#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 20, 2025; 6:53 GMT TreeBASE (cc) 1994-2008 Study reference: Halanych K., & Robinson T. 1999. The utility of cytochrome b and 12S rDNA data for phylogeny reconstruction of leporid (Lagomorpha) genera. Journal of Molecular Evolution, 48: 369-379. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S422] [ The following blocks are input data for analysis step 527 ] BEGIN TAXA; TITLE TaxaForAnalysisStep527; DIMENSIONS NTAX=12; TAXLABELS Brachylagus_idahoensis Bunolagus_monticularis Lepus_americanus Lepus_californicus Lepus_capensis Ochotona_princeps Oryctolagus_cuniculus Pronolagus_crassicaudatus Romerolagus_diazi Sylvilagus_aquaticus Sylvilagus_audubonii Sylvilagus_floridanus ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2143] TITLE Cyt_b; LINK TAXA = TaxaForAnalysisStep527; DIMENSIONS NCHAR=672; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Brachylagus_idahoensis CCCCTGCTAAAAATAGTCAATCACTCTTTAATTGACCTCCCCGCCCCATCGAATATCTCCGCCTGATGAAATTTCGGCTCCCTTCTAGGCCTGTGCCTAATTATCCAAATCCTAACCGGCCTATTTCTAGCTATACATTATACCTCAGACACACTAACAGCATTCTCATCAGTCACCCATATTTGCCGAGATGTAAACTACGGCTGACTTATCCGTTATCTTCACGCAAACGGAGCATCAATATTCTTTGTCTGCCTCTATATGCACGTAGGCCGTGGAATTTACTACGGATCCTACACTTACCTAGAAACCTGAAATATTGGCATCATCCTACTATTCGCTGTAATAGCCACAGCATTCATAGGCTATGTCCTCCCATGGGGCCAGATATCTTTCTGAGGTGCAACTGTAATTACTAACCTCCTGTCAGCCATTCCCTATATTGGAACAACCCTAGTTGAATGGATTTGAGGCGGGTTTTCAGTCGACAAAGCCACACTCACCCGATTCTTCGCCTTCCACTTCATTCTCCCATTCATCATTGCGGCCTTAGTAATAATTCACCTACTCTTCCTCCATGAAACTGGCTCTAATAACCCATCAGGTATCCCCTCAGATTCAGATAAAATTCCATTTCACCCCTACTACACTATTAAAGATATCCTAGGATTC Bunolagus_monticularis CCCCTATTAAAAATCATCAATCACTCCCTAATTGACCTCCCCGCCCCATCAAACATTTCTGCTTGATGAAACTTCGGCTCTCTCTTAGGCTTATGCCTGATAATTCAAATCCTAACTGGCCTTTTCTTAGCCATACACTACACCTCAGACACTACAACAGCATTCTCATCAGTTACTCACATCTGTCGTGACGTAAACTATGGCTGACTCATTCGATACCTCCATGCCAACGGAGCATCAATGTTCTTTATCTGCCTTTATATACATGTAGGCCGCGGAATCTACTATGGCTCATATACTTATTTAGAAACCTGAAATATCGGCATCATCCTCCTATTCGCAGTAATAGCCACAGCATTCATAGGCTACGTCCTCCCATGAGGCCAAATATCATTCTGAGGCGCAACCGTAATTACTAATCTCCTATCGGCGATCCCTTACATCGGGACCACCCTAGTTGAATGGATCTGAGGCGGATTCTCAGTCGACAAAGCTACACTTACTCGCTTTTTCGCATTCCACTTCATTCTCCCATTCATCATTGCAGCCCTAGTTATAGTCCATCTACTTTTCCTTCACGAAACTGGATCCAACAACCCATCAGGAATCCCCTCAGACTCCGACAAAATCCCCTTCCACCCTTACTATACAATCAAAGACGCCCTAGGATTT Lepus_americanus CCCCTACTAAAAATTGTTAACCACTCCCTAATTGACCTTCCCGCCCCCTCAAACATCTCAGCCTGATGAAACTTTGGCTCTCTACTAGGCCTATGCCTAATGATCCAAATCTTAACTGGCCTGTTCCTTGCTATACACTATACATCGGACACAGCAACAGCATTCTCCTCAGTCACTCATATCTGCCGAGACGTAAACTACGGCTGACTTATCCGTTATCTACACGCTAACGGAGCATCAATGTTCTTTATTTGTCTATACATACACGTAGGCCGTGGAATTTATTATGGATCATATACTTATCTGGAAACCTGAAATATTGGTATCGTTCTCCTATTTGCAGTAATAGCCACGGCATTCATAGGCTACGTCCTCCCATGAGGACAAATATCATTCTGAGGGGCTACCGTAATTACTAACCTCCTATCAGCTATCCCCTACATTGGGACAACCCTAGTTGAATGAATCTGAGGTGGATTTTCAGTTGATAAAGCCACTCTCACCCGATTCTTCGCTTTCCACTTCATCCTCCCATTCATCATTGCAGCGCTAGTAATAATTCACTTACTTTTCCTTCATGAAACCGGCTCCAATAACCCATCAGGCATCCCATCAGACTCCGACAAAATCCCATTCCACCCCTATTATACAATCAAAGACGTCCTAGGATTT Lepus_californicus ?CCCTACTAAAAATTGTTAACCACTCCCTAATTGACCTTCCCGCCCCCTCAAACTTTTCAGCCTGATGAAACTTCGGCTCTCTATTAGGCCTATGCCTAATAATCCAAATCCTAACTGGTCTCTTCCTAGCTATACACTATACATCAGACACAGCGACAC?GTTCTCCTCAGTCACACATATTTGCCGAGACGTAAACTATGGCTGACTTATCCGTTACCTGCACGCTAACGGAGCATCAATATTCTTTATTTGCCTATATATACATGTAGGCCGTGGAATTTACTACGGCTCATATACTTATTTAG?AACCTGAAATATCGGGATTATTCTGCTATTCGCAGTAATAGCCACAGCATTTATAGGTTATGTCCTCCCATGAGGACAAATATCATTCTGAGGAGCTACCGTAATTACTAATCTTCTATCA?CTATCCCCTACATTGGAACAACCCTAGTTGAATGAATCTGAGGAGGATTTTCAGTTGACAAATCCACACTAACCCGATTCTTCGCTTTCCACTTTATTCTCCCATTCATCATTGCAGCATTAGTAATAATTCACTTACTCTTCCTCCATGAAACGGGCTCCAATAACCCTTCAGGCATTCCATCAGATTCCGATAAAATTCCATTCCACCCCTATTATACAATTAAAGAGGCC?TAGGATTT Lepus_capensis CCCCTACTAAAAATTGTTAACCACTCCCTAATTGACCTTCCCGCCCCCTCAAACATCTCAGCCTGATGAAACTTCGGCTCTCTATTAGGCCTATGCCTAATAATCCAAATCCTAACTGGCCTGTTCCTAGCTATACACTACACATCAGACACAGCAACAGCGTTTTCCTCAGTCACACATATTTGTCGAGACGTAAACTACGGTTGACTTATCCGTTACCTACACGCCAACGGAGCATCAATATTCTTTATTTGCTTATATATACATGTAGGCCGTG?AATCTACTACGGCTCATACACTTATCTAGAAACCTGAAACATTGGCATTATTCTGTTATTCGCAGTAATAGCAACAGCGTTCATAGGCTATGTCCTCCCATGAGGGCAAATATCATTCTGAGGTGCCACCGTAATTACTAATCTTCTATCAGCCATTCCTTACATCGGAACAACCCTAGTTGAATGAATCTGAGGAGGATTTTCAGTCGACAAAGCCACACTAACCCGATTCTTCGCTTTCCATTTCATCCTACCATTTATCATCGCAGCTCTAGTAATAATCCATTTACTTTTCCTCCATGAAACCGGTTCTAATAATCCATCAGGAATCCCATCAGACTCTGATAAAATCCCATTTGACCCCTATTATACAAT?AAAGATGTCCTAGGATTT Ochotona_princeps ?CCCTAATAAAAATC?TAAACCACTCTTTAATCGATCTCCCAACCCCCTCAAACATCTCCGCATGATGAAACTTTGGGTCCCTCCTAGGCCTATGCCTAGGTATCCAAATCATCACCGGCTTATTCCTGGCCATACACTACACGTCAGACACACTAACAGCATTCTCATCAGTCACTCACATCTGCCGAGATGTAAACTACGGCTGAATTATCCGCTACCTACACGCCAACGGCGCATCCATATTCTTCATCTGCCTCTTCTTACACGTAGGTCGAGGTATCTATTACGGCTCCTACACCTACTCAGAGACATGAAACATCGGAATCCTACTACTATTTGCAGTTATAGCTACCGCCTTCATGGGCTACGTCCTACCATGAGGACAAATATCTTTCTGAGGAGCAACCGTAATCACCAACCTCCTATCTGCAATCCCATACATCGGCACCGACCTCGTCCAATGAATCTGAGGAGGCTTTTCAGTAGACAAAGCCACCCTAACTCGATTCTTTGCCTTCCACTTCATCCTACCTTTCATCATTGCAGCCCTAGTCATAGTCCACTTACTCTTCCTCCACGAAACAGGCTCAAACAACCCCACAGGAATTATCTCAGACGCAGACAAAATCCCATTCCACCCCTACTACACAAT??????????????????? Oryctolagus_cuniculus CCCCTATTAAAAATTGTTAACCACTCCCTAATTGACCTTCCTGCTCCATCAAACATCTCTGCCTGATGAAACTTTGGCTCTCTACTAGGCCTGTGCCTTATAATTCAAATTTTCACTGGCCTATTCTTAGCCATACACTACACCTCTGACACAACAACAGCATTCTCATCAGTAACCCATATTTGCCGAGATGTTAACTATGGCTGACTTATCCGATACCTCCACGCTAACGGAGCATCTATATTCTTTATTTGCCTCTACATACACGTAGGCCGCGGAATCTACTATGGATCATACACATACCTAGAGACCTGAAACATTGGCATCATCCTCCTATTCGCAGTAATAGCCACAGCATTTATCGGTTATGTCCTCCCATGAGGACAAATATCATTATGGGGAGCAACCGTAATCACTAACCTCCTATCAGCAATCCCATATATCGGAACAACCTTAGTTGAATGAATCTGAGGAGGATTTTCAGTTGATAAAGCCACTCTTACCCGATTCTTCGCTTTTCACTTCATCTTGCCATTTATCATTGCAACTTTAGTCTTAATTCACCTCCTCTTTCTACATGAAACTGGCTCCAACAACCCAACAGGAATTCCTTCAAACTCAGATAAAATCCCTTTCCACCCCTACTACACAATCAAAGACACCCTAGGTTTC Pronolagus_crassicaudatus CCCTTATTTAAAATCTTGAACCACTCCCTAATTGACCTCCCAACCCCATCAAATATCTCTGCTTGATGAAACTTTGGATCTCTCCTAGGCTTATGCCTAGCCATCCAAATTTTTACCGGGCTCTTCCTAGCCATACATTACACATCAGATACAATAACAGCATTTTCATCTGTCACTCATATTTGTCGAGATGTTAATTATGGTTGACTAATTCGCTACCTCCACGCCAACGGAGCCTCTATGTTCTTTATCTGCCTTTACTTGCACGTAGGTCGAGGAATTTACTACGGCTCATACACATACTCAGAAACCTGAAACATTGGCATTCTCCTTCTATTCGCAGTTATAGCTACTGCATTCATGGGCTATGTACTCCCATGAGGACAAATAT?CTGTAAGGGAGCAACAGTTATTACCAATCTTTTATCCGCCATCCCCTACATCGGAACAAATCTAGTGGAATGAATTTGAGGGGGCTTCTCAGTAGACAAAGCCACCCTCACCCGCTTCTTCGCCTTCCACTTTATTCTGCCATTCATTATTGCAGCCCTAGCAACCACCCACCTACTCTTTCTACACGAAACCGGCTCCAATAACCCATCAGGCATCCCCTCAGACTCAGACAAAATCCCATTCCACCCGTATTACACAATTAAAGACACTCTAGGGTTC Romerolagus_diazi ?CCCTACTAAAAATTGTTAACCACTCCTTAATTGACCGCCCCGCCCCATCAAACATTTCCTCCTGATGAAATTTTGGCTCTCTCTTAGGTCTATGTCTAATAATCCAAATTTTTACCGGGCTCTTCCTAGCCATACACTACACTTCAGATACAACAACAGCATTCTCATCAGTAACACACATCTGTCGAGACGTAAACTATGGCTGACTAATCCGATATATTCACGCCAACGGGGCATCCATATTTTTCATCTGCCTGTACATGCATGTAGGCCGTGGAATCTATTATGGTTCATACACCTACCAAGAAACCTGAAATATCGGGATCCTTCTACTATTTGCAGTGATAGCCACAGCATTCATAGGCTATGTTCTCCCATGAGGACAAATATCATTCTGAGGAGCAACAGTAATTACTAACCTCCTATCAGCCATGCCCTATATTGGAGCAACCTTAGTAGAATGAATTTGAGGGGGCTTTTCAGTTGATAAAGCCACTCTTACCCGCTTCTTTGCATTCCACTTCATTCTTCCATTTATCATCGCGGCCCTAGCCATAGTTCACCTACTATTCCTCCACGAAACCGGCTCCAACAACCCCTCAGGGAATCCCTCAGATGCAGATAAAATCCCTTTGATCCCTTATTACACAATTAAAGATGCACTAGGATTT Sylvilagus_aquaticus CCTCTAC????AATCGTCAACCACTCTCTAATTGACCTTCCCACCCCATCAAATATCTCTGCCTGATGAAACTTCGGATCCCTCCTAGGCCTATGCCTAATCATTCAAATCCTAACCGGCCTATTCTTAGCCATGCACTACACCTCCGACACACTTACAGCATTCTCATCGGTAACTCATATTTGCCGAGACGTAAACTACGGCTGGCTAATTCGATACCTTCACGCTAACGGAGCATCAATGTTCTTCATCTGCCTCTATATGCACGTCGGCCGCGGTATTTACTACGGCTCCTACACTTATCTAGAAACCTGAAATATTGGTATTATTCTACTATTTGCAGTAATAGCCACAGCTTTCATGGGCTATGTACTTCCATGAGGCCAAATATTCTTCTGAGGCGCAACCGTAATCACCAACCTTTTATCTGCCATCCCCTACATCGGGACAACCCTTGTCGAATGAATCTGAGGGGGATTCTCAGTCGACAAAGCCACACTCACCCGCTTCTTCGCATTCCACTTTATTCTACCATTTATCATTGCAGCCCTAGTAATAGTCCACTTACTATTCCTTCACGAGACTGGCTCTAACAACCCGTCAGGAATTCCTTCAGACTCAGACAAAATCCCCTTCCACCCTTACTACACAATCAAAGACGCCCTAGGATTT Sylvilagus_audubonii CCTCTACTAAAAATCATCAACCACTCCTTAATTGACCTTCCCACCCCATCAAACATCTCTGCCTGATGAAACTTCGGGTCCCTCCTAGGCCTATGCCTAATCATTCAAATCCTAACCGGCCTATTCTTAGCCATGCACTACACCTCCGACACACTTACAGCCTTCTCGTCAGTAACTCATATTTGTCGAGACGTAAACTACGGCTGACTAATCCGATATCTTCATGCTAACGGAGCATCAATATTCTTCATCTGCCTTTACATACACGTCGGCCGCGGTATTTACTACGGCTCCTACACTTACCTAGAAACCTGAAATATTGGCATTATCCTGCTATTCGCAGTAATAGCCACAGCTTTCATAGGCTATGTACTCCCATGAGGCCAAATATCCTTCTGAGGCGCAACCGTAATCACTAATCTTTTATCAGCCATCCCCTATATTGGAACAGCCCTAGTCGAATGGATCTGAGGGGGGTTCTCAGTCGACAAAGCCACACTCACCCGCTTCTTCGCATTCCACTTTATCCTACCATTTATCATCGCAGCTCTAGTTATAGTCCACTTACTGTTCCTCCACGAAACTGGCTCTAACAACCCAACAGGCATCCCTTCAGACTCAGACAAAATCCCTTTCCACCCTTACTACACAATTAAAGACGCCCTGGGATTT Sylvilagus_floridanus CCCCTATTAAAAATTGTAAACCATTCTCTAATTGACCTCCCTGCACCATCAAACATCTCCGCCTGATGAAACTTCGGATCTCTTCTAGGCCTGTGCCTAATAATTCAAATCCTAACCGGCCTGTTCTTAGCTATGCACTATACCTCGGACACCCTCACAGCATTCTCATCAGTAACTCACATTTGCCGAGATGTAAACTACGGCTGACTGATTCGTTATCTTCACGCTAATGGAGCATCAATATTCTTCATCTGCCTTTATATACACGTCGGCCGCGGCATTTACTATGGCTCCTACACTTACCTGGAAACCTGAAATATTGGTATTATCCTATTATTCGCAGTGATAGCTACAGCATTCATAGGCTATGTACTCCCATGAGGCCAAATATCCTTTTGAGGCGCAACTGTAATTACCAACCT?CTATCAGCTAGCCCCTACATCGGAACAACCCTGGTCGAATGAATCTGAGGAGGATTCTCAGTCGACAAAGCCACACTCACCCGCTTCTTCGCATTCCACTTTATCCTACCATTTATCATTGCAGCCCTAGTCATAGTCCACTTACTCTTCCTCCATGAAACCGGCTCTAACAACCCATCAGGGATCCCTTCAGACTCAGACAAAATTCCCTTCCACCCCTATTACACAATTAAGGACGCCCTAGGTTTT ; END; BEGIN SETS; CHARSET cytB_2nd (CHARACTERS = Cyt_b) = 290 293 296 299 302 305 308 311 314 317 320 323 326 329 332 335 338 341 344 347 350 353 356 359 362 365 2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47 50 53 56 59 62 65 68 71 74 77 80 83 86 89 92 95 98 101 104 107 110 113 116 119 122 125 128 131 134 137 140 143 146 149 152 155 158 161 164 167 170 173 176 179 182 185 188 191 194 197 200 203 206 209 212 215 218 221 224 227 230 233 236 239 242 245 248 251 254 257 260 263 266 269 272 275 278 281 284 287 368 371 374 377 380 383 386 389 392 395 398 401 404 407 410 413 416 419 422 425 428 431 434 437 440 443 446 449 452 455 458 461 464 467 470 473 476 479 482 485 488 491 494 497 500 503 506 509 512 515 518 