  =============================================
  AUTO                                         
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version 2.3

  Program started at Fri Mar 20 18:12:58 2009
         finished at Fri Mar 20 18:12:59 2009
     


Options in use:
---------------

Analysis strategy is                          Maximum likelihood



Datatype: Microsatellite data [Brownian motion]
Missing data is not included

Pseudo-random number generator: Mersenne-Twister                                
Random number seed (with internal timer)            153119415

Start parameters:
   First genealogy was started using a random tree
   Theta values were generated  from an FST-calculation
   M values were generated from the FST-calculation

Migration model:
   Migration matrix model with variable Theta  

Mutation rate is constant 

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
   Output file (PDF):                            outfile.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:                                             1

Population                                    Locus  Gene copies
                                                     data (missing)
----------------------------------------------------------------
  1 population_number_0                          1     50 (0)
  2 population_number_1                          1     42 (0)
Total of all populations                         1     92 (0)

Allele frequency spectra
========================

Locus 0
Allele  Pop1   Pop2   All
----------------------------
    16  0.220  0.167  0.193
    19  0.040  0.071  0.056
    18  0.060  0.119  0.090
    15  0.220  0.024  0.122
    21  0.020  0.167  0.093
    23  0.020  0.119  0.070
    17  0.280  0.095  0.188
    22  0.060  0.119  0.090
    25  0.060  0.024  0.042
    24  0.020    -    0.010
    26    -    0.024  0.012
    27    -    0.048  0.024
    29    -    0.024  0.012
Total     10     12     13





==============================================================================
MCMC estimates 
==============================================================================
Population [x] Loc.  Ln(L)   Theta    M [m/mu] [+=receiving population]  
                             [m / mu]    1,+     2,+    
-------------- ---- -------- -------- ----------------------------------------
 1: population  1 1    0.943  3.47446 -------  5.9023 
                1 2    0.087  2.61757 -------  3.0587 
                1 A    1.887  3.47446 -------  5.9023 
 2: population  1 1    0.943  4.24288  4.4097 -------
                1 2    0.087  6.10522  4.0565 -------
                1 A    1.887  4.24288  4.4097 -------

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  -1.431      2.4046   2.404596   4.115773   5.550633   4.266510 
0.025  -0.033     2.62087   2.620868   4.166417   5.679672   4.305868 
0.050   0.534     2.74007   2.740070   4.190200   5.742156   4.327711 
0.250   1.660     3.14886   3.148862   4.233164   5.864481   4.382546 
MLE     1.887*    3.47446   3.474460   4.242879   5.902264   4.409726 
0.750   1.660     3.84141   3.841407   4.244507   5.920313   4.430843 
0.950   0.534     4.45811   4.458108   4.240680   5.929281   4.453336 
0.975  -0.033     4.68365   4.683651   4.238816   5.929983   4.458992 
0.995  -1.431     5.16832   5.168320   4.234932   5.929873   4.468211 
==------------------------------------------------------------------------------




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  -1.430     2.85949   3.398467   2.859489   5.708911   4.354665 
0.025  -0.033     3.13103   3.435505   3.131033   5.782750   4.378749 
0.050   0.533     3.28196   3.447823   3.281958   5.810825   4.387261 
0.250   1.658     3.80934   3.468722   3.809338   5.872595   4.403576 
MLE     1.887*    4.24288   3.474460   4.242879   5.902264   4.409726 
0.750   1.659     4.74118   3.476561   4.741185   5.925305   4.413593 
0.950   0.534     5.59997   3.476517   5.599967   5.950444   4.416976 
0.975  -0.035     5.92222   3.476152   5.922225   5.957002   4.417759 
0.995  -1.430     6.62302   3.475317   6.623018   5.967867   4.419049 
==------------------------------------------------------------------------------




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  -1.431     2.41761   2.639041   6.091029   2.417608   4.050806 
0.025  -0.034     4.60317   3.263105   4.085413   4.603175   4.236252 
0.050   0.533     4.81504   3.301246   4.110811   4.815038   4.262954 
0.250   1.658     5.46907   3.435027   4.204910   5.469072   4.371733 
MLE     1.887*    5.90226   3.474460   4.242879   5.902264   4.409726 
0.750   1.660     6.33117   3.485072   4.265001   6.331173   4.424647 
0.950   0.534     6.96314   3.482294   4.284499   6.963140   4.430159 
0.975  -0.035     7.17358   3.479789   4.288972   7.173577   4.430222 
0.995  -1.431     7.59295   3.474377   4.295804   7.592945   4.429344 
==------------------------------------------------------------------------------




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  -1.430     3.28415   3.299706   4.123093   5.522380   3.284148 
0.025  -0.034     3.54576   3.342404   4.157169   5.629471   3.545757 
0.050   0.534     3.68286   3.369825   4.178679   5.696119   3.682861 
0.250   1.659     4.10876   3.442254   4.229129   5.852660   4.108759 
MLE     1.887*    4.40973   3.474460   4.242879   5.902264   4.409726 
0.750   1.659     4.71915   3.498287   4.245817   5.924363   4.719146 
0.950   0.534     5.18252   3.524680   4.240535   5.932427   5.182522 
0.975  -0.034     5.33853   3.531809   4.237668   5.931895   5.338532 
0.995  -1.432     5.65218   3.543838   4.231527   5.928598   5.652179 
==------------------------------------------------------------------------------




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


Parameter                          Lower percentiles
            --------------------------------------------------------------------
                0.005         0.025         0.050         0.250         MLE
--------------------------------------------------------------------------------
Theta_1         2.404596      2.620868      2.740070      3.148862      3.474460  
Theta_2         2.859489      3.131033      3.281958      3.809338      4.242879  
  M_21          2.417608      4.603175      4.815038      5.469072      5.902264  
  M_12          3.284148      3.545757      3.682861      4.108759      4.409726  




Parameter                          Upper percentiles
            --------------------------------------------------------------------
                MLE           0.750         0.950         0.975         0.995
--------------------------------------------------------------------------------
Theta_1         3.474460      3.841407      4.458108      4.683651      5.168320  
Theta_2         4.242879      4.741185      5.599967      5.922225      6.623018  
  M_21          5.902264      6.331173      6.963140      7.173577      7.592945  
  M_12          4.409726      4.719146      5.182522      5.338532      5.652179  

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


