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Forum "Analyse phylogénétique"

Thread subject: Hypothèse des événements évolutifs d'une espèce: DA ou HTG?

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Hypothèse des événements évolutifs d'une espèce: DA ou HTG?
voyagel3
31 Oct 2016 10:54
Non evaluated contribution

Bonjour, 

Lors de la construction des arbres, PhyML et BioNJ, on a choisi comme groupe d'étude les rickettsiale, et comme groupe extérieur les autres alphaprotéobactéries. Nous avons remarqué que l'espèce alphaprotéobacterie rhizobiales n'est pas regoupé entre elles: [1] et [2]. 

Quelle hypothése nous pourrions faire sur [1] et sur [2]? Est-qu'il s'agit d'une duplication ancienne (DA) ou d'un HTG? 

Nous sommes en déssaccord sur les événements évolutifs de ces 2 groupes. L'un pense qu'il y a DA sur les 2 groupes alors que l'autre pense qu'il y a DA sur [1] et HTG sur [2]. 

Pourriez-vous nous éclairer s'il vous plaît? 

 

Bien respectueusement

 

 

=============

Arbre PhyML

==============

   , BPARPC2 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
     ,+ 0.456000                                                                                                        
     ,'0.861000 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
     |                                                                                                                  
     ' TO9D 6007030 Traduction 148-1158 sens direct                                                                     
   ,-+ 0.833000                                                                                                         
   | , BPARPC4 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                 
   | ' 0.854000                                                                                                         
 ,-+ 0.000000C3 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
 | |                                                                                                                    
 | | , BPARPP2 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                 
 | '-+ 0.886000                                                                                                         
 |   ' BPARPP1 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                 
 |                                                                                                                      
 |                   , BPARRT4 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                 
 |                  ,+ 0.781000                                                                                         
 |                  |' BPARRT1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                 
 |                ,-+ 0.915000                                                                                          
 |                | ,+ BPARRT2 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                 
 |                | ' 0.000000                                                                                          
 |                | '-+ BPARRT3 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                
 |          ,-----+ 0.989000                                                                                            
 |          |     |  , BPARRR2 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                 
 |          |     | ,+ 0.824000                                                                                         
 |          |     '-+'0.857000 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                 
 |          |       |                                                                                                   
 |        ,-+ 0.889000 BPARR1 Bacteria Proteobacteria Alphaproteobacteria Rhodobacteral                                 
=+        | |                                                                                                           
 |        | |     ,+ BPARRP1 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                   
 |        | |    ,+ 0.854000                                                                                            
 |        | |   ,+'0.8190003 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                   
 |      ,-+ 0.491000                                                                                                    
 |      | | '---+'0.9540004 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                    
 |      | |     |                                                                                                       
 |      | |     '---+ BPARRF1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                  
 |     ,+ 0.694000                                                                                                      
 |     || '---+ BPARRD1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                        
 |     ||                                                                                                               
 |     ||     , BPASSS2 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad                                     
 |     |'-----+ 0.995000                                                                                             
 | ,---+ 0.766000PASSS1 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad                                      
 | |   |                                                                                                                
 | |   |    ,+ BPARHH3 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales   |                                       
 | |   | ,--+ 0.954000                                                           |                                       
 | |   '-+ 0.816000RHH2 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales  |  [1]                                     
 | |     |                                                                       |                                       
 '-+ 0.929000BPARHH1 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales     |                                       
   |                                                                                                                    
   |                                       ,+ BPARHD2 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales           |
   |                 ,---------------------+ 0.972000                                                                   | [2]
   |                 |                     ' BPARHD1 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales            |
   |                 |                                                                                                  
   |                 |                             ,+ BPACCA3 Bacteria Proteobacteria Alphaproteobacteria Caulobactera  
   '-----------------+ 0.973000                    , 0.686000                                                           
                     |                         ,---' 0.798000Bacteria Proteobacteria Alphaproteobacteria Caulobactera  
                     |                         |   |                                                                    
                     |                         |   '+ BPACCA2 Bacteria Proteobacteria Alphaproteobacteria Caulobactera  
                     '-------------------------+ 0.117000                                                               
                                               | ,-+ BPASSS3 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad   
                                               | |                                                                      
                                               '-+ 0.894000SSS4 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad
                                                 '-+                                                                    
                                                   '-+ BPASSS5 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad 
                                                                                                                        
 |----------|-----------|----------|----------|--------                                                                 
 0        0.5           1        1.5          2                                                                         
 substitutions/site                                         

