  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version debug 3.0.5

  Program started at Fri Mar 20 16:49:30 2009
         finished at Fri Mar 20 16:49:56 2009
     


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)  Exponential  0.000000   1.000000  10.000000           -
Migration rate      (M)  Exponential  0.000000  10.000000  1000.00000          -



Datatype: Microsatellite data [Brownian motion]
Missing data is not included

Pseudo-random number generator: Mersenne-Twister                                
Random number seed (with internal timer)           2132887175

Start parameters:
   First genealogy was started using a random tree
   Theta values were generated  from an FST-calculation
   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):                  6400
      Steps recorded (sample*rep):                      3200
   Combining over replicates:                              2
   Static heating scheme
      4 chains with  temperatures
       1.00, 2.33, 3.67, 5.00
      Swapping interval is 1
   Number of discard trees per chain:                    130

Print options:
   Data file:                                    infile.msat
   Output file (ASCII text):                   outfile-bayes
   Output file (PDF):                            outfile.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

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




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

Locus Parameter        2.5%      25.0%    mode     75.0%   97.5%     median   mean
-----------------------------------------------------------------------------------
    1  Theta_1         0.15000  0.20000  0.47500  0.95000  4.05000  2.97500  1.23841
    1  Theta_2         0.30000  0.45000  0.77500  1.20000  2.10000  3.17500  1.38481
    1  M_2->1             0.00     5.00    17.50    25.00    35.00    22.50    13.84
    1  M_1->2             0.00     5.00    17.50    30.00    40.00    22.50    23.37
    2  Theta_1         0.00000  0.00000  0.02500  0.10000  0.35000  0.12500  0.04938
    2  Theta_2         0.00000  0.00000  0.02500  0.15000  0.25000  0.17500  0.04517
    2  M_2->1           160.00   215.00   247.50   280.00   455.00   307.50   218.67
    2  M_1->2            85.00   100.00   132.50   160.00   185.00   317.50   217.52
    3  Theta_1         0.00000  0.90000  1.12500  1.35000  3.20000  1.17500  0.43231
    3  Theta_2         0.05000  0.15000  0.37500  0.70000  2.40000  1.07500  0.31901
    3  M_2->1            15.00    35.00    47.50    60.00    75.00    52.50    24.85
    3  M_1->2            15.00    45.00    62.50    75.00   100.00    67.50    32.71
    4  Theta_1         0.00000  0.00000  0.27500  0.70000  5.30000  2.72500  0.73201
    4  Theta_2         0.10000  1.50000  1.97500  2.25000  2.85000  1.62500  0.50114
    4  M_2->1             5.00    20.00    32.50    50.00    70.00    42.50    16.39
    4  M_1->2             0.00    20.00    42.50    50.00    65.00    42.50    14.57
    5  Theta_1         0.00000  0.10000  0.32500  0.55000  2.55000  1.37500  0.27929
    5  Theta_2         0.00000  0.00000  0.17500  0.35000  0.90000  0.37500  0.11151
    5  M_2->1             0.00     5.00    22.50    30.00    50.00    27.50     6.42
    5  M_1->2            40.00    60.00    82.50   100.00   175.00    97.50    29.13
    6  Theta_1         0.55000  0.75000  1.37500  1.65000  3.60000  1.67500  0.35263
    6  Theta_2         0.05000  0.10000  0.32500  0.55000  3.55000  1.07500  0.27980
    6  M_2->1             5.00    10.00    27.50    40.00    80.00    37.50     8.65
    6  M_1->2            30.00    45.00    57.50    70.00    90.00    67.50    16.75
    7  Theta_1         0.00000  0.00000  0.02500  0.10000  0.20000  0.12500  0.00529
    7  Theta_2         0.00000  0.00000  0.02500  0.20000  1.30000  0.22500  0.13374
    7  M_2->1           420.00   635.00   657.50   805.00   915.00   697.50   207.68
    7  M_1->2           580.00   625.00   707.50   780.00   880.00   687.50   216.14
    8  Theta_1         0.00000  1.10000  1.27500  1.45000  2.10000  1.07500  0.28226
    8  Theta_2         0.00000  0.05000  0.27500  1.00000  5.75000  2.72500  0.58405
    8  M_2->1            15.00    30.00    42.50    55.00    80.00    47.50    12.11
    8  M_1->2            10.00    20.00    37.50    45.00    90.00    52.50    19.49
    9  Theta_1         0.35000  0.55000  0.82500  1.15000  2.85000  1.12500  0.28240
    9  Theta_2         0.15000  0.25000  0.52500  0.85000  5.95000  2.87500  0.50904
    9  M_2->1             0.00     5.00    17.50    25.00    35.00    22.50     4.01
    9  M_1->2             0.00    10.00    22.50    35.00    50.00    27.50     6.30
   10  Theta_1         0.10000  0.20000  0.42500  0.70000  4.75000  1.77500  0.64683
   10  Theta_2         0.00000  0.00000  0.27500  0.70000  1.85000  0.67500  0.19282
   10  M_2->1             0.00     0.00     7.50    15.00    30.00    17.50     2.95
   10  M_1->2             0.00     5.00    27.50    40.00    60.00    52.50    17.73
  All  Theta_1         0.05000  0.25000  0.37500  0.50000  0.65000  0.42500  0.39901
  All  Theta_2         0.00000  0.15000  0.27500  0.35000  0.45000  0.32500  0.26968
  All  M_2->1             0.00    10.00    22.50    30.00    40.00    27.50    24.35
  All  M_1->2            15.00    25.00    42.50    50.00    65.00    47.50    41.72
-----------------------------------------------------------------------------------



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]

(1) Thermodynamic integration: log(Prob(D|Model))=-134216.191397 (-130685.266543 with Bezier-approximation) 
(2) Harmonic mean:             log(Prob(D|Model))=-2097799.382357
(1) and (2) should give a similar result, (2) is considered more
crude than (1), but (1) needs heating with several well-spaced chains

MCMC run characteristics
========================




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

Parameter           Accepted changes               Ratio
Theta_1                   8225/8225              1.00000
Theta_2                   8518/8518              1.00000
M_2->1                    8262/8262              1.00000
M_1->2                    8313/8313              1.00000
Genealogies               9416/32037             0.29391
Autocorrelation and Effective sample size
-------------------------------------------------------------------

  Parameter         Autocorrelation(*)   Effective Sample size
  ---------         ---------------      ---------------------
  Theta_1                0.96633               549.53
  Theta_2                0.95886               917.21
  M_(2,1)                0.92459              1278.31
  M_(1,2)                0.94441               934.23
  Ln[Prob(D|P)]          0.98486               246.64
  (*) averaged over loci.

