APPENDIX 3 DATA MATRIX AND STEP MATRICES
Shown below is the data matrix used in the phylogenetic analyses, including step matrices and the constraint tree for outgroup relationships. The sets of character weights ("WTSET") for both the between-state scaling and between-character scaling analyses are both shown, but were not used simultaneously. The data matrix was constructed using MacClade and the maximum value used was therefore 999 instead of 1000.#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=17 NCHAR=56;
FORMAT MISSING=? GAP=- SYMBOLS= " 0 1 2 3 4 5 6 7 8 9 A B C D E F";
MATRIX
[ 10 20 30 40 50 ]
Leiolepis 0200C0C000?????000000E000?0000?0?0501002C00101??00010100
Physignathus 0200B0?001100000000009000?2000?0?0F00000E000010?10011100
Pristidactylus 030090A000?????000000B000A0020?0?0301000B000000123000000
Polychrus 0000064100?????000400C000?0000?0?71200027000000180300100
Brachylophus 0?0039?04110000000400D000?2000?0?07000008000010?31300100
Ctenosaura 020098D00110000000000A10020000?0?0800000D000000?3C300000
Dipsosarus 0200B8A02102000000000F00012000?0?06000003000000?31300000
H.spinosus 0200A8B000?????42402081110002201130010002001110027000111
M.annularis 010070800102???42402161105002201244100021011000162302000
M.groi 0200109000?????42402171103002200?02000000000000154120000
E.cofanorum 1540332141105014244001100B210200?770000290110?0185101000
E.heterolepis 1720321141102014232215100C20120106E01000400101114A320000
E.laticeps 14105071411200110030040007000200?0D00000C001010178200000
E.microlepis 18406561411030140140031009200200?2A01002A00101026B300000
E.oshaughness 16402131111000120440011008200210?1900000F001011269001100
E.palpebralis 1A4187013111021414420010062000?0?4B201126111000159301100
E.praestabilis 19304451411011130211021004120100?5C00001500101026600?000
;
ENDBLOCK;
BEGIN ASSUMPTIONS;
USERTYPE char2 STEPMATRIX = 11
0 1 2 3 4 5 6 7 8 9 A
[0] . 213 333 556 736 832 846 852 929 966 999
[1] 213 . 120 343 523 619 633 639 716 753 786
[2] 333 120 . 223 403 499 513 519 596 633 666
[3] 556 343 223 . 180 276 290 296 373 410 443
[4] 736 523 403 180 . 96 110 116 193 230 263
[5] 832 619 499 276 96 . 14 20 97 134 167
[6] 846 633 513 290 110 14 . 6 83 120 153
[7] 852 639 519 296 116 20 6 . 77 114 147
[8] 929 716 596 373 193 97 83 77 . 37 70
[9] 966 753 633 410 230 134 120 114 37 . 33
[A] 999 786 666 443 263 167 153 147 70 33 .
;
USERTYPE char3 STEPMATRIX = 5
0 1 2 3 4
[0] . 500 556 800 999
[1] 500 . 56 300 499
[2] 556 56 . 244 443
[3] 800 300 244 . 199
[4] 999 499 443 199 .
;
USERTYPE char5 STEPMATRIX = 13
0 1 2 3 4 5 6 7 8 9 A B C
[0] . 107 212 250 255 277 295 322 447 500 562 749 999
[1] 107 . 105 143 148 170 188 215 340 393 455 642 892
[2] 212 105 . 38 43 65 83 110 235 288 350 537 787
[3] 250 143 38 . 5 27 45 72 197 250 312 499 749
[4] 255 148 43 5 . 22 40 67 192 245 307 494 744
[5] 277 170 65 27 22 . 18 45 170 223 285 472 722
[6] 295 188 83 45 40 18 . 27 152 205 267 454 704
[7] 322 215 110 72 67 45 27 . 125 178 240 427 677
[8] 447 340 235 197 192 170 152 125 . 53 115 302 552
[9] 500 393 288 250 245 223 205 178 53 . 62 249 499
[A] 562 455 350 312 307 285 267 240 115 62 . 187 437
[B] 749 642 537 499 494 472 454 427 302 249 187 . 250
[C] 999 892 787 749 744 722 704 677 552 499 437 250 .
