  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version debug 3.3.2

  Program started at Thu Sep  6 15:07:54 2012
         finished at Thu Sep  6 15:08:18 2012
     


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

Analysis strategy is                                    Bayesian

Proposal distribution:
Parameter group          Proposal type
-----------------------  -------------------
Population size (Theta)       Slice sampling
Migration rate      (M)       Slice sampling


Prior distribution:
Parameter group          Prior type   Minimum    Mean(*)    Maximum    Delta
-----------------------  ------------ ---------- ---------- ---------- ----------
Population size (Theta)      Uniform  0.000000  10.000000  20.000000   2.000000 
Migration rate      (M)      Uniform  0.000000  10.000000  20.000000   2.000000 



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)            310705631

Start parameters:
   First genealogy was started using a UPGMA-tree
   Theta values were generated  RANDOM start value from U(min,max)
   M values were generated from the FST-calculation

Migration model: Arbitrary migration matrix model            
[Legend: m = average (average over a group of Thetas or M]
[s = symmetric M, S = symmetric 4Nm,
 0 = zero, and not estimated,   ]
[* = free to vary, Thetas are on diagonal]
population     * 0 
population     * * 



Mutation rate is constant for all loci

Markov chain settings:
   Long chains (long-chains):                              1
      Steps sampled (inc*samples*rep):                 10000
      Steps recorded (sample*rep):                     10000
   Combining over replicates:                              2
   Static heating scheme
      4 chains with  temperatures
       1.00, 1.50, 3.00,1000000.00
      Swapping interval is 1
   Burn-in per chain:                                1000

Print options:
   Data file:                                    infile.msat
   Output file (ASCII text):                   outfile-bayes
   Output file (PDF):                      outfile-bayes.pdf
   Posterior distribution:                         bayesfile
   Print data:                                            No
   Print genealogies:                                     No
   Plot data: No                                            

Summary of data:
Title:                      Example: Microsatellite data set
Data file:                                       infile.msat
Datatype:                                Microsatellite data
[Data was used as repeat-length information]
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  0.196
    19  0.040  0.071  0.054
    18  0.060  0.119  0.087
    15  0.220  0.024  0.130
    21  0.020  0.167  0.087
    23  0.020  0.119  0.065
    17  0.280  0.095  0.196
    22  0.060  0.119  0.087
    25  0.060  0.024  0.043
    24  0.020    -    0.011
    26    -    0.024  0.011
    27    -    0.048  0.022
    29    -    0.024  0.011
Total      10     12     13
H_exp   0.811  0.883  0.874

Locus 2
Allele  Pop1   Pop2   All
----------------------------
    16  0.520  0.571  0.543
    19  0.040    -    0.022
    18  0.220  0.119  0.174
    17  0.160  0.167  0.163
    15  0.020    -    0.011
    21  0.020  0.071  0.043
    20  0.020  0.024  0.022
    22    -    0.048  0.022
Total       7      6      8
H_exp   0.653  0.624  0.644

Locus 3
Allele  Pop1   Pop2   All
----------------------------
    19  0.240  0.262  0.250
    20  0.280  0.476  0.370
    18  0.080  0.095  0.087
    21  0.280  0.119  0.207
    22  0.120  0.048  0.087
Total       5      5      5
H_exp   0.765  0.679  0.743

Locus 4
Allele  Pop1   Pop2   All
----------------------------
    16  0.080  0.071  0.076
    24  0.180  0.024  0.109
    15  0.020  0.048  0.033
    25  0.160  0.167  0.163
    14  0.020  0.048  0.033
    19  0.100  0.143  0.120
    12  0.060    -    0.033
    20  0.080  0.190  0.130
    23  0.060  0.119  0.087
    28  0.020    -    0.011
    22  0.060  0.024  0.043
    21  0.160  0.119  0.141
    13    -    0.024  0.011
    26    -    0.024  0.011
Total      12     12     14
H_exp   0.882  0.875  0.892

Locus 5
Allele  Pop1   Pop2   All
----------------------------
    20  0.400  0.524  0.457
    21  0.420  0.357  0.391
    19  0.180  0.119  0.152
Total       3      3      3
H_exp   0.631  0.584  0.615

Locus 6
Allele  Pop1   Pop2   All
----------------------------
    19  0.060    -    0.033
    20  0.100  0.024  0.065
    18  0.300  0.214  0.261
    22  0.200  0.119  0.163
    21  0.120  0.476  0.283
    16  0.060    -    0.033
    24  0.160  0.048  0.109
    17    -    0.119  0.054
Total       7      6      8
H_exp   0.813  0.696  0.804

