  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version 3.0.1

  Program started at Mon Oct 20 12:00:27 2008
         finished at Mon Oct 20 12:00:51 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 (with internal timer)           1028171259

Start parameters:
   First genealogy was started using a UPGMA-tree
   Theta values were generated  from guessed values
   Theta = 1.00000,1.00000
   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):                           10
      Trees sampled (short-inc*samples):                1000
      Trees recorded (short-sample):                     500
   Long chains (long-chains):                              3
      Trees sampled (long-inc*samples):                 2000
      Trees recorded (long-sample):                     1000
   Averaging over replicates:                              2
   Number of discard trees per chain:                   1000

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
Datatype:                                 Microsatellite data
Number of loci:                                             4

Population                                    Locus  Gene copies
                                                     data (missing)
----------------------------------------------------------------
  1 population__number___0                       1     50 (0)
                                                 2     50 (0)
                                                 3     50 (0)
                                                 4     50 (0)
  2 population__number___1                       1     42 (0)
                                                 2     42 (0)
                                                 3     42 (0)
                                                 4     42 (0)
Total of all populations                         1     92 (0)
                                                 2     92 (0)
                                                 3     92 (0)
                                                 4     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





==============================================================================
MCMC estimates 
==============================================================================
Population [x] Loc.  Ln(L)   Theta    M [m/mu] [+=receiving population]  
                             [xN mu]    1,+     2,+    
-------------- ---- -------- -------- ----------------------------------------
 1: population  1 1    3.265  4.81872 -------  1.6220 
                1 2    1.354  1.79551 -------  2.7628 
                1 A    6.530  4.81872 -------  1.6220 
                2 1    3.094  4.88575 -------  0.6691 
                2 2    3.698  3.46159 -------  2.9537 
                2 A    6.187  4.88575 -------  0.6691 
                3 1    8.629  2.84797 -------  1.1362 
                3 2    0.532  3.39406 -------  5.4719 
                3 A   17.258  2.84797 -------  1.1362 
                4 1    2.084  7.26908 -------  2.5194 
                4 2    2.868  8.41944 -------  1.7748 
                4 A    4.171  7.27561 -------  2.5163 
                All  -29.895  4.34155 -------  1.7583 
 2: population  1 1    3.265 13.31855  2.6956 -------
                1 2    1.354 12.89439  1.3184 -------
                1 A    6.530 13.31855  2.6956 -------
                2 1    3.094  1.47551  4.4192 -------
                2 2    3.698  2.84593  4.4167 -------
                2 A    6.187  1.47551  4.4192 -------
                3 1    8.629  2.61727 13.6303 -------
                3 2    0.532  3.50980  0.8512 -------
                3 A   17.258  2.61727 13.6303 -------
                4 1    2.084  7.82133  3.0405 -------
                4 2    2.868  6.33887  3.5508 -------
                4 A    4.171  7.81470  3.0416 -------
                All  -29.895  5.47309  3.7810 -------

Comments:
 The x is 1, 2, or 4 for mtDNA, haploid, or diploid data, respectively
There were 10 short chains (500 used trees out of sampled 1000)
  and 3 long chains (1000 used trees out of sampled 2000)
  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=67.790152, num(param)=4]

-------------------------------------------------------------------------------
H0: 4.9073 2.7697 2.7697 4.9073                    | LnL(test) = -40.192940
 =  4.3415 1.7583 3.7810 5.4731                    | LnL(full) = -29.895076
[ m, m, m, m,]                                     | LRT       = 20.595727
                                                   | df        = 4
                                                   | Prob      = 0.000381
                                                   | Probc     = 0.000381
                                                   | AIC       = 84.385879
                                                   | 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 -33.213     3.67656   3.676561   5.386757   1.764714   3.826169 
0.025 -31.816     3.82186   3.821864   5.401487   1.763336   3.818010 
0.050 -31.248     3.89926   3.899258   5.410702   1.762635   3.813082 
0.250 -30.122     4.15236   4.152364   5.445168   1.760252   3.795175 
MLE   -29.895*    4.34155   4.341546   5.473090   1.758270   3.781041 
0.750 -30.123     4.54332   4.543318   5.502791   1.755948   3.766325 
0.950 -31.248     4.85551   4.855512   5.545729   1.752040   3.745832 
0.975 -31.816     4.96328   4.963284   5.559396   1.750633   3.739602 
0.995 -33.213     5.18313   5.183132   5.585425   1.747713   3.728344 
==------------------------------------------------------------------------------




