Web document 7.11. Sample output from a Bayesian phylogenetic analysis using MrBayes.

 

   Logging screen output to file "log.out"

 

MrBayes > sumt

   Summarizing trees in files "13globins.nex.run1.t" and "13globins.nex.run2.t"

   DOS line termination

   Examining first file ...

   Found one tree block in file "13globins.nex.run1.t" with 5944 trees in last block

   Expecting the same number of trees in the last tree block of all files

 

   Tree reading status:

 

   0      10      20      30      40      50      60      70      80      90     100

   v-------v-------v-------v-------v-------v-------v-------v-------v-------v-------v

   *********************************************************************************

 

   Read a total of 11888 trees in 2 files (sampling 11888 of them)

      (Each file contained 5944 trees of which 5944 were sampled)

 

   File "13globins.nex.parts" already exists

   Overwrite information in this file (yes/no):    Overwriting file "13globins.nex.parts"

 

   File "13globins.nex.con" already exists

   Overwrite information in this file (yes/no):    Overwriting file "13globins.nex.con"

 

   File "13globins.nex.trprobs" already exists

   Overwrite information in this file (yes/no):    Overwriting file "13globins.nex.trprobs"

                                                                                   

   General explanation:                                                         

                                                                                  

   A taxon bibartition is specified by removing a branch, thereby dividing the  

   species into those to the left and those to the right of the branch. Here,   

   taxa to one side of the removed branch are denoted "." and those to the    

   other side are denoted "*". The output includes the bipartition number     

   (ID; sorted from highest to lowest probability), bipartition (e.g., ...**..),

   number of times the bipartition was observed (#obs), the posterior probabil- 

   ity of the bipartition, and, if branch lengths were recorded on the trees in 

   the file, the average (Mean(v)) and variance (Var(v)) of the lengths. Each   

   "." or "*" in the bipartition represents a taxon that is to the left or  

   right of the removed branch. A list of the taxa in the bipartition is given  

   before the list of bipartitions. If you summarize several independent analy- 

   ses, convergence diagnostics are presented for both the posterior probabil-  

   ities of bipartitions (bipartition or split frequencies) and branch lengths  

   (if recorded on the trees in the files). In the former case, the diagnostic is

   the standard deviation of the partition frequencies (Stdev(s)), in the second

   case it is the potential scale reduction factor (PSRF) of Gelman and Rubin   

   (1992). Stdev(s) is expected to approach 0 and PSRF is expected to approach 1

   as runs converge onto the posterior probability distribution. Note that these

   values may be unreliable if the partition is not present in all runs (the    

   last column indicates the number of runs that sampled the partition if more  

   than one run is summarized). The PSRF is also sensitive to small sample      

   sizes and it should only be considered a rough guide to convergence since    

   some of the assumptions allowing one to interpret it as a true potential     

   scale reduction factor are violated in the phylogenetic context.             

                                                                                

   List of taxa in bipartitions:                                                

                                                                                  

      1 -- mbkangaro

      2 -- mbharbor_

      3 -- mbgray_se

      4 -- alphahors

      5 -- alphakang

      6 -- alphadog

      7 -- betadog

      8 -- betarabbi

      9 -- betakanga

     10 -- globinlam

     11 -- globinsea

     12 -- globinsoy

     13 -- globinins

                                                                                  

   Summary statistics for taxon bipartitions:                               

 

