  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version debug 3.2.10

  Program started at Wed May 18 11:00:24 2011
         finished at Wed May 18 11:01:43 2011
     


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

Analysis strategy is                          Maximum likelihood



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

Inheritance scalers in use for Thetas (specified scalars=1)
1.00 1.00 1.00 1.00 1.00 
1.00 1.00 1.00 1.00 1.00 

[Each Theta uses the (true) ineritance scalar of the first locus as a reference]


Pseudo-random number generator: Mersenne-Twister                                
Random number seed (from parmfile)           1407071073

Start parameters:
   First genealogy was started using a UPGMA-tree
   Theta values were generated  from an FST-calculation
   M values were generated from guessed values
   M-matrix: -----  1.00 
                1.00 ----- 
               

Migration model:
   Migration matrix model with variable Theta  

Mutation rate is constant for all loci

Markov chain settings:
   Short chains (short-chains):                            2
      Trees sampled (short-inc*samples):                 100
      Trees recorded (short-sample):                     100
   Long chains (long-chains):                              2
      Trees sampled (long-inc*samples):                 1000
      Trees recorded (long-sample):                     1000
   Averaging over replicates:                              2
   Static heating scheme
      4 chains with  temperatures
       1.00, 1.50, 3.00,1000000.00
      Swapping interval is 1
   Number of discard trees per chain:                  10000

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:
Title:                      Example: Microsatellite data set
Data file:                                       infile.msat
Datatype:                                Microsatellite data
Number of loci:                                           10

Population                   Locus   Gene copies    
                                     ---------------
                                     data  (missing)
----------------------------------------------------
  1 population_number___0        1     50 (0)
  1                              2     50 (0)
  1                              3     50 (0)
  1                              4     50 (0)
  1                              5     50 (0)
  1                              6     50 (0)
  1                              7     50 (0)
  1                              8     50 (0)
  1                              9     50 (0)
  1                             10     50 (0)
  2 population_number___1        1     42 (0)
  2                              2     42 (0)
  2                              3     42 (0)
  2                              4     42 (0)
  2                              5     42 (0)
  2                              6     42 (0)
  2                              7     42 (0)
  2                              8     42 (0)
  2                              9     42 (0)
  2                             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)

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

Locus 3
Allele  Pop1   Pop2   All
----------------------------
    19  0.240  0.262  0.251
    20  0.280  0.476  0.378
    18  0.080  0.095  0.088
    21  0.280  0.119  0.200
    22  0.120  0.048  0.084
Total      5      5      5

Locus 4
Allele  Pop1   Pop2   All
----------------------------
    16  0.080  0.071  0.076
    24  0.180  0.024  0.102
    15  0.020  0.048  0.034
    25  0.160  0.167  0.163
    14  0.020  0.048  0.034
    19  0.100  0.143  0.121
    12  0.060    -    0.030
    20  0.080  0.190  0.135
    23  0.060  0.119  0.090
    28  0.020    -    0.010
    22  0.060  0.024  0.042
    21  0.160  0.119  0.140
    13    -    0.024  0.012
    26    -    0.024  0.012
Total     12     12     14

Locus 5
Allele  Pop1   Pop2   All
----------------------------
    20  0.400  0.524  0.462
    21  0.420  0.357  0.389
    19  0.180  0.119  0.150
Total      3      3      3

Locus 6
Allele  Pop1   Pop2   All
----------------------------
    19  0.060    -    0.030
    20  0.100  0.024  0.062
    18  0.300  0.214  0.257
    22  0.200  0.119  0.160
    21  0.120  0.476  0.298
    16  0.060    -    0.030
    24  0.160  0.048  0.104
    17    -    0.119  0.060
Total      7      6      8

Locus 7
Allele  Pop1   Pop2   All
----------------------------
    23  0.040  0.238  0.139
    20  0.660  0.143  0.401
    22  0.180  0.190  0.185
    21  0.100  0.333  0.217
    19  0.020  0.095  0.058
Total      5      5      5

Locus 8
Allele  Pop1   Pop2   All
----------------------------
    19  0.520  0.524  0.522
    17  0.040  0.048  0.044
    18  0.100  0.071  0.086
    20  0.140  0.190  0.165
    16  0.080    -    0.040
    22  0.100  0.048  0.074
    15  0.020  0.048  0.034
    23    -    0.071  0.036
Total      7      7      8

