  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version 3.0.6

  Program started at Thu May 14 10:45:25 2009
         finished at Thu May 14 10:46:29 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 (from parmfile)           1407071073

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
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    4.494  5.71817 -------  1.9363 
                1 2    0.875  2.51299 -------  3.6355 
                1 A    8.989  5.71817 -------  1.9363 
                2 1    1.443 24.85558 -------  3.3274 
                2 2    0.261  2.93328 -------  2.2686 
                2 A    2.887 24.85558 -------  3.3274 
                3 1    1.756  1.95083 -------  1.7200 
                3 2    1.446  3.23842 -------  6.3889 
                3 A    3.159  1.48409 -------  1.7875 
                4 1    1.166  8.59037 -------  2.9965 
                4 2    1.391 11.35904 -------  1.2912 
                4 A    2.782 11.35904 -------  1.2912 
                5 1    1.586  1.00239 -------  0.6291 
                5 2    2.804  2.43793 ------- 11.8152 
                5 A    3.172  1.00239 -------  0.6291 
                6 1    1.129  4.13263 -------  1.7354 
                6 2    0.322  3.31961 -------  0.9002 
                6 A    2.241  4.13595 -------  1.7351 
                7 1    1.966  1.62830 -------  4.2412 
                7 2    0.463  1.54851 -------  3.6268 
                7 A    3.326  1.78583 -------  3.9846 
                8 1    1.852  1.41617 -------  2.8382 
                8 2   10.768  1.61472 -------  3.5992 
                8 A    5.966  1.79520 -------  3.6474 
                9 1    7.785  3.90136 -------  5.6159 
                9 2    3.697  1.61023 -------  3.5337 
                9 A   15.570  3.90136 -------  5.6159 
               10 1    2.730  6.18105 -------  2.9551 
               10 2    0.163  4.15722 -------  1.5018 
               10 A    0.326  4.15722 -------  1.5018 
                All -130.117  2.92907 -------  2.0973 
 2: population  1 1    4.494 11.37400  0.8386 -------
                1 2    0.875  7.07001  2.2638 -------
                1 A    8.989 11.37400  0.8386 -------
                2 1    1.443  1.69057  2.0156 -------
                2 2    0.261  1.29972  1.9062 -------
                2 A    2.887  1.69057  2.0156 -------
                3 1    1.756  3.63998  3.1300 -------
                3 2    1.446  1.00114  5.8769 -------
                3 A    3.159  2.36372  6.4411 -------
                4 1    1.166  6.84123  0.5425 -------
                4 2    1.391  7.52449  2.2049 -------
                4 A    2.782  7.52449  2.2049 -------
                5 1    1.586  2.34566  3.0129 -------
                5 2    2.804  0.72186  0.0000 -------
                5 A    3.172  2.34566  3.0129 -------
                6 1    1.129  1.96864  1.7413 -------
                6 2    0.322  1.87556  1.8653 -------
                6 A    2.241  1.96865  1.7569 -------
                7 1    1.966  3.14470  0.2293 -------
                7 2    0.463  2.93961  0.7729 -------
                7 A    3.326  3.19435  0.1970 -------
                8 1    1.852  6.08634  3.8056 -------
                8 2   10.768  4.33522  5.2952 -------
                8 A    5.966  2.39486  4.2312 -------
                9 1    7.785  3.30185  4.7622 -------
                9 2    3.697  7.95754  4.8791 -------
                9 A   15.570  3.30184  4.7622 -------
               10 1    2.730  8.11011  4.8652 -------
               10 2    0.163  2.67751  1.9143 -------
               10 A    0.326  2.67751  1.9143 -------
                All -130.117  3.80341  2.4751 -------

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=268.234491, num(param)=4]

