  =============================================
  AUTO                                         
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version 2.1.2

  Program started at Mon Jan 23 16:35:51 2006
         finished at Mon Jan 23 16:37:23 2006
     


Options in use:
---------------
Datatype: Microsatellite data [Stepwise mutation]
Missing data is not included
Pseudo-random number generator: Least Congruental Generator                     
Random number seed (with internal timer)           1138052151
Start parameters:
   Theta values were generated  from the FST-calculation
   M values were generated from the FST-calculation
Migration model:
   Migration matrix model with variable Theta  
Mutation rate is constant for all loci
Analysis strategy is                          Maximum likelihood
Markov chain settings:
   Short chains (short-chains):                           10
      Trees sampled (short-inc*samples):                 100
      Trees recorded (short-sample):                      50
   Long chains (long-chains):                              3
      Trees sampled (long-inc*samples):                  200
      Trees recorded (long-sample):                      100
   Averaging over replicates:                              2
   Number of discard trees per chain:                     10
Print options:
   Data file:                                    infile.msat
   Output file (ASCII text):                      outfile-ml
   Output file (PDF):                         outfile-ml.pdf
   Print data:                                            No
   Print genealogies:                                     No
   Plot data: No                                            
   Profile likelihood: Yes, tables and summary             
             Percentile method
             with df=1 and for Theta and M=m/mu



Summary of data:
---------------
Datatype:                                 Microsatellite data
Number of loci:                                            10

Population                                    Locus  Gene copies
                                                     data (missing)
----------------------------------------------------------------
  1 population__number___0                       1     50 (0)
                                                 2     50 (0)
                                                 3     50 (0)
                                                 4     50 (0)
                                                 5     50 (0)
                                                 6     50 (0)
                                                 7     50 (0)
                                                 8     50 (0)
                                                 9     50 (0)
                                                10     50 (0)
  2 population__number___1                       1     42 (0)
                                                 2     42 (0)
                                                 3     42 (0)
                                                 4     42 (0)
                                                 5     42 (0)
                                                 6     42 (0)
                                                 7     42 (0)
                                                 8     42 (0)
                                                 9     42 (0)
                                                10     42 (0)
Total of all populations                         1     92 (0)
                                                 2     92 (0)
                                                 3     92 (0)
                                                 4     92 (0)
                                                 5     92 (0)
                                                 6     92 (0)
                                                 7     92 (0)
                                                 8     92 (0)
                                                 9     92 (0)
                                                10     92 (0)





