  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version 3.1.7

  Program started at Thu Aug  5 10:56:51 2010
         finished at Thu Aug  5 11:13:24 2010
     


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

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:
   Migration matrix model with variable Theta  

Mutation rate is constant for all loci

Markov chain settings:
   Long chains (long-chains):                              1
      Steps sampled (inc*samples*rep):                200000
      Steps recorded (sample*rep):                      1000
   Combining over replicates:                              2
   Static heating scheme
      4 chains with  temperatures
       1.00, 1.50, 3.00,1000000.00
      Swapping interval is 1
   Number of discard trees per chain:                  10000

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     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      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

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     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

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      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

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      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      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     10




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

Locus Parameter        2.5%      25.0%    mode     75.0%   97.5%     median   mean
-----------------------------------------------------------------------------------
    1  Theta_1         0.76000  2.32000  3.34000  5.36000 12.64000  5.58000  6.59041
    1  Theta_2         6.08000 15.36000 18.54000 19.80000 20.00000 15.18000 14.22092
    1  M_2->1             3.64     4.36     6.06     6.68    11.92     6.78     7.19
    1  M_1->2             2.88     3.92     4.70     5.12     6.12     4.58     4.55
    2  Theta_1         2.12000  3.20000  5.02000  6.12000 10.92000  5.58000  3.02212
    2  Theta_2         1.32000  1.80000  2.46000  5.04000 12.96000  7.22000  4.23683
    2  M_2->1             0.00     0.08     0.50     0.96     2.84     0.90     0.53
    2  M_1->2             0.92     4.12     5.82     9.04    13.64     7.18     3.76
    3  Theta_1         4.40000  5.12000  7.46000  9.88000 17.32000  9.26000  3.47165
    3  Theta_2         0.08000  0.32000  1.38000  2.36000  6.36000  2.26000  1.56737
    3  M_2->1             0.76     1.20     2.10     2.92     5.52     2.62     0.93
    3  M_1->2             8.00    15.12    15.58    19.12    19.88    12.10     3.83
    4  Theta_1        10.48000 17.52000 18.18000 18.76000 20.00000 15.94000  3.84416
    4  Theta_2         9.04000 16.24000 19.34000 19.92000 20.00000 16.42000  3.87965
    4  M_2->1             0.16     0.28     0.74     1.20     2.92     1.34     0.43
    4  M_1->2             0.08     0.36     0.74     1.24     2.68     1.18     0.32
    5  Theta_1         0.60000  0.96000  2.26000  4.68000  6.48000  4.46000  1.40698
    5  Theta_2         1.08000  1.36000  2.22000  4.40000  9.12000  4.22000  1.42288
    5  M_2->1             0.00     0.00     0.34     1.92     6.16     5.26     1.57
    5  M_1->2             0.00     0.00     0.02     3.92     4.92     4.74     1.62
    6  Theta_1         2.32000  4.32000  4.74000  6.92000 10.56000  6.14000  1.07252
    6  Theta_2         0.12000  0.56000  0.98000  2.32000  7.08000  2.14000  0.45631
    6  M_2->1             0.00     0.36     0.74     1.20     2.16     1.06     0.21
    6  M_1->2             0.16     2.00     2.74     4.16    12.56     3.54     0.82
    7  Theta_1         0.04000  0.36000  0.86000  2.32000  6.00000  2.14000  0.36836
    7  Theta_2         1.12000  2.12000  3.58000  5.56000 13.92000  5.18000  0.94528
    7  M_2->1             0.08     1.00     1.58     2.60     9.08     4.18     0.62
    7  M_1->2             0.00     0.00     0.02     2.08     4.92     2.10     0.61
    8  Theta_1         2.40000  3.32000  4.26000  7.04000 15.64000  7.22000  1.02955
    8  Theta_2         1.44000  1.84000  2.42000  6.00000 12.72000  6.58000  0.99931
    8  M_2->1             0.28     0.96     1.78     2.04     3.36     1.70     0.22
    8  M_1->2             1.56     3.32     5.02     5.64    13.36     7.02     0.92
    9  Theta_1         1.96000  3.68000  4.46000  6.68000 11.60000  5.86000  0.71100
    9  Theta_2         1.00000  1.68000  2.54000  5.24000 10.44000  6.10000  0.85300
    9  M_2->1             0.00     0.00     0.02     0.44     5.16     2.42     0.27
    9  M_1->2             1.52     1.88     3.74     6.96    15.92     6.66     0.89
   10  Theta_1         1.56000  2.60000  3.50000  7.60000 14.80000  7.86000  0.90640
   10  Theta_2         5.04000  6.08000  7.10000  8.16000 18.96000 11.26000  1.13829
   10  M_2->1             0.76     2.08     3.38     4.28    11.28     4.66     0.55
   10  M_1->2             0.00     0.88     1.26     1.80     3.48     1.50     0.17
  All  Theta_1         3.24000  4.12000  4.54000  4.80000  5.20000  4.46000  4.40411
  All  Theta_2         1.52000  1.92000  2.18000  2.40000  3.64000  2.30000  2.39049
  All  M_2->1             0.48     0.84     1.10     1.40     2.12     1.22     1.24
  All  M_1->2             1.16     2.88     3.38     3.72     4.20     3.22     2.95
-----------------------------------------------------------------------------------



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              -7636.41                      -1346.67                -115.66
      2              -2913.00                       -559.26                 -78.37
      3              -1204.14                       -292.12                 -74.13
      4              -7792.32                      -1378.82                -129.88
      5               -883.89                       -216.25                 -55.86
      6              -4265.14                       -788.37                 -77.29
      7              -1593.18                       -346.27                 -76.84
      8              -2813.17                       -552.12                 -91.10
      9              -2858.41                       -563.54                 -77.50
     10              -3804.78                       -729.55                 -99.33
---------------------------------------------------------------------------------------
  All               -35837.26                      -6845.79                -948.77
[Scaling factor = -72.817552]
MCMC run characteristics
========================




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

Parameter           Accepted changes               Ratio
Theta_1                 276107/276107            1.00000
Theta_2                 276097/276097            1.00000
M_2->1                  274642/274642            1.00000
M_1->2                  275913/275913            1.00000
Genealogies             310443/1001187           0.31007
Autocorrelation and Effective sample size
-------------------------------------------------------------------

  Parameter         Autocorrelation(*)   Effective Sample size
  ---------         ---------------      ---------------------
  Theta_1                0.79950              1190.18
  Theta_2                0.81841              1344.70
  M_2->1                 0.95344               656.66
  M_1->2                 0.92559               648.58
  Ln[Prob(D|P)]          0.92862               498.24
  (*) averaged over loci.

