  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version 3.5.0

  Program started at Sun Mar  3 14:20:09 2013
         finished at Sun Mar  3 14:20:17 2013
     


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

Analysis strategy is BAYESIAN INFERENCE

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


Prior distribution (Proposal-delta will be tuned to acceptance frequence 0.440000):
Parameter group          Prior type   Minimum    Mean(*)    Maximum    Delta
-----------------------  ------------ ---------- ---------- ---------- ----------
Population size (Theta)      Uniform  0.000000  10.000000  20.000000   5.000000 
Migration rate      (M)      Uniform  0.000000  10.000000  20.000000   5.000000 



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
Alleles        10     12     13
Samplesize     50     42     92
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
Alleles         7      6      8
Samplesize     50     42     92
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
Alleles         5      5      5
Samplesize     50     42     92
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
Alleles        12     12     14
Samplesize     50     42     92
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
Alleles         3      3      3
Samplesize     50     42     92
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
Alleles         7      6      8
Samplesize     50     42     92
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
Alleles         5      5      5
Samplesize     50     42     92
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
Alleles         7      7      8
Samplesize     50     42     92
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
Alleles         7      8      8
Samplesize     50     42     92
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
Alleles         9      8     10
Samplesize     50     42     92
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         4.88000  5.44000  0.00000  8.88000  0.00000  0.00000 10.82314
    1  Theta_2        11.48000 14.52000  0.00000 16.28000  0.00000 14.18000 13.60132
    1  M_1->2             0.00     0.28     0.00     0.80     0.00     1.26     1.22
    2  Theta_1         2.80000  3.56000  0.00000  4.84000  0.00000  0.00000  4.70100
    2  Theta_2         0.44000  0.60000  0.00000  2.48000  0.00000  2.94000  5.27173
    2  M_1->2             0.00     7.96     0.00    11.04     0.00     9.66     9.73
    3  Theta_1         5.12000  6.08000  0.00000  7.92000  0.00000  0.00000  8.05833
    3  Theta_2         2.16000  2.88000  0.00000  4.96000  0.00000  7.50000  8.53377
    3  M_1->2             0.00     3.60     0.00     5.84     0.00     5.46     5.67
    4  Theta_1         1.60000  1.80000  0.00000  4.44000  0.00000  0.00000  9.12468
    4  Theta_2         0.12000  0.24000  0.00000  1.68000  0.00000  1.82000  8.22277
    4  M_1->2             0.00     1.56     0.00     3.52     0.00     4.58     9.72
    5  Theta_1         1.32000  2.28000  0.00000  3.36000  0.00000  0.00000  2.83023
    5  Theta_2         5.80000  8.56000  0.00000 12.24000  0.00000 12.38000 12.70291
    5  M_1->2             0.00     5.36     0.00     7.88     0.00     6.18     6.59
    6  Theta_1         5.92000  7.24000  0.00000  9.24000  0.00000  0.00000  8.88443
    6  Theta_2         0.28000  0.60000  0.00000  1.24000  0.00000  1.06000  1.05900
    6  M_1->2             0.00     3.20     0.00     5.92     0.00     9.06    10.92
    7  Theta_1         1.00000  1.20000  0.00000  2.32000  0.00000  0.00000  3.45695
    7  Theta_2         2.24000  2.76000  0.00000  5.08000  0.00000  6.66000  7.15833
    7  M_1->2             0.00     0.12     0.00     1.44     0.00     1.38     1.62
    8  Theta_1         2.80000  5.32000  0.00000  7.20000  0.00000  0.00000  6.17402
    8  Theta_2         4.72000  5.52000  0.00000  9.32000  0.00000  9.90000 10.69693
    8  M_1->2             0.00     1.00     0.00     1.84     0.00     1.66     1.76
    9  Theta_1         1.32000  1.64000  0.00000  3.80000  0.00000  0.00000  5.27911
    9  Theta_2         1.88000  3.12000  0.00000  5.32000  0.00000  4.66000  4.97139
    9  M_1->2             0.00     1.40     0.00     3.00     0.00     4.42     4.62
   10  Theta_1         0.00000  0.00000  0.00000  0.56000  0.00000  0.00000  7.64207
   10  Theta_2         0.12000  0.20000  0.00000  1.24000  0.00000 10.78000  8.47570
   10  M_1->2             0.00     0.40     0.00     1.80     0.00     2.10     5.55
  All  Theta_1         0.00000  0.04000  0.22000  0.32000  0.52000  0.30000  0.20407
  All  Theta_2         0.48000  0.72000  0.94000  1.08000  1.32000  0.98000  0.92455
  All  M_1->2             0.04     0.16     0.46     0.72     0.84     1.30     1.46
-----------------------------------------------------------------------------------


