Automated phylogeny reconstruction

Methods

• (Prior to inclusion in database: base calling with phred; contig assembly with phrap)
• Progressive multiple sequence alignment with clustalw2
• Maximum likelihood phylogeny estimation from DNA sequences using dnaml (from Joseph Felsenstein's phylip package; uses a Hidden Markov Model method of inferring rates of evolution)
• DNA similarity using dnadist (F84 algorithm), also from phylip

Primers

• rbcL_1F
• rbcL_724R

Settings

• $ clustalw2 -align -output=phylip -outorder=input -type=dna
• $ echo -n "o\n1\ny\n" | dnaml
• $ echo -n "y\n" | dnadist
• Outgroup added: Amborella trichopoda, GENBANK ID: gi|37194760
• Run time: 2010-07-28 12:10 GMT-0700

dnaml output

Nucleic acid sequence Maximum Likelihood method, version 3.65


Empirical Base Frequencies:

   A       0.28420
   C       0.20434
   G       0.22752
  T(U)     0.28394

Transition/transversion ratio =   2.000000


     +Leeain41  
  +-11  
  |  +Vitisel2  
  |  
  |        +Sympl36   
  |     +--9  
  |  +--1  +Adinaco4  
  |  |  |  
  |  |  +Ilex11    
  |  |  
  |  |        +---Streb199  
  |  |     +-13  
  3--6     |  +Archi35   
  |  |  +--8  
  |  |  |  |  +Gynotax45 
  |  |  |  +-12  
  |  |  |     |  +Flaco30   
  |  |  |     +--7  
  |  +--4        +-Macartr9  
  |     |  
  |     |     +-------Lepis204  
  |     |  +-14  
  |     |  |  |  +Melic10   
  |     |  |  +--5  
  |     +--2     +Buchaar3  
  |        |  
  |        |  +Syzyg39   
  |        +-10  
  |           +Syzyglo1  
  |  
  +---Amborella 


remember: (although rooted by outgroup) this is an unrooted tree!

Ln Likelihood = -3451.93438

 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------

     3          Amborella         0.06255     (  0.04331,     0.08185) **
     3            11              0.01462     (  0.00539,     0.02385) **
    11          Leeain41          0.01131     (  0.00326,     0.01934) **
    11          Vitisel2          0.01576     (  0.00632,     0.02529) **
     3             6              0.00439     (     zero,     0.00985) **
     6             1              0.00713     (  0.00048,     0.01382) **
     1             9              0.01297     (  0.00429,     0.02173) **
     9          Sympl36           0.01607     (  0.00587,     0.02624) **
     9          Adinaco4          0.01274     (  0.00399,     0.02152) **
     1          Ilex11            0.02576     (  0.01351,     0.03809) **
     6             4              0.00365     (     zero,     0.00876) **
     4             8              0.01231     (  0.00193,     0.02269) **
     8            13              0.01165     (  0.00107,     0.02223) **
    13          Streb199          0.06766     (  0.04539,     0.08996) **
    13          Archi35           0.02564     (  0.01308,     0.03821) **
     8            12              0.00905     (  0.00137,     0.01678) **
    12          Gynotax45         0.02670     (  0.01415,     0.03927) **
    12             7              0.00307     (     zero,     0.00754) **
     7          Flaco30           0.01953     (  0.00900,     0.03002) **
     7          Macartr9          0.02843     (  0.01576,     0.04114) **
     4             2              0.00881     (  0.00059,     0.01709) **
     2            14              0.02524     (  0.01137,     0.03919) **
    14          Lepis204          0.14172     (  0.10776,     0.17575) **
    14             5              0.00378     (     zero,     0.01018)
     5          Melic10           0.02833     (  0.01541,     0.04127) **
     5          Buchaar3          0.02007     (  0.00923,     0.03089) **
     2            10              0.02338     (  0.01160,     0.03515) **
    10          Syzyg39           0.00414     (     zero,     0.00893) **
    10          Syzyglo1          0.00709     (  0.00086,     0.01334) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01

phylogeny (newick format)

((Leeain41:0.01131,Vitisel2:0.01576):0.01462,(((Sympl36:0.01607, Adinaco4:0.01274):0.01297,Ilex11:0.02576):0.00713, (((Streb199:0.06766,Archi35:0.02564):0.01165,(Gynotax45:0.02670, (Flaco30:0.01953,Macartr9:0.02843):0.00307):0.00905):0.01231, ((Lepis204:0.14172,(Melic10:0.02833,Buchaar3:0.02007):0.00378):0.02524, (Syzyg39:0.00414,Syzyglo1:0.00709):0.02338):0.00881):0.00365):0.00439, Amborella:0.06255);

DNA similarity

Adinaco4   is most similar to Sympl36    (DNA dist: 0.029779)
Amborella  is most similar to Adinaco4   (DNA dist: 0.078474)
Archi35    is most similar to Gynotax45  (DNA dist: 0.053562)
Buchaar3   is most similar to Melic10    (DNA dist: 0.046745)
Flaco30    is most similar to Macartr9   (DNA dist: 0.048715)
Gynotax45  is most similar to Flaco30    (DNA dist: 0.049137)
Ilex11     is most similar to Sympl36    (DNA dist: 0.048392)
Leeain41   is most similar to Vitisel2   (DNA dist: 0.027276)
Lepis204   is most similar to Buchaar3   (DNA dist: 0.124069)
Macartr9   is most similar to Flaco30    (DNA dist: 0.048715)
Melic10    is most similar to Buchaar3   (DNA dist: 0.046745)
Streb199   is most similar to Macartr9   (DNA dist: 0.069457)
Sympl36    is most similar to Adinaco4   (DNA dist: 0.029779)
Syzyg39    is most similar to Syzyglo1   (DNA dist: 0.011280)
Syzyglo1   is most similar to Syzyg39    (DNA dist: 0.011280)
Vitisel2   is most similar to Leeain41   (DNA dist: 0.027276)