  =============================================
    Example: Microsatellite data set           
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  Version debug 2.4.2

  Program started at Sun Feb 17 16:45:15 2008
         finished at Sun Feb 17 16:45:22 2008
     


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

Analysis strategy is                          Maximum likelihood



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

Pseudo-random number generator: Mersenne-Twister                                
Random number seed (with internal timer)           1881505405

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:
   Short chains (short-chains):                           10
      Trees sampled (short-inc*samples):                 100
      Trees recorded (short-sample):                      50
   Long chains (long-chains):                              3
      Trees sampled (long-inc*samples):                  200
      Trees recorded (long-sample):                      100
   Averaging over replicates:                              2
   Number of discard trees per chain:                     10

Print options:
   Data file:                                    infile.msat
   Output file (ASCII text):                      outfile-ml
   Output file (PDF):                         outfile-ml.pdf
   Print data:                                            No
   Print genealogies:                                     No
   Plot data: No                                            
   Profile likelihood: Yes, tables and summary             
             Percentile method
             with df=1 and for Theta and M=m/mu




Summary of data:
Title:   Example: Microsatellite data set
Datatype:                                 Microsatellite data
Number of loci:                                            10

Population                                    Locus  Gene copies
                                                     data (missing)
----------------------------------------------------------------
  1 population__number___0                       1     50 (0)
                                                 2     50 (0)
                                                 3     50 (0)
                                                 4     50 (0)
                                                 5     50 (0)
                                                 6     50 (0)
                                                 7     50 (0)
                                                 8     50 (0)
                                                 9     50 (0)
                                                10     50 (0)
  2 population__number___1                       1     42 (0)
                                                 2     42 (0)
                                                 3     42 (0)
                                                 4     42 (0)
                                                 5     42 (0)
                                                 6     42 (0)
                                                 7     42 (0)
                                                 8     42 (0)
                                                 9     42 (0)
                                                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 0
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 1
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 2
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 3
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 4
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 5
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 6
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 7
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 8
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 9
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





==============================================================================
MCMC estimates 
==============================================================================
Population [x] Loc.  Ln(L)   Theta    M [m/mu] [+=receiving population]  
                             [xN mu]    1,+     2,+    
-------------- ---- -------- -------- ----------------------------------------
 1: population  1 1    0.680  0.69526 -------  8.7627 
                1 2    0.080  1.10787 ------- 10.3484 
                1 A    0.159  1.10787 ------- 10.3484 
                2 1    0.562  0.04264 ------- 145.1094 
                2 2    0.732  0.03213 ------- 260.0000 
                2 A    1.465  0.03213 ------- 260.0000 
                3 1    0.361  0.26224 ------- 25.2561 
                3 2    0.826  0.24587 ------- 63.0160 
                3 A    1.651  0.24587 ------- 63.0160 
                4 1    0.180  0.39604 ------- 27.4574 
                4 2    0.086  0.43761 ------- 32.5418 
                4 A    0.171  0.43761 ------- 32.5418 
                5 1    0.294  1.52168 -------  8.8020 
                5 2    1.831  1.24639 -------  2.3841 
                5 A    3.662  1.24639 -------  2.3841 
                6 1    0.045  0.82371 ------- 71.7697 
                6 2    0.083  1.59345 ------- 56.8819 
                6 A    0.167  1.59345 ------- 56.8819 
                7 1    2.065  0.00404 ------- 570.9661 
                7 2    0.916  0.00928 ------- 687.3997 
                7 A    1.832  0.00928 ------- 687.3997 
                8 1    0.229  0.19169 ------- 32.8581 
                8 2    0.745  0.36894 ------- 33.9389 
                8 A    1.490  0.36894 ------- 33.9389 
                9 1    0.373  1.02923 ------- 26.4238 
                9 2    4.613  0.77450 ------- 16.4786 
                9 A    9.226  0.77450 ------- 16.4786 
               10 1    0.179  2.04994 -------  7.1778 
               10 2    1.039  1.97557 -------  2.7472 
               10 A    2.078  1.97557 -------  2.7472 
                All -1366.269  0.70189 ------- 21.8125 
 2: population  1 1    0.680  3.27893  4.1015 -------
                1 2    0.080  2.47546 11.8363 -------
                1 A    0.159  2.47546 11.8363 -------
                2 1    0.562  0.44908 78.1743 -------
                2 2    0.732  0.63530 64.4723 -------
                2 A    1.465  0.63530 64.4723 -------
                3 1    0.361  0.71204 17.0793 -------
                3 2    0.826  0.64063 16.9555 -------
                3 A    1.651  0.64063 16.9555 -------
                4 1    0.180  1.26957 25.4841 -------
                4 2    0.086  1.88710 11.0882 -------
                4 A    0.171  1.88710 11.0882 -------
                5 1    0.294  0.06529 24.6457 -------
                5 2    1.831  0.10092 25.7732 -------
                5 A    3.662  0.10092 25.7732 -------
                6 1    0.045  0.34762 56.5380 -------
                6 2    0.083  0.45178 78.3467 -------
                6 A    0.167  0.45178 78.3467 -------
                7 1    2.065  0.16006 250.7189 -------
                7 2    0.916  0.14562 173.4268 -------
                7 A    1.832  0.14562 173.4268 -------
                8 1    0.229  0.87347 44.3484 -------
                8 2    0.745  1.44077 23.9641 -------
                8 A    1.490  1.44077 23.9641 -------
                9 1    0.373  4.36758 19.2244 -------
                9 2    4.613  1.79879 12.9673 -------
                9 A    9.226  1.79879 12.9673 -------
               10 1    0.179  0.17293 83.5540 -------
               10 2    1.039  0.07533 279.8212 -------
               10 A    2.078  0.07533 279.8212 -------
                All -1366.269  0.80589 26.9293 -------

Comments:
 The x is 1, 2, or 4 for mtDNA, haploid, or diploid data, respectively
There were 10 short chains (50 used trees out of sampled 100)
  and 3 long chains (100 used trees out of sampled 200)
  COMBINATION OF 2 MULTIPLE RUNS)




==============================================================================
Likelihood ratio tests
==============================================================================
Over all loci
Legend for the LRT tables
-------------------------------------------------------------------------------
Null-Hypothesis: your test model         | Log(likelihood) of test model
=same=                                   | Log(likelihood) of full model
full model (the model under which the    | Likelihood ratio test value
genealogies were sampled)                | Degrees of freedom of test
[Theta values are on the diagonal of the | Probability*
Migration matrix, migration rates are    | Probability**
specified as M]                          | Akaike's Information Criterion***
                                         | Number of parameters used
-------------------------------------------------------------------------------
  *) Probability under the assumption that parameters have range -Inf to Inf
 **) Probability under the assumption that parameters have range 0 to Inf
***) AIC: the smaller the value the better the model
          [the full model has AIC=2740.537132, num(param)=4]

-------------------------------------------------------------------------------
H0: 0.7539 24.371 24.371 0.7539                    | LnL(test) = -1378.296196
 =  0.7019 21.813 26.929 0.8059                    | LnL(full) = -1366.268566
[ m, m, m, m,]                                     | LRT       = 24.055261
                                                   | df        = 4
                                                   | Prob      = 0.000078
                                                   | Probc     = 0.000078
                                                   | AIC       = 2760.592392
                                                   | num(param)= 2
-------------------------------------------------------------------------------