==============================================================================
MCMC estimates 
==============================================================================
Population [x] Loc.  Ln(L)   Theta    M [m/mu] [+=receiving population]  
                             [xNe mu]    1,+     2,+    
-------------- ---- -------- -------- ----------------------------------------
 1: population  1 1    0.165  0.36286 ------- 10.3043 
                1 2    0.024  0.40508 ------- 11.4465 
                1 A    0.307  0.37420 ------- 10.6309 
                2 1    0.193  0.15271 ------- 42.8912 
                2 2    0.022  0.20715 ------- 51.2639 
                2 A    0.031  0.20618 ------- 51.1602 
                3 1    0.060  0.52345 ------- 17.7521 
                3 2    1.120  0.61631 ------- 34.6869 
                3 A    2.240  0.61631 ------- 34.6869 
                4 1    0.187  0.43508 ------- 25.5646 
                4 2    0.202  0.52069 ------- 32.2090 
                4 A    0.356  0.43733 ------- 25.7672 
                5 1    1.052  0.18815 ------- 11.1966 
                5 2    2.175  0.18293 -------  7.7804 
                5 A    2.998  0.18430 -------  7.6365 
                6 1    0.351  1.05814 -------  6.0660 
                6 2    0.281  0.72671 -------  6.6431 
                6 A    0.488  0.73026 -------  6.6379 
                7 1    0.665  0.08094 ------- 63.3447 
                7 2    1.603  0.06636 ------- 41.5876 
                7 A    3.189  0.06637 ------- 41.5931 
                8 1    1.414  0.35519 ------- 10.9241 
                8 2    0.946  0.47240 ------- 10.8024 
                8 A    2.827  0.35612 ------- 10.9168 
                9 1    0.256  0.75454 ------- 11.6942 
                9 2    0.118  0.55183 -------  9.2043 
                9 A    0.209  0.55402 -------  9.2408 
               10 1    0.259  0.49595 -------  8.9629 
               10 2    0.982  0.47786 ------- 10.6164 
               10 A    1.755  0.47834 ------- 10.5950 
                All -226.499  0.39957 ------- 13.6856 
 2: population  1 1    0.165  0.39744 21.7652 -------
                1 2    0.024  0.40250 28.0609 -------
                1 A    0.307  0.39878 23.3023 -------
                2 1    0.193  0.13297 61.0445 -------
                2 2    0.022  0.10214 54.9198 -------
                2 A    0.031  0.10245 54.9917 -------
                3 1    0.060  0.49225 22.9766 -------
                3 2    1.120  0.52254 17.6252 -------
                3 A    2.240  0.52254 17.6252 -------
                4 1    0.187  0.46855  8.1975 -------
                4 2    0.202  0.58856  8.7721 -------
                4 A    0.356  0.47158  8.2252 -------
                5 1    1.052  0.23072 21.4420 -------
                5 2    2.175  0.17412 18.0026 -------
                5 A    2.998  0.17699 18.2025 -------
                6 1    0.351  0.31770 20.9691 -------
                6 2    0.281  0.36363 19.3947 -------
                6 A    0.488  0.36261 19.4339 -------
                7 1    0.665  0.10222 22.9821 -------
                7 2    1.603  0.09143 47.3604 -------
                7 A    3.189  0.09145 47.3447 -------
                8 1    1.414  0.56634 16.3066 -------
                8 2    0.946  0.48343 22.1595 -------
                8 A    2.827  0.56627 16.3172 -------
                9 1    0.256  0.58823 17.8494 -------
                9 2    0.118  0.53848 16.4694 -------
                9 A    0.209  0.53918 16.4954 -------
               10 1    0.259  0.30728 50.3781 -------
               10 2    0.982  0.43307 40.5789 -------
               10 A    1.755  0.43144 40.6637 -------
                All -226.499  0.35147 21.4359 -------

Comments:
 The x is 1, 2, or 4 for mtDNA, haploid, or diploid data, respectively
There were 10 short chains (50 used trees out of sampled 100)
  and 3 long chains (100 used trees out of sampled 200)
  COMBINATION OF 2 MULTIPLE RUNS)


===============================================================================
Profile likelihood tables   [Summary is at the end of the file]
===============================================================================


Profile likelihood for parameter Theta_1
Parameters are evaluated at percentiles
using bisection method (slow, but exact).
-------------------------------------------------------------------------------
Per.  Ln(L)     Theta_1     *Theta_1*   Theta_2      M_21       M_12     
=-------------------------------------------------------------------------------
0.005 -229.817    0.35259   0.352590   0.354383  13.652625  20.911559 
0.025 -228.419   0.363533   0.363533   0.353462  13.657752  21.055190 
0.050 -227.851   0.369235   0.369235   0.352992  13.660816  21.134618 
0.250 -226.725   0.387012   0.387012   0.351890  13.673894  21.340729 
MLE   -226.499   0.399574   0.399574   0.351470  13.685637  21.435893 
0.750 -226.726   0.412453   0.412453   0.351230  13.698760  21.503559 
0.950 -227.851    0.43174   0.431740   0.351040  13.719451  21.574115 
0.975 -228.419   0.438211   0.438211   0.350997  13.726587  21.592937 
0.995 -229.816   0.451191   0.451191   0.350924  13.741207  21.625982 
==------------------------------------------------------------------------------