--------------------------------------------------------------------
Correlation matrix of parameters
--------------------------------------------------------------------
   Q1    Q2   M21   M12 
Locus 1:
 1.00  0.54   --  -0.73 
 0.54  1.00   --  -0.38 
  --    --    --    --  
-0.73 -0.38   --   1.00 

Locus 2:
 1.00  0.02   --   0.23 
 0.02  1.00   --   0.11 
  --    --    --    --  
 0.23  0.11   --   1.00 

Locus 3:
 1.00 -0.16   --  -0.05 
-0.16  1.00   --  -0.20 
  --    --    --    --  
-0.05 -0.20   --   1.00 

Locus 4:
 1.00  0.90   --  -0.90 
 0.90  1.00   --  -0.94 
  --    --    --    --  
-0.90 -0.94   --   1.00 

Locus 5:
 1.00  0.10   --  -0.39 
 0.10  1.00   --  -0.17 
  --    --    --    --  
-0.39 -0.17   --   1.00 

Locus 6:
 1.00  0.21   --  -0.18 
 0.21  1.00   --  -0.57 
  --    --    --    --  
-0.18 -0.57   --   1.00 

Locus 7:
 1.00  0.73   --  -0.63 
 0.73  1.00   --  -0.52 
  --    --    --    --  
-0.63 -0.52   --   1.00 

Locus 8:
 1.00  0.01   --   0.12 
 0.01  1.00   --  -0.44 
  --    --    --    --  
 0.12 -0.44   --   1.00 

Locus 9:
 1.00 -0.01   --   0.73 
-0.01  1.00   --  -0.31 
  --    --    --    --  
 0.73 -0.31   --   1.00 

Locus 10:
 1.00  0.95   --  -0.90 
 0.95  1.00   --  -0.89 
  --    --    --    --  
-0.90 -0.89   --   1.00 



Over all loci
--------------------------------------------------------------------
 1.00  0.64   --  -0.53 
 0.64  1.00   --  -0.53 
  --    --    --    --  
-0.53 -0.53   --   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              -5883.42                      -1068.00                -108.06
      2               -828.99                       -218.53                 -46.36
      3               -626.43                       -199.04                 -79.22
      4              -4614.04                       -854.34                -116.23
      5              -1548.62                       -321.00                 -56.18
      6              -9113.30                      -1561.10                 -58.56
      7               -833.90                       -222.87                 -58.27
      8               -694.38                       -214.34                 -75.01
      9               -908.52                       -247.97                 -73.39
     10             -40186.21                      -6568.10                -184.60
---------------------------------------------------------------------------------------
  All               -65064.46                     -11301.94                -682.53
[Scaling factor = 173.345379]
MCMC run characteristics
========================




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

Parameter           Accepted changes               Ratio
Theta_1                  16696/16696             1.00000
Theta_2                  16846/16846             1.00000
M_1->2                   16633/16633             1.00000
Genealogies              15280/49825             0.30667
Autocorrelation and Effective sample size
-------------------------------------------------------------------

[  0]   Parameter         Autocorrelation(*)   Effective Sample size
  ---------         ---------------      ---------------------
  Theta_1                0.93619              4731.39
  Theta_2                0.91603              6325.69
  M_1->2                 0.91515              6631.69
  Ln[Prob(D|P)]          0.99658               278.71
  (*) averaged over loci.

