  ==========================================================
    Example: sequence data set wit two loci [simulated data]
  ==========================================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  ==========================================================
  Version 3.5.2

  Program started at Wed Apr 24 15:38:15 2013
         finished at Wed Apr 24 15:38:16 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   2.000000 
Migration rate      (M)      Uniform  0.000000  10.000000  20.000000   2.000000 



Datatype: DNA sequence data

Inheritance scalers in use for Thetas (specified scalars=1)
1.00 1.00 
[Each Theta uses the (true) ineritance scalar of the first locus as a reference]


Data set was subsampled: used a random sample of size: 5
with private random number seed 13


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]
    Africa     * 0 * * 
  Americas     * * * * 
   Pacific     * * * * 
      Asia     * * * * 



Mutation rate is constant for all loci

Markov chain settings:
   Long chains (long-chains):                              1
      Steps sampled (inc*samples*rep):                  1000
      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
   Burn-in per replicate (samples*inc):                  100

Print options:
   Data file:                                     infile.seq
   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: sequence data set wit two loci [simulated d
Data file:                                        infile.seq
Datatype:                                      Sequence data
Number of loci:                                            2


Data set was subsampled and used a random sample of size: 5

Locus Population Individuals
----- ---------- ---------------------------------------------------------------------
    1 Africa     0BAX 0BAI 0BAH 0BAO 0BAF 
      Americas   1BAQ 1BAX 1BAR 1BAV 1BAL 
      Pacific    2BAS 2BAD 2BAG 2BAM 2BAC 
      Asia       3BAJ 3BAQ 3BAX 3BAO 3BAP 
    2 Africa     0BAR 0BAK 0BAT 0BAL 0BAE 
      Americas   1BAH 1BAF 1BAQ 1BAO 1BAX 
      Pacific    2BAO 2BBA 2BAQ 2BAB 2BAP 
      Asia       3BAW 3BAA 3BAG 3BAL 3BAB 
Population                   Locus   Gene copies    
----------------------------------------------------
  1 Africa                       1        25
  1                              2        25
  2 Americas                     1        25
  2                              2        25
  3 Pacific                      1        25
  3                              2        25
  4 Asia                         1        25
  4                              2        25
    Total of all populations     1       100
                                 2       100


Empirical Base Frequencies
------------------------------------------------------------
Locus     Nucleotide                        Transition/
          ------------------------------  Transversion ratio
          A       C       G       T(U)
------------------------------------------------------------
   1      0.3103  0.1869  0.2766  0.2262       2.00000
   2      0.2770  0.2245  0.2052  0.2933       2.00000



