#NEXUS [MacClade 4.03 registered to Claude dePamphilis, Penn State University] BEGIN TAXA; DIMENSIONS NTAX=16; TAXLABELS Arabidopsis Nicotiana Oryza Pinus Marchantia Mesostigma Nephroselmis Chlorella Cyanidium Odontella Guillardia Porphyra Cyanophora Chlamydomonas Synechocystis Nostoc; END; BEGIN CHARACTERS; DIMENSIONS NCHAR=245; FORMAT MISSING=? GAP=- MATCHCHAR=. TRANSPOSE ; MATRIX [ 10 ] [ . ] accA 0.......1..1..11 accB 0.......1..1..11 accD 1....0...00.00..[3 orf106, 5 orf316, 8 AccD] acpP 0.......11111.11[11 acpA, 10 acp] apcA 0.......1..11.11 apcB 0.......1..11.11 apcD 0.......1..11.11 apcE 0.......1..11.11 apcF 0.......1..11.11 argB 0.......1..1..11 atpA 1............... atpB 1............... atpD 0.......11111.11 atpE 1............... atpF 1............... atpG 0.......11111.11 atpH 1............... atpI 1...........0... carA 0.......1..1..11 ccsA 1...............[1 ycf5,2 ycf5,3 orf321,4 orf320, 5 small,8-13 ycf5] cemA 1........0..0...[2 hypothetical 3 orf230,4 orf261,5 orf434,8-9 ycf10,] cfxQ 0.......1111..11[9 cfxX,12 orf301] chlB 0..11111...11111[5 orf513] chlI 0....11111111111[add 14chlI] chlL 0..11111...11111[5 frxC] chlN 0..11111...11111 clpC 0.......1111..11 clpP 1.1.....0000....[3 rps12, 5 orf203] cobA 0.......1.....11 cpcA 0.......1..11.11 cpcB 0.......1..11.11 cpcG 0.......1..1..11 cpeA 0..........1.... cpeB 0.........11.... crtE 0...........1.11 cysA 0...11111.....11[5 mbpX,9 ycf85] cysT 0...1111......11[5 small] dnaB 0.......1111..11 dnaK 0.......11111.11 fabH 0..........1..11 ftrB 0.......1.11..11[9 ftrC] ftsH 0......11111..11[10-12 ycf25] ftsI 0....11.......11 ftsW 0....11.....1.11 glmS 0.......1.....11 glnB 0.......1..1..11 gltB 0.......1..1..11 groL 0.......11111.11[9-13 groEL] groS 0...........1.11[13 groES] hemA 0...........1.11 hisH 0.......1...1.11 hisS 0...........1.11 hup 0.........1...11[11 hlp] ilvB 0.......1.11..11 ilvH 0.......1.11..11 infA 0.111111......11 infB 0.........11..11 infC 0.......1..1..11 lipB 0.......1.....11 lpxA 0.......1.....11 lpxC 0.......1.....11 matK 1....00000000000[3 orf542, 5orf370i] menB 0.......1.....11 minD 0....111..1...11 minE 0......1..1...11 nadA 0...........1.11 ndhA 1..0...0000000..[5 ndh1] ndhB 1..0...0000000..[5 ndh2] ndhC 1..0...0000000..[5 ndh3] ndhD 1..0...0000000..[5 ndh4] ndhE 1..0...0000000..[5 ndh4L] ndhF 1..0...0000000..[5 ndh5] ndhG 1..0...0000000..[5 orf191] ndhH 1..0...0000000..[3 NADH dehydrogenase 49kDa protein ,5 orf392] ndhI 1..0...0000000..[3 18kDa protein related to a subunit of NADH dehydro, 5 frxB] ndhJ 1..0..00000000..[3 orf159, 5 orf169] ndhK 1..0...0000000..[1,3,5 psbG] pbsA 0.........11..11 pdhA 0.............11 pdhB 0.............11 petA 1............... petB 1............... petD 1............... petF 0.......11111.11 petG 1...............[add 3 petG, 5 orf37] petJ 0.......1..1..11 petL 1.......0.....00[1 orf31, 4 orf62b,5 orf31,add 9 petL, add11 -13 petL] petM 0.............11 petN 0.............11 pgmA 0..........1..11 pheT 0.............11 preA 0.......1..11.11 psaA 1...............[add 2 psaA] psaB 1............... psaC 1............... psaD 0.......11111.11[add 13 psaD] psaE 0.......11111.11 psaF 0.......11111.11 psaI 1............0..[3 orf36, 5 orf36b] psaJ 1...............[3 orf44 5 orf42b] psaK 0.......1.11..11 psaL 0.......1111..11 psaM 0..111.111111.11[add 5 psaM,9psaM] psbA 1............... psbB 1............... psbC 1...............[add 2psbC] psbD 1...............[add 2psbD] psbE 1............... psbF 1............... psbH 1...............[5 orf74] psbI 1...............[add 2psbI, 5 orf36a] psbJ 1...............[5 orf40] psbK 1...............[2 hypothetical protein, 5 orf55] psbL 1...............[5 orf38] psbM 1.......0000....[5 orf34] psbN 1...............[add 14 psbN] psbT 1...............