1 ============================================= 2 Example: Microsatellite data set 3 ============================================= 4 MIGRATION RATE AND POPULATION SIZE ESTIMATION 5 using Markov Chain Monte Carlo simulation 6 ============================================= 7 Version debug 3.1.2 8 9 Program started at Sun Feb 7 16:01:09 2010 10 finished at Sun Feb 7 16:01:14 2010 11 12 13 14Options in use: 15--------------- 16 17Analysis strategy is Bayesian 18 19Proposal distribution: 20Parameter group Proposal type 21----------------------- ------------------- 22Population size (Theta) Slice sampling 23 24 25Prior distribution: 26Parameter group Prior type Minimum Mean(*) Maximum Delta 27----------------------- ------------ ---------- ---------- ---------- ---------- 28Population size (Theta) Uniform 0.000000 10.000000 20.000000 2.000000 29 30 31 32Datatype: Microsatellite data [Brownian motion] 33Missing data is not included 34 35Pseudo-random number generator: Mersenne-Twister 36Random number seed (from parmfile) 310705631 37 38Start parameters: 39 First genealogy was started using a UPGMA-tree 40 Theta values were generated RANDOM start value from U(min,max) 41 M values were generated from the FST-calculation 42 43Migration model: 44 Migration matrix model with variable Theta 45 46Mutation rate is constant for all loci 47 48Markov chain settings: 49 Long chains (long-chains): 1 50 Steps sampled (inc*samples*rep): 640 51 Steps recorded (sample*rep): 320 52 Combining over replicates: 2 53 Static heating scheme 54 4 chains with temperatures 55 1.00, 1.50, 3.00,1000000.00 56 Swapping interval is 1 57 58Print options: 59 Data file: infile.msat 60 Output file (ASCII text): outfile-bayes 61 Output file (PDF): outfile-bayes.pdf 62 Posterior distribution: bayesfile 63 All values of Post.Dist: bayesallfile 64 Print data: No 65 Print genealogies: No 66 Plot data: No 67 68Summary of data: 69Title: Example: Microsatellite data set 70Data file: infile.msat 71Datatype: Microsatellite data 72Number of loci: 10 73 74Population Locus Gene copies 75 --------------- 76 data (missing) 77---------------------------------------------------- 78 1 population__number___0 1 50 (0) 79 1 2 50 (0) 80 1 3 50 (0) 81 1 4 50 (0) 82 1 5 50 (0) 83 1 6 50 (0) 84 1 7 50 (0) 85 1 8 50 (0) 86 1 9 50 (0) 87 1 10 50 (0) 88 1 population__number___1 1 42 (0) 89 1 2 42 (0) 90 1 3 42 (0) 91 1 4 42 (0) 92 1 5 42 (0) 93 1 6 42 (0) 94 1 7 42 (0) 95 1 8 42 (0) 96 1 9 42 (0) 97 1 10 42 (0) 98 Total of all populations 1 92 (0) 99 2 92 (0) 100 3 92 (0) 101 4 92 (0) 102 5 92 (0) 103 6 92 (0) 104 7 92 (0) 105 8 92 (0) 106 9 92 (0) 107 10 92 (0) 108 109Allele frequency spectra 110======================== 111 112Locus 1 113Allele Pop1 Pop1 All 114---------------------------- 115 16 0.196 0.196 0.196 116 19 0.054 0.054 0.054 117 18 0.087 0.087 0.087 118 15 0.130 0.130 0.130 119 21 0.087 0.087 0.087 120 23 0.065 0.065 0.065 121 17 0.196 0.196 0.196 122 22 0.087 0.087 0.087 123 25 0.043 0.043 0.043 124 24 0.011 0.011 0.011 125 26 0.011 0.011 0.011 126 27 0.022 0.022 0.022 127 29 0.011 0.011 0.011 128Total 13 129 130Locus 2 131Allele Pop1 Pop1 All 132---------------------------- 133 16 0.543 0.543 0.543 134 19 0.022 0.022 0.022 135 18 0.174 0.174 0.174 136 17 0.163 0.163 0.163 137 15 0.011 0.011 0.011 138 21 0.043 0.043 0.043 139 20 0.022 0.022 0.022 140 22 0.022 0.022 0.022 141Total 8 142 143Locus 3 144Allele Pop1 Pop1 All 145---------------------------- 146 19 0.250 0.250 0.250 147 20 0.370 0.370 0.370 148 18 0.087 0.087 0.087 149 21 0.207 0.207 0.207 150 22 0.087 0.087 0.087 151Total 5 152 153Locus 4 154Allele Pop1 Pop1 All 155---------------------------- 156 16 0.076 0.076 0.076 157 24 0.109 0.109 0.109 158 15 0.033 0.033 0.033 159 25 0.163 0.163 0.163 160 14 0.033 0.033 0.033 161 19 0.120 0.120 0.120 162 12 0.033 0.033 0.033 163 20 0.130 0.130 0.130 164 23 0.087 0.087 0.087 165 28 0.011 0.011 0.011 166 22 0.043 0.043 0.043 167 21 0.141 0.141 0.141 168 13 0.011 0.011 0.011 169 26 0.011 0.011 0.011 170Total 14 171 172Locus 5 173Allele Pop1 Pop1 All 174---------------------------- 