATRIX
14 [ 10 20 30 40 50 60 70 80 ]
15 [ . . . . . . . . ]
17 Struthio_camelus VKYPNTNEEGKEVVLPKILSPIGSDGVYSNELANIEYTNVSK??????FAT--VDDYKPVPLDYMLDSKTSNKNNVVESSGTLRHFGK [86]
18 Rhea_americana .............L..E..N.V.T................?.D?????...--...H...S.E..........D.....N...S.... [86]
19 Pterocnemia_pennata .............L..E..N.V.A..................DHD?EV...--...H...S.E..........D.....N...S.... [86]
20 Casuarius_casuarius ........D....L.....N.........DD......A....DHDKEV...--..E....SPE.......N..DS....N...G.... [86]
21 Dromaius_novaehollandiae ........D....L.....N..........D......A..??D?????...--.......S.E.......N..D.....N...G.... [86]
22 Nothoprocta_cinerascens .....A.D.....P...TP...A.NA.FGS....V....I..DHDK?????T-..G...AT.E.F..NQ.A..A....KNV....L.. [87]
23 Eudromia_elegans .R.....D.....P...TP..V.AN....S....V....I?.?????????S-I.G...AT.EFF..NQ....A.A..KNV..N.I.E [87]
24 Pygoscelis_adeliae_f .TF..........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S.... [86]
25 Pygoscelis_adeliae_y .T...........LVT.......T..................DHDKEVI..--.......S.E..............D.N...S.... [86]
26 Spheniscus_humboldti .T.S.........LIT.......T..................D?DKEVI..--I......S.E..............D.N.I.S.... [86]
27 Phalacrocorax_sulcirostris .S.SK.......ALVT.......T..............KI..DHDKEVI..--.......S.E.............AD.N...S.... [86]
28 Anhinga_novaehollandeae .L.S.........LVT.......T................T.DHDKEVI.S--.......S.E..............D.N...S.... [86]
29 Nycticorax_nycticorax .T.S.A....R..LVT.......A..........M....I..DHDGEVIV.--.......SPEN.V.......D..AD.N...S.... [86]
30 Chauna_chavaria .R...........L.T.T.....T..................DRDKEAV..--......AT.E....NQ....S...D.N...S.... [86]
31 Anseranas_semipalmata .R...S.......L.T.D...................A....DHDKEAV..--..E...AT.E....NQ........D.N...S.... [86]
32 Dendrocygna_arcuata .RF..........L.T.E...V.................I..D?DKEAV..--......AT.E....N..G......D.N...S.... [86]
33 Dendrocygna_autumnalis .RF..........L.T.D.....................I..DHDKEAV..--......AT.E....N..G......D.N...S.... [86]
34 Dendrocygna_eytoni_d .RF..........L.T.DVI.V............L....I..DHDKEAV..--....R.DT.E....N..G......D.N...S.... [86]
35 Dendrocygna_eytoni_e .RF..........L.T.DVI.V............L....I..DHDKEAV..--..E.R.DT.E....N..G......D.N...S.... [86]
36 Dendrocygna_viduata .RFS.........L.T.E...V.................I..D?D?EAV..--......AT.E....N..G.R....D.N...S.... [86]
37 Coscoroba_coscoroba ..F..........L.T.D.I...T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S.... [86]
38 Cygnus_atratus .RF..........L.T.D.....T...............I..DHDKEAV..--......ATME....N..G......D.N...S.... [86]
39 Goose .RF..........L.T.D.....T...............I..DHDKEAV..--......ATVE....N..D......D.N...S.... [86]
40 Anser_indicus .RF..........L.T.D.A...T...............I..DHDKEAV..--......ATVE....N..D......D.N...S.... [86]
41 Branta_canadensis .RF.......R..L.T.D.....T...............I..DHD???V..--......ATVE....N..G......D.N...S.... [86]
42 Cereopsis_novaehollandiae ..F..........L...DVI.T.T...............I..D?D??AV..--......ARME....N..G......D.N...S.... [86]
43 Chloephaga_picta .RF..........L.T.E.....T...............I..D??KEAV..--..G...ATME....N..G......D.N...S...E [86]
44 Duck .RF..........L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E [86]
45 Anas_platyrhynchos .RF........D.L.T.E...V.T...............I..DHDKEAV..--..G...ATME....N..G......D.N...S...E [86]
