Phylogenetic trees of class II sequences

These gene trees' were constructed using the DRB3, DQA and DQB exon 2 peptide sequence alignments found elsewhere in the BoLA site. The phylogenies were calculated using the SEQBOOT, PROTDIST and CONSENSE programs from the PHYLIP package of Dr Joe Felsenstein to define the consensus tree from 500 replicates. Distances were calculated using the neighbour-joining method, but were not included in the trees.

Remember! These trees are not meant to be definitive indicators of the evolution of the class II alleles. They are only intended to illustrate the similarities between the various alleles. In fact, I think that the mode of evolution of MHC alleles is such that using gene trees for exon 2 may not be the best way to display the evolutionary relationships involved.

Trees

 

• DRB3 tree
• DQA tree
• DQB tree

   

  DRB3 tree

  PROTDIST and neighbour-joining tree of DRB3 exon 2 peptide sequences.
  In this consensus tree the numbers at the forks indicate the number of times the group consisting of the alleles which are to the right of that fork occurred among 500 trees

   

  
                                                 +----DRB3*0201  
                                       +-------170  
                                       !         +----DRB3*1201     
                                  +---61  
                                  !    !    +---------DRB3*2601     
                                  !    +--224  
                   +-------------47         !    +----DRB3*1002     
                   !              !         +--476
                   !              !              +----DRB3*1001     
                   !              !
                   !              +-------------------DRB3*1601     
                   !
                   !                   +--------------DRB3*2002     
                   !              +--455  
                   !              !    !    +---------DRB3*2003     
                   !              !    +--381  
                   +-------------84         ! 
                   !              !         +---------DRB3*2001
                   !              !          
                   !              +-------------------DRB3*3301
                   !               
                   !
         +---------1                        +---------DRB3*3701     
         !         !                   +--263  
         !         !                   !    !       
         !         !              +---75    +---------DRB3*2501
         !         !              !    !      
         !         !              !    !
         !         !              !    +--------------DRB3*0801     
         !         !    +--------36  
         !         !    !         !         +---------DRB3*2901     
         !         !    !         !    +--225  
         !         !    !         !    !    !    +----DRB3*1801     
         !         !    !         !    !    +--306  
         !         !    !         +--128         +----DRB3*1802     
         !         !    !              !
         !         !    !              !         +----DRB3*1502     
         !         !    !              +-------500  
         !         !    !                        +----DRB3*1501     
         !         +----6  
         !              !                        +----DRB3*1701     
         !              !                   +--496  
         !              !              +--274    +----DRB3*1702     
         !              !              !    !
         !              !         +--173    +---------DRB3*1703     
         !              !         !    !
         !              !         !    !         +----DRB3*3202     
         !              !    +---53    +-------408  
         !              !    !    !              +----DRB3*3201     
         !              +---18    !
         !                   !    +-------------------DRB3*3901     
         !                   !
         !                   +------------------------DRB3*0401     
         !
         !                                       +----DRB3*0701     
         !                   +-----------------185  
         !                   !                   +----DRB3*2704        
         !                   !
         !                   !                   +----DRB3*2702     
         !              +--180              +--265  
         !              !    !         +--411    +----DRB3*2701     
         !              !    !         !    !
         !              !    !    +--184    +---------DRB3*2703     
    +----8         +---65    !    !    !
    !    !         !    !    +--391    +--------------DRB3*2706        
    !    !         !    !         !
    !    !         !    !         +-------------------DRB3*2705        
    !    !    +----5    !
    !    !    !    !    +-----------------------------DRB3*0601     
    !    !    !    !
    !    !    !    !                   +--------------DRB3*2401     
    !    !    !    !                   !
    !    !    !    +------------------98         +----DRB3*0902     
    !    !    !                        !    +--500  
    !    !    !                        +--417    +----DRB3*1202     
    !    !    !                             !
    !    !    !                             +---------DRB3*0901     
    !    !    !
    !    +----3                             +---------DRB3*1101     
    !    !    !                        +--161  
    !    !    !                        !    !    +----DRB3*2801     
    !    !    !                        !    +--460  
    !    !    !                   +--102         +----DRB3*2802     
    !    !    !                   !    !
    !    !    !                   !    !    +---------DRB3*1401  
    !    !    !                   !    !    ! 
    !    !    !              +--110    +--221     
    !    !    !              !    !         +---------DRB3*3101 
    !    !    !              !    !            
    !    !    !              !    !              +----DRB3*2202
    !    !    +-------------39    +------------495    
    !    !                   !                   +----DRB3*2201
    !    !                   !                       
    !    !                   +------------------------DRB3*4001
    !    !                       
    !    !
    !    !                                  +---------DRB3*3601     
    !    !                             +--225  
    !    !                             !    !    +----DRB3*3001     
    !    !                        +--315    +--260  
    !    !                        !    !         +----DRB3*3002     
    !    !                        !    !
    !    !                   +--103    +--------------DRB3*2301     
    !    !                   !    !
    !    !                   !    !              +----DRB3*0101     
    !    +------------------30    +------------500  
    !                        !                   +----DRB3*0102     
    !                        !
    !                        +------------------------DRB3*2101     
    !
    !                                            +----DRB3*3402     
    !                                       +--467  
    !                                       !    +----DRB3*3401     
    !                                  +--357  
    !                                  !    !    +----DRB3*0302     
    !                        +-------239    +--306  
    !                        !         !         +----DRB3*0301     
    !                        !         !
    !                        !         +--------------DRB3*1301     
    !                        !
    +-----------------------41                   +----DRB3*1901     
                             !         +-------140  
                             !         !         +----DRB3*3801     
                             !    +--103  
                             !    !    !         +----DRB3*0503     
                             !    !    !    +--330  
                             +---85    !    !    +----DRB3*0501     
                                  !    +--306
                                  !         +---------DRB3*0502     
                                  !
                                  +-------------------DRB3*3501     
  