Profile likelihood for parameter Theta_2
Parameters are evaluated at percentiles
using bisection method (slow, but exact).
-------------------------------------------------------------------------------
Per.  Ln(L)     Theta_2      Theta_1   *Theta_2*     M_21       M_12     
=-------------------------------------------------------------------------------
0.005 -229.817   0.307804   0.400621   0.307804  13.726401  21.469599 
0.025 -228.419    0.31758   0.400390   0.317580  13.715639  21.463637 
0.050 -227.852   0.322727   0.400269   0.322727  13.710392  21.460157 
0.250 -226.727   0.339288   0.399877   0.339288  13.695307  21.447193 
MLE   -226.499    0.35147   0.399574   0.351470  13.685637  21.435893 
0.750 -226.727   0.364228   0.399228   0.364228  13.676342  21.422503 
0.950 -227.851   0.383648   0.398613   0.383648  13.662694  21.399398 
0.975 -228.419   0.390258   0.398371   0.390258  13.657885  21.390910 
0.995 -229.816   0.403629   0.397812   0.403629  13.647372  21.373056 
==------------------------------------------------------------------------------




Profile likelihood for parameter   M_21
Parameters are evaluated at percentiles
using bisection method (slow, but exact).
-------------------------------------------------------------------------------
Per.  Ln(L)        M_21      Theta_1    Theta_2   *  M_21*      M_12     
=-------------------------------------------------------------------------------
0.005 -229.816    11.8542   0.398347   0.352313  11.854231  21.373911 
0.025 -228.419    12.2763   0.398648   0.352113  12.276313  21.387205 
0.050 -227.851    12.4958   0.398798   0.352012  12.495831  21.394515 
0.250 -226.727    13.1883   0.399256   0.351698  13.188335  21.418491 
MLE   -226.499    13.6856   0.399574   0.351470  13.685637  21.435893 
0.750 -226.726    14.1943   0.399891   0.351232  14.194336  21.453299 
0.950 -227.852      14.95   0.400345   0.350868  14.949976  21.477653 
0.975 -228.420    15.2008   0.400490   0.350746  15.200772  21.485215 
0.995 -229.817    15.6993   0.400770   0.350503  15.699263  21.499350 
==------------------------------------------------------------------------------




Profile likelihood for parameter   M_12
Parameters are evaluated at percentiles
using bisection method (slow, but exact).
-------------------------------------------------------------------------------
Per.  Ln(L)        M_12      Theta_1    Theta_2      M_21    *  M_12*    
=-------------------------------------------------------------------------------
0.005 -229.817    18.5301   0.392586   0.352983  13.652691  18.530063 
0.025 -228.420    19.1983   0.394537   0.352508  13.658792  19.198347 
0.050 -227.852    19.5469   0.395513   0.352279  13.662338  19.546871 
0.250 -226.727    20.6463   0.398146   0.351717  13.675137  20.646341 
MLE   -226.499    21.4359   0.399574   0.351470  13.685637  21.435893 
0.750 -226.726    22.2426   0.400704   0.351321  13.697057  22.242592 
0.950 -227.853     23.436   0.401940   0.351214  13.713946  23.436038 
0.975 -228.420    23.8314   0.402262   0.351194  13.719225  23.831389 
0.995 -229.817    24.6154   0.402798   0.351165  13.728847  24.615398 
==------------------------------------------------------------------------------




===============================================================================
Summary of profile likelihood percentiles of all parameters
===============================================================================


Parameter                          Lower percentiles
            --------------------------------------------------------------------
                0.005         0.025         0.050         0.250         MLE
--------------------------------------------------------------------------------
Theta_1         0.352590      0.363533      0.369235      0.387012      0.399574  
Theta_2         0.307804      0.317580      0.322727      0.339288      0.351470  
  M_21         11.854231     12.276313     12.495831     13.188335     13.685637  
  M_12         18.530063     19.198347     19.546871     20.646341     21.435893  




Parameter                          Upper percentiles
            --------------------------------------------------------------------
                MLE           0.750         0.950         0.975         0.995
--------------------------------------------------------------------------------
Theta_1         0.399574      0.412453      0.431740      0.438211      0.451191  
Theta_2         0.351470      0.364228      0.383648      0.390258      0.403629  
  M_21         13.685637     14.194336     14.949976     15.200772     15.699263  
  M_12         21.435893     22.242592     23.436038     23.831389     24.615398  

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


