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

• matK-3F_kim
• matK-1R_kim

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|33333411
• Run time: 2010-09-08 12:11 GMT-0700

dnaml output

Nucleic acid sequence Maximum Likelihood method, version 3.65


Empirical Base Frequencies:

   A       0.29491
   C       0.18260
   G       0.16154
  T(U)     0.36096

Transition/transversion ratio =   2.000000


               +------Flaco30   
            +--8  
            |  |  +-----Melic10   
            |  +--6  
         +--2     +--Buchaar3  
         |  |  
         |  |  +------Archi35   
         |  +-10  
      +--1     |  +Syzyg39   
      |  |     +-12  
      |  |        +Syzyglo1  
      |  |  
      |  |  +Leeain41  
      |  +-13  
  +---3     +Vitisel2  
  |   |  
  |   |     +----Prism44   
  |   |  +-14  
  |   |  |  +---Ilex11    
  |   +--7  
  |      |  +--Palaqbe95 
  |      +-16  
  |         |  +--Gordo6    
  |         +--4  
  |            |  +-Sympl36   
  |            +-11  
  |               +Adinaco4  
  |  
  |  +---------Dendrcr7  
  9--5  
  |  |  +----Polya82   
  |  +-15  
  |     +---Matthsa33 
  |  
  +-------Amborella 


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

Ln Likelihood = -6541.27639

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

     9          Amborella         0.13229     (  0.10449,     0.16020) **
     9             3              0.06578     (  0.04562,     0.08595) **
     3             1              0.01126     (  0.00216,     0.02040) **
     1             2              0.02058     (  0.00959,     0.03162) **
     2             8              0.00633     (     zero,     0.01359) **
     8          Flaco30           0.11122     (  0.08630,     0.13615) **
     8             6              0.03053     (  0.01648,     0.04456) **
     6          Melic10           0.10188     (  0.07806,     0.12568) **
     6          Buchaar3          0.05361     (  0.03624,     0.07106) **
     2            10              0.01443     (  0.00462,     0.02426) **
    10          Archi35           0.11677     (  0.09102,     0.14258) **
    10            12              0.05238     (  0.03546,     0.06932) **
    12          Syzyg39           0.00641     (  0.00060,     0.01227) **
    12          Syzyglo1          0.00234     (     zero,     0.00599) *
     1            13              0.03356     (  0.02014,     0.04698) **
    13          Leeain41          0.01290     (  0.00453,     0.02133) **
    13          Vitisel2          0.02167     (  0.01107,     0.03222) **
     3             7              0.02099     (  0.00925,     0.03279) **
     7            14              0.01424     (  0.00401,     0.02454) **
    14          Prism44           0.08996     (  0.06748,     0.11238) **
    14          Ilex11            0.06075     (  0.04248,     0.07903) **
     7            16              0.01837     (  0.00812,     0.02864) **
    16          Palaqbe95         0.03855     (  0.02438,     0.05279) **
    16             4              0.00065     (     zero,     0.00338)
     4          Gordo6            0.04090     (  0.02697,     0.05474) **
     4            11              0.00447     (     zero,     0.00965) **
    11          Sympl36           0.03403     (  0.02104,     0.04702) **
    11          Adinaco4          0.02527     (  0.01432,     0.03628) **
     9             5              0.01317     (  0.00146,     0.02491) **
     5          Dendrcr7          0.17009     (  0.13743,     0.20271) **
     5            15              0.01284     (  0.00182,     0.02396) **
    15          Polya82           0.08285     (  0.06009,     0.10566) **
    15          Matthsa33         0.07235     (  0.05200,     0.09270) **

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

phylogeny (newick format)

(((((Flaco30:0.11122,(Melic10:0.10188,Buchaar3:0.05361):0.03053):0.00633, (Archi35:0.11677,(Syzyg39:0.00641,Syzyglo1:0.00234):0.05238):0.01443):0.02058, (Leeain41:0.01290,Vitisel2:0.02167):0.03356):0.01126, ((Prism44:0.08996,Ilex11:0.06075):0.01424,(Palaqbe95:0.03855, (Gordo6:0.04090,(Sympl36:0.03403,Adinaco4:0.02527):0.00447):0.00065):0.01837):0.02099):0.06578, (Dendrcr7:0.17009,(Polya82:0.08285,Matthsa33:0.07235):0.01284):0.01317, Amborella:0.13229);

DNA similarity

Adinaco4   is most similar to Sympl36    (DNA dist: 0.060070)
Amborella  is most similar to Matthsa33  (DNA dist: 0.220722)
Archi35    is most similar to Syzyglo1   (DNA dist: 0.175364)
Buchaar3   is most similar to Syzyglo1   (DNA dist: 0.148977)
Dendrcr7   is most similar to Matthsa33  (DNA dist: 0.256238)
Flaco30    is most similar to Syzyglo1   (DNA dist: 0.179078)
Gordo6     is most similar to Adinaco4   (DNA dist: 0.067503)
Ilex11     is most similar to Adinaco4   (DNA dist: 0.113464)
Leeain41   is most similar to Vitisel2   (DNA dist: 0.034548)
Matthsa33  is most similar to Polya82    (DNA dist: 0.157659)
Melic10    is most similar to Buchaar3   (DNA dist: 0.155042)
Palaqbe95  is most similar to Adinaco4   (DNA dist: 0.071133)
Polya82    is most similar to Matthsa33  (DNA dist: 0.157659)
Prism44    is most similar to Adinaco4   (DNA dist: 0.132880)
Sympl36    is most similar to Adinaco4   (DNA dist: 0.060070)
Syzyg39    is most similar to Syzyglo1   (DNA dist: 0.008947)
Syzyglo1   is most similar to Syzyg39    (DNA dist: 0.008947)
Vitisel2   is most similar to Leeain41   (DNA dist: 0.034548)