Locus 9
Allele  Pop1   Pop2   All
----------------------------
    24  0.080  0.024  0.052
    19  0.300  0.429  0.364
    20  0.300  0.167  0.233
    23  0.180  0.143  0.161
    22  0.080  0.024  0.052
    18  0.020  0.071  0.046
    21  0.040  0.095  0.068
    25    -    0.048  0.024
Total      7      8      8

Locus 10
Allele  Pop1   Pop2   All
----------------------------
    22  0.100  0.214  0.157
    20  0.440  0.214  0.327
    23  0.080  0.167  0.123
    24  0.020    -    0.010
    19  0.160  0.167  0.163
    21  0.060  0.048  0.054
    18  0.080    -    0.040
    15  0.020  0.071  0.046
    17  0.040  0.048  0.044
    25    -    0.071  0.036
Total      9      8     10





==============================================================================
MCMC estimates 
==============================================================================
Population [x] Loc.  Ln(L)   Theta    M [m/mu] [+=receiving population]  
                             [xN mu]    1,+     2,+    
-------------- ---- -------- -------- ----------------------------------------
 1: population  1 1    6.096  1.19521 -------  3.5124 
                1 2    5.184  1.20020 -------  2.3208 
                1 A   12.131  1.19329 -------  3.5163 
                2 1   13.406  0.84499 -------  3.0563 
                2 2   49.920  1.40952 -------  0.8257 
                2 A   43.591  1.40952 -------  0.8257 
                3 1    3.124  0.96026 -------  2.4503 
                3 2    3.132  1.05091 -------  5.8105 
                3 A    6.277  1.05091 -------  5.8104 
                4 1    1.572  2.13816 -------  2.4519 
                4 2   40.603  2.45870 -------  1.2144 
                4 A   80.167  2.46373 -------  1.2462 
                5 1    6.610  1.09422 -------  4.4302 
                5 2    7.307  0.81168 -------  4.1413 
                5 A   13.563  0.81975 -------  4.1293 
                6 1    7.134  1.76410 -------  2.9646 
                6 2    1.870  1.35311 -------  3.7410 
                6 A   12.030  2.24022 -------  2.2500 
                7 1    2.428  1.01522 -------  3.1778 
                7 2   14.340  1.10149 -------  2.8900 
                7 A   10.589  0.90543 -------  1.8585 
                8 1    2.568  1.66546 -------  5.6357 
                8 2    4.534  1.51201 -------  4.3252 
                8 A    6.265  1.50965 -------  4.3055 
                9 1    2.351  2.73075 -------  2.7228 
                9 2    4.271  1.16554 -------  3.8618 
                9 A    8.267  1.15808 -------  3.8705 
               10 1    3.940  2.16240 -------  4.2483 
               10 2    2.606  1.16861 -------  1.5292 
               10 A    5.221  1.16861 -------  1.5292 
                All  126.704  1.44885 -------  1.9917 
 2: population  1 1    6.096  2.02918  3.8645 -------
                1 2    5.184  1.82935  2.8790 -------
                1 A   12.131  2.03279  3.8631 -------
                2 1   13.406  1.22911  3.5624 -------
                2 2   49.920  1.43300  0.7753 -------
                2 A   43.591  1.43300  0.7753 -------
                3 1    3.124  1.17667  2.8898 -------
                3 2    3.132  1.44645  5.6147 -------
                3 A    6.277  1.44644  5.6147 -------
                4 1    1.572  1.35754  8.1841 -------
                4 2   40.603  2.08324  1.6827 -------
                4 A   80.167  2.15790  1.6744 -------
                5 1    6.610  1.43033  3.9282 -------
                5 2    7.307  0.67942 14.9086 -------
                5 A   13.563  0.67044 15.3001 -------
                6 1    7.134  1.16185  3.2330 -------
                6 2    1.870  1.37709  5.4239 -------
                6 A   12.030  1.22336  3.2673 -------
                7 1    2.428  1.78569  3.1330 -------
                7 2   14.340  1.13854  5.1861 -------
                7 A   10.589  1.54856  1.2443 -------
                8 1    2.568  1.39146  8.0800 -------
                8 2    4.534  2.10093  7.7527 -------
                8 A    6.265  2.10703  7.6146 -------
                9 1    2.351  1.65607  3.2399 -------
                9 2    4.271  1.20468  3.9008 -------
                9 A    8.267  1.20490  3.8805 -------
               10 1    3.940  1.64599  2.1636 -------
               10 2    2.606  1.35767  1.3163 -------
               10 A    5.221  1.35767  1.3163 -------
                All  126.704  1.50760  2.7512 -------

