  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version debug 3.0

  Program started at Thu Oct 16 11:06:09 2008
         finished at Thu Oct 16 11:07:44 2008
     


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 (from parmfile)               134623

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 for all loci

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: Yes, only those in last chain, e1
   Plot data: No                                            
   Profile likelihood: Yes, tables and summary             
             Percentile method
             with df=1 and for Theta and M=m/mu




Summary of data:
Title:   Example: Microsatellite data set
Datatype:                                 Microsatellite data
Number of loci:                                             2

Population                                    Locus  Gene copies
                                                     data (missing)
----------------------------------------------------------------
  1 population__number___0                       1     50 (0)
                                                 2     50 (0)
  2 population__number___1                       1     42 (0)
                                                 2     42 (0)
Total of all populations                         1     92 (0)
                                                 2     92 (0)

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

Locus 1
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

Locus 2
Allele  Pop1   Pop2   All
----------------------------
    16  0.520  0.571  0.546
    19  0.040    -    0.020
    18  0.220  0.119  0.170
    17  0.160  0.167  0.163
    15  0.020    -    0.010
    21  0.020  0.071  0.046
    20  0.020  0.024  0.022
    22    -    0.048  0.024
Total      7      6      8





==============================================================================
MCMC estimates 
==============================================================================
Population [x] Loc.  Ln(L)   Theta    M [m/mu] [+=receiving population]  
                             [xN mu]    1,+     2,+    
-------------- ---- -------- -------- ----------------------------------------
 1: population  1 1    0.488  0.75436 -------  9.3405 
                1 2    0.952  0.91784 ------- 10.5935 
                1 A    1.629  0.91204 ------- 10.5404 
                2 1    1.858  0.01491 ------- 208.1020 
                2 2    1.128  0.04852 ------- 269.7020 
                2 A    2.257  0.04852 ------- 269.7020 
                All -364.517  0.37980 ------- 20.3067 
 2: population  1 1    0.488  1.56933 11.0827 -------
                1 2    0.952  1.86469 12.0892 -------
                1 A    1.629  1.85136 12.0341 -------
                2 1    1.858  0.22083 74.3429 -------
                2 2    1.128  0.46354 68.7575 -------
                2 A    2.257  0.46354 68.7575 -------
                All -364.517  0.83287 19.8611 -------

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)




==============================================================================
Likelihood ratio tests
==============================================================================
Over all loci
Legend for the LRT tables
-------------------------------------------------------------------------------
Null-Hypothesis: your test model         | Log(likelihood) of test model
=same=                                   | Log(likelihood) of full model
full model (the model under which the    | Likelihood ratio test value
genealogies were sampled)                | Degrees of freedom of test
[Theta values are on the diagonal of the | Probability*
Migration matrix, migration rates are    | Probability**
specified as M]                          | Akaike's Information Criterion***
                                         | Number of parameters used
-------------------------------------------------------------------------------
  *) Probability under the assumption that parameters have range -Inf to Inf
 **) Probability under the assumption that parameters have range 0 to Inf
***) AIC: the smaller the value the better the model
          [the full model has AIC=737.034030, num(param)=4]

-------------------------------------------------------------------------------
H0: 0.6063 20.084 20.084 0.6063                    | LnL(test) = -378.791510
 =  0.3798 20.307 19.861 0.8329                    | LnL(full) = -364.517015
[ m, m, m, m,]                                     | LRT       = 28.548990
                                                   | df        = 4
                                                   | Prob      = 0.000010
                                                   | Probc     = 0.000010
                                                   | AIC       = 761.583020
                                                   | num(param)= 2
-------------------------------------------------------------------------------
===============================================================================
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 -367.835   0.300452   0.300452   0.833206  20.289941  19.838497 
0.025 -366.438   0.317229   0.317229   0.833124  20.293166  19.842393 
0.050 -365.869   0.326303   0.326303   0.833083  20.294992  19.844705 
0.250 -364.745     0.3565   0.356500   0.832958  20.301414  19.853397 
MLE   -364.517   0.379801   0.379801   0.832872  20.306652  19.861058 
0.750 -364.745   0.405196   0.405196   0.832786  20.312547  19.870193 
0.950 -365.870   0.445802   0.445802   0.832660  20.322161  19.886030 
0.975 -366.439   0.460164   0.460164   0.832617  20.325562  19.891865 
0.995 -367.835   0.490037   0.490037   0.832533  20.332554  19.904178 
==------------------------------------------------------------------------------