;
USERTYPE char6 STEPMATRIX = 10
0 1 2 3 4 5 6 7 8 9
[0] . 27 37 83 117 143 166 286 666 999
[1] 27 . 10 56 90 116 139 259 639 972
[2] 37 10 . 46 80 106 129 249 629 962
[3] 83 56 46 . 34 60 83 203 583 916
[4] 117 90 80 34 . 26 49 169 549 882
[5] 143 116 106 60 26 . 23 143 523 856
[6] 166 139 129 83 49 23 . 120 500 833
[7] 286 259 249 203 169 143 120 . 380 713
[8] 666 639 629 583 549 523 500 380 . 333
[9] 999 972 962 916 882 856 833 713 333 .
;
USERTYPE char7 STEPMATRIX = 14
0 1 2 3 4 5 6 7 8 9 A B C D
[0] . 15 70 92 125 179 216 264 313 452 562 616 780 999
[1] 15 . 55 77 110 164 201 249 298 437 547 601 765 984
[2] 70 55 . 22 55 109 146 194 243 382 492 546 710 929
[3] 92 77 22 . 33 87 124 172 221 360 470 524 688 907
[4] 125 110 55 33 . 54 91 139 188 327 437 491 655 874
[5] 179 164 109 87 54 . 37 85 134 273 383 437 601 820
[6] 216 201 146 124 91 37 . 48 97 236 346 400 564 783
[7] 264 249 194 172 139 85 48 . 49 188 298 352 516 735
[8] 313 298 243 221 188 134 97 49 . 139 249 303 467 686
[9] 452 437 382 360 327 273 236 188 139 . 110 164 328 547
[A] 562 547 492 470 437 383 346 298 249 110 . 54 218 437
[B] 616 601 546 524 491 437 400 352 303 164 54 . 164 383
[C] 780 765 710 688 655 601 564 516 467 328 218 164 . 219
[D] 999 984 929 907 874 820 783 735 686 547 437 383 219 .
;

USERTYPE char9 STEPMATRIX = 5
0 1 2 3 4
[0] . 231 500 714 999
[1] 231 . 269 483 768
[2] 500 269 . 214 499
[3] 714 483 214 . 285
[4] 999 768 499 285 .
;
USERTYPE char12 STEPMATRIX = 3
0 1 2
[0] . 141 999
[1] 141 . 858
[2] 999 858 .
;
USERTYPE char13 STEPMATRIX = 6
0 1 2 3 4 5
[0] . 77 167 200 929 999
[1] 77 . 90 123 852 922
[2] 167 90 . 33 762 832
[3] 200 123 33 . 729 799
[4] 929 852 762 729 . 70
[5] 999 922 832 799 70 .
;
USERTYPE char14 STEPMATRIX = 3
0 1 2
[0] . 50 857
[1] 50 . 807
[2] 857 807 .
;
USERTYPE char16 STEPMATRIX = 5
0 1 2 3 4
[0] . 167 846 950 999
[1] 167 . 679 783 832
[2] 846 679 . 104 153
[3] 950 783 104 . 50
[4] 999 832 153 50 .
;
USERTYPE char17 STEPMATRIX = 3
0 1 2
[0] . 857 999
[1] 857 . 142
[2] 999 142 .
;
USERTYPE char18 STEPMATRIX = 5
0 1 2 3 4
[0] . 214 250 833 999
[1] 214 . 36 619 785
[2] 250 36 . 583 749
[3] 833 619 583 . 166
[4] 999 785 749 166 .