Comments:
 The x is 1, 2, or 4 for mtDNA, haploid, or diploid data, respectively
There were 2 short chains (100 used trees out of sampled 100)
  and 2 long chains (1000 used trees out of sampled 1000)
  Static heating with 4 chains was active
  COMBINATION OF 2 MULTIPLE RUNS)


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


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  123.386    1.30622   1.422645   1.306224   2.033453   2.706307 
0.025  124.784    1.35018   1.426619   1.350177   2.026703   2.712154 
0.050  125.351    1.37354   1.429074   1.373545   2.022806   2.715983 
0.250  126.476       1.45   1.439145   1.450000   2.007288   2.733086 
MLE    126.704     1.5076   1.448848   1.507602   1.991697   2.751203 
0.750  126.477    1.56882   1.459956   1.568815   1.972425   2.773444 
0.950  125.351    1.66237   1.473564   1.662373   1.946533   2.802789 
0.975  124.784    1.69384   1.476711   1.693837   1.940080   2.810059 
0.995  123.386    1.75705   1.481217   1.757052   1.930253   2.821214 
==------------------------------------------------------------------------------




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  123.388    1.26438   1.264382   1.481224   2.055649   2.686732 
0.025  124.784    1.30509   1.305094   1.484521   2.043639   2.695803 
0.050  125.352    1.32671   1.326713   1.486795   2.036902   2.701603 
0.250  126.476    1.39661   1.396607   1.497023   2.012794   2.726218 
MLE    126.704    1.44885   1.448848   1.507602   1.991697   2.751203 
0.750  126.477     1.5039   1.503900   1.519950   1.967416   2.780728 
0.950  125.351    1.58736   1.587358   1.535377   1.935053   2.817045 
0.975  124.784    1.61552   1.615516   1.539338   1.926862   2.825130 
0.995  123.388     1.6726   1.672601   1.546175   1.915401   2.835315 
==------------------------------------------------------------------------------




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  123.387     1.5813   1.491756   1.538687   1.581298   2.854420 
0.025  124.783    1.67268   1.484985   1.534583   1.672676   2.834915 
0.050  125.351    1.72128   1.480253   1.531538   1.721277   2.822352 
0.250  126.477    1.87761   1.461474   1.517885   1.877613   2.777381 
MLE    126.704     1.9917   1.448848   1.507602   1.991697   2.751203 
0.750  126.478    2.11298   1.442165   1.500998   2.112984   2.741427 
0.950  125.352    2.34057   1.467273   1.509731   2.340568   2.808985 
0.975  124.785    2.44333   1.477174   1.513713   2.443333   2.836210 
0.995  123.387    2.63225   1.479507   1.515038   2.632245   2.858411 
==------------------------------------------------------------------------------




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  123.387    2.26465   1.423018   1.490515   2.029875   2.264655 
0.025  124.783    2.37275   1.427064   1.492232   2.023885   2.372750 
0.050  125.352    2.43004   1.429501   1.493544   2.020307   2.430036 
0.250  126.477    2.61446   1.439296   1.500114   2.006015   2.614456 
MLE    126.704     2.7512   1.448848   1.507602   1.991697   2.751203 
0.750  126.476    2.89558   1.460401   1.517301   1.972976   2.895581 
0.950  125.352    3.11356   1.476182   1.531022   1.943591   3.113564 
0.975  124.783    3.18672   1.480286   1.534615   1.935126   3.186716 
0.995  123.386    3.33227   1.486706   1.540225   1.921365   3.332265 
==------------------------------------------------------------------------------




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


Parameter                          Lower percentiles
            --------------------------------------------------------------------
                0.005         0.025         0.050         0.250         MLE
--------------------------------------------------------------------------------
 Theta_1        1.264382      1.305094      1.326713      1.396607      1.448848  
 Theta_2        1.306224      1.350177      1.373545      1.450000      1.507602  
   M_21         1.581298      1.672676      1.721277      1.877613      1.991697  
   M_12         2.264655      2.372750      2.430036      2.614456      2.751203  




Parameter                          Upper percentiles
            --------------------------------------------------------------------
                MLE           0.750         0.950         0.975         0.995
--------------------------------------------------------------------------------
 Theta_1        1.448848      1.503900      1.587358      1.615516      1.672601  
 Theta_2        1.507602      1.568815      1.662373      1.693837      1.757052  
   M_21         1.991697      2.112984      2.340568      2.443333      2.632245  
   M_12         2.751203      2.895581      3.113564      3.186716      3.332265  

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