   ID -- Partition      #obs    Probab.  Stdev(s)   Mean(v)   Var(v)    PSRF  Nruns

   --------------------------------------------------------------------------------

    1 -- ..*..........  11888  1.000000  0.000000  0.043107  0.000418  1.000    2

    2 -- ......*......  11888  1.000000  0.000000  0.070789  0.000586  1.000    2

    3 -- .........*...  11888  1.000000  0.000000  0.037674  0.000654  1.001    2

    4 -- ..........*..  11888  1.000000  0.000000  0.064191  0.000791  1.002    2

    5 -- ...*.........  11888  1.000000  0.000000  0.088738  0.000754  1.000    2

    6 -- .************  11888  1.000000  0.000000  0.116869  0.001562  1.000    2

    7 -- .*...........  11888  1.000000  0.000000  0.067826  0.000461  1.000    2

    8 -- ...........*.  11888  1.000000  0.000000  0.852265  0.033478  1.001    2

    9 -- ....*........  11888  1.000000  0.000000  0.105215  0.001036  1.000    2

   10 -- .....*.......  11888  1.000000  0.000000  0.126253  0.001089  1.000    2

   11 -- ............*  11888  1.000000  0.000000  0.756330  0.026074  1.000    2

   12 -- .......*.....  11888  1.000000  0.000000  0.083162  0.000663  1.000    2

   13 -- ........*....  11888  1.000000  0.000000  0.158580  0.001857  1.000    2

   14 -- ...**********  11886  0.999832  0.000000  0.675390  0.023884  1.000    2

   15 -- ...***.......  11885  0.999748  0.000119  0.328362  0.005318  1.000    2

   16 -- .........**..  11885  0.999748  0.000119  0.505679  0.014589  1.000    2

   17 -- ......***....  11879  0.999243  0.000119  0.295652  0.005753  1.001    2

   18 -- ...*.*.......  10654  0.896198  0.006186  0.051493  0.000632  1.000    2

   19 -- ...........**  10577  0.889721  0.005353  0.433231  0.016810  1.000    2

   20 -- ......**.....  10281  0.864822  0.004402  0.061645  0.000833  1.000    2

   21 -- ...******....  10097  0.849344  0.009398  0.223350  0.007999  1.000    2

   22 -- .........****   6260  0.526581  0.002141  0.225533  0.009590  1.000    2

   23 -- .**..........   5840  0.491252  0.006186  0.049463  0.001080  1.000    2

   24 -- ..***********   5284  0.444482  0.005234  0.026841  0.000303  1.000    2

   25 -- ...********..   4253  0.357756  0.008208  0.224796  0.010708  1.002    2

   26 -- ...*********.   1288  0.108345  0.005234  0.331364  0.013494  1.005    2

   27 -- ...******..*.   1154  0.097073  0.008327  0.251456  0.008839  1.000    2

   28 -- ...**........   1147  0.096484  0.006781  0.037934  0.000569  1.002    2

   29 -- ......*.*....   1111  0.093456  0.002498  0.029859  0.000319  1.000    2

   30 -- ...***...****    830  0.069818  0.005948  0.122319  0.003635  1.013    2

   31 -- .*.**********    762  0.064098  0.000952  0.015361  0.000199  1.000    2

   --------------------------------------------------------------------------------

 

 

   Clade credibility values:

 

   /---------------------------------------------------------------- mbkangaro (1)

   |                                                                              

   |---------------------------------------------------------------- mbharbor_ (2)

   |                                                                              

   |---------------------------------------------------------------- mbgray_se (3)

   |                                                                               

   |                                                  /------------- alphahors (4)

   |                                     /-----90-----+                           

   |                                     |            \------------- alphadog (6)

   +                         /----100----+                                        

   |                         |           \-------------------------- alphakang (5)

   |                         |                                                     

   |            /-----85-----+                        /------------- betadog (7)

   |            |            |           /-----86-----+                           

   |            |            |           |            \------------- betarabbi (8)

   |            |            \----100----+                                        

   |            |                        \-------------------------- betakanga (9)

   \-----100----+                                                                  

                |                                     /------------- globinlam (10)

                |                        /-----100----+                           

                |                        |            \------------- globinsea (11)

                \-----------53-----------+                                        

                                         |            /------------- globinsoy (12)

                                         \-----89-----+                            

                                                      \------------- globinins (13)

                                                                                  

 

   Phylogram:

 

                                                                                 /--- mbkangaro (1)

   |                                                                              

   |-- mbharbor_ (2)

   |                                                                              

   |- mbgray_se (3)

   |                                                                              

   |                                    /--- alphahors (4)

   |                                   /+                                         

   |                                   |\---- alphadog (6)

   +                         /---------+                                          

   |                         |         \--- alphakang (5)

   |                         |                                                     

   |                   /-----+          /-- betadog (7)

   |                   |     |        /-+                                         

   |                   |     |        | \-- betarabbi (8)

   |                   |     \--------+                                            

   |                   |              \----- betakanga (9)

   \-------------------+                                                          

                       |                    /- globinlam (10)

                       |     /--------------+                                     

                       |     |              \-- globinsea (11)

                       \-----+                                                    

                             |            /------------------------- globinsoy (12)

                             \------------+                                       

                                          \---------------------- globinins (13)

                                                                                   

   |--------------| 0.500 expected changes per site

 

   Calculating tree probabilities...

 

   Credible sets of trees (194 trees sampled):

      50 % credible set contains 4 trees

      90 % credible set contains 28 trees

      95 % credible set contains 47 trees

      99 % credible set contains 109 trees

 

 

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