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 -367.834   0.618554   0.379787   0.618554  20.301979  19.870753 
0.025 -366.437   0.662401   0.379813   0.662401  20.303099  19.869234 
0.050 -365.871   0.686374   0.379821   0.686374  20.303702  19.868258 
0.250 -364.744   0.768207   0.379823   0.768207  20.305546  19.864412 
MLE   -364.517   0.832872   0.379801   0.832872  20.306652  19.861058 
0.750 -364.744   0.904898   0.379762   0.904898  20.307442  19.857234 
0.950 -365.870    1.02395   0.379675   1.023946  20.307724  19.851086 
0.975 -366.439    1.06705   0.379639   1.067055  20.307539  19.848972 
0.995 -367.835    1.15825   0.379560   1.158250  20.306719  19.844751 
==------------------------------------------------------------------------------




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 -367.834    16.1967   0.379355   0.832995  16.196736  19.859939 
0.025 -366.438    17.1219   0.379462   0.832919  17.121869  19.860571 
0.050 -365.869    17.6102   0.379516   0.832889  17.610161  19.860830 
0.250 -364.744    19.1691   0.379685   0.832845  19.169070  19.861246 
MLE   -364.517    20.3067   0.379801   0.832872  20.306652  19.861058 
0.750 -364.744    21.4884   0.379917   0.832966  21.488377  19.860286 
0.950 -365.870    23.2725   0.380079   0.833271  23.272549  19.857625 
0.975 -366.437    23.8713   0.380129   0.833427  23.871298  19.856215 
0.995 -367.834     25.075   0.380224   0.833843  25.075036  19.852384 
==------------------------------------------------------------------------------




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 -367.834    16.0268   0.379250   0.834123  20.316306  16.026797 
0.025 -366.437    16.8936   0.379355   0.833744  20.312358  16.893625 
0.050 -365.870    17.3486   0.379414   0.833573  20.310791  17.348592 
0.250 -364.745    18.8011   0.379625   0.833123  20.307603  18.801111 
MLE   -364.517    19.8611   0.379801   0.832872  20.306652  19.861058 
0.750 -364.745    20.9598   0.380005   0.832664  20.306610  20.959813 
0.950 -365.870    22.6053   0.380352   0.832432  20.307992  22.605266 
0.975 -366.439    23.1593   0.380481   0.832372  20.308789  23.159261 
0.995 -367.834    24.2644   0.380758   0.832276  20.310821  24.264395 
==------------------------------------------------------------------------------




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


Parameter                          Lower percentiles
            --------------------------------------------------------------------
                0.005         0.025         0.050         0.250         MLE
--------------------------------------------------------------------------------
 Theta_1        0.300452      0.317229      0.326303      0.356500      0.379801  
 Theta_2        0.618554      0.662401      0.686374      0.768207      0.832872  
   M_21        16.196736     17.121869     17.610161     19.169070     20.306652  
   M_12        16.026797     16.893625     17.348592     18.801111     19.861058  




Parameter                          Upper percentiles
            --------------------------------------------------------------------
                MLE           0.750         0.950         0.975         0.995
--------------------------------------------------------------------------------
 Theta_1        0.379801      0.405196      0.445802      0.460164      0.490037  
 Theta_2        0.832872      0.904898      1.023946      1.067055      1.158250  
   M_21        20.306652     21.488377     23.272549     23.871298     25.075036  
   M_12        19.861058     20.959813     22.605266     23.159261     24.264395  

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


