Pig and wild boar mtDNA tree Build 1 (Jun 1, 2014)
Nucleotide position numbers are relative to the EF545567. Mutations are transitions unless an exact base change is specified.
Coding region mutations (np 1255-16690) are shown in black; control region mutations (np 1-1254) in blue.
Mutations toward a base identical-by-state to the EF545567 are indicated with the prefix @.
"R" and "Y" specify the heteroplasmic status of A/G and C/T at a certain site, respectively.
Deletions are indicated by a "d" after the deleted nucleotide position.
Insertions are indicated by a "+" followed by the position number and type of inserted nucleotide(s).
Undetermined mutatiions are noted by "N".
The phantom mutation 6261d is shown in parenthesis.
Repetitive and difficult-to-align region np 700-921 is not considered.
The length variation in the  A tract scored at np 142 (135+C, 136+A, 136+CA, 137C, 142+XA) and the  A tract scored at np 1638 (1638d,1638+A), and the mutation 691 were not considered for phylogenetic reconstruction and are therefore excluded from the tree.
EF545592 appears remote to AE and serves as an outgroup sequence which is excluded from the tree.
Accession numbers of sequences are in bold for wild boar.
mt-MRCA
 
A 322 389 1175 1225 1304 1639 1990 2335 3088 3999 4342 4369 4711 4846 5369 5873 6092 7009 7108 7447 8498 8773 9157 9789 9837 10529 10816 10944 11071 11366 12109 13581 13997 14399 14738 14839 14998 15151 15277 @15337 16492
     
A1 3064 5636
     
  A1a'b 4939 5463A 5753 6296 6970 7513 9156 14639
       
    A1a 180 305 451 500 1412 2339 4015 4459 5628 5672 5708 7339 7669 7837 8017 9435 10070 10100 10680 11184 11259 12649 13049 14213 15685 16111 16258
         
      D 240 1315 5797 6164 6952 11944 15025 15721 16292
           
        D1 500 2374 11432 12064 16301
             
          D1a 14198
               
            D1a1'3 278
               
              D1a1 451 15220
                   
                D1a1a 240
                     
                    181 3798 9699 10680 14639                                 EF545577
                                           
                    7081 8291A 8292 10762 13803                                                       EF545590
                   
                D1a1b 559 
                     
                    12061                                                           AF486873
                     
                    389 1167                                                           KC493608
                   
                D1a1c (6261d)
                   
                    @278 @451                                                         AF486860
                     
                    180 10043 AF486863
                                                                               
                    5430T 5745 12085 14908 AF486862
                                                                               
                      62 180 390 5066                                                        AF486865
                       
                      4858 @14198                                                       AF486871
                     
                    386 11665 13830 14405 14697                                                       AF486864
                     
                    9625 AF486872
                                                                               
                    5471 12241 14312 15772                                                       AF486874
                   
                  276                                       EF545593
                                                                     
                  247 3571 5927 10977                                                           JN601070 JN601071
                   
                  5471 14312 15772                                                           JN601074
                   
                  390 473 2514+A 7291 9625                                                         AF486855
                   
                  5430T 5745 9727 12085 14642 14908 16219 16292 16313 16393                                                   KC493609
                   
                  61 386 939 1057 1675T 2735 3457+C 5597 6449d 7507 9119d 9195 11401C 11665 11831 12374 13830 14405 14877 15002 15626 16489                                       KF971862
                   
                  7321 9288C 14476                                                           KF472179
                                                                               
                  1167 11555 16042                                                           KC505408
                                                                               
                  3048 4429 8491 14710N 16594                                                         EF545591
                 
              D1a3 8071 9209 10616
                   
                D1a3a 240 5449 10740 15767                                     EF545581
                                           
                  180                                                 EF545582
                           
                  559 4043 9090 9373 14862                                   EF545583
                                     
            D1a2 240 
                 
                639 6958 8282 10704 11402 11414 @12064 12241G 12692 13337 16492 16681                                                   GQ220329
                 