-------------------------------------------------------------------------------
H0: 3.3662 2.2862 2.2862 3.3662                    | LnL(test) = -138.564111
 =  2.9291 2.0973 2.4751 3.8034                    | LnL(full) = -130.117245
[ m, m, m, m,]                                     | LRT       = 16.893730
                                                   | df        = 4
                                                   | Prob      = 0.002027
                                                   | Probc     = 0.002027
                                                   | AIC       = 281.128221
                                                   | 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 -133.434    2.60227   2.602268   3.794195   2.092156   2.478423 
0.025 -132.038    2.67623   2.676230   3.797277   2.093480   2.477701 
0.050 -131.471      2.715   2.714995   3.798619   2.094113   2.477277 
0.250 -130.346    2.83876   2.838758   3.801877   2.095976   2.475932 
MLE   -130.117    2.92907   2.929071   3.803407   2.097289   2.475092 
0.750 -130.345    3.02275   3.022745   3.804330   2.098699   2.474417 
0.950 -131.469    3.16417   3.164174   3.804527   2.101060   2.473819 
0.975 -132.038    3.21197   3.211969   3.804279   2.101945   2.473729 
0.995 -133.435    3.30799   3.307995   3.803311   2.103887   2.473709 
==------------------------------------------------------------------------------




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 -133.435    3.28387   2.923113   3.283874   2.116093   2.469409 
0.025 -132.039    3.40183   2.925109   3.401835   2.110389   2.471348 
0.050 -131.470     3.4638   2.926000   3.463796   2.107724   2.472217 
0.250 -130.344     3.6608   2.928113   3.660797   2.100870   2.474214 
MLE   -130.117    3.80341   2.929071   3.803407   2.097289   2.475092 
0.750 -130.345    3.95137   2.929686   3.951367   2.094520   2.475711 
0.950 -131.470    4.17476   2.930067   4.174758   2.091621   2.476374 
0.975 -132.038    4.25025   2.930075   4.250250   2.090887   2.476565 
0.995 -133.434    4.40212   2.929937   4.402121   2.089668   2.476935 
==------------------------------------------------------------------------------




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 -133.435    1.80946   2.918602   3.812412   1.809462   2.481172 
0.025 -132.038     1.8758   2.922174   3.812417   1.875797   2.480350 
0.050 -131.470     1.9103   2.923674   3.811929   1.910297   2.479798 
0.250 -130.345    2.01913   2.927268   3.808196   2.019132   2.477424 
MLE   -130.117    2.09729   2.929071   3.803407   2.097289   2.475092 
0.750 -130.346    2.17778   2.930416   3.796533   2.177783   2.472122 
0.950 -131.471    2.29735   2.931565   3.782383   2.297353   2.466651 
0.975 -132.038    2.33732   2.931726   3.776520   2.337319   2.464544 
0.995 -133.434    2.41712   2.931708   3.762978   2.417121   2.459922 
==------------------------------------------------------------------------------




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 -133.435    2.14372   2.924549   3.768013   2.109293   2.143725 
0.025 -132.038    2.22131   2.927263   3.783764   2.105662   2.221308 
0.050 -131.471    2.26121   2.928185   3.789597   2.104043   2.261210 
0.250 -130.345    2.38611   2.929418   3.800576   2.099775   2.386114 
MLE   -130.117    2.47509   2.929071   3.803407   2.097289   2.475092 
0.750 -130.344     2.5658   2.927887   3.803066   2.095098   2.565803 
0.950 -131.469    2.70055   2.924896   3.797398   2.092319   2.700548 
0.975 -132.038    2.74543   2.923641   3.794198   2.091492   2.745428 
0.995 -133.435    2.83484   2.920855   3.785814   2.089960   2.834837 
==------------------------------------------------------------------------------




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


Parameter                          Lower percentiles
            --------------------------------------------------------------------
                0.005         0.025         0.050         0.250         MLE
--------------------------------------------------------------------------------
Theta_1         2.602268      2.676230      2.714995      2.838758      2.929071  
Theta_2         3.283874      3.401835      3.463796      3.660797      3.803407  
  M_21          1.809462      1.875797      1.910297      2.019132      2.097289  
  M_12          2.143725      2.221308      2.261210      2.386114      2.475092  




Parameter                          Upper percentiles
            --------------------------------------------------------------------
                MLE           0.750         0.950         0.975         0.995
--------------------------------------------------------------------------------
Theta_1         2.929071      3.022745      3.164174      3.211969      3.307995  
Theta_2         3.803407      3.951367      4.174758      4.250250      4.402121  
  M_21          2.097289      2.177783      2.297353      2.337319      2.417121  
  M_12          2.475092      2.565803      2.700548      2.745428      2.834837  

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