521 524 527 530 533 536 539 542 545 548 551 554 557 560 563 566 569 572 575 578 581 584 587 590 593 596 599 602 605 608 611 614 617 620 623 626 629 632 635 638 641 644 647 650 653 656 659 662 665 668 671; CHARSET cytB_3out (CHARACTERS = Cyt_b) = 1-2 4-5 7-8 10-11 13-14 16-17 19-20 22-23 25-26 28-29 31-32 34-35 37-38 40-41 43-44 46-47 49-50 52-53 55-56 58-59 61-62 64-65 67-68 70-71 73-74 76-77 79-80 82-83 85-86 88-89 91-92 94-95 97-98 100-101 103-104 106-107 109-110 112-113 115-116 118-119 121-122 124-125 127-128 130-131 133-134 136-137 139-140 142-143 145-146 148-149 151-152 154-155 157-158 160-161 163-164 166-167 169-170 172-173 175-176 178-179 181-182 184-185 187-188 190-191 193-194 196-197 199-200 202-203 205-206 208-209 211-212 214-215 217-218 220-221 223-224 226-227 229-230 232-233 235-236 238-239 241-242 244-245 247-248 250-251 253-254 256-257 259-260 262-263 307-308 310-311 313-314 316-317 319-320 322-323 325-326 328-329 331-332 334-335 337-338 340-341 343-344 346-347 349-350 352-353 355-356 358-359 361-362 364-365 367-368 370-371 373-374 376-377 379-380 382-383 385-386 388-389 391-392 394-395 397-398 400-401 403-404 406-407 409-410 412-413 415-416 418-419 421-422 424-425 427-428 430-431 433-434 436-437 439-440 442-443 445-446 448-449 451-452 454-455 457-458 460-461 463-464 466-467 469-470 472-473 475-476 478-479 481-482 484-485 487-488 490-491 493-494 496-497 499-500 502-503 505-506 508-509 511-512 514-515 517-518 520-521 523-524 526-527 529-530 532-533 535-536 538-539 541-542 544-545 547-548 550-551 553-554 556-557 559-560 562-563 565-566 568-569 571-572 574-575 577-578 580-581 583-584 586-587 589-590 592-593 595-596 598-599 601-602 604-605 607-608 610-611 613-614 616-617 619-620 622-623 625-626 628-629 631-632 634-635 637-638 640-641 643-644 646-647 649-650 652-653 655-656 658-659 661-662 664-665 667-668 670-671 265-266 268-269 271-272 274-275 277-278 280-281 283-284 286-287 289-290 292-293 295-296 298-299 301-302 304-305; CHARSET cytB_3rd (CHARACTERS = Cyt_b) = 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 3 6 9 12 15 18 21 24 27 30 33 36 501 504 507 510 513 516 519 522 525 528 531 534 537 540 543 546 549 552 555 558 561 564 567 570 573 576 117 120 123 126 129 132 135 138 141 144 147 150 153 156 159 162 165 168 171 174 177 180 183 186 189 192 195 198 201 204 207 210 213 216 219 222 225 228 231 234 237 240 243 246 249 252 255 258 261 264 267 270 273 276 279 282 285 288 291 294 297 300 303 306 309 312 315 318 321 324 327 330 333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 381 384 387 390 393 396 399 402 405 408 411 414 417 420 423 426 429 432 435 438 441 444 447 450 453 456 459 462 465 468 471 474 477 480 483 486 489 492 495 498 579 582 585 588 591 594 597 600 603 606 609 612 615 618 621 624 627 630 633 636 639 642 645 648 651 654 657 660 663 666 669 672; CHARSET 12S (CHARACTERS = Cyt_b) = 247-248 250-251 253-254 256-257 259-260 262-263 265-266 268-269 271-272 274-275 277-278 280-281 283-284 286-287 289-290 292-293 295-296 298-299 301-302 304-305 307-308 310-311 313-314 316-317 319-320 322-323 1-2 4-5 7-8 10-11 13-14 16-17 19-20 22-23 25-26 28-29 31-32 34-35 37-38 40-41 43-44 46-47 49-50 52-53 55-56 58-59 61-62 64-65 67-68 70-71 73-74 76-77 79-80 82-83 85-86 88-89 91-92 94-95 97-98 100-101 103-104 106-107 109-110 112-113 115-116 118-119 