============================================= AUTO ============================================= MIGRATION RATE AND POPULATION SIZE ESTIMATION using Markov Chain Monte Carlo simulation ============================================= Version 2.1.2 Program started at Mon Jan 23 16:35:51 2006 finished at Mon Jan 23 16:37:23 2006 Options in use: --------------- Datatype: Microsatellite data [Stepwise mutation] Missing data is not included Pseudo-random number generator: Least Congruental Generator Random number seed (with internal timer) 1138052151 Start parameters: Theta values were generated from the 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 Analysis strategy is Maximum likelihood 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: --------------- 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) ============================================================================== MCMC estimates ============================================================================== Population [x] Loc. Ln(L) Theta M [m/mu] [+=receiving population] [xNe mu] 1,+ 2,+ -------------- ---- -------- -------- ---------------------------------------- 1: population 1 1 0.165 0.36286 ------- 10.3043 1 2 0.024 0.40508 ------- 11.4465 1 A 0.307 0.37420 ------- 10.6309 2 1 0.193 0.15271 ------- 42.8912 2 2 0.022 0.20715 ------- 51.2639 2 A 0.031 0.20618 ------- 51.1602 3 1 0.060 0.52345 ------- 17.7521 3 2 1.120 0.61631 ------- 34.6869 3 A 2.240 0.61631 ------- 34.6869 4 1 0.187 0.43508 ------- 25.5646 4 2 0.202 0.52069 ------- 32.2090 4 A 0.356 0.43733 ------- 25.7672 5 1 1.052 0.18815 ------- 11.1966 5 2 2.175 0.18293 ------- 7.7804 5 A 2.998 0.18430 ------- 7.6365 6 1 0.351 1.05814 ------- 6.0660 6 2 0.281 0.72671 ------- 6.6431 6 A 0.488 0.73026 ------- 6.6379 7 1 0.665 0.08094 ------- 63.3447 7 2 1.603 0.06636 ------- 41.5876 7 A 3.189 0.06637 ------- 41.5931 8 1 1.414 0.35519 ------- 10.9241 8 2 0.946 0.47240 ------- 10.8024 8 A 2.827 0.35612 ------- 10.9168 9 1 0.256 0.75454 ------- 11.6942 9 2 0.118 0.55183 ------- 9.2043 9 A 0.209 0.55402 ------- 9.2408 10 1 0.259 0.49595 ------- 8.9629 10 2 0.982 0.47786 ------- 10.6164 10 A 1.755 0.47834 ------- 10.5950 All -226.499 0.39957 ------- 13.6856 2: population 1 1 0.165 0.39744 21.7652 ------- 1 2 0.024 0.40250 28.0609 ------- 1 A 0.307 0.39878 23.3023 ------- 2 1 0.193 0.13297 61.0445 ------- 2 2 0.022 0.10214 54.9198 ------- 2 A 0.031 0.10245 54.9917 ------- 3 1 0.060 0.49225 22.9766 ------- 3 2 1.120 0.52254 17.6252 ------- 3 A 2.240 0.52254 17.6252 ------- 4 1 0.187 0.46855 8.1975 ------- 4 2 0.202 0.58856 8.7721 ------- 4 A 0.356 0.47158 8.2252 ------- 5 1 1.052 0.23072 21.4420 ------- 5 2 2.175 0.17412 18.0026 ------- 5 A 2.998 0.17699 18.2025 ------- 6 1 0.351 0.31770 20.9691 ------- 6 2 0.281 0.36363 19.3947 ------- 6 A 0.488 0.36261 19.4339 ------- 7 1 0.665 0.10222 22.9821 ------- 7 2 1.603 0.09143 47.3604 ------- 7 A 3.189 0.09145 47.3447 ------- 8 1 1.414 0.56634 16.3066 ------- 8 2 0.946 0.48343 22.1595 ------- 8 A 2.827 0.56627 16.3172 ------- 9 1 0.256 0.58823 17.8494 ------- 9 2 0.118 0.53848 16.4694 ------- 9 A 0.209 0.53918 16.4954 ------- 10 1 0.259 0.30728 50.3781 ------- 10 2 0.982 0.43307 40.5789 ------- 10 A 1.755 0.43144 40.6637 ------- All -226.499 0.35147 21.4359 ------- 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) =============================================================================== Profile likelihood tables [Summary is at the end of the file] =============================================================================== Profile likelihood for parameter Theta_1 Parameters are evaluated at percentiles using bisection method (slow, but exact). ------------------------------------------------------------------------------- Per. Ln(L) Theta_1 *Theta_1* Theta_2 M_21 M_12 =------------------------------------------------------------------------------- 0.005 -229.817 0.35259 0.352590 0.354383 13.652625 20.911559 0.025 -228.419 0.363533 0.363533 0.353462 13.657752 21.055190 0.050 -227.851 0.369235 0.369235 0.352992 13.660816 21.134618 0.250 -226.725 0.387012 0.387012 0.351890 13.673894 21.340729 MLE -226.499 0.399574 0.399574 0.351470 13.685637 21.435893 0.750 -226.726 0.412453 0.412453 0.351230 13.698760 21.503559 0.950 -227.851 0.43174 0.431740 0.351040 13.719451 21.574115 0.975 -228.419 0.438211 0.438211 0.350997 13.726587 21.592937 0.995 -229.816 0.451191 0.451191 0.350924 13.741207 21.625982 ==------------------------------------------------------------------------------ Profile likelihood for parameter Theta_2 Parameters are evaluated at percentiles using bisection method (slow, but exact). ------------------------------------------------------------------------------- Per. Ln(L) Theta_2 Theta_1 *Theta_2* M_21 M_12 =------------------------------------------------------------------------------- 0.005 -229.817 0.307804 0.400621 0.307804 13.726401 21.469599 0.025 -228.419 0.31758 0.400390 0.317580 13.715639 21.463637 0.050 -227.852 0.322727 0.400269 0.322727 13.710392 21.460157 0.250 -226.727 0.339288 0.399877 0.339288 13.695307 21.447193 MLE -226.499 0.35147 0.399574 0.351470 13.685637 21.435893 0.750 -226.727 0.364228 0.399228 0.364228 13.676342 21.422503 0.950 -227.851 0.383648 0.398613 0.383648 13.662694 21.399398 0.975 -228.419 0.390258 0.398371 0.390258 13.657885 21.390910 0.995 -229.816 0.403629 0.397812 0.403629 13.647372 21.373056 ==------------------------------------------------------------------------------ Profile likelihood for parameter M_21 Parameters are evaluated at percentiles using bisection method (slow, but exact). ------------------------------------------------------------------------------- Per. Ln(L) M_21 Theta_1 Theta_2 * M_21* M_12 =------------------------------------------------------------------------------- 0.005 -229.816 11.8542 0.398347 0.352313 11.854231 21.373911 0.025 -228.419 12.2763 0.398648 0.352113 12.276313 21.387205 0.050 -227.851 12.4958 0.398798 0.352012 12.495831 21.394515 0.250 -226.727 13.1883 0.399256 0.351698 13.188335 21.418491 MLE -226.499 13.6856 0.399574 0.351470 13.685637 21.435893 0.750 -226.726 14.1943 0.399891 0.351232 14.194336 21.453299 0.950 -227.852 14.95 0.400345 0.350868 14.949976 21.477653 0.975 -228.420 15.2008 0.400490 0.350746 15.200772 21.485215 0.995 -229.817 15.6993 0.400770 0.350503 15.699263 21.499350 ==------------------------------------------------------------------------------ Profile likelihood for parameter M_12 Parameters are evaluated at percentiles using bisection method (slow, but exact). ------------------------------------------------------------------------------- Per. Ln(L) M_12 Theta_1 Theta_2 M_21 * M_12* =------------------------------------------------------------------------------- 0.005 -229.817 18.5301 0.392586 0.352983 13.652691 18.530063 0.025 -228.420 19.1983 0.394537 0.352508 13.658792 19.198347 0.050 -227.852 19.5469 0.395513 0.352279 13.662338 19.546871 0.250 -226.727 20.6463 0.398146 0.351717 13.675137 20.646341 MLE -226.499 21.4359 0.399574 0.351470 13.685637 21.435893 0.750 -226.726 22.2426 0.400704 0.351321 13.697057 22.242592 0.950 -227.853 23.436 0.401940 0.351214 13.713946 23.436038 0.975 -228.420 23.8314 0.402262 0.351194 13.719225 23.831389 0.995 -229.817 24.6154 0.402798 0.351165 13.728847 24.615398 ==------------------------------------------------------------------------------ =============================================================================== Summary of profile likelihood percentiles of all parameters =============================================================================== Parameter Lower percentiles -------------------------------------------------------------------- 0.005 0.025 0.050 0.250 MLE -------------------------------------------------------------------------------- Theta_1 0.352590 0.363533 0.369235 0.387012 0.399574 Theta_2 0.307804 0.317580 0.322727 0.339288 0.351470 M_21 11.854231 12.276313 12.495831 13.188335 13.685637 M_12 18.530063 19.198347 19.546871 20.646341 21.435893 Parameter Upper percentiles -------------------------------------------------------------------- MLE 0.750 0.950 0.975 0.995 -------------------------------------------------------------------------------- Theta_1 0.399574 0.412453 0.431740 0.438211 0.451191 Theta_2 0.351470 0.364228 0.383648 0.390258 0.403629 M_21 13.685637 14.194336 14.949976 15.200772 15.699263 M_12 21.435893 22.242592 23.436038 23.831389 24.615398 --------------------------------------------------------------------------------