;
USERTYPE char19 STEPMATRIX = 5
0 1 2 3 4
[0] . 150 333 714 999
[1] 150 . 183 564 849
[2] 333 183 . 381 666
[3] 714 564 381 . 285
[4] 999 849 666 285 .
;
USERTYPE char20 STEPMATRIX = 3
0 1 2
[0] . 50 999
[1] 50 . 949
[2] 999 949 .
;
USERTYPE char22 STEPMATRIX = 16
0 1 2 3 4 5 6 7 8 9 A B C D E F
[0] . 52 61 93 95 97 99 133 204 256 267 325 465 650 720 999
[1] 52 . 9 41 43 45 47 81 152 204 215 273 413 598 668 947
[2] 61 9 . 32 34 36 38 72 143 195 206 264 404 589 659 938
[3] 93 41 32 . 2 4 6 40 111 163 174 232 372 557 627 906
[4] 95 43 34 2 . 2 4 38 109 161 172 230 370 555 625 904
[5] 97 45 36 4 2 . 2 36 107 159 170 228 368 553 623 902
[6] 99 47 38 6 4 2 . 34 105 157 168 226 366 551 621 900
[7] 133 81 72 40 38 36 34 . 71 123 134 192 332 517 587 866
[8] 204 152 143 111 109 107 105 71 . 52 63 121 261 446 516 795
[9] 256 204 195 163 161 159 157 123 52 . 11 69 209 394 464 743
[A] 267 215 206 174 172 170 168 134 63 11 . 58 198 383 453 732
[B] 325 273 264 232 230 228 226 192 121 69 58 . 140 325 395 674
[C] 465 413 404 372 370 368 366 332 261 209 198 140 . 185 255 534
[D] 650 598 589 557 555 553 551 517 446 394 383 325 185 . 70 349
[E] 720 668 659 627 625 623 621 587 516 464 453 395 255 70 . 279
[F] 999 947 938 906 904 902 900 866 795 743 732 674 534 349 279 .
;
USERTYPE char26 STEPMATRIX = 13
0 1 2 3 4 5 6 7 8 9 A B C
[0] . 165 330 523 572 577 588 645 722 800 824 866 999
[1] 165 . 165 358 407 412 423 480 557 635 659 701 834
[2] 330 165 . 193 242 247 258 315 392 470 494 536 669
[3] 523 358 193 . 49 54 65 122 199 277 301 343 476
[4] 572 407 242 49 . 5 16 73 150 228 252 294 427
[5] 577 412 247 54 5 . 11 68 145 223 247 289 422
[6] 588 423 258 65 16 11 . 57 134 212 236 278 411
[7] 645 480 315 122 73 68 57 . 77 155 179 221 354
[8] 722 557 392 199 150 145 134 77 . 78 102 144 277
[9] 800 635 470 277 228 223 212 155 78 . 24 66 199
[A] 824 659 494 301 252 247 236 179 102 24 . 42 175
[B] 866 701 536 343 294 289 278 221 144 66 42 . 133
[C] 999 834 669 476 427 422 411 354 277 199 175 133 .
;
USERTYPE char27 STEPMATRIX = 3
0 1 2
[0] . 950 999
[1] 950 . 49
[2] 999 49 .
;
USERTYPE char28 STEPMATRIX = 3
0 1 2
[0] . 250 947
[1] 250 . 697
[2] 947 697 .
;
USERTYPE char29 STEPMATRIX = 3
0 1 2
[0] . 231 999
[1] 231 . 768
[2] 999 768 .
;
USERTYPE char30 STEPMATRIX = 3
0 1 2
[0] . 857 999
[1] 857 . 142
[2] 999 142 .
;
USERTYPE char33 STEPMATRIX = 3
0 1 2
[0] . 250 999
[1] 250 . 749
[2] 999 749 .