Locus 7
Allele  Pop1   Pop2   All
----------------------------
    23  0.040  0.238  0.130
    20  0.660  0.143  0.424
    22  0.180  0.190  0.185
    21  0.100  0.333  0.207
    19  0.020  0.095  0.054
Total       5      5      5
H_exp   0.520  0.766  0.724

Locus 8
Allele  Pop1   Pop2   All
----------------------------
    19  0.520  0.524  0.522
    17  0.040  0.048  0.043
    18  0.100  0.071  0.087
    20  0.140  0.190  0.163
    16  0.080    -    0.043
    22  0.100  0.048  0.076
    15  0.020  0.048  0.033
    23    -    0.071  0.033
Total       7      7      8
H_exp   0.682  0.672  0.682

Locus 9
Allele  Pop1   Pop2   All
----------------------------
    24  0.080  0.024  0.054
    19  0.300  0.429  0.359
    20  0.300  0.167  0.239
    23  0.180  0.143  0.163
    22  0.080  0.024  0.054
    18  0.020  0.071  0.043
    21  0.040  0.095  0.065
    25    -    0.048  0.022
Total       7      8      8
H_exp   0.773  0.751  0.775

Locus 10
Allele  Pop1   Pop2   All
----------------------------
    22  0.100  0.214  0.152
    20  0.440  0.214  0.337
    23  0.080  0.167  0.120
    24  0.020    -    0.011
    19  0.160  0.167  0.163
    21  0.060  0.048  0.054
    18  0.080    -    0.043
    15  0.020  0.071  0.043
    17  0.040  0.048  0.043
    25    -    0.071  0.033
Total       9      8     10
H_exp   0.752  0.838  0.813

Average expected heterozygosity
Pop1   Pop2   All
---------------------
0.728  0.737  0.757




Bayesian estimates
==================

Locus Parameter        2.5%      25.0%    mode     75.0%   97.5%     median   mean
-----------------------------------------------------------------------------------
    1  Theta_1         3.20000  3.60000  0.00000  5.92000  0.00000  0.00000  8.76607
    1  Theta_2         2.64000  3.32000  0.00000  6.56000  0.00000  7.86000 10.22227
    1  M_1->2             0.00     0.36     0.00     1.36     0.00     2.26     2.76
    2  Theta_1         3.32000  3.88000  0.00000  6.40000  0.00000  0.00000 11.29370
    2  Theta_2         2.60000  2.84000  0.00000  6.92000  0.00000  7.22000  8.57817
    2  M_1->2             0.00     0.08     0.00     0.92     0.00     1.30     1.87
    3  Theta_1         4.12000  6.00000  0.00000  8.72000  0.00000  0.00000  7.96846
    3  Theta_2         1.28000  1.68000  0.00000  3.88000  0.00000  3.74000  5.10644
    3  M_1->2             0.00     0.00     0.00     1.68     0.00     4.14     3.97
    4  Theta_1         1.64000  1.92000  0.00000  3.92000  0.00000  0.00000  9.59679
    4  Theta_2         0.00000  0.08000  0.00000  1.04000  0.00000  4.34000  4.44228
    4  M_1->2             0.00     0.00     0.00     1.08     0.00     8.94     7.78
    5  Theta_1         1.68000  2.08000  0.00000  3.24000  0.00000  0.00000  3.30713
    5  Theta_2         0.04000  0.16000  0.00000  3.40000  0.00000  5.74000  8.50986
    5  M_1->2             0.00     3.20     0.00     6.28     0.00     9.02    10.37
    6  Theta_1         4.64000  5.20000  0.00000  8.88000  0.00000  0.00000 10.14170
    6  Theta_2         2.56000  3.68000  0.00000  6.32000  0.00000  6.02000  6.61751
    6  M_1->2             0.00     1.68     0.00     2.76     0.00     2.46     2.52
    7  Theta_1         1.08000  1.48000  0.00000  2.24000  0.00000  0.00000  2.06001
    7  Theta_2         2.04000  2.92000  0.00000  4.44000  0.00000  3.98000  4.12102
    7  M_1->2             0.00     0.68     0.00     1.60     0.00     1.38     1.43
    8  Theta_1         2.28000  2.48000  0.00000  5.60000  0.00000  0.00000  9.70360
    8  Theta_2         6.52000  7.72000  0.00000 12.08000  0.00000 11.34000 11.82580
    8  M_1->2             0.00     0.20     0.00     1.12     0.00     1.22     1.30
    9  Theta_1         5.20000  6.08000  0.00000  9.32000  0.00000  0.00000 10.06655
    9  Theta_2         3.20000  4.72000  0.00000  8.60000  0.00000  8.14000  8.89753
    9  M_1->2             0.00     1.36     0.00     2.88     0.00     3.22     3.43
   10  Theta_1         1.32000  1.56000  0.00000  3.56000  0.00000  0.00000  8.05323
   10  Theta_2         1.68000  1.84000  0.00000  4.00000  0.00000  6.10000  8.29181
   10  M_1->2             0.00     0.40     0.00     0.84     0.00     0.70     0.66
  All  Theta_1         2.08000  2.28000  2.46000  2.64000  2.84000  2.50000  2.46523
  All  Theta_2         0.20000  0.40000  0.62000  0.76000  1.00000  0.66000  0.60114
  All  M_1->2             0.00     0.16     0.34     0.48     0.72     0.42     0.36
-----------------------------------------------------------------------------------