  

   

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  DQA tree

  PROTDIST and neighbour-joining tree of DQA exon 2 peptide sequences
  In this consensus tree the numbers at the forks indicate the number of times the group consisting of the alleles which are to the right of that fork occurred among 500 trees

   

  
  
                                                                          +----DQA*2701
                                                 +----------------------500  
                                                 !                        +----DQA*2702  
                                                 !
                                                 !                        +----DQA*2001 
                                                 !                   +--110  
                                                 !                   !    +----DQA*2002
                                                 !              +--169  
                                            +--158              !    !    +----DQA*2201 
                                            !    !         +--186    +--173  
                                            !    !         !    !         +----DQA*2205 
                                            !    !         !    !
                                            !    !    +--488    +--------------DQA*2101
                                            !    !    !    !
                                            !    !    !    !              +----DQA*2202
                                       +--235    !    !    !         +--300  
                                       !    !    +--177    +-------189    +----DQA*2204 
                                       !    !         !              !
                                       !    !         !              +---------DQA*2203
                                       !    !         !
                                       !    !         +------------------------DQA*2401
                                  +--476    !
                                  !    !    +----------------------------------DQA*2301
                                  !    !
                                  !    !                             +---------DQA*2502
                                  !    !                        +--361  
                                  !    !                        !    !    +----DQA*2501
                             +--485    !                        !    +--391  
                             !    !    +----------------------498         +----DQA*2603
                             !    !                             !
                             !    !                             !         +----DQA*2602
                             !    !                             +-------394  
                        +--189    !                                       +----DQA*2601
                        !    !    !
                        !    !    +--------------------------------------------DQA*2801
                        !    !
                        !    !                                  +--------------DQA*1001
                        !    +--------------------------------209  
                        !                                       !    +---------DQA*1203
                        !                                       +--262  
                        !                                            !    +----DQA*1201
                        !                                            +--389  
                   +---89                                                 +----DQA*1202
                   !    !
                   !    !                                                 +----DQA*0802
                   !    !                                       +-------498  
                   !    !                                       !         +----DQA*0801
                   !    !                                  +--161  
                   !    !                                  !    !    +---------DQA*1401
                   !    !                                  !    +--458  
                   !    !                             +--113         !    +----DQA*1301 
              +--195    !                             !    !         +--468  
              !    !    !                             !    !              +----DQA*1302
              !    !    +----------------------------84    !
              !    !                                  !    +-------------------DQA*0103
              !    !                                  !
              !    !                                  !                   +----DQA*0101
         +--160    !                                  +-----------------208  
         !    !    !                                                      +----DQA*0102
         !    !    !
         !    !    +-----------------------------------------------------------DQA*1101
         !    !
    +--237    !                                                           +----DQA*0301
    !    !    !                                                      +--407  
    !    !    +----------------------------------------------------220    +----DQA*0302
    !    !                                                           !
    !    !                                                           +---------DQA*0401
    !    !
    !    +---------------------------------------------------------------------DQA*0204
    !
    !                                                           +--------------DQA*0201
    !                                                           !
    +----------------------------------------------------------86         +----DQA*0501
                                                                !    +--108  
                                                                +--100    +----DQA*0202
                                                                     !
                                                                     +---------DQA*0203
  