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 -33.213     4.23977   4.299354   4.239774   1.760715   3.834370 
0.025 -31.816     4.49481   4.305944   4.494808   1.759824   3.826305 
0.050 -31.247     4.63429   4.310175   4.634290   1.759396   3.821022 
0.250 -30.123     5.10448   4.327132   5.104477   1.758379   3.799598 
MLE   -29.895*    5.47309   4.341546   5.473090   1.758270   3.781041 
0.750 -30.123     5.87826   4.355594   5.878256   1.759273   3.761614 
0.950 -31.249     6.53148   4.367995   6.531483   1.765927   3.732771 
0.975 -31.816     6.76486   4.366900   6.764859   1.771874   3.720759 
0.995 -33.212     7.42696   4.151461   7.426962   2.003495   3.519916 
==------------------------------------------------------------------------------




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 -33.213     1.46192   4.381952   5.494214   1.461916   3.727152 
0.025 -31.815     1.53065   4.369298   5.488572   1.530650   3.746582 
0.050 -31.247     1.56622   4.363254   5.484842   1.566216   3.755258 
0.250 -30.122       1.678   4.348233   5.474945   1.677997   3.774562 
MLE   -29.895*    1.75827   4.341546   5.473090   1.758270   3.781041 
0.750 -30.123     1.84155   4.337814   5.480012   1.841553   3.781126 
0.950 -31.248     1.96936   4.331981   5.551125   1.969364   3.754696 
0.975 -31.817      2.0173   4.295062   5.773393   2.017299   3.679302 
0.995 -33.213     2.24856   4.154058   6.375429   2.248559   3.491949 
==------------------------------------------------------------------------------




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 -33.212     3.16337   4.393824   5.606792   1.764617   3.163368 
0.025 -31.816     3.30557   4.386740   5.587251   1.757991   3.305572 
0.050 -31.247     3.37986   4.381413   5.573713   1.756698   3.379864 
0.250 -30.122     3.61415   4.359109   5.518073   1.756737   3.614145 
MLE   -29.895*    3.78104   4.341546   5.473090   1.758270   3.781041 
0.750 -30.123     3.95019   4.326322   5.431781   1.760030   3.950195 
0.950 -31.248     4.19742   4.312460   5.386142   1.762654   4.197420 
0.975 -31.817     4.27914   4.310222   5.374546   1.763606   4.279139 
0.995 -33.212      4.4413   4.309098   5.355153   1.765789   4.441302 
==------------------------------------------------------------------------------




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


Parameter                          Lower percentiles
            --------------------------------------------------------------------
                0.005         0.025         0.050         0.250         MLE
--------------------------------------------------------------------------------
Theta_1         3.676561      3.821864      3.899258      4.152364      4.341546  
Theta_2         4.239774      4.494808      4.634290      5.104477      5.473090  
  M_21          1.461916      1.530650      1.566216      1.677997      1.758270  
  M_12          3.163368      3.305572      3.379864      3.614145      3.781041  




Parameter                          Upper percentiles
            --------------------------------------------------------------------
                MLE           0.750         0.950         0.975         0.995
--------------------------------------------------------------------------------
Theta_1         4.341546      4.543318      4.855512      4.963284      5.183132  
Theta_2         5.473090      5.878256      6.531483      6.764859      7.426962  
  M_21          1.758270      1.841553      1.969364      2.017299      2.248559  
  M_12          3.781041      3.950195      4.197420      4.279139      4.441302  

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


