1 ============================================= 2 Example: Microsatellite data set 3 ============================================= 4 MIGRATION RATE AND POPULATION SIZE ESTIMATION 5 using Markov Chain Monte Carlo simulation 6 ============================================= 7 Version 3.6.6 8 9 Program started at Tue Jan 20 15:37:10 2015 10 finished at Tue Jan 20 15:37:31 2015 11 12 13 14Options in use: 15--------------- 16 17Analysis strategy is BAYESIAN INFERENCE 18 19Proposal distribution: 20Parameter group Proposal type 21----------------------- ------------------- 22Population size (Theta) Slice sampling 23Migration rate (M) Slice sampling 24 25 26Prior distribution (Proposal-delta will be tuned to acceptance frequence 0.440000): 27Parameter group Prior type Minimum Mean(*) Maximum Delta 28----------------------- ------------ ---------- ---------- ---------- ---------- 29Population size (Theta) Uniform 0.000000 10.000000 20.000000 2.000000 30Migration rate (M) Uniform 0.000000 10.000000 20.000000 2.000000 31 32 33 34Datatype: Microsatellite data [Brownian motion] 35Missing data is not included 36 37Inheritance scalers in use for Thetas (specified scalars=1) 381.00 1.00 1.00 1.00 1.00 391.00 1.00 1.00 1.00 1.00 40 41[Each Theta uses the (true) ineritance scalar of the first locus as a reference] 42 43 44Pseudo-random number generator: Mersenne-Twister 45Random number seed (from parmfile) 310705631 46 47Start parameters: 48 First genealogy was started using a UPGMA-tree 49 Theta values were generated RANDOM start value from U(min,max) 50 M values were generated from the FST-calculation 51 52Migration model: Arbitrary migration matrix model 53[Legend: m = average (average over a group of Thetas or M] 54[s = symmetric M, S = symmetric 4Nm, 55 0 = zero, and not estimated, ] 56[* = free to vary, Thetas are on diagonal] 57population * 0 58population * * 59 60 61 62Mutation rate is constant for all loci 63 64Markov chain settings: 65 Long chains (long-chains): 1 66 Steps sampled (inc*samples*rep): 10000 67 Steps recorded (sample*rep): 10000 68 Combining over replicates: 2 69 Static heating scheme 70 4 chains with temperatures 71 1.00, 1.50, 3.00,1000000.00 72 Swapping interval is 1 73 Burn-in per replicate (samples*inc): 10000 74 75Print options: 76 Data file: infile.msat 77 Output file (ASCII text): outfile-bayes 78 Output file (PDF): outfile-bayes.pdf 79 Posterior distribution: bayesfile 80 Print data: No 81 Print genealogies: No 82 Plot data: No 83 84Summary of data: 85Title: Example: Microsatellite data set 86Data file: infile.msat 87Datatype: Microsatellite data 88[Data was used as repeat-length information] 89Number of loci: 10 90 91Population Locus Gene copies 92 --------------- 93 data (missing) 94---------------------------------------------------- 95 1 population_number___0 1 50 (0) 96 1 2 50 (0) 97 1 3 50 (0) 98 1 4 50 (0) 99 1 5 50 (0) 100 1 6 50 (0) 101 1 7 50 (0) 102 1 8 50 (0) 103 1 9 50 (0) 104 1 10 50 (0) 105 2 population_number___1 1 42 (0) 106 2 2 42 (0) 107 2 3 42 (0) 108 2 4 42 (0) 109 2 5 42 (0) 110 2 6 42 (0) 111 2 7 42 (0) 