  

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  DQB tree

  PROTDIST and neighbour-joining tree of DQB exon 2 peptide sequences
  In this consensus tree the numbers at the forks indicate the number of times the group consisting of the alleles which are to the right of that fork occurred among 500 trees

   

  
  
                                            +----DQB*0501         
                                       +--452
                             +-------233    +----DQB*0502         
                             !         !
                             !         +---------DQB*1601         
         +-----------------298  
         !                   !              +----DQB*1701         
         !                   !    +-------476  
         !                   !    !         +----DQB*1702         
         !                   +--196  
         !                        !    +---------DQB*0901         
         !                        +--497  
         !                             !    +----DQB*0903         
         !                             +--210  
         !                                  +----DQB*0902         
         !
         !                                  +----DQB*0102         
         !                             +--285  
         !                        +--126    +----DQB*0101         
         !                        !    !
         !                        !    +---------DQB*0103         
         !                   +---29  
         !                   !    !         +----DQB*1401         
         !                   !    !    +--128  
    +--156         +--------63    +--164    +----DQB*1402         
    !    !         !         !         !
    !    !         !         !         +---------DQB*1201         
    !    !         !         !
    !    !         !         +-------------------DQB*2101         
    !    !         !
    !    !         !                        +----DQB*0701         
    !    !    +---45                   +--175  
    !    !    !    !                   !    +----DQB*0601         
    !    !    !    !    +-------------30  
    !    !    !    !    !              !    +----DQB*2001         
    !    !    !    !    !              +---54  
    !    !    !    !    !                   +----DQB*0201         
    !    !    !    !    !
    !    !    !    !    !                   +----DQB*1801         
    !    !    !    +--102              +--272  
    !    !    !         !         +--130    +----DQB*1802         
    !    !    !         !         !    !
    !    !    !         !    +--181    +---------DQB*1901         
    !    +---47         !    !    !
    !         !         !    !    +--------------DQB*0301         
    !         !         +---43  
    !         !              !              +----DQB*0801         
    !         !              !         +---97  
    !         !              !         !    +----DQB*1501         
    !         !              +--------47  
    !         !                        !    +----DQB*0402         
    !         !                        +--399  
    !         !                             +----DQB*0401         
    !         !
    !         !                             +----DQB*1101         
    !         +---------------------------219  
    !                                       +----DQB*1301         
    !
    !                                       +----DQB*1002         
    !                                  +--133  
    !                             +--147    +----DQB*1008         
    !                             !    !
    !                        +---85    +---------DQB*1003         
    !                        !    !
    !                        !    !    +---------DQB*1001         
    !                        !    +--127  
    +----------------------190         !    +----DQB*1004         
                             !         +--290  
                             !              +----DQB*1005         
                             !
                             !              +----DQB*1006         
                             +------------482  
                                            +----DQB*1007         
  
  

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