;
USERTYPE char34 STEPMATRIX = 8
0 1 2 3 4 5 6 7
[0] . 167 231 500 571 737 944 999
[1] 167 . 64 333 404 570 777 832
[2] 231 64 . 269 340 506 713 768
[3] 500 333 269 . 71 237 444 499
[4] 571 404 340 71 . 166 373 428
[5] 737 570 506 237 166 . 207 262
[6] 944 777 713 444 373 207 . 55
[7] 999 832 768 499 428 262 55 .
;

USERTYPE char35 STEPMATRIX = 16
0 1 2 3 4 5 6 7 8 9 A B C D E F
[0] . 141 350 366 424 518 523 544 580 596 628 633 664 811 868 999
[1] 141 . 209 225 283 377 382 403 439 455 487 492 523 670 727 858
[2] 350 209 . 16 74 168 173 194 230 246 278 283 314 461 518 649
[3] 366 225 16 . 58 152 157 178 214 230 262 267 298 445 502 633
[4] 424 283 74 58 . 94 99 120 156 172 204 209 240 387 444 575
[5] 518 377 168 152 94 . 5 26 62 78 110 115 146 293 350 481
[6] 523 382 173 157 99 5 . 21 57 73 105 110 141 288 345 476
[7] 544 403 194 178 120 26 21 . 36 52 84 89 120 267 324 455
[8] 580 439 230 214 156 62 57 36 . 16 48 53 84 231 288 419
[9] 596 455 246 230 172 78 73 52 16 . 32 37 68 215 272 403
[A] 628 487 278 262 204 110 105 84 48 32 . 5 36 183 240 371
[B] 633 492 283 267 209 115 110 89 53 37 5 . 31 178 235 366
[C] 664 523 314 298 240 146 141 120 84 68 36 31 . 147 204 335
[D] 811 670 461 445 387 293 288 267 231 215 183 178 147 . 57 188
[E] 868 727 518 502 444 350 345 324 288 272 240 235 204 57 . 131
[F] 999 858 649 633 575 481 476 455 419 403 371 366 335 188 131 .
;

USERTYPE char36 STEPMATRIX = 3
0 1 2
[0] . 250 999
[1] 250 . 749
[2] 999 749 .
;
USERTYPE char40 STEPMATRIX = 3
0 1 2
[0] . 333 999
[1] 333 . 666
[2] 999 666 .
;
USERTYPE char41 STEPMATRIX = 16
0 1 2 3 4 5 6 7 8 9 A B C D E F
[0] . 6 106 337 508 514 562 591 644 650 703 887 904 922 981 999
[1] 6 . 100 331 502 508 556 585 638 644 697 881 898 916 975 993
[2] 106 100 . 231 402 408 456 485 538 544 597 781 798 816 875 893
[3] 337 331 231 . 171 177 225 254 307 313 366 550 567 585 644 662
[4] 508 502 402 171 . 6 54 83 136 142 195 379 396 414 473 491
[5] 514 508 408 177 6 . 48 77 130 136 189 373 390 408 467 485
[6] 562 556 456 225 54 48 . 29 82 88 141 325 342 360 419 437
[7] 591 585 485 254 83 77 29 . 53 59 112 296 313 331 390 408
[8] 644 638 538 307 136 130 82 53 . 6 59 243 260 278 337 355
[9] 650 644 544 313 142 136 88 59 6 . 53 237 254 272 331 349
[A] 703 697 597 366 195 189 141 112 59 53 . 184 201 219 278 296
[B] 887 881 781 550 379 373 325 296 243 237 184 . 17 35 94 112
[C] 904 898 798 567 396 390 342 313 260 254 201 17 . 18 77 95
[D] 922 916 816 585 414 408 360 331 278 272 219 35 18 . 59 77
[E] 981 975 875 644 473 467 419 390 337 331 278 94 77 59 . 18
[F] 999 993 893 662 491 485 437 408 355 349 296 112 95 77 18 .