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

Locus Parameter        2.5%      25.0%    mode     75.0%   97.5%     median   mean
-----------------------------------------------------------------------------------
    1  Theta_1         0.00000  0.00000  0.02000  0.20000  0.68000  0.22000  0.26641
    1  Theta_2         0.00000  0.00000  0.14000  0.44000  0.76000  0.46000  6.58620
    1  Theta_3         0.00000  0.00000  0.02000  0.24000  1.44000  0.26000  5.44908
    1  Theta_4         0.00000  0.00000  0.18000  0.32000  1.00000  0.34000  0.39966
    1  M_3->1             1.80     1.92     2.26     2.56     4.72     6.30     7.54
    1  M_4->1             0.00     0.88     1.22     1.52     1.84     2.46     6.66
    1  M_1->2            16.72    17.56    17.98    18.40    18.48    14.74    11.99
    1  M_3->2             5.24     5.44     5.78     6.12     6.20     6.86     7.66
    1  M_4->2             5.96     6.16     6.50     6.84     6.96     6.46     6.95
    1  M_1->3             1.40     1.48     1.98     2.40     3.08     4.78     5.90
    1  M_2->3             8.28     9.72    10.30    10.64    10.92     8.42     8.16
    1  M_4->3            13.80    13.88    14.30    14.60    15.52    14.02    13.75
    1  M_1->4             6.40     6.44     6.86     7.20     7.84     8.54     8.59
    1  M_2->4             0.00     0.00     0.34     0.84     2.72     1.30     2.23
    1  M_3->4             0.00     0.00     0.02     0.36     0.56    10.46    10.20
    2  Theta_1         0.00000  0.00000  0.02000  0.16000  0.64000  0.18000  0.17854
    2  Theta_2         0.00000  0.00000  0.02000  0.20000  0.72000  0.22000  1.05921
    2  Theta_3         0.00000  0.00000  0.02000  0.16000  0.48000  0.18000  0.28333
    2  Theta_4         0.00000  0.00000  0.14000  0.32000  1.12000  0.34000  0.34611
    2  M_3->1             6.84     7.08     7.62     8.08     8.24     7.18     7.66
    2  M_4->1             0.00     0.08     0.94     1.24     1.96     5.90     6.51
    2  M_1->2             0.00     0.56     1.06     1.56     2.68     2.14     4.52
    2  M_3->2            17.08    17.12    17.50    17.84    17.88     9.78     8.80
    2  M_4->2             0.00     0.00     0.26     1.00     1.28     5.02     6.87
    2  M_1->3             0.00     0.00     0.02     0.32     2.88     2.66     7.02
    2  M_2->3             0.00     0.76     1.26     1.76     1.88     3.78     4.81
    2  M_4->3             0.00     0.00     0.02     0.88     2.60     1.82     4.04
    2  M_1->4             0.00     0.00     0.46     0.80     2.76     2.38     5.30
    2  M_2->4             0.00     0.00     0.02     1.16     2.68     2.38     5.48
    2  M_3->4            16.32    16.52    16.98    17.36    17.48    10.26    10.05
  All  Theta_1         0.00000  0.04000  0.22000  0.36000  0.56000  0.30000  0.21505
  All  Theta_2         0.00000  0.04000  0.26000  0.40000  0.80000  0.34000  1.13590
  All  Theta_3         0.00000  0.00000  0.18000  0.32000  0.72000  0.30000  0.97998
  All  Theta_4         0.00000  0.08000  0.30000  0.44000  0.76000  0.38000  0.32552
  All  M_3->1             0.04     2.96     3.42     3.84     4.64     4.30     6.45
  All  M_4->1             0.00     0.12     1.02     1.36     3.56     2.14     4.27
  All  M_1->2            16.56    17.48    18.02    18.44    18.64    14.70    10.43
  All  M_3->2             0.00     0.00     0.26     0.64     4.44     5.86     7.30
  All  M_4->2             0.00     1.16     1.66     2.08     2.32     5.42     7.39
  All  M_1->3             0.00     1.48     1.94     2.40     2.92     2.50     4.99
  All  M_2->3             8.32     9.64    10.26    10.68    10.96     8.86     7.99
  All  M_4->3             0.00     0.00     0.42     0.88     2.72     1.62     4.38
  All  M_1->4             0.00     0.04     0.38     0.68     2.36     6.66     5.61
  All  M_2->4             0.00     0.04     0.38     0.64     2.72     0.62     2.00
  All  M_3->4            15.64    16.44    16.98    17.36    17.60    10.62     9.53
-----------------------------------------------------------------------------------


--------------------------------------------------------------------
Correlation matrix of parameters
--------------------------------------------------------------------
   Q1    Q2    Q3    Q4   M21   M31   M41   M12   M32   M42   M13   M23   M43   M14   M24   M34 
Locus 1:
 1.00 -0.04 -0.27  0.67   --  -0.62 -0.11  0.14  0.19 -0.12 -0.06 -0.44 -0.23 -0.06 -0.05 -0.02 
-0.04  1.00 -0.63  0.03   --   0.01  0.78  0.65  0.56 -0.36 -0.40  0.20 -0.17  0.40  0.30  0.49 
-0.27 -0.63  1.00 -0.34   --   0.42 -0.61 -0.66 -0.62  0.16  0.43  0.11  0.56 -0.19 -0.25 -0.31 
 0.67  0.03 -0.34  1.00   --  -0.39 -0.02  0.21  0.37 -0.24 -0.09 -0.25 -0.41  0.07  0.14  0.10 
  --    --    --    --    --    --    --    --    --    --    --    --    --    --    --    --  
-0.62  0.01  0.42 -0.39   --   1.00  0.04 -0.08 -0.13  0.04  0.01  0.24  0.31  0.02  0.06  0.25 
-0.11  0.78 -0.61 -0.02   --   0.04  1.00  0.53  0.50 -0.08 -0.27  0.21 -0.29  0.39  0.10  0.52 
 0.14  0.65 -0.66  0.21   --  -0.08  0.53  1.00  0.55 -0.36 -0.39 -0.01 -0.40  0.27  0.30  0.49 
 0.19  0.56 -0.62  0.37   --  -0.13  0.50  0.55  1.00 -0.54 -0.50 -0.06 -0.38  0.13  0.19  0.60 
-0.12 -0.36  0.16 -0.24   --   0.04 -0.08 -0.36 -0.54  1.00  0.22  0.06 -0.05 -0.10 -0.04 -0.23 
-0.06 -0.40  0.43 -0.09   --   0.01 -0.27 -0.39 -0.50  0.22  1.00  0.27  0.20  0.03 -0.34 -0.57 
-0.44  0.20  0.11 -0.25   --   0.24  0.21 -0.01 -0.06  0.06  0.27  1.00  0.11  0.31  0.18 -0.08 
-0.23 -0.17  0.56 -0.41   --   0.31 -0.29 -0.40 -0.38 -0.05  0.20  0.11  1.00  0.02 -0.11 -0.26 
-0.06  0.40 -0.19  0.07   --   0.02  0.39  0.27  0.13 -0.10  0.03  0.31  0.02  1.00  0.02  0.12 
-0.05  0.30 -0.25  0.14   --   0.06  0.10  0.30  0.19 -0.04 -0.34  0.18 -0.11  0.02  1.00  0.13 
-0.02  0.49 -0.31  0.10   --   0.25  0.52  0.49  0.60 -0.23 -0.57 -0.08 -0.26  0.12  0.13  1.00 