                4484 6643 13404 14618 15770                                                           KF601700
               
            D1a3 11414
                 
              D1a3a 2424 
                   
                D1a3a1 240 13694
                   
                    @500 3090 @16301                                                          KC505406
                                                                               
                    442 16042 16219 16292 16393                                                       KC505407
                   
                  7777                                                              AF486859
                                                                               
                169+T 7486 14216                                                             KC493610
                                                                               
                639 660 5006+T 13337                                                             KC505409
               
              964d 4483 11414 16042 16051 16144A 16166 16219 16292 16313 16393                                                     KC493611
               
              247 1175 2548 11414 13694                                                             KC493607
             
          D1b 404 3434 9372 13472C
               
            D1b1 8267
                 
                1107+TAAAACACTTA 15329C 16095                                   KC250274
                                                                     
                1313 6988 8545 16552                                                             JN601075
                 
                1107+TAAAACACTTA 12580                                                           KF767443
               
              180 1107+TAAAACACTTA 5669 14341                                                             KF888634
               
              559 3357 7151 8935 10466                                       EF545576
                                     
              4591 11000 15850 16317                                                             EF545575
               
          D1c 442
               
            D1c1 9699
                 
              D1c1a 181 559 10493
                   
                  3048                                                             EF545589
                   
                  240 300 14507                                                           AF486861
                 
              D1c1b 4558 7534 9902 15614
                   
                D1c1b1 (6261d) 
                     
                    278 9047G 9424 14088+A                                                       AF486868
                     
                    240 @442 6296G @9699                                                       AB298688
                   
                  1175 14063 14351                                                            EF545587
               
              240 3971 (6261d) 9136 15850 15886                                                           AF486867
               
              305 4831 5188 5417 8114                                       EF545574
                                   
            240
               
            D1d 4228 8860 8932 10161 12331 15485 16511                                                           EF545569
               
            D1e'g'h 559
                 
              D1e 300 8135 11014A                                       EF545570
                                         
                  7033 7702 8207 9953 15527 15595T 15998 16285                                                     KF660222
                   
                  12782                                                             AF486857
                   
                  8207 15998                                                           KF472178
                   
                  1391 7843 8698 14594                                                         AF486870
                 
              D1g 2065T 4831 10810                                                             EF545588
                 
              D1h 278 389 9788 12046 13399 14862                                     EF545578
                                     
            D1f 299 10354 13202                                                               EF545580
               
              1906 2182 6179 6829 7138 8860 9132 12313 15485 16291                                                         AF486856
             
          D1i 6539 7289 8701 8774 10243 11414 12892                                                             EF545579
           
        D2 4471 8581 15337 15838
             
            583 6300 11597 14558                                         EF545573
                                   
            2065C 3594 14710                                                                 EF545567
             
            1990 6077 8011 9542 14205T                                                               KC493612
           
        D3'4 451
             
          D3 240
               
          D3a 278 1311 5393 5435 7309 7468 7540 7615 8686 11539 11552 15154 15850 16468
             
            D3a1 10030 15634
               
              D3a1a 3565+T 6841 KF752550
                                                                             
                573d 15770                                                           KC505410
                 
                8533                                                          EF545572
                     
              3565+T 7688                                                              KF472177
                                             
          D3b 239 559 1199A 6442 6961 8590 8875 12805 13115 13131 13304 13632 14862 15379                                                   GU147934
           
          D4 3099 7559 12241G 
             
          D4a 24 181 213 559 3568 5409 5417 5516 6262 7886 8211d 10150 11070 12760 14676  AF486869
                                                                           
            1103 4030 9058 14594                                                             GQ220328
           
          D4b 240 2340 8344 13550 14955 15232 14594                                     EF545584
                               
      A1a2 213 442 559 1412A 2338 4606 5984 6850 8967 11134 11276 13220 13236 14249 14312 14370 14459 16120 16270                                                     EF545571
       