121-122 124-125 127-128 130-131 133-134 136-137 139-140 142-143 145-146 148-149 151-152 154-155 157-158 160-161 163-164 166-167 169-170 172-173 175-176 178-179 181-182 184-185 187-188 190-191 193-194 196-197 199-200 202-203 205-206 208-209 211-212 214-215 217-218 220-221 223-224 226-227 229-230 232-233 235-236 238-239 241-242 244-245 325-326 328-329 331-332 334-335 337-338 340-341 343-344 346-347 349-350 352-353 355-356 358-359 361-362 364-365 367-368 370-371 373-374 376-377 379-380 382-383 385-386 388-389 391-392 394-395 397-398 400-401 403-404 406-407 409-410 412-413 415-416 418-419 421-422 424-425 427-428 430-431 433-434 436-437 439-440 442-443 445-446 448-449 451-452 454-455 457-458 460-461 463-464 466-467 469-470 472-473 475-476 478-479 481-482 484-485 487-488 490-491 493-494 496-497 499-500 502-503 505-506 508-509 511-512 514-515 517-518 520-521 523-524 526-527 529-530 532-533 535-536 538-539 541-542 544-545 547-548 550-551 553-554 556-557 559-560 562-563 565-566 568-569 571-572 574-575 577-578 580-581 583-584 586-587 589-590 592-593 595-596 598-599 601-602 604-605 607-608 610-611 613-614 616-617 619-620 622-623 625-626 628-629 631-632 634-635 637-638 640-641 643-644 646-647 649-650 652-653 655-656 658-659 661-662 664-665 667-668 670-671; CHARSET cytB_1st (CHARACTERS = Cyt_b) = 595 598 601 604 607 610 613 616 619 622 625 628 631 634 637 640 643 646 649 652 655 658 661 664 667 670 1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 97 100 103 106 109 112 115 118 121 124 127 130 133 136 139 142 145 148 151 154 157 160 163 166 169 172 175 178 181 184 187 190 193 196 199 202 205 208 211 214 217 220 223 226 229 232 235 238 241 244 247 250 253 256 259 262 265 268 271 274 277 280 283 286 289 292 295 298 301 304 307 310 313 316 319 322 325 328 331 334 337 340 343 346 349 352 355 358 361 364 367 370 373 376 379 382 385 388 391 394 397 400 403 406 409 412 415 418 421 424 427 430 433 436 439 442 445 448 451 454 457 460 463 466 469 472 475 478 481 484 487 490 493 496 499 502 505 508 511 514 55 58 61 64 67 70 73 76 79 82 85 88 91 94 517 520 523 526 529 532 535 538 541 544 547 550 553 556 559 562 565 568 571 574 577 580 583 586 589 592; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Cyt_b) = 1: 1-670\3, 2: 2-671\3, 3: 3-672\3; CODONPOSSET CodonPositions (CHARACTERS = Cyt_b) = 1: 1-670\3, 2: 2-671\3, 3: 3-672\3; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2144] TITLE 12S; LINK TAXA = TaxaForAnalysisStep527; DIMENSIONS NCHAR=739; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Brachylagus_idahoensis TTCCCCGC---ACCAGTGAGAATGCCCTTAACATCAGTTCAAAGATCAAGAGGAGCAGGTATTAAGCACACTATTAAGTAGCTCAAGATGCCTTGCTTAACCACACCCCCAAGGGAAACAGCAGTGATAGAAATTTAGCAATAAACGAAAGTTTGACTAAGTTATACTACTC-AGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTAATAAACACTCGGCGTAAAGCGTGATTAGGATTAGAC---GTAACAAAATAGAATCAAATATCAACTAAACTGTAAAAAGTAATAGTTGCAAACAAAAATTAACAACGAAAGTGGTTTTATTATCTTCGAATTCACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCGATAATTTCATAACAAAATTACCCGCCAGAGAACTACAAGCCAGAGCTTCAAACTCAAAGGACTTGGCGGTGCTTTATACCCGCCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAGACCTCACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCGAACCCTAAAAAGGGACAAAAGTAAGCTCAATTATTTCCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGGAAGCAATGGGCTACATTTTCTATATCAGAATACA--CGAAGACCCTGATGAAACTCAAAGGGTTAAAGGAGGATTT