 

===========

Arbre BioNJ

===========

       , BPARPC2 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                               
      ,+ 0.5                                                                                                            
     ,+'0.86RPC1 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                               
     ||                                                                                                                 
     |' TO9D 6007030 Traduction 148-1158 sens direct                                                                    
    ,+ 0.97                                                                                                             
    ||,+ BPARPC4 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                               
    |'+ 1                                                                                                               
 ,--+ 0.99PARPC3 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                               
 |  |                                                                                                                   
 |  | , BPARPP2 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
 |  '-+ 1                                                                                                               
 |    ' BPARPP1 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
 |                                                                                                                      
 |                                       ,+ BPARHD2 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales   |          
 |                   ,-------------------+ 1                                                                  | [1]         
 |                   |                   '+ BPARHD1 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales   |          
 |                   |                                                                                                  
=+                   |                           ,+ BPASSS4 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad    
 |  ,----------------+ 0.98                    ,-+ 0.41                                                                 
 |  |                |                       ,-+ 0.59-+ BPASSS5 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad
 |  |                |                       | |                                                                        
 |  |                |                       | '----+ BPASSS3 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad  
 |  |                |                       |                                                                          
 |  |                '-----------------------+ 1  , BPACCA3 Bacteria Proteobacteria Alphaproteobacteria Caulobactera    
 |  |                                        |   ,+ 0.78                                                                
 |  |                                        '---+'0.93ACCA1 Bacteria Proteobacteria Alphaproteobacteria Caulobactera   
 |  |                                            |                                                                      
 |  |                                            '-+ BPACCA2 Bacteria Proteobacteria Alphaproteobacteria Caulobactera   
 '--+ 0.65                                                                                                              
    |      ,-+ BPARHH3 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales |                                         
    |   ,--+ 0.99                                                              |                                         
    | ,-+ 0.95BPARHH2 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales  |   [2]                                      
    | | |                                                                      |                                         
    | | '---+ BPARHH1 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales  |                                         
    | |                                                                                                                 
    | |       , BPASSS2 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad                                        
    | |,------+ 1                                                                                                       
    | ,+ 0.35 ' BPASSS1 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad                                        
    '-||0.2                                                                                                             
      |'-----+ BPARRD1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                         
      |                                                                                                                 
      |        , BPARRP1 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                       
      |      ,-+ 0.96                                                                                                   
      |     ,+ 0.82ARRR3 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                       
      ' 0.61||                                                                                                          
      |,----+'0.99PARRR4 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                       
      ||    |                                                                                                           
      ||    '----+ BPARRF1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                     
      ||                                                                                                                
      ||       ,+ BPARRR2 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                      
      '+ 0.99 ,+ 0.95                                                                                                   
       |     ,+'0.95ARRR1 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                      
       |     ||                                                                                                         
       |     |'-+ BPARR1 Bacteria Proteobacteria Alphaproteobacteria Rhodobacteral                                      
       '-----+ 1                                                                                                        
             | ,+ BPARRT2 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                      
             | |                                                                                                        
             '-+, BPARRT4 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                      
               |, 0.44                                                                                                  
               ''+0.26RRT3 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                     
                |                                                                                                       
                ' BPARRT1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                      
                                                                                                                        
 |-----------------|----------------|-----------------|                                                                 
 0               0.5                1               1.5                                                                 
 substitutions/site                                       

 

 

 

P_Hingamp_BC16
4 Nov 2016 10:56
Game master

Bonjour,

Il y a souvent plusieurs interprétations possibles à partir d'un arbre phylogénétique, et quelques fois il n'est pas possible de trancher, auquel cas il est tout à fait acceptable de proposer deux hypothèses alternatives! Il faut se résoudre quelque fois à reconnaitre qu'on ne sait pas...