46 Megapodius_freycinet .R...........LVTQDV?...T....?....G...??I????????LV.--......ST.EDK..NQ....S...D.N...S.... [86]
47 Leipoa_ocellata IRH..........LVTEDS....T...............I..E?DK??VV.--..G.THAT.ELK..NQ....G..AQ.N...S.... [86]
48 Ortalis_vetula ...........D.LA.EDPNL.......T-.......???????????..PN-...H..ALQEQKI.N..D..S...D.N...S.... [86]
49 Penelope_jacquacu ...........D.LA.EDP.........T-.........I..ERDKEA..PN-...H..ALQEQK..N..D..S...D.N...S.... [86]
50 Penelope_superciliaris ...........D.LVAEDP....................I..E?DKEA..PN-...H..ALQEQK..N..D..S...D.N...S.... [87]
51 Bonasa_umbellus .RF........V.LV.EDPR...T.A.....M.......I..EHD???L.AS-..E...ATME.R..N..G........N.N.S...T [87]
52 Tympanuchus_cupido .RF........D.LVTED.H...T...............I..EHD???L.AS-..E...ATME.R..N..G........N...S.... [87]
53 Oreortyx_pictus .RF........D.LAT.E.H...T........S......I..EHDTEA..AS-..E...AT.E.R.....A........N...S.... [87]
54 Callipepla_squamata_n .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..A........N...S.... [87]
55 Callipepla_squamata_s .RF........D.LAT.E.H...T........Y......I..EHD??A..AS-..E...DT.E.R..N..AS.......N...S.... [87]
56 Lophortyx_californicus .RF........D.LVT.E.Q...T........Y......I..EHD?EA..AS-..E...AT.E.R..N..A........N...S.... [87]
57 Colinus_virginianus .RF........D.LATEE.H...T....MS.MF......T..EHDTEA..AS-..E...AMSE.R..N..V........N...S.... [87]
58 Cyrtonyx_montezumae_l .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...AT.E.VI.N..G........N...S.... [87]
59 Cyrtonyx_montezumae_s .RF........D.LVTEEV....T........S..A.?.I.?E?D???..AS-..E...ATSE.VI.N..G........N...S.... [87]
60 Alectoris_chukar ARF..A.....D..VTED.R...T....T-.........I..EHDGETL.A--..E...AT.E.R.....G........N...S.... [85]
61 Alectoris_rufa ARF..A.....D..VTED.H...T....T-.........I..EHD???L.A--..E...AT.E.R.....G........N...S.... [85]
62 Francolinus_afer .RF..A....RD..VSEN.R...TH........SM....I..EHDREAP.AS-..E...ATME.RV.NI.G......K.N...S.... [87]
63 Francolinus_erckelii .RF..A.....D.AVSEN.R...T...N-.....M....I??EHD?EAP.AS-..E...ATME.RV.NI.G......K.N...S.K.. [86]
64 Francolinus_coqui_v .RF..A....RD..VSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S.... [87]
65 Francolinus_coqui_a .RF..A....RD.AVSEN.R...T.........SMN...I..E?D?EA???S-..E...GTME.RV.NI.G......K.N...S.... [87]
66 Francolinus_francolinus_a ARF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........ [87]
67 Francolinus_francolinus_v .RF........V.LDS.D.I...T..LHDS..S...H.KIK.EHDRE????S-..G...ETAEET..N..R........N........ [87]
68 Francolinus_pondicerianus ARFS.A.....D.LVIDDPR.M.T....DS..F.M....I..EHD???LPAS-..E...DTTEER..N..G........N...S.... [87]
69 Perdix_perdix .RF........D.LVTED.Q...T...............I..EHT???L.AS-..E...ATME.R..N..G..D.....N...N.... [87]
70 Coturnix_delegorguei .RF........DE.V.DE.RF..T....NH.MF.K....I..EQDGET???S-..E...A.K..RV.N..G........N...NR... [87]
71 Coturnix_coturnix_japonica_1 .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N...........N...N.... [87]
72 Coturnix_coturnix_japonica_2 .RF........DE.V.DE.RL..T....NH.MF.K....I..EQDGETL.AS-..E...A.K..RV.N..G........N...N.... [87]
73 Arborophilia_torqueola .RF..S.....V..VKEDPR...T.........H..T??I?.?????????S-....M.ATME.RV.N..G........N...S.... [87]
74 Bambusicola_thoracica ARF..A.....V.LDTQE.R...T.......MS......I.IK?DKE?L.AS-..E...ETAEERI.N..G........N....N... [87]
75 Tragopan_satyra .RF........D.LVTED.H...T...............I..GHDREAL.AS-..E...ATME.R..N..G........N...S.... [87]
