  =============================================
    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 10:45:13 2008
         finished at Thu Oct 16 10:45:51 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 (from parmfile)                   34

Start parameters:
   First genealogy was started using a random tree
   Theta values were generated  from guessed values
   Theta = 10.00000,10.00000
   M values were generated from guessed values
   M-matrix: ----- 10.00 
               10.00 ----- 
               

Migration model:
   Migration matrix model with variable Theta  

Mutation rate is constant for all loci

Markov chain settings:
   Short chains (short-chains):                            0
      Trees sampled (short-inc*samples):                 100
      Trees recorded (short-sample):                      50
   Long chains (long-chains):                              1
      Trees sampled (long-inc*samples):                   20
      Trees recorded (long-sample):                       10
   Averaging over replicates:                              2

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   69.753  3.14711 -------  3.8035 
                1 2   69.365  3.07958 -------  4.2745 
                1 A  138.951  3.12460 -------  3.9514 
                2 1   50.819  3.40219 -------  6.8496 
                2 2   58.232  2.90978 -------  6.4071 
                2 A  109.050  2.90979 -------  6.4071 
                All  244.945  3.01577 -------  5.6127 
 2: population  1 1   69.753  2.69308  5.4200 -------
                1 2   69.365  2.62843  4.4548 -------
                1 A  138.951  2.66885  5.0882 -------
                2 1   50.819  2.79929 10.0702 -------
                2 2   58.232  2.93868  8.0071 -------
                2 A  109.050  2.93868  8.0071 -------
                All  244.945  2.80136  7.1204 -------

Comments:
 The x is 1, 2, or 4 for mtDNA, haploid, or diploid data, respectively
There were 0 short chains (50 used trees out of sampled 100)
  and 1 long chain (10 used trees out of sampled 20)
  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=-481.890149, num(param)=4]

-------------------------------------------------------------------------------
H0: 2.9086 6.3666 6.3666 2.9086                    | LnL(test) = 243.262069
 =  3.0158 5.6127 7.1204 2.8014                    | LnL(full) = 244.945074
[ m, m, m, m,]                                     | LRT       = 3.366010
                                                   | df        = 4
                                                   | Prob      = 0.498542
                                                   | Probc     = 0.498542
                                                   | AIC       = -482.524138
                                                   | 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  241.627    2.37484   2.374843   2.796448   5.636068   7.090583 
0.025  243.024    2.51035   2.510351   2.797991   5.628586   7.100198 
0.050  243.592    2.58365   2.583646   2.798683   5.625263   7.104459 
0.250  244.717    2.82756   2.827558   2.800439   5.616980   7.115036 
MLE    244.945    3.01577   3.015767   2.801360   5.612739   7.120406 
0.750  244.717    3.22081   3.220810   2.802063   5.609587   7.124355 
0.950  243.592    3.54867   3.548671   2.802733   5.606734   7.127841 
0.975  243.024    3.66463   3.664630   2.802870   5.606196   7.128466 
0.995  241.628    3.90613   3.906133   2.803031   5.605667   7.129010 
==------------------------------------------------------------------------------




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  241.628    2.10564   3.014034   2.105637   5.621134   7.107258 
0.025  243.025    2.24865   3.014247   2.248654   5.620324   7.108793 
0.050  243.592    2.32692   3.014407   2.326918   5.619600   7.109991 
0.250  244.717    2.59194   3.015109   2.591939   5.616140   7.115334 
MLE    244.945    2.80136   3.015767   2.801360   5.612739   7.120406 
0.750  244.717    3.03409   3.016541   3.034090   5.608677   7.126397 
0.950  243.591    3.41557   3.017803   3.415575   5.602029   7.136169 
0.975  243.025     3.5528   3.018237   3.552801   5.599751   7.139523 
0.995  241.628    3.84401   3.019102   3.844009   5.595226   7.146211 
==------------------------------------------------------------------------------




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  241.627    4.36097   3.020894   2.806831   4.360972   7.158264 
0.025  243.025     4.6403   3.020048   2.806020   4.640297   7.152404 
0.050  243.592    4.78749   3.019541   2.805507   4.787493   7.148781 
0.250  244.718    5.26298   3.017572   2.803398   5.262977   7.134208 
MLE    244.945    5.61274   3.015767   2.801360   5.612739   7.120406 
0.750  244.718    5.97901   3.013539   2.798769   5.979010   7.103039 
0.950  243.592    6.53654   3.009564   2.794048   6.536536   7.071565 
0.975  243.024    6.72564   3.008103   2.792299   6.725643   7.059907 
0.995  241.627    7.10633   3.005104   2.788700   7.106335   7.035881 
==------------------------------------------------------------------------------




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  241.628    5.56238   3.004938   2.787567   5.679654   5.562383 
0.025  243.025    5.91347   3.007929   2.791242   5.661059   5.913471 
0.050  243.593    6.09852   3.009406   2.793090   5.651915   6.098518 
0.250  244.717     6.6893   3.013470   2.798308   5.626845   6.689297 
MLE    244.945    7.12041   3.015767   2.801360   5.612739   7.120406 
0.750  244.718    7.56757   3.017610   2.803881   5.601449   7.567575 
0.950  243.593    8.23997   3.019563   2.806650   5.589497   8.239967 
0.975  243.025    8.46598   3.020049   2.807361   5.586522   8.465982 
0.995  241.627    8.91919   3.020834   2.808526   5.581749   8.919191 
==------------------------------------------------------------------------------




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


Parameter                          Lower percentiles
            --------------------------------------------------------------------
                0.005         0.025         0.050         0.250         MLE
--------------------------------------------------------------------------------
 Theta_1        2.374843      2.510351      2.583646      2.827558      3.015767  
 Theta_2        2.105637      2.248654      2.326918      2.591939      2.801360  
   M_21         4.360972      4.640297      4.787493      5.262977      5.612739  
   M_12         5.562383      5.913471      6.098518      6.689297      7.120406  




Parameter                          Upper percentiles
            --------------------------------------------------------------------
                MLE           0.750         0.950         0.975         0.995
--------------------------------------------------------------------------------
 Theta_1        3.015767      3.220810      3.548671      3.664630      3.906133  
 Theta_2        2.801360      3.034090      3.415575      3.552801      3.844009  
   M_21         5.612739      5.979010      6.536536      6.725643      7.106335  
   M_12         7.120406      7.567575      8.239967      8.465982      8.919191  

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