Toutefois dans votre arbre, n'observons-nous pas un deuxième groupe taxonomique réparti entre deux branches distinctes: les "Sphingomonad" ? Ceci aurait tendance à donner un peu plus de crédibilité à l'hypothèse de la duplication qui aurait pu avoir lieu à la base de la branche A des "non-Ricketsiales". Sauf que dans ce cas on s'attendrait peut -être à voir des "Caulobactera" aussi dans l'autre branche B, ainsi que des "Rhodospirill" et des "Rhodobactera" dans l'autre branche C? Quelques fois lorsqu'un gène se duplique, l'une des copies est perdue dans une branche taxonomique et pas dans les autres, ce qui peut produire de tels arbres (encore faut-il s'assurer qu'en enrichissant vos arbres avec des Caulobactera/Rhodospirill/Rhodobactera cela ne change pas la topologie de ces arbres).

En bref: si vous pensez avoir de bons arguments, tranchez entre les deux hypothèses (quitte à les citer toutes les deux), sinon proposez deux hypothèses alternatives!

 

   , BPARPC2 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                               
     ,+ 0.456000                                                                                                       
     ,'0.861000 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                               
     |                                                                                                                 
     ' TO9D 6007030 Traduction 148-1158 sens direct                                                                    
   ,-+ 0.833000                                                                                                        
   | , BPARPC4 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
   | ' 0.854000                                                                                                        
,-+ 0.000000C3 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                               
| |                                                                                                                   
| | , BPARPP2 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
| '-+ 0.886000                                                                                                        
|   ' BPARPP1 Bacteria Proteobacteria Alphaproteobacteria Rickettsiale                                                
|                                                                                                                     
|                   , BPARRT4 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                
|                  ,+ 0.781000                                                                                        
|                  |' BPARRT1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                
|                ,-+ 0.915000                                                                                         
|                | ,+ BPARRT2 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                
|                | ' 0.000000                                                                                         
|                | '-+ BPARRT3 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                               
|          ,-----+ 0.989000                                                                                           
|          |     |  , BPARRR2 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                
|          |     | ,+ 0.824000                                                                                        
|          |     '-+'0.857000 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                
|          |       |                                                                                                  
|        ,-+ 0.889000 BPARR1 Bacteria Proteobacteria Alphaproteobacteria Rhodobacteral                                
=+        | |                                                                                                          
|        | |     ,+ BPARRP1 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                  
|        | |    ,+ 0.854000                                                                                           
|        | |   ,+'0.8190003 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                  
|      ,-+ 0.491000                                                                                                   
|      | | '---+'0.9540004 Bacteria Proteobacteria Alphaproteobacteria Rhodobactera                                   
|      | |     |                                                                                                      
|      | |     '---+ BPARRF1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                 
|     ,+ 0.694000                                                                                                     
|     || '---+ BPARRD1 Bacteria Proteobacteria Alphaproteobacteria Rhodospirill                                       
|     ||                                                                                                              
|     ||     , BPASSS2 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad                                    
|     |'-----+ 0.995000                                                                                            
| ,-B-+ 0.766000PASSS1 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad                                     
| |   |                                                                                                               
| |   |    ,+ BPARHH3 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales   |                                      
| |   | ,--+ 0.954000                                                           |                                      
| |   '-+ 0.816000RHH2 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales  |  [1]                                    
| |     |                                                                       |                                      
'-+ 0.929000BPARHH1 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales     |                                      
 A |                                                                                                                   
   |                                       ,+ BPARHD2 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales           |
   |                 ,---------------------+ 0.972000                                                                   | [2]
   |                 |                     ' BPARHD1 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales            |
   |                 |                                                                                                 
   |                 |                             ,+ BPACCA3 Bacteria Proteobacteria Alphaproteobacteria Caulobactera 
   '---------C-------+ 0.973000                    , 0.686000                                                          
                     |                         ,---' 0.798000Bacteria Proteobacteria Alphaproteobacteria Caulobactera 
                     |                         |   |                                                                   
                     |                         |   '+ BPACCA2 Bacteria Proteobacteria Alphaproteobacteria Caulobactera 
                     '-------------------------+ 0.117000                                                              
                                               | ,-+ BPASSS3 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad  
                                               | |                                                                     
                                               '-+ 0.894000SSS4 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad
                                                 '-+                                                                   
                                                   '-+ BPASSS5 Bacteria Proteobacteria Alphaproteobacteria Sphingomonad 
 |----------|-----------|----------|----------|--------                                                                
0        0.5           1        1.5          2                                                                        
substitutions/site