Locus 2:
 1.00  0.64  0.53  0.82   --  -0.45 -0.21 -0.28 -0.61 -0.33 -0.57 -0.33 -0.14 -0.26 -0.28 -0.70 
 0.64  1.00  0.81  0.43   --  -0.38 -0.28 -0.23 -0.34 -0.38 -0.31 -0.22 -0.17 -0.25 -0.31 -0.52 
 0.53  0.81  1.00  0.32   --  -0.34 -0.23 -0.23 -0.40 -0.39 -0.36 -0.28 -0.14 -0.23 -0.30 -0.51 
 0.82  0.43  0.32  1.00   --  -0.33 -0.22 -0.15 -0.52 -0.13 -0.53 -0.27 -0.10 -0.14 -0.18 -0.51 
  --    --    --    --    --    --    --    --    --    --    --    --    --    --    --    --  
-0.45 -0.38 -0.34 -0.33   --   1.00 -0.11  0.03  0.17  0.01  0.28  0.15  0.30  0.24  0.22  0.49 
-0.21 -0.28 -0.23 -0.22   --  -0.11  1.00  0.28  0.09  0.30 -0.06 -0.11 -0.19 -0.51 -0.18 -0.13 
-0.28 -0.23 -0.23 -0.15   --   0.03  0.28  1.00  0.24  0.25 -0.00  0.04 -0.34  0.30  0.14  0.11 
-0.61 -0.34 -0.40 -0.52   --   0.17  0.09  0.24  1.00  0.13  0.61  0.25  0.00  0.17  0.10  0.40 
-0.33 -0.38 -0.39 -0.13   --   0.01  0.30  0.25  0.13  1.00 -0.04 -0.09 -0.24 -0.00  0.16  0.28 
-0.57 -0.31 -0.36 -0.53   --   0.28 -0.06 -0.00  0.61 -0.04  1.00  0.64  0.01  0.15  0.02  0.46 
-0.33 -0.22 -0.28 -0.27   --   0.15 -0.11  0.04  0.25 -0.09  0.64  1.00 -0.14  0.09  0.28  0.21 
-0.14 -0.17 -0.14 -0.10   --   0.30 -0.19 -0.34  0.00 -0.24  0.01 -0.14  1.00  0.13  0.06  0.33 
-0.26 -0.25 -0.23 -0.14   --   0.24 -0.51  0.30  0.17 -0.00  0.15  0.09  0.13  1.00  0.29  0.46 
-0.28 -0.31 -0.30 -0.18   --   0.22 -0.18  0.14  0.10  0.16  0.02  0.28  0.06  0.29  1.00  0.23 
-0.70 -0.52 -0.51 -0.51   --   0.49 -0.13  0.11  0.40  0.28  0.46  0.21  0.33  0.46  0.23  1.00 