112 2 8 42 (0) 113 2 9 42 (0) 114 2 10 42 (0) 115 Total of all populations 1 92 (0) 116 2 92 (0) 117 3 92 (0) 118 4 92 (0) 119 5 92 (0) 120 6 92 (0) 121 7 92 (0) 122 8 92 (0) 123 9 92 (0) 124 10 92 (0) 125 126Allele frequency spectra 127======================== 128 129Locus 1 130Allele Pop1 Pop2 All 131-------------------------------- 13216 0.220 0.167 0.196 13319 0.040 0.071 0.054 13418 0.060 0.119 0.087 13515 0.220 0.024 0.130 13621 0.020 0.167 0.087 13723 0.020 0.119 0.065 13817 0.280 0.095 0.196 13922 0.060 0.119 0.087 14025 0.060 0.024 0.043 14124 0.020 - 0.011 14226 - 0.024 0.011 14327 - 0.048 0.022 14429 - 0.024 0.011 145Alleles 10 12 13 146Samplesize 50 42 92 147H_exp 0.811 0.883 0.874 148 149Locus 2 150Allele Pop1 Pop2 All 151-------------------------------- 15216 0.520 0.571 0.543 15319 0.040 - 0.022 15418 0.220 0.119 0.174 15517 0.160 0.167 0.163 15615 0.020 - 0.011 15721 0.020 0.071 0.043 15820 0.020 0.024 0.022 15922 - 0.048 0.022 160Alleles 7 6 8 161Samplesize 50 42 92 162H_exp 0.653 0.624 0.644 163 164Locus 3 165Allele Pop1 Pop2 All 166-------------------------------- 16719 0.240 0.262 0.250 16820 0.280 0.476 0.370 16918 0.080 0.095 0.087 17021 0.280 0.119 0.207 17122 0.120 0.048 0.087 172Alleles 5 5 5 173Samplesize 50 42 92 174H_exp 0.765 0.679 0.743 175 176Locus 4 177Allele Pop1 Pop2 All 178-------------------------------- 17916 0.080 0.071 0.076 18024 0.180 0.024 0.109 18115 0.020 0.048 0.033 18225 0.160 0.167 0.163 18314 0.020 0.048 0.033 18419 0.100 0.143 0.120 18512 0.060 - 0.033 18620 0.080 0.190 0.130 18723 0.060 0.119 0.087 18828 0.020 - 0.011 18922 0.060 0.024 0.043 19021 0.160 0.119 0.141 19113 - 0.024 0.011 19226 - 0.024 0.011 193Alleles 12 12 14 194Samplesize 50 42 92 195H_exp 0.882 0.875 0.892 196 197Locus 5 198Allele Pop1 Pop2 All 199-------------------------------- 20020 0.400 0.524 0.457 20121 0.420 0.357 0.391 20219 0.180 0.119 0.152 203Alleles 3 3 3 204Samplesize 50 42 92 205H_exp 0.631 0.584 0.615 206 207Locus 6 208Allele Pop1 Pop2 All 209-------------------------------- 21019 0.060 - 0.033 21120 0.100 0.024 0.065 21218 0.300 0.214 0.261 21322 0.200 0.119 0.163 21421 0.120 0.476 0.283 21516 0.060 - 0.033 21624 0.160 0.048 0.109 21717 - 0.119 0.054 218Alleles 7 6 8 219Samplesize 50 42 92 220H_exp 0.813 0.696 0.804 221 222Locus 7 223Allele Pop1 Pop2 All 224-------------------------------- 22523 0.040 0.238 0.130 22620 0.660 0.143 0.424 22722 0.180 0.190 0.185 22821 0.100 0.333 0.207 22919 0.020 0.095 0.054 230Alleles 5 5 5 231Samplesize 50 42 92 232H_exp 0.520 0.766 0.724 233 234Locus 8 235Allele Pop1 Pop2 All 236-------------------------------- 23719 0.520 0.524 0.522 23817 0.040 0.048 0.043 23918 0.100 0.071 0.087 24020 0.140 0.190 0.163 24116 0.080 - 0.043 24222 0.100 0.048 0.076 24315 0.020 0.048 0.033 24423 - 0.071 0.033 245Alleles 7 7 8 246Samplesize 50 42 92 247H_exp 0.682 0.672 0.682 248 249Locus 9 250Allele Pop1 Pop2 All 251-------------------------------- 25224 0.080 0.024 0.054 25319 0.300 0.429 0.359 25420 0.300 0.167 0.239 25523 0.180 0.143 0.163 25622 0.080 0.024 0.054 25718 0.020 0.071 0.043 