Bunolagus_monticularis ATCTCCGC---ACCAGTGAGAATGCCCTTAATATCAAT--ACTGATCAAAAGGAGCAGACATTAAGCACACTAACCAGTAGCTCAAGATGTCTTGCTTAACCACGCCCCCAAGGGATACAGCAGTGATAAAAATTTAGCAATAAACGTAAGTTTGACTAAGTTATGCTACTACAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTAATAAACACTCGGCGTAAAGCGTGATTAGAGATAAAA------TAAAAATAAGTTCAAATAACAACTAAGCCGTAAAAAGTAATAGTTGCAAACAAAAATAAACAACGAAAGTGATTTTACAGTACTCGAATTCACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAATAATTTCATAACAAAATTATTCGCCAGAGAACTACAAGCCACAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCC-CCTAGAGGAGCCTGTTCTATAATCGATGAACCCCGATAAACCTTACCACTCTTTGCTAAATCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGAACAAAAGTGAGCTCAATTATCCTCATAAAGACGTTAGGTCAAGGTGTAGCCCATAGAGTGGAAAGCAATGGGCTACATTTTCTACCTCAGAACACA--CGAAAGCCCTAATGAAACT-TAAGG-CTAAAGGAGGATTT Lepus_americanus CTCCCCTC---CCCAGTGAGAATGCCCTTAATATCAAT--CTAGATCAAGAGGAGCAGGTATTAAGCACACTAACTAGTAGCTCAAGATGCCTTGCTTAACCACACCCCCAAGGGATACAGCAGTGATAAAAATTTAGCAATGAACGTAAGTTTGACTAAGCTATGCTACTCCAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATAAACACCCGGCGTAAAGCGTGATTAGAACATAAG---AAAAAAAAATAAAATCAAATAACAACTAAGCTGTAAAAAGTAATAGTTATAAACAAAAATAAACAACGAAAGTGATTTTATAACCTTCGAACTCACGATAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTAGATAATTCCAGAACAAAATTATTCGCCAGAGAACTACAAGCCAGAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCGCCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAATTCAGCCTATATACCGCCATCTTCAGCGAACTCTAAAAAGGAGCAAAAGTAAGCTCAATCATCACCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGAAAGCAATGGGCTACATTTTCTACTTTAGAACACA--CGAAAGCCCCTATGAAACTCTAGAGGCCAAAGGAGGATTT Lepus_californicus ??????????????????????TGCCCTTAATATCAAT--TTAGATCAAGAGGAGCAGGTATTAAGCACACTAACTAGTAGCTCAAGATGCCTTGCTTAACCACACCCCCAAGGGATACAGCAGTGATAAAAATTTAGCAATAAACGTAAGTTTGACTAAGCTATGCTACTCCAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATAAACA-TCGGCGTAAAGCGTGATTAGAACAAAAAACAAAAAAAAAATAAAAT?AAATAACAACTAAGCTGTAAAAAGTAATAGTTGTAAACAAAAATAAACAACGAAAGTGATTT?ATAGTCTTCGAACTCACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACTTAGATAATTTCCTAACAAAATTATTCGCCAGAGAACTACAAGCCAGAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCGCCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGAGCAAAAGTAAGCTCAATCATCACCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGAAAGCAATGGGCTACATTTTCTACCTTAGAACACA--CGAAAGCCCCTATGAAACTCTAGGGGCCAAAGGAGGATTT Lepus_capensis CTCCCCTC---TCCAGTGAGAATGCCCTTAATATCAAT--CTAGATCAAGAGGAGCAGGTATTAAGCACACTAACTAGTAGCTCAAGATATCTTGCTTAACCACACCCCCAAGGGATACAGCAGTGATAAAAATTTAGCAATGAACGCAAGTTTGACTAAGCTATGCTACTTTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATAAACACCCGGCGTAAAGCGTGATTAGAACACAAA-----ATAAAAATAAAATCAAATAACAACTAAGCTGTAAAAAGTAATAGTTGCAAACAAAAATAAACGACGAAAGTGATTTCATAGTCTTCGAACTCACGATAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGCCTTAAACCTAGATAATTTCATAACAAAATTATTCGCCAGAGAACTACAAGCCAGAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCGCCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCAAACCCTAAAAAGGAACAAAAGTAAGCTCAATCATCACCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGAAAGCAATGGGCTACATTTTCTAGTTCAGAACACA--CGAAAGCCCCTAT?AAACTCTA?????????????????? Ochotona_princeps