  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version debug 3.0.7

  Program started at Mon Jun  8 12:14:08 2009
         finished at Mon Jun  8 12:14:10 2009
     


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

Analysis strategy is                                    Bayesian

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


Prior distribution:
Parameter group          Prior type   Minimum    Mean(*)    Maximum    Delta
-----------------------  ------------ ---------- ---------- ---------- ----------
Population size (Theta)      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 (with internal timer)            938952981

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):                   640
      Steps recorded (sample*rep):                       320
   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.msat1
   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.msat1
Datatype:               Microsatellite data
Number of loci:                          10

Population                   Locus   Gene copies    
                                     ---------------
                                     data  (missing)
----------------------------------------------------
  1 population__number___0       1    100 (0)
  1                              2    100 (0)
  1                              3    100 (0)
  1                              4    100 (0)
  1                              5    100 (0)
  1                              6    100 (0)
  1                              7    100 (0)
  1                              8    100 (0)
  1                              9    100 (0)
  1                             10    100 (0)
    Total of all populations     1    100 (0)
                                 2    100 (0)
                                 3    100 (0)
                                 4    100 (0)
                                 5    100 (0)
                                 6    100 (0)
                                 7    100 (0)
                                 8    100 (0)
                                 9    100 (0)
                                10    100 (0)

Allele frequency spectra
========================

Locus 1
Allele  Pop1   All
---------------------
    16  0.180  0.180
    19  0.050  0.050
    18  0.080  0.080
    15  0.120  0.120
    21  0.080  0.080
    23  0.060  0.060
    17  0.180  0.180
    22  0.080  0.080
    25  0.040  0.040
    24  0.010  0.010
    26  0.010  0.010
    27  0.020  0.020
    29  0.010  0.010
Total     13

Locus 2
Allele  Pop1   All
---------------------
    16  0.500  0.500
    19  0.020  0.020
    18  0.160  0.160
    17  0.150  0.150
    15  0.010  0.010
    21  0.040  0.040
    20  0.020  0.020
    22  0.020  0.020
Total      8

Locus 3
Allele  Pop1   All
---------------------
    19  0.310  0.310
    20  0.340  0.340
    18  0.080  0.080
    21  0.190  0.190
    22  0.080  0.080
Total      5

Locus 4
Allele  Pop1   All
---------------------
    16  0.070  0.070
    24  0.100  0.100
    15  0.030  0.030
    25  0.150  0.150
    14  0.030  0.030
    19  0.110  0.110
    12  0.030  0.030
    20  0.120  0.120
    23  0.080  0.080
    28  0.010  0.010
    22  0.040  0.040
    21  0.130  0.130
    13  0.010  0.010
    26  0.010  0.010
Total     14

Locus 5
Allele  Pop1   All
---------------------
    20  0.500  0.500
    21  0.360  0.360
    19  0.140  0.140
Total      3

Locus 6
Allele  Pop1   All
---------------------
    19  0.030  0.030
    20  0.060  0.060
    18  0.240  0.240
    22  0.150  0.150
    21  0.260  0.260
    16  0.030  0.030
    24  0.100  0.100
    17  0.050  0.050
Total      8

Locus 7
Allele  Pop1   All
---------------------
    23  0.200  0.200
    20  0.390  0.390
    22  0.170  0.170
    21  0.190  0.190
    19  0.050  0.050
Total      5

Locus 8
Allele  Pop1   All
---------------------
    19  0.480  0.480
    17  0.040  0.040
    18  0.080  0.080
    20  0.150  0.150
    16  0.040  0.040
    22  0.070  0.070
    15  0.030  0.030
    23  0.030  0.030
Total      8

Locus 9
Allele  Pop1   All
---------------------
    24  0.130  0.130
    19  0.330  0.330
    20  0.220  0.220
    23  0.150  0.150
    22  0.050  0.050
    18  0.040  0.040
    21  0.060  0.060
    25  0.020  0.020
Total      8

Locus 10
Allele  Pop1   All
---------------------
    22  0.220  0.220
    20  0.310  0.310
    23  0.110  0.110
    24  0.010  0.010
    19  0.150  0.150
    21  0.050  0.050
    18  0.040  0.040
    15  0.040  0.040
    17  0.040  0.040
    25  0.030  0.030
Total     10




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

Locus Parameter        2.5%      25.0%    mode     75.0%   97.5%     median   mean
-----------------------------------------------------------------------------------
    1  Theta_1         3.64000  4.00000  4.62000  5.44000  5.96000  6.46000  7.31036
    2  Theta_1         0.60000  0.80000  1.06000  1.28000  1.48000  1.74000  0.92954
    3  Theta_1         0.24000  0.44000  0.74000  1.00000  1.48000  0.90000  0.28815
    4  Theta_1         4.92000  5.92000  6.54000  7.04000  9.12000  6.94000  1.74491
    5  Theta_1         5.08000  5.64000  6.30000  6.80000 10.56000  7.50000  1.54859
    6  Theta_1         2.88000  3.12000  3.58000  4.12000  4.88000  5.34000  1.01658
    7  Theta_1         0.00000  0.00000  0.22000  0.44000  0.56000  2.22000  0.20255
    8  Theta_1         0.00000  0.00000  0.22000  0.56000  0.60000  7.06000  0.53164
    9  Theta_1         4.16000  4.92000  5.62000  6.00000  7.60000  5.66000  0.63852
   10  Theta_1         1.56000  1.80000  2.22000  2.64000  3.04000  4.94000  0.46367
  All  Theta_1         0.00000  0.00000  0.30000  0.64000  1.56000  1.10000  1.92921
-----------------------------------------------------------------------------------



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             -15654.86                      -2711.43                 -78.82
      2              -8861.55                      -1617.13                -145.92
      3              -7872.16                      -1472.20                -236.81
      4              -5592.50                      -1107.97                 -74.36
      5              -7040.84                      -1316.56                 -55.46
      6             -22763.27                      -3838.22                 -59.95
      7              -6827.29                      -1335.26                -715.21
      8              -5333.25                      -1096.96                -778.24
      9             -10236.93                      -1834.31                 -56.14
     10             -13903.91                      -2425.35                -103.89
---------------------------------------------------------------------------------------
  All              -104086.55                     -18755.38               -2304.80
MCMC run characteristics
========================




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

Parameter           Accepted changes               Ratio
Theta_1                   3200/3200              1.00000
Genealogies                629/3240              0.19414
Autocorrelation and Effective sample size
-------------------------------------------------------------------

  Parameter         Autocorrelation(*)   Effective Sample size
  ---------         ---------------      ---------------------
  Theta_1                0.38490              1763.60
  Ln[Prob(D|P)]          0.96896                84.28
  (*) averaged over loci.