25821 0.040 0.095 0.065 25925 - 0.048 0.022 260Alleles 7 8 8 261Samplesize 50 42 92 262H_exp 0.773 0.751 0.775 263 264Locus 10 265Allele Pop1 Pop2 All 266-------------------------------- 26722 0.100 0.214 0.152 26820 0.440 0.214 0.337 26923 0.080 0.167 0.120 27024 0.020 - 0.011 27119 0.160 0.167 0.163 27221 0.060 0.048 0.054 27318 0.080 - 0.043 27415 0.020 0.071 0.043 27517 0.040 0.048 0.043 27625 - 0.071 0.033 277Alleles 9 8 10 278Samplesize 50 42 92 279H_exp 0.752 0.838 0.813 280 281Average expected heterozygosity 282Pop1 Pop2 All 283--------------------- 2840.728 0.737 0.757 285 286 287 288 289Bayesian estimates 290================== 291 292Locus Parameter 2.5% 25.0% mode 75.0% 97.5% median mean 293----------------------------------------------------------------------------------- 294 1 Theta_1 1.08000 1.36000 1.86000 2.36000 2.76000 3.02000 3.71518 295 1 Theta_2 0.68000 0.96000 1.46000 2.60000 6.52000 2.46000 3.00004 296 1 M_1->2 2.08 3.12 4.22 4.84 7.12 4.34 4.44 297 2 Theta_1 3.80000 4.76000 5.82000 6.56000 9.12000 6.06000 6.23930 298 2 Theta_2 1.92000 2.72000 3.74000 6.76000 15.64000 6.70000 7.90481 299 2 M_1->2 2.52 4.64 5.10 6.96 9.28 5.90 5.92 300 3 Theta_1 4.16000 6.68000 7.90000 9.24000 11.08000 7.90000 7.84903 301 3 Theta_2 10.36000 14.20000 15.86000 19.36000 20.00000 13.98000 12.94539 302 3 M_1->2 0.48 0.72 1.30 1.96 4.32 1.82 2.13 303 4 Theta_1 1.60000 1.96000 2.54000 3.08000 3.64000 15.62000 10.55422 304 4 Theta_2 1.60000 1.84000 3.10000 4.32000 5.12000 6.10000 9.17295 305 4 M_1->2 1.04 1.32 1.98 2.56 6.88 3.30 3.62 306 5 Theta_1 2.24000 2.52000 3.22000 4.12000 8.20000 4.22000 4.85088 307 5 Theta_2 2.48000 9.04000 10.14000 12.80000 15.36000 10.42000 10.58751 308 5 M_1->2 5.80 7.96 8.30 8.72 18.08 11.46 11.75 309 6 Theta_1 2.08000 2.68000 3.14000 3.80000 9.96000 4.78000 5.25820 310 6 Theta_2 0.00000 0.08000 0.54000 0.92000 1.08000 1.38000 1.98602 311 6 M_1->2 1.56 2.04 3.18 5.72 14.80 5.54 7.50 312 7 Theta_1 1.48000 2.20000 2.78000 3.20000 4.56000 2.90000 2.95964 313 7 Theta_2 2.24000 3.60000 5.82000 6.72000 13.44000 6.98000 7.44128 314 7 M_1->2 0.08 0.48 0.74 1.00 1.96 0.86 0.91 315 8 Theta_1 3.12000 4.16000 5.14000 7.04000 8.16000 8.46000 9.63487 316 8 Theta_2 0.72000 0.92000 1.66000 2.60000 3.16000 3.46000 6.61854 317 8 M_1->2 0.44 0.64 1.38 2.20 7.04 2.46 3.36 318 9 Theta_1 3.84000 4.16000 5.58000 6.72000 12.24000 6.86000 7.52431 319 9 Theta_2 1.64000 2.12000 3.02000 4.92000 13.16000 6.30000 6.80907 320 9 M_1->2 1.32 1.92 2.30 3.48 5.80 3.14 3.30 321 10 Theta_1 2.56000 2.80000 3.82000 5.16000 5.60000 7.42000 8.05189 322 10 Theta_2 5.24000 6.64000 7.38000 9.76000 15.16000 9.34000 9.72418 323 10 M_1->2 0.00 0.32 0.58 0.88 1.56 0.74 0.75 324 All Theta_1 4.16000 4.60000 4.90000 5.20000 5.88000 5.02000 5.11582 325 All Theta_2 1.76000 2.72000 3.02000 3.28000 4.24000 3.02000 3.04385 326 All M_1->2 2.44 2.84 3.18 3.48 3.76 3.14 3.22 327----------------------------------------------------------------------------------- 328 329 330 331Log-Probability of the data given the model (marginal likelihood = log(P(D|thisModel)) 