ATCCCCGA---ACCGGTGAAAATGCCCTCCAACTCACCCACC-GATTAAGAGGGGCGGGTATTAAG--CACACACTAGTAGCTCAAAATACCTTGCTTAACCACACCCCCAAGGGACACAGCAGTGATAAATCTTAAGCAATAAACGAAAGTTTGACTAAGTTAAACTACATCAGAGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTAACAAAACCCCGGCGTAAAGCGTGTTTAAGACTACAA-------CTCAATAAAGTTAAATAATACCCAAGCTGTAAAAAGCTATAGCTATAATTAAGCCCCT-CAACGAAAGTGACTTTATCACCCTTGAATACACGAAAGCTAGGACCCAAACTGGGATTAGATACCCCACTATGCCTAGCCACAAACCTAAATAGTTAAACAACAAAACTATTCGCCAGAGAACTACTAGCAACAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCACTTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCCACCTCACCACCCTTTGCTAACTCAGCCTGTATACCGCCATCTCCAGCAAACCCTAAAAAGGTATCATAGTAAGCCCAATAA-CCCCATAAAAACGTTAGGTCAAGGTGTAGCCCATAGGGTGGGAAGCAATGGGCTACATTTTCTTATATAGAACACATACGAAAGCCCATGTGAAACCATAGG--CCGAAGGCGGATTT Oryctolagus_cuniculus CTACTCCTCACGCCAGTGA-AATGCCCTTAACATCAAA--CTAGATCAAGAGGAGCGGACATTAAGCACAGTAATCAGTAGCTCAAGATGCCTTGCTTAACCACACCCCCAAGGGATACAGCAGTGATAAATATTTAGCAATGAACGTAAGTTTGACTAAGTTATGCTACTTTAGGGTTGGTAAATCTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTAATAAATATCCGGCGTAAAGCGTGATTAGAATAAACA------ACAAAATAAAATCAAATAACAACTAAGCTGTAGAAAGTAATAGTTGCAAACAAAAATAAACAACGAAAGTGATTTTATACTCTTCGAACTCACGATAGCTAAGGCCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACTTTGATAATTTCATAACAAAATTATTCGCCAGAGAACTACAAGCCAAAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCACCTAGAGGAGCCTGTTCCGTAATCGATAAACCCCGATAAACCCTACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCGAACCCTAAAAAGGAGCAAAAGTAAGCTCAATTACCACCGTAAAAACGTTAGGTCAAGGTGTAGCCCATAGAGTGGAGAGCAATGGGCTACATTTTCTACTTCAGAATATA--CGAAAGCCCTTATGAAACTCTAAGGGCCAAAGGAGGATTT Pronolagus_crassicaudatus TTCCCCAT---GCCAGTGAGAATGCCCTTAACATCAAC--CCAGATCAAGAGGAGTAGGCATTAAGCACACCAGCCGGTAGCTCACGACGCCTTGCTCACCCACACCCCCAAGGGATACAGCAGTGAATTAAACTTAGCAATGAACGAAAGTTCGACTGAGTTATGCTACTTAAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATAAATACCCGGCGTAAAGTGTGATTAGAAGTAAAT------GAAAAATAAAATCAAATAGCGTTTAAGCTGTAAAAAGTACTAACCACGAACAAAAATAATCAACGAAAGTGATCTTATAATTTTCGAACTCACGAGAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTTAATAGTTTCATAACAAAACTATTCGCCAGAGAACTACAAGCCAGAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCGCCTAGAGGAGCCTGTTCTATAATCGATAATCCCCGATAAACCCTACCTCTCTTTGCCAACTCAGCCTATATACCGCCATCTCCAGCGAACCCTGAAAAGGAGCAAAAGTGAGCTCAATCA-CCCCATAAAAACGTTAGGTCAAGGTGTAGCCTATGGAGTGGAAAGCAATGGGCTACATTTTCTACTATAGAATACA--CGGAACTCCCTGTGAAACC-TAGGGACCAAAGGAGGATTT Romerolagus_diazi AACCCCGC---ACCAGTGAGAATGCCCTTAACATCAAC--CCAGATCAAGAGGAGCAGACATTAAGTACACTTCCCAGTAGCTCAAAATGTCTTGCTCAACCACACCCCCAAGGGATACAGCAGTGATAAAAATTTAGCAATCAACGTAAGTTTGACTAAGTTATACTACTTCAGGGTTGGTAAATCTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTAATAAACACCCGGCGTAAAGCGTGATTAGAAACAAAA------CACAAATAAAATCAAATAACAACTAAGCTGTAAAAAGTAATAGTTGTAAACAAAAATAAACTACGAAAGTGATTTTATAACATTCGAACTCACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTAAATAATTT-ATAACAAAATTGTTCGCCAGAGAAGTACAAGCCAGAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTACACCCACCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAATTCAGCCTATATACCGCCATCTTCAGCGAACCCTAAAAAGGAACAAAAGTAAGCTTAATTATTCTCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGAAAGTAATGGGCTACATTTTCTATATTAGAACATA--CGAAAGCCCTTATGAAATCTTAGGG-CCAAAGGAGGATTT Sylvilagus_aquaticus