--------------------------------------------------------------------
Correlation matrix of parameters
--------------------------------------------------------------------
   Q1    Q2   M21   M12 
Locus 1:
 1.00  0.75   --  -0.86 
 0.75  1.00   --  -0.83 
  --    --    --    --  
-0.86 -0.83   --   1.00 

Locus 2:
 1.00 -0.79   --   0.87 
-0.79  1.00   --  -0.74 
  --    --    --    --  
 0.87 -0.74   --   1.00 

Locus 3:
 1.00 -0.08   --  -0.07 
-0.08  1.00   --   0.66 
  --    --    --    --  
-0.07  0.66   --   1.00 

Locus 4:
 1.00  0.92   --  -0.94 
 0.92  1.00   --  -0.91 
  --    --    --    --  
-0.94 -0.91   --   1.00 

Locus 5:
 1.00 -0.51   --   0.70 
-0.51  1.00   --  -0.80 
  --    --    --    --  
 0.70 -0.80   --   1.00 

Locus 6:
 1.00 -0.55   --   0.02 
-0.55  1.00   --   0.01 
  --    --    --    --  
 0.02  0.01   --   1.00 

Locus 7:
 1.00 -0.08   --  -0.02 
-0.08  1.00   --  -0.00 
  --    --    --    --  
-0.02 -0.00   --   1.00 

Locus 8:
 1.00 -0.33   --  -0.75 
-0.33  1.00   --   0.12 
  --    --    --    --  
-0.75  0.12   --   1.00 

Locus 9:
 1.00  0.16   --  -0.47 
 0.16  1.00   --  -0.24 
  --    --    --    --  
-0.47 -0.24   --   1.00 

Locus 10:
 1.00  0.91   --   0.46 
 0.91  1.00   --   0.41 
  --    --    --    --  
 0.46  0.41   --   1.00 



Over all loci
--------------------------------------------------------------------
 1.00  0.19   --  -0.33 
 0.19  1.00   --  -0.46 
  --    --    --    --  
-0.33 -0.46   --   1.00 
--------------------------------------------------------------------



Log-Probability of the data given the model (marginal likelihood = log(P(D|thisModel))
--------------------------------------------------------------------
[Use this value for Bayes factor calculations:
BF = Exp[log(P(D|thisModel) - log(P(D|otherModel)]
shows the support for thisModel]



Locus      Raw Thermodynamic score(1a)  Bezier approximated score(1b)     Harmonic mean(2)
------------------------------------------------------------------------------------------
      1              -4829.68                       -896.70                -112.33
      2               -881.80                       -238.51                 -88.77
      3               -801.03                       -229.76                 -80.23
      4             -32648.26                      -5351.21                -117.40
      5               -245.89                       -110.70                 -61.89
      6             -14465.22                      -2418.43                 -84.40
      7              -2857.90                       -545.07                 -45.16
      8               -640.93                       -211.85                 -96.42
      9              -2057.46                       -435.15                -104.15
     10              -3309.13                       -643.93                -106.07
---------------------------------------------------------------------------------------
  All               -62788.76                     -11132.78                -948.28
[Scaling factor = -51.476468]
MCMC run characteristics
========================




Acceptance ratios for all parameters and the genealogies
---------------------------------------------------------------------

Parameter           Accepted changes               Ratio
Theta_1                  80226/80226             1.00000
Theta_2                  79926/79926             1.00000
M_1->2                   79784/79784             1.00000
Genealogies              24144/80122             0.30134
Autocorrelation and Effective sample size
-------------------------------------------------------------------

[  0]   Parameter         Autocorrelation(*)   Effective Sample size
  ---------         ---------------      ---------------------
  Theta_1                0.95300              5153.44
  Theta_2                0.92662              7440.50
  M_1->2                 0.92052              8289.76
  Ln[Prob(D|P)]          0.99855               201.17
  (*) averaged over loci.

