Chicken and red junglefowl mtDNA tree Build 1 (Jun 1, 2014)
Nucleotide position numbers are relative to the AP003321. Mutations are transitions unless an exact base change is specified.
Coding region mutations (np 1233-16785) are shown in black; control region mutations (np 1-1232) in blue.
Mutations toward a base identical-by-state to the AP003321 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).
The length variations scored at np 859 (859d) and around 3941 (3946+C,3946+CC,3946+CCC, 3945d,3946d) were not considered for phylogenetic reconstruction and are therefore excluded from the tree.
Accession numbers of sequences are in bold for red junglefowl.
mt-MRCA
 
ABZY 3837 9602
   
Y 197 270 281 391A 1587 3514 3898A 6252 6965 7370 7868T 7964A 8597 12491 12557 12593 14301 14331 15292             GU261693
   
ABZ 243 261
   
  Z 306 889 1385 4451 4829 10300 11684 11979 15976 16269 16356
     
    391A 7370 10833 15030                       GU261674
                               
    199 291 3514+C 8358 12429                       GU261696
   
  AB 256 310 11007 16596
     
  A 167 225 2071 9806 10447 12104 12689 12961 16263 16371
     
  A1 16356
       
    A1a 3125 8612 12054 14232T
         
        9484                     GU261684
                             
        256 391A 11103 15088                   GU261700
       
      396 2295 15958A                     GU261695
       
    355 686 5688G 13229                       AB086102
     
    240 13351                         KF981434
   
  B 212 246 315 1215 1699C 2209 5106 5832 10270 13884
     
  B1 10669
     
  B1a 792
       
      296                     GU261714
                           
      686 3098 15652Y                   GU261705
       
      256 4805 9313                   GU261699
     
    223 296 2792A                      GU261704
     
  B2 15693T 15875                       AP003321
   
CD 281 306 5724G 15409
   
C 363 3900 7886 8223 9042 9440 14399 15211 15331 15400 15706 16257
     
  C1 242 @261 @306 367 2885+C 3269A 5700T 5960 6236 7214 15391
     
  C1a 9848                           GU261675
                               
      248 @281 342 6112 6890 11531 12057                   GU261681
     
  C1b 342
       
      3157 7715                         GU261718
                               
      391 13783R                       GU261679
     
  C1c @212 14208                         GU261701
                               
  C2 @281 342 362 1264 1588 2876 3514+C 7268 8059 9556 11064 11695 12135 12644 12864               GU261680
   
  C3 177T 265 10279 12557 14010 14734
     
  342 686 2385 3838 7101 7589 9407T 11023                     GU261716
                             
  1786 2830 2963 4382 11422T                       GU261707
 
D 2595 11693
   
  D1 4291 4772 8642
       
    D1a 342
         
    D1a1 11381G
         
        296 686 11447 12215 @15875                   AP003322
                               
        8192 10107 11465 11636 14514 15615 16466                 AP003323
       
    D1a2 6236                         GU261687
       
      220 344 9550 16674A GU261682
                                 
      7011                           KF939304
     
  D2 1762 2942 3480 6758 7031 7155 10697 12539 13722 15229A 15545 16447 GU261683
                                 
  D3 15235
   
  D3a 4572 9461A 13737 15391 16356
     
    @281 6738                         GU261697
                             
    210 221 342 2361+C 4586 5557 5690 10620 12143 15606Y                 GU261685
   
  D3b 220 @281 302 391A 5381 10170 11260 12678 14468 15403                   GU261677
   
EFGHIWZ 446 9542
 
I 171 207 @212 221 229 @246 322A 354 362 363 391 521 686 2275 2768 4598 4607 4874A 5840C 6011 6194 7022 7364 7769 7979 8141 8192 8444 9184 9347 11024 13779 14208 15403 16103 16257 @16596 16676 GU261698
 
EFGHWX 4586 6905 8618 10081 11973
   
H 198 199 281 306 363 391 2799 5875 6041 6095 7292 14802 16356 16397                   GU261715
   
EFGWX 1214
 
WX 363 417
     
W 133 167 @310 391 521 4095 4457 @6905 7181 7577 7715 7739 10432 11603 11708 11732 12003T 12191 12725T 15835 16665     GU261706
                           
X 242 326 4526 4613 8681 11744 11773 12218 12383 12410 14877 14957 15277 15943 16356 16442           GU261692
 
EFG 3941 16131
   
E 217 8079 8339 10978 11388 15445
     
E1 6764 6806 8473 12464
     
  E1a 13569                     GU261712 KF954727
                         
      12690                   AP003318
     
  E1b 686
       
      @243 1525+A 8783 12008 15835               GU261694
                         
      342 14220                   AP003319
     
  E1c 330
       
      222 1297 13227                 AY235571 KF826490
       
      207 238 @246 12705 14046               HQ857210
                         
    @246 5375 15505                   GU261686
                         
    199 6236                     GU261713
                         
    10814 10996 11797 13542                 GU261709
                         
    2022 11187 15362                   AY235570
                         
    6437 13257                   AP003580
                         
    2027 2361+C                   AP003317
                         
E2 224 @246 1174 2886 2890+2C 9870C 11040 12200 14712 14871 16356             HQ857209
   
E3 249 355 8796 9014 9794T 15545
     
  E3a 222
     
    3050 5749                   HQ857212
                       
    281 686 8137 12819 14468 15951               HQ857211
   
  E3b @246 344 3099 9587 10255 12224                 GU261708
   
FG @315 16339
   
F 234 236 254 317C 904 7385 7463 10115 11573 14034G
   
F1 396                     GU261691
                       
    347 10300                   GU261702
   
F2 11531
     
    342 12247 12830 15734               GU261689
                       
    5299 6000 10229 15443 15471               GU261703
   
F3 @246 686
     
    12167T 13509                 GU261717
                       
    6799 8903T                 DQ648776
   
F4 265 15992A                   GU261688
                       
F5 4325 11024 13949 14847C                 GU261711
                       
G @212 296A 302 6236 7031 7475 11504 15017 15232 @16131
   
G1 6536
   
G1a 322
     
    9914                 GU261719
                     
    362 4395 @16596               GU261690
   
  13706A                   GU261676
                     
  281 317C 391A 686 11656 16556               GU261710
   
G2 322 347 1988 4229 13328                 GU261678