76 Tragopan_temmincki .RF........D.LVTED.R...T...............I..GHD???L.AS-..E...ATME.R..N..G........N...S.... [87]
77 Lophophorus_impejanus .RF..A.....D.LVTED.R...T...............I..EHDREAL.AS-..E...ATME.R..N..G........N...S.... [87]
78 Crossoptilon_auritum .RF........D.LVAED.R...T...............I..ERDGEAL.AS-..E...ATME.R..N..G........N...S.... [87]
79 Lophura_edwardsi .RF........D.LVAED.R...T.......M.......I..ERDGEAL.AS-..E...ATME.R..N..G........N...S.... [87]
80 Lophura_ignita .RF........D.LVGEDIR...T.......M.......N..ERDGEAL.AS-..E...ATME.R..N.SD........N...S.... [87]
81 Gallus_gallus ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTAEDR..N..G........N...S.... [87]
82 Grey_jungle_fowl ARF..ADK...D.LVN.D.R...T....T.D..S..F..I..EHDKETL.AS-..E...DTVEDR..N..G........N...S.... [87]
83 Phasianus_colchicus .RF..........LVAED.R.V.T.....S.........I..EHEGEAL.AS-..E...ATME.R..N..G........N...NR..Q [87]
84 Syrmaticus_ellioti .RF..K.....D.LVAED.H...T...............I..ER?G??L.AS-..E...ATME.R..N..G........N...S.... [87]
85 Syrmaticus_reevesii .RF..K.......LVAED.H...T.....S.........I..ERNGEAL.AS-..E...ATME.R..N..G........N...SR..E [87]
86 Chrysolophus_amherstiae .RFL.....S.D-LVAED.H...T...............I..EHDG?AL.AS-..E...ATME.R..N..G........N...N.... [86]
87 Polyplectron_bicalcaratum .RF....K...D.LA.EEVR...T.....D.S..RD...I..EHDR?????S-..E.Q.TTTEHRVNNE.G......K.N..VS.... [87]
88 Argusianus_argus_argus .RF........D.LVSEDRH...T.....H..T......I..EHD?EAL.A--..EH..AT.EDR..N.I...D..L..N...S.... [86]
89 Pavo_cristatus .RF..A.....D.LVSED.H...T.....H.........I..EHDREAL.AS-..E...AT.EHR..N..G........N...S.... [87]
90 Afropavo_congensis .RF........D.SAS.D.R...T.....H.........I..EHDGEAL.AS-..E...ATMEQR..N..G........N...S.... [87]
91 Numida_meleagris .RF..A.....D.LVTED.R...T......D........I.?????EAL.A--..E...ATME.R..N..D........N...S.... [86]
92 Acryllium_vulturinum .RF..A.....D.LVIED.R...T......D........I..EHD???L.A--..E...ATME.R..N..D........N...S.... [86]
93 Meleagris_gallopavo .RF........D.LVTED.R...T...H.-.........I..EHDREAL.AS-..E...AT.E.R..N..G........N...S.... [86]
94 Grus_carunculatus .T...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S.... [86]
95 Anthropoides_virgo .T...........LVT.......T..................DHDKEVT..--......AT.E..F...........D.N...S.... [86]
96 Grus_vipio IT...........LVT.......T..................DHDKEAT..--......AT.E..F...........D.N...S.... [86]
97 Fulica_atra .T...........LVT.....V.TN......S..........DYDKEVT..--..G.Q.AS.E.VF.N.....D..AD.N...S.... [86]
98 Vanellus_spinosus .T...........LVT.......T..........L.......DYDKEVI..--......AS................D.N...S..E. [86]
99 Larus_rudibundus .T...........LAT.A...V....................DYDKEDI..--......AS................D.N...S..E. [86]
100 Turnix_sylvatica .RF........DT.AD.D.P.........-.M.......I..EHD??T???S-..E...GMMERL..N..ND.......N...N...E [86]
101 Gallirallus_australis .T.........V.LVT.NI..V.TN...T..S.I...S....DYD???T..??..G.QSA.Q..VF.N........AD.N...S.... [88]
102 Geococcyx_californianus .A...A......ALVTTARLH..T....G.....L.H..I..DYNKEVI.S--.N.....S.L....N..G.....AD.N...S.... [86]
103 Dacelo_novaeguineae .......D.....LVTE......T.R................EHDKEAI..-Q..EH..AT...RI.......D..MD.N...S.... [87]
104 Carpococcyx_renauldi .R...S......GLATT.R....T....G.....L....I..DYD???I..--.......T.ED...NI.H..Y..AH.N..FS.... [86]