175 20 0.457 0.457 0.457 176 21 0.391 0.391 0.391 177 19 0.152 0.152 0.152 178Total 3 179 180Locus 6 181Allele Pop1 Pop1 All 182---------------------------- 183 19 0.033 0.033 0.033 184 20 0.065 0.065 0.065 185 18 0.261 0.261 0.261 186 22 0.163 0.163 0.163 187 21 0.283 0.283 0.283 188 16 0.033 0.033 0.033 189 24 0.109 0.109 0.109 190 17 0.054 0.054 0.054 191Total 8 192 193Locus 7 194Allele Pop1 Pop1 All 195---------------------------- 196 23 0.130 0.130 0.130 197 20 0.424 0.424 0.424 198 22 0.185 0.185 0.185 199 21 0.207 0.207 0.207 200 19 0.054 0.054 0.054 201Total 5 202 203Locus 8 204Allele Pop1 Pop1 All 205---------------------------- 206 19 0.522 0.522 0.522 207 17 0.043 0.043 0.043 208 18 0.087 0.087 0.087 209 20 0.163 0.163 0.163 210 16 0.043 0.043 0.043 211 22 0.076 0.076 0.076 212 15 0.033 0.033 0.033 213 23 0.033 0.033 0.033 214Total 8 215 216Locus 9 217Allele Pop1 Pop1 All 218---------------------------- 219 24 0.054 0.054 0.054 220 19 0.359 0.359 0.359 221 20 0.239 0.239 0.239 222 23 0.163 0.163 0.163 223 22 0.054 0.054 0.054 224 18 0.043 0.043 0.043 225 21 0.065 0.065 0.065 226 25 0.022 0.022 0.022 227Total 8 228 229Locus 10 230Allele Pop1 Pop1 All 231---------------------------- 232 22 0.152 0.152 0.152 233 20 0.337 0.337 0.337 234 23 0.120 0.120 0.120 235 24 0.011 0.011 0.011 236 19 0.163 0.163 0.163 237 21 0.054 0.054 0.054 238 18 0.043 0.043 0.043 239 15 0.043 0.043 0.043 240 17 0.043 0.043 0.043 241 25 0.033 0.033 0.033 242Total 10 243 244 245 246 247Bayesian estimates 248================== 249 250Locus Parameter 2.5% 25.0% mode 75.0% 97.5% median mean 251----------------------------------------------------------------------------------- 252 1 Theta_1 0.24000 0.32000 0.70000 1.04000 1.12000 1.34000 3.33784 253 2 Theta_1 1.52000 1.72000 2.18000 2.60000 3.00000 5.26000 2.35192 254 3 Theta_1 6.56000 7.68000 8.14000 8.96000 10.20000 8.38000 2.78226 255 4 Theta_1 3.04000 3.28000 3.74000 4.36000 4.76000 5.30000 1.57289 256 5 Theta_1 4.52000 5.64000 5.82000 6.16000 7.64000 5.78000 1.16801 257 6 Theta_1 1.40000 1.60000 2.06000 2.52000 2.80000 3.14000 0.88223 258 7 Theta_1 4.64000 6.08000 7.10000 7.40000 8.60000 6.62000 0.93965 259 8 Theta_1 3.32000 3.76000 4.30000 4.68000 7.68000 5.50000 0.68725 260 9 Theta_1 0.64000 0.80000 1.14000 1.40000 1.56000 1.86000 0.34611 261 10 Theta_1 2.52000 3.00000 3.42000 3.84000 4.28000 5.02000 0.53229 262 All Theta_1 0.04000 0.36000 0.70000 1.08000 1.28000 0.98000 1.14876 263----------------------------------------------------------------------------------- 264 265 266 267Log-Probability of the data given the model (marginal likelihood = log(P(D|thisModel)) 268-------------------------------------------------------------------- 269[Use this value for Bayes factor calculations: 270BF = Exp[log(P(D|thisModel) - log(P(D|otherModel)] 271shows the support for thisModel] 272 273 274 275Locus Raw Thermodynamic score(1a) Bezier approximated score(1b) Harmonic mean(2) 276------------------------------------------------------------------------------------------ 277 1 -6453.33 -1219.74 -125.49 278 2 -1025.64 -326.95 -27.69 279 3 -821.61 -295.96 -48.28 280 4 -5064.36 -997.20 -46.07 281 5 -361.80 -211.03 -25.42 282 6 -3515.91 -734.52 -32.59 283 7 -982.78 -318.23 -31.55 284 8 -2296.16 -529.95 -30.84 285 9 -1340.39 -382.41 -25.65 286 10 -1240.75 -372.81 -33.12 287--------------------------------------------------------------------------------------- 288 All -23197.53 -5483.59 -426.69 289MCMC run characteristics 290======================== 291 292 293 294 295Acceptance ratios for all parameters and the genealogies 296--------------------------------------------------------------------- 297 298Parameter Accepted changes Ratio 299Theta_1 3153/3153 1.00000 300Genealogies 787/3287 0.23943 301Autocorrelation and Effective sample size 302------------------------------------------------------------------- 303 304 Parameter Autocorrelation(*) Effective Sample size 305 --------- --------------- --------------------- 306 Theta_1 0.31917 1748.74 307 Ln[Prob(D|P)] 0.90861 100.66 308 (*) averaged over loci. 309 310