Over all loci
--------------------------------------------------------------------
 1.00  0.08 -0.20  0.70   --  -0.54 -0.14 -0.01 -0.16 -0.20 -0.27 -0.39 -0.19 -0.14 -0.15 -0.26 
 0.08  1.00 -0.57  0.09   --  -0.08  0.52  0.42  0.24 -0.31 -0.30  0.08 -0.15  0.14  0.06  0.24 
-0.20 -0.57  1.00 -0.28   --   0.28 -0.48 -0.51 -0.40  0.07  0.22  0.06  0.37 -0.12 -0.15 -0.26 
 0.70  0.09 -0.28  1.00   --  -0.36 -0.08  0.09 -0.00 -0.18 -0.26 -0.25 -0.28 -0.02 -0.01 -0.10 
  --    --    --    --    --    --    --    --    --    --    --    --    --    --    --    --  
-0.54 -0.08  0.28 -0.36   --   1.00 -0.03 -0.03  0.04  0.02  0.16  0.19  0.30  0.14  0.15  0.36 
-0.14  0.52 -0.48 -0.08   --  -0.03  1.00  0.43  0.28  0.11 -0.15  0.07 -0.24 -0.11 -0.06  0.25 
-0.01  0.42 -0.51  0.09   --  -0.03  0.43  1.00  0.38 -0.04 -0.18  0.01 -0.36  0.27  0.19  0.33 
-0.16  0.24 -0.40 -0.00   --   0.04  0.28  0.38  1.00 -0.12  0.21  0.12 -0.16  0.15  0.13  0.48 
-0.20 -0.31  0.07 -0.18   --   0.02  0.11 -0.04 -0.12  1.00  0.05 -0.03 -0.16 -0.04  0.09  0.04 
-0.27 -0.30  0.22 -0.26   --   0.16 -0.15 -0.18  0.21  0.05  1.00  0.48  0.08  0.11 -0.09 -0.01 
-0.39  0.08  0.06 -0.25   --   0.19  0.07  0.01  0.12 -0.03  0.48  1.00 -0.02  0.17  0.24  0.05 
-0.19 -0.15  0.37 -0.28   --   0.30 -0.24 -0.36 -0.16 -0.16  0.08 -0.02  1.00  0.09 -0.00  0.02 
-0.14  0.14 -0.12 -0.02   --   0.14 -0.11  0.27  0.15 -0.04  0.11  0.17  0.09  1.00  0.21  0.30 
-0.15  0.06 -0.15 -0.01   --   0.15 -0.06  0.19  0.13  0.09 -0.09  0.24 -0.00  0.21  1.00  0.18 
-0.26  0.24 -0.26 -0.10   --   0.36  0.25  0.33  0.48  0.04 -0.01  0.05  0.02  0.30  0.18  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               -667.88                       -540.30                -603.55
      2              -1775.81                      -1317.35               -3516.81
---------------------------------------------------------------------------------------
  All                -2353.48                      -1767.44               -4030.15
[Scaling factor = 90.212376]
MCMC run characteristics
========================




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

Parameter           Accepted changes               Ratio
Theta_1                     76/76                1.00000
Theta_2                     72/72                1.00000
Theta_3                     53/53                1.00000
Theta_4                     66/66                1.00000
M_3->1                      86/86                1.00000
M_4->1                      65/65                1.00000
M_1->2                      71/71                1.00000
M_3->2                      67/67                1.00000
M_4->2                      64/64                1.00000
M_1->3                      65/65                1.00000
M_2->3                      61/61                1.00000
M_4->3                      74/74                1.00000
M_1->4                      73/73                1.00000
M_2->4                      66/66                1.00000
M_3->4                      59/59                1.00000
Genealogies                264/982               0.26884
Autocorrelation and Effective sample size
-------------------------------------------------------------------

  Parameter         Autocorrelation(*)   Effective Sample size
  ---------         ---------------      ---------------------
  Theta_1                0.98040                20.02
  Theta_2                0.97869                21.50
  Theta_3                0.96791                32.78
  Theta_4                0.97359                26.73
  M_3->1                 0.96986                30.63
  M_4->1                 0.98153                18.63
  M_1->2                 0.96394                36.72
  M_3->2                 0.97655                23.77
  M_4->2                 0.97601                24.27
  M_1->3                 0.97256                27.86
  M_2->3                 0.97718                23.12
  M_4->3                 0.96679                33.78
  M_1->4                 0.96585                34.99
  M_2->4                 0.97404                26.27
  M_3->4                 0.97274                27.72
  Ln[Prob(D|P)]          0.98512                14.99
  (*) averaged over loci.


POTENTIAL PROBLEMS
------------------------------------------------------------------------------------------
This section reports potential problems with your run, but such reporting is often not 
very accurate. Whith many parameters in a multilocus analysis, it is very common that 
some parameters for some loci will not be very informative, triggering suggestions (for 
example to increase the prior range) that are not sensible. This suggestion tool will 
improve with time, therefore do not blindly follow its suggestions. If some parameters 
are flagged, inspect the tables carefully and judge wether an action is required. For 
example, if you run a Bayesian inference with sequence data, for macroscopic species 
there is rarely the need to increase the prior for Theta beyond 0.1; but if you use 
microsatellites it is rather common that your prior distribution for Theta should have a 
range from 0.0 to 100 or more. With many populations (>3) it is also very common that 
some migration routes are estimated poorly because the data contains little or no 
information for that route. Increasing the range will not help in such situations, 
reducing number of parameters may help in such situations.
------------------------------------------------------------------------------------------
Param 8 (Locus 1): Upper prior boundary seems too low! 
Param 8 (all loci): Upper prior boundary seems too low! 
Param 7: Effective sample size of run seems too short! 
------------------------------------------------------------------------------------------