;
USERTYPE char49 STEPMATRIX = 9
0 1 2 3 4 5 6 7 8
[0] . 185 444 555 592 666 777 888 999
[1] 185 . 259 370 407 481 592 703 814
[2] 444 259 . 111 148 222 333 444 555
[3] 555 370 111 . 37 111 222 333 444
[4] 592 407 148 37 . 74 185 296 407
[5] 666 481 222 111 74 . 111 222 333
[6] 777 592 333 222 185 111 . 111 222
[7] 888 703 444 333 296 222 111 . 111
[8] 999 814 555 444 407 333 222 111 .
;

USERTYPE char50 STEPMATRIX = 13
0 1 2 3 4 5 6 7 8 9 A B C
[0] . 56 71 75 283 339 368 374 518 565 594 678 999
[1] 56 . 15 19 227 283 312 318 462 509 538 622 943
[2] 71 15 . 4 212 268 297 303 447 494 523 607 928
[3] 75 19 4 . 208 264 293 299 443 490 519 603 924
[4] 283 227 212 208 . 56 85 91 235 282 311 395 716
[5] 339 283 268 264 56 . 29 35 179 226 255 339 660
[6] 368 312 297 293 85 29 . 6 150 197 226 310 631
[7] 374 318 303 299 91 35 6 . 144 191 220 304 625
[8] 518 462 447 443 235 179 150 144 . 47 76 160 481
[9] 565 509 494 490 282 226 197 191 47 . 29 113 434
[A] 594 538 523 519 311 255 226 220 76 29 . 84 405
[B] 678 622 607 603 395 339 310 304 160 113 84 . 321
[C] 999 943 928 924 716 660 631 625 481 434 405 321 .
;
USERTYPE char51 STEPMATRIX = 4
0 1 2 3
[0] . 500 625 999
[1] 500 . 125 499
[2] 625 125 . 374
[3] 999 499 374 .
;

USERTYPE char52 STEPMATRIX = 3
0 1 2
[0] . 667 999
[1] 667 . 332
[2] 999 332 .
;
OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ;
TYPESET * UNTITLED = unord: 53, ord: 1 4 8 10-11 15 21 23-25 31-32 48 53, char2: 2, char3: 3, char5: 5, char6: 6, char7: 7, char9: 9, char12: 12, char13: 13, char14: 14, char16: 16, char17: 17, char18: 18, char19: 19, char20: 20, char22: 22, char26: 26, char27: 27, char28: 28, char29: 29, char30: 30, char33: 33, char34: 34, char35: 35, char36: 36, char40: 40, char41: 41, char49: 49, char50: 50, char51: 51, char52: 52;
WTSET * BETWEEN-STATE = 999.00: 1 4 8 10-11 15 21 23-25 31-32 37-39 42-48 53-56, 3.00: 2 6, 1.00: 3 9 12-14 16-20 27-30 33-35 36 40-41 51-52, 4.00: 5, 4.57: 7, 21.50: 22, 6.05: 26, 9.00: 49, 17.84: 50;
WTSET * BETWEEN-CHARACTER = 999: 1 4 8 10-11 15 21 23-25 31-32 37-39 42-48 53-56, 1: 2-3 5-7 9 12-14 16-20 22 26-30 33-35 36 40-41 49-52;
ENDBLOCK;
BEGIN TREES;
TRANSLATE
1 Leiolepis,
2 Physignathus,
3 Pristidactylus,
4 Polychrus,
5 Brachylophus,
6 Ctenosaura,
7 Dipsosarus,
8 H.spinosus,
9 M.annularis,
10 M.groi,
11 E.cofanorum,
12 E.heterolepis,
13 E.laticeps,
14 E.microlepis,
15 E.oshaughnessy,
16 E.palpebralis,
17 E.praestabilis
;
TREE * UNTITLED = [andR] ((1,2),((6,17),5),(3,4),16,9,14,7,13,10,12,11,15,8);
ENDBLOCK;