105 Podargus_strigoides .T.......S...LVDEV.....T..........L.-..I..DRDK??I..--....Q..MG...............D.N...N.... [85]
106 ;
107 END;
108 BEGIN GENETICCode;
109 StandardNUCLEAR;
110 END;
112 BEGIN CODONS;
113 CODESET * UNTITLED = Universal: all ;
114 END;
116 BEGIN ASSUMPTIONS;
117 OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ;
118 END;
120 BEGIN TREES;
122 TRANSLATE
123 1 Struthio_camelus,
124 2 Rhea_americana,
125 3 Pterocnemia_pennata,
126 4 Casuarius_casuarius,
127 5 Dromaius_novaehollandiae,
128 6 Nothoprocta_cinerascens,
129 7 Eudromia_elegans,
130 8 Pygoscelis_adeliae_f,
131 9 Pygoscelis_adeliae_y,
132 10 Spheniscus_humboldti,
133 11 Phalacrocorax_sulcirostris,
134 12 Anhinga_novaehollandeae,
135 13 Nycticorax_nycticorax,
136 14 Chauna_chavaria,
137 15 Anseranas_semipalmata,
138 16 Dendrocygna_arcuata,
139 17 Dendrocygna_autumnalis,
140 18 Dendrocygna_eytoni_d,
141 19 Dendrocygna_eytoni_e,
142 20 Dendrocygna_viduata,
143 21 Coscoroba_coscoroba,
144 22 Cygnus_atratus,
145 23 Goose,
146 24 Anser_indicus,
147 25 Branta_canadensis,
148 26 Cereopsis_novaehollandiae,
149 27 Chloephaga_picta,
150 28 Duck,
151 29 Anas_platyrhynchos,
152 30 Megapodius_freycinet,
153 31 Leipoa_ocellata,
154 32 Ortalis_vetula,
155 33 Penelope_jacquacu,
156 34 Penelope_superciliaris,
157 35 Bonasa_umbellus,
158 36 Tympanuchus_cupido,
159 37 Oreortyx_pictus,
160 38 Callipepla_squamata_n,
161 39 Callipepla_squamata_s,
162 40 Lophortyx_californicus,
163 41 Colinus_virginianus,
164 42 Cyrtonyx_montezumae_l,
165 43 Cyrtonyx_montezumae_s,
166 44 Alectoris_chukar,
167 45 Alectoris_rufa,
168 46 Francolinus_afer,
169 47 Francolinus_erckelii,
170 48 Francolinus_coqui_v,
171 49 Francolinus_coqui_a,
172 50 Francolinus_francolinus_a,
173 51 Francolinus_francolinus_v,
174 52 Francolinus_pondicerianus,
175 53 Perdix_perdix,
176 54 Coturnix_delegorguei,
177 55 Coturnix_coturnix_japonica_1,
178 56 Coturnix_coturnix_japonica_2,
179 57 Arborophilia_torqueola,
180 58 Bambusicola_thoracica,
181 59 Tragopan_satyra,
182 60 Tragopan_temmincki,
183 61 Lophophorus_impejanus,
184 62 Crossoptilon_auritum,
185 63 Lophura_edwardsi,
186 64 Lophura_ignita,
187 65 Gallus_gallus,
188 66 Grey_jungle_fowl,
189 67 Phasianus_colchicus,
190 68 Syrmaticus_ellioti,
191 69 Syrmaticus_reevesii,
192 70 Chrysolophus_amherstiae,
193 71 Polyplectron_bicalcaratum,
194 72 Argusianus_argus_argus,
195 73 Pavo_cristatus,
196 74 Afropavo_congensis,
197 75 Numida_meleagris,
198 76 Acryllium_vulturinum,
199 77 Meleagris_gallopavo,
200 78 Grus_carunculatus,
201 79 Anthropoides_virgo,
202 80 Grus_vipio,
203 81 Fulica_atra,
204 82 Vanellus_spinosus,
205 83 Larus_rudibundus,
206 84 Turnix_sylvatica,
207 85 Gallirallus_australis,
208 86 Geococcyx_californianus,
209 87 Dacelo_novaeguineae,
210 88 Carpococcyx_renauldi,
211 89 Podargus_strigoides
212 ;
213 TREE * PAUP_1 = [&R] (1,(((2,3),(4,5)),((((((((((6,7),((30,31),(((32,33),34),(((((((35,57),((((53,67),70),(62,(63,64),(68,69))),(((54,(55,56)),84),74))),(((46,(48,49)),47),71)),((36,59),60),(61,(75,76))),(72,73),77),((44,45),((((50,51),58),52),(65,66)))),(((37,((38,39),40)),41),(42,43)))))),14),15),((((16,20),(18,19)),17),((((21,26),(27,(28,29))),22),((23,24),25)))),(78,79,80)),87),((81,85),(82,83))),(8,9,(10,((11,(86,88)),13),12))),89)));
215 END;
218 BEGIN NOTES;
219 TEXT TAXON=26 TEXT= G_removed_from_end_of_sequence;
220 END;
222 BEGIN MACCLADE;
223 Version 3.05;
224 LastModified -1425155265;
225 Singles 1000&/0;
226 END;