332-------------------------------------------------------------------- 333[Use this value for Bayes factor calculations: 334BF = Exp[log(P(D|thisModel) - log(P(D|otherModel)] 335shows the support for thisModel] 336 337 338 339Locus Raw Thermodynamic score(1a) Bezier approximated score(1b) Harmonic mean(2) 340------------------------------------------------------------------------------------------ 341 1 -16501.65 -2750.99 -62.75 342 2 -901.94 -231.19 -65.87 343 3 -443.23 -172.83 -98.74 344 4 -5182.96 -949.44 -113.33 345 5 -658.82 -180.93 -54.92 346 6 -2602.87 -513.16 -53.67 347 7 -340.80 -144.57 -60.91 348 8 -3309.11 -634.56 -102.97 349 9 -973.06 -261.24 -82.72 350 10 -1895.79 -426.97 -101.19 351--------------------------------------------------------------------------------------- 352 All -32800.06 -6255.75 -786.94 353[Scaling factor = 10.139731] 354MCMC run characteristics 355======================== 356 357 358 359 360Acceptance ratios for all parameters and the genealogies 361--------------------------------------------------------------------- 362 363Parameter Accepted changes Ratio 364Theta_1 16446/16446 1.00000 365Theta_2 16684/16684 1.00000 366M_1->2 16656/16656 1.00000 367Genealogies 15970/50214 0.31804 368Autocorrelation and Effective sample size 369------------------------------------------------------------------- 370 371 Parameter Autocorrelation(*) Effective Sample size 372 --------- --------------- --------------------- 373 Theta_1 0.93347 3458.04 374 Theta_2 0.91976 4198.60 375 M_1->2 0.91389 4517.46 376 Ln[Prob(D|P)] 0.99554 223.86 377 (*) averaged over loci. 378 379 380POTENTIAL PROBLEMS 381------------------------------------------------------------------------------------------ 382This section reports potential problems with your run, but such reporting is often not 383very accurate. Whith many parameters in a multilocus analysis, it is very common that 384some parameters for some loci will not be very informative, triggering suggestions (for 385example to increase the prior range) that are not sensible. This suggestion tool will 386improve with time, therefore do not blindly follow its suggestions. If some parameters 387are flagged, inspect the tables carefully and judge wether an action is required. For 388example, if you run a Bayesian inference with sequence data, for macroscopic species 389there is rarely the need to increase the prior for Theta beyond 0.1; but if you use 390microsatellites it is rather common that your prior distribution for Theta should have a 391range from 0.0 to 100 or more. With many populations (>3) it is also very common that 392some migration routes are estimated poorly because the data contains little or no 393information for that route. Increasing the range will not help in such situations, 394reducing number of parameters may help in such situations. 395------------------------------------------------------------------------------------------ 396Param 2 (Locus 3): Upper prior boundary seems too low! 397------------------------------------------------------------------------------------------ 398