ATCCCCAC---ACCGGTGAGAATGCCCTCAACATCAGC--ATAGATCAAGAGGAGCGGGCATTAAGCAC?CCAATCAGCAGCTCAAGATGCCTTGCTTAACCACACCCCCAAGGAAAACAGCAGTGATAAAAATTTAGCAATGAACGTAAGTTTGACTAAGTTATGCTACTCTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCGAACTAATAAACACCCGGCGTAAAGCGTGATTAGAACTAAAG-----ATACAAATAGAGTCAAATAACAACTAAGCTGTAAAAAGTAATAGCTGTAAACAAAAATAAACAACGAAAGTGATTCTACAACCTTCGAACTCACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACTTAAATAATTTCATAACAAAATTACTCGCCAGAGAACTACAAGCCAGAGCTTGAAACTCAAAGGACTTGGCGGTGCTTTATACCCACCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCGAACCCTAAAAAGGAACAAAAGTAAGCTCAATTATCCCCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGAAAGCAATGGGCTACATTTTCTTCTCCAGAACATA--CGAAAGCCCTTATGAAACTCTGAGGGCCAAAGGAGGATTT Sylvilagus_audubonii ATCCCCAT---ACCGGTGAGAATGCCCTTAACATCAAC--ATAGATCAAGAGGAGCAGGCATTAAGCACACTAATAAGTAGCTCAAGATGCCTTGCTTAACCACACCCCCAAGGGAAACAGCAGTGATAGAAATTTAGCAATGAACGTAAGTTTGACTAAGTTATGCTACTCTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATAAATACCCGGCGTAAAGCGTGATTAGAGCTAAAA----TAGAAAAATAAAATCAAATAACAACTAAGCTGTAAAAAGTAATAGTTGTAAACAAAAATAAACAACGAAAGTGATTTTACAACCTTCGAACTCACGATAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTGAATAATTTTATAACAAAATTACTCGCCAGAGAACTACAAGCCAGAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCGCCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCGAACCCTAAAAAGGAATAAAAGTAAGCTCAACTATTGCCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGAAAGCAATGGGCTACATTTTCTTCTTCAGAACAT?--CGAAAGCCCTTATGAAATTCTAAGGGCCAAAGGAGGATTT Sylvilagus_floridanus ????????????????????AATGCCCTTAACAT?AAT--TTAGATCAAGAGGAGCAGGCATTAAGCACACTATTTAGTAGCTCAAGATGCCTTGCTTAACCACACCCCCAAGGAAAACAGCAGTGATAGAAATTTAGCAATGAACGCAAGTTTGACTAAGTTATGCTACTCTAGGGTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCC-AACTAATAAATTCCCGGCGTAAAGCGTGATTAGAATCAAAA---CAGAAAAAATAAAATCAAATAACAACTAAGCTGTAAAAAGTAATAGTTACAAACAAAAATAAACAACGAAAGTGATTTTATAACCTTCGAACTCACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCTTAAACTTAAATAATTCCATAACAAAATTACTCGCCAGAGAACTACAAGCCAGAGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCACCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCGAACCCTAAAAAGGAAAAAAACTAAGC?CAATTATCCCCATAAAAACGTTAGGTCAAGGTGTAGCCTATAGAGTGGAAAGTAATGGGCTAGATTTTCTACTTCAGAACATA--CGAAAGCCCTTATGAAACTCTGAGAGCCAAAGGAGGATTT ; END; BEGIN SETS; CHARSET 12S (CHARACTERS = 12S) = 1-6 13-36 43-261 271-695 700-739; CHARSET all_but_ambig (CHARACTERS = 12S) = 1-6 13-36 43-261 271-695 700-739; CHARSET 12S (CHARACTERS = 12S) = 1-6 13-36 43-261 271-695 700-739; CHARSET 12Sambig (CHARACTERS = 12S) = 7-12 37-42 262-270 696-699; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 12S) = N: 1-739; CODONPOSSET CodonPositions (CHARACTERS = 12S) = N: 1-739; END; [ The following blocks are output data for analysis step 527 ] BEGIN TREES; TITLE Tb5307; LINK TAXA = TaxaForAnalysisStep527; TREE Fig._5B = [&R] (((Brachylagus_idahoensis,Sylvilagus_floridanus,(Sylvilagus_aquaticus,Sylvilagus_audubonii)),(((Lepus_americanus,Lepus_californicus),Lepus_capensis),Oryctolagus_cuniculus),(Bunolagus_monticularis,Romerolagus_diazi)),Pronolagus_crassicaudatus,Ochotona_princeps); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3441] END; BEGIN TREES; TITLE Tb5307; LINK TAXA = TaxaForAnalysisStep527; TREE Fig._5A = [&R] (((Brachylagus_idahoensis,((Sylvilagus_aquaticus,Sylvilagus_audubonii),Sylvilagus_floridanus)),((Bunolagus_monticularis,Romerolagus_diazi),((Lepus_americanus,(Lepus_californicus,Lepus_capensis)),Oryctolagus_cuniculus))),Pronolagus_crassicaudatus,Ochotona_princeps); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3442] END;