    A1b 109 213 323 386 534 583 1446 2241 2372 3880 5435 5465 5648C 7159 7798 7825 8551 9022 9343 9346 9699 10020 10691 12169 13051 13391 13674 14523 14568 14738 14774 15301T 15640 15749 15862 16036                                     EF545586
                                                                               
      213 278 321 323 386 387 390 405 442 559 980 1178 1224 1248 1275+T 1628 1638+A 2383 3862 3880 4036 4090 4210 4393 5001+G 5465 5875 7264 7585 7798 8074 8365 8449 8551 8755 9187 10340 11776 12085 12142 12169 13056 14738 15551 16036 16291 16504                             KC505411
     
  A1c 90 278 300 301 322 390 534 541 574 656 950T 1087+2ACAAACCAC 1175 1834 1906 2514+A 2726 3102 5405 @6164 6582 6925 7465 7540 8398 8668 9052 9309 9414 9480 9699 9727 9822 10205 10457 11174 11279 11341 11411 11735 12787 12909 13159 13175 13227A 13460 13781 14369 14540 14541 15700 16036 16400                     EF375877
   
A2 213 278 442 559 1253 3772 6859A 9286 9917 12909 12959 13667 
     
  157 @500 636 952 1199A 4393 5288 5417 5495 @5672 @6164 6805 6841 9438 9775 10658 11231 11433 12061 12241 12301 13643 14312 14370 16132A 16252 16255 16552                         EF545585
                         
  239 @451 461 541 639 1717 4063A 4369 5564 6077 6802 8229 8359 8713 9217 11154 11414 11980 12442 12929T 13560 14205 14956 15694 15784A 16018 16136A 16610 @16258                                               EF545568
 
E 109 131 137C 142+XA 144 152 157 293 574 1168 2064 2071 2613 3102 3366 3451 3640 3873T 4030 4081 4420 4438 4489A 4737 4754 5168T 5207 5552 5678 5880 5963 6138 6171 6298 6508 6925T 7022 7321 7486 7750 8371 8413 8605 8713 8743 8761 9058 9225 9234 9553 9752 9973 10484 10517 10753 11018 11162 11189 11289 11372 11683 11786 11830 12241 12298 12370 12469 12518 12583 12675 12958 12962 13433A 13605 13838 14209 14313A 14561C 14812 14947 15109 15127 15362 15625 15661 15961 16294 16297 16358 16456 16552 16564 16608
   
E1 5948
     
E1a 9605 @9837 13478                   FJ237000
                                                           
  E1a1 124T
       
    E1a1a @180
         
      E1a1a1 @10517
           
        E1a1a1a 4297
             
            @322 461G 13253 13994 16010A 16339                                                           AP003428
                                             
            4483 @6138 7160 7417A 13307 14742                                                           JN601072 JN601073
           
          @3640 14763                                                                 JN601068 JN601069
         
        278 4748 9699 @10484                                 FJ236998
                                         
        11176 15209                                                                   FJ236997
       
    E1a1b @4471
       
      E1a1b1 278 1246 11327 13113
           
        949 @10517 16330                                                                 KC250275 KF569218
         
        6787 9412                                                                   FJ236996
       
      E1a1b2 @10517
       
      E1a1b2a 949 
           
          14477T 15333                                                               JN601066 JN601067
           
          3962 7312T 10797 13084 16131                                                             KF767444
         
        1254+A 4860T 6688 6856                                                                KC469587
       
        @305 5770 11966                                                                   FJ236994
     
  E1a2 7234 9149 13307 14361 14495                                     FJ237003
                                   
E1b 386 8442 10478 11537
     
  E1b1 5187                                                                         FJ237002
       
    13158                                       FJ237001
                                   
  E1b2 10845 11776                                                                       FJ236999
 
E2 9252 10365 15973
   
110 278 279 1272 7759 9345T 15565                                     EU117375
                                 
14725N                                                                           FJ236993
 
1969 10358                                         FJ236992
                                 
5358T 10899 15996                                                                         FJ236991
                                           
@3640 9601 11186 13166 14003 16520                                                                     FJ236995