[3 orf35, 14 ycf8(orf31)] psbU 0.............11 psbV 0.......11111.11 psbW 0.......11111.11 psbX 0........1111.11 psbY 0.............11 rbcL 1............... rbcS 0.......11111.11 rne 0.....1...11..11 rpl1 0.......11111.11 rpl2 1...............[5 orf203] rpl3 0.......11111.11 rpl4 0.......1111..11 rpl5 0....11111111111 rpl6 0.......11111.11 rpl9 0..........1..11 rpl11 0.......11111.11 rpl12 0.....1111111.11 rpl13 0.......1111..11 rpl14 1............... rpl16 1............... rpl18 0.......11111.11 rpl19 0....11111111.11 rpl20 1............... rpl21 0...1...11111.11 rpl22 1.....00.....0.. rpl23 1...........0... rpl24 0.......1111..11 rpl27 0.......1111..11 rpl28 0.......1..11.11 rpl29 0.......1111..11 rpl31 0.......1111..11 rpl32 1...........00..[add 2,3,5 rpl32] rpl33 1.....00.....0.. rpl34 0.......11111.11 rpl35 0.......11111.11 rpl36 1...............[add 14 rpl36] rpoA 1............... rpoB 1............... rpoC1 1............... rpoC2 1............... rpoZ 0.............11 rps1 0..........1..11 rps2 1............... rps3 1............... rps4 1............... rps5 0.......11111.11 rps6 0.......11111.11 rps7 1............... rps8 1............... rps9 0....11111111111 rps10 0.......11111.11 rps11 1............0.. rps12 1............... rps13 0.......11111.11 rps14 1............... rps15 1.....00000000..[add 2 rps15] rps16 1..00.00.....0.. rps17 0.......11111.11 rps18 1............... rps19 1............... rps20 0........1111.11 secA 0.......1111..11 secY 0.......11111.11 thiG 0.......11.1..11 trmE 0.............11 trpA 0.......1..1..11 trpG 0.......1..11.11 trxA 0.......1..1..11 tsf 0.......1.11..11 tufA 0....11111111111 ycf1 1.0.....00000000[2 hypothetical protein, 4 rps12, 5orf1068] ycf2 1.0..00000000000[4 orf2054, 5 orf2136] ycf3 1..0............[3 orf170, 4 rps12] ycf4 1............... ycf9 1............... ycf12 0..??11111111111[ 4 orf33, 5 orf33] ycf13 0.............11 ycf15 1.00000000000000[ 1 rpl23] ycf16 0.......11111.11 ycf17 0.......1.111.11 ycf18 0.......1..1.... ycf19 0.......1.11..11 ycf20 0....1..1.11..11 ycf21 0..........11.11 ycf22 0..........1..11 ycf23 0.......1..11.11 ycf24 0.......11111.11 ycf26 0.......1..1..11 ycf27 0.......1.111.11 ycf28 0.......1..1..11 ycf29 0.......1.111.11[9 ompR] ycf30 0.......11111.11 ycf32 0.......11111.11 ycf33 0........1111.11 ycf34 0..........11.11 ycf35 0........1111.11 ycf36 0.........111.11 ycf37 0.......1.111.11 ycf38 0..........11.11 ycf39 0.......11111.11 ycf40 0.......11.1..11[12 orf71] ycf41 0........1...... ycf42 0........1.1..11[12 orf199] ycf43 0.......1111..11[12 orf254] ycf44 0.......1111..11[12 orf437] ycf45 0.......11.1..11[12 trnS] ycf46 0........111..11[12 orf491] ycf47 0........111..11[12 orf71] ycf48 0.............11 ycf49 0.......1...1.11[13 orf102] ycf50 0.............11 ycf51 0.............11 ycf52 0.............11 ycf53 0.......1..1..11[12 orf238] ycf54 0.......1..1..11[12 orf108] ycf55 0.......1..1....[12 orf320] ycf56 0.............11 ycf62 0....1111..1..11[8 orf504,12 orf327] ycf65 0....1..1.11..11[11 unknown,12 orf99] ycf66 0...11........11[5 orf135] ycf67 0.............11 ycf68 0.............11 ycf70 0.............11 ycf72 0.............11 ycf80 0.......1....... ycf81 0....11.......11 ycf82 0.......1.....11 ycf83 0.......1.....11 ; END; BEGIN ASSUMPTIONS; USERTYPE loss (STEPMATRIX) = 2 0 1 [0] . i [1] 1 . ; OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ; TYPESET * UNTITLED = unord: 34 62 87 188-189 195 198 219 233 242, loss: 1-33 35-61 63-86 88-187 190-194 196-197 199-218 220-232 234-241 243-245; END; BEGIN TREES; TRANSLATE 1 Arabidopsis, 2 Nicotiana, 3 Oryza, 4 Pinus, 5 Marchantia, 6 Mesostigma, 7 Nephroselmis, 8 Chlorella, 9 Cyanidium, 10 Odontella, 11 Guillardia, 12 Porphyra, 13 Cyanophora, 14 Chlamydomonas, 15 Synechocystis, 16 Nostoc ; TREE * UNTITLED = [&R] (((((((((1,2),3),4),5),(7,(8,14))),6),((9,10),(11,12))),13),(15,16)); END;