  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version debug 3.2.17

  Program started at Sun Oct  9 20:24:30 2011
         finished at Sun Oct  9 20:25:19 2011
     


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

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

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
H_exp   0.811  0.883  0.847

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
H_exp   0.653  0.624  0.638

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
H_exp   0.765  0.679  0.722

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
H_exp   0.882  0.875  0.878

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
H_exp   0.631  0.584  0.608

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
H_exp   0.813  0.696  0.754

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
H_exp   0.520  0.766  0.643

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
H_exp   0.682  0.672  0.677

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
H_exp   0.773  0.751  0.762

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
H_exp   0.752  0.838  0.795

Average expected heterozygosity
Pop1   Pop2   All
---------------------
0.728 0.737 0.732




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

Locus Parameter        2.5%      25.0%    mode     75.0%   97.5%     median   mean
-----------------------------------------------------------------------------------
    1  Theta_1         0.40000  0.56000  1.22000  2.08000  2.32000  2.74000  4.45556
    1  Theta_2         0.52000  0.72000  1.18000  2.32000  2.92000  3.58000  4.73761
    1  M_1->2             0.00     0.00     0.30     0.76     0.92     2.42     2.56
    2  Theta_1         2.80000  3.96000  4.50000  5.64000  8.96000  5.22000  2.72766
    2  Theta_2         4.56000  6.08000  7.02000  8.68000 12.92000  8.02000  4.22616
    2  M_1->2             0.00     0.24     0.46     0.68     1.28     0.58     0.28
    3  Theta_1         2.40000  3.60000  4.66000  5.32000  7.32000  4.70000  1.59238
    3  Theta_2         1.44000  2.08000  2.66000  3.36000  8.08000  3.10000  1.25279
    3  M_1->2             0.00     0.12     0.62     1.32     5.80     2.18     0.81
    4  Theta_1         4.60000  5.72000  6.98000  8.08000 11.88000  7.62000  1.98870
    4  Theta_2         3.36000  4.60000  5.50000  6.68000 10.12000  6.02000  1.62657
    4  M_1->2             0.12     0.64     1.02     1.40     2.12     1.14     0.28
    5  Theta_1         2.36000  2.68000  3.30000  4.40000 11.92000  6.06000  1.34937
    5  Theta_2         1.72000  6.00000  6.46000  8.84000 13.88000  7.02000  1.46795
    5  M_1->2             0.24     0.68     1.02     1.52     3.68     1.86     0.38
    6  Theta_1         1.44000  3.04000  3.82000  4.64000  5.88000  3.78000  0.62760
    6  Theta_2         0.80000  1.20000  1.54000  1.84000  2.68000  1.70000  0.28551
    6  M_1->2             2.16     4.48     5.50     6.04    10.68     6.54     1.11
    7  Theta_1         2.28000  3.92000  4.66000  5.68000  7.56000  4.90000  0.70744
    7  Theta_2         1.96000  2.76000  3.98000  5.44000  9.40000  5.18000  0.80050
    7  M_1->2             0.20     0.52     0.78     1.88     3.72     1.70     0.26
    8  Theta_1         2.44000  2.72000  3.86000  5.04000 12.44000  5.78000  0.83500
    8  Theta_2         2.00000  2.40000  3.10000  5.44000 12.04000  5.66000  0.94295
    8  M_1->2             0.20     0.68     1.02     1.28     1.96     1.10     0.14
    9  Theta_1         5.24000  6.36000  7.10000  8.36000 11.16000  7.78000  0.88399
    9  Theta_2         4.04000  5.28000  5.90000  7.16000 10.04000  6.54000  0.75126
    9  M_1->2             0.24     0.64     0.94     1.32     2.08     1.10     0.13
   10  Theta_1         0.20000  0.28000  0.78000  1.48000  1.76000  4.34000  0.46388
   10  Theta_2         0.00000  0.16000  0.62000  1.04000  1.52000  3.66000  0.37738
   10  M_1->2             0.08     0.32     1.06     2.28     2.76     3.50     0.58
  All  Theta_1         4.56000  5.48000  6.10000  6.48000  7.20000  5.94000  5.91176
  All  Theta_2         5.16000  6.72000  7.18000  7.36000  7.96000  6.62000  6.56064
  All  M_1->2             0.32     0.56     0.78     0.92     1.20     0.82     0.77
-----------------------------------------------------------------------------------



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             -28361.13                      -4631.15                 -84.72
      2               -818.49                       -214.46                 -71.72
      3               -741.76                       -194.19                 -50.64
      4              -4314.87                       -789.95                 -86.77
      5               -535.14                       -156.61                 -76.49
      6              -3340.26                       -595.30                 -46.93
      7               -722.15                       -189.26                 -71.86
      8              -1427.39                       -316.14                 -81.59
      9              -1119.87                       -275.76                 -88.54
     10              -6074.74                      -1050.17                -157.09
---------------------------------------------------------------------------------------
  All               -47504.49                      -8461.67                -865.03
[Scaling factor = -48.672332]
MCMC run characteristics
========================




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

Parameter           Accepted changes               Ratio
Theta_1                  16707/16707             1.00000
Theta_2                  16672/16672             1.00000
M_1->2                   16825/16825             1.00000
Genealogies              14890/49816             0.29890
Autocorrelation and Effective sample size
-------------------------------------------------------------------

  Parameter         Autocorrelation(*)   Effective Sample size
  ---------         ---------------      ---------------------
  Theta_1                0.92931              3619.95
  Theta_2                0.89824              4375.93
  M_1->2                 0.91471              4134.21
  Ln[Prob(D|P)]          0.99589               285.94
  (*) averaged over loci.

