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. 2010 Jul 28;11:401. doi: 10.1186/1471-2105-11-401

Table 1.

Model checking for introduction scenarios 1, 2 and 3.

Probability (tsimulated<tobserved)

Test quantity (t) Observed value Scenario 1 Scenario 2 Scenario 3
Test quantities NAL_S 13.6000 0.7275 0.2871 0.6235
corresponding NAL_1 3.4000 0.7542 0.9865 (*) 0.4252
to thesummary NAL_2 3.6500 0.6455 0.4102 0.4761
statistics used HET_S 0.8429 0.5621 0.2471 0.4488
to discriminate HET_1 0.5151 0.4938 0.9890 (*) 0.4339
among HET_2 0.5725 0.9125 0.9188 0.8221
scenarios and MGW_S 0.8242 0.3593 0.7656 0.5230
compute MGW_1 0.4072 0.3782 0.6713 0.4524
parameter MGW_2 0.4834 0.6117 0.8499 0.7297
posterior FST_S_1 0.2170 0.7882 0.0371 (*) 0.8105
distributions FST_S_2 0.2050 0.6180 0.4606 0.6052
FST_2_3 0.1761 0.0001 (***) 0.9580 (*) 0.6289

Test quantities VAR_S 21.7561 0.7476 0.2538 0.6209
corresponding VAR_1 9.3385 0.4861 0.3561 0.3598
to summary VAR_2 9.5277 0.5232 0.1792 0.3748
statistics NOT LIK_1_S 38.5648 0.7867 0.4503 0.7240
used to LIK_1_2 31.7504 0.0001 (***) 1.0000 (***) 0.7162
discriminate LIK_2_1 32.1075 0.0001 (***) 0.9850 (*) 0.7836
among H2P_S_1 0.7734 0.6563 0.8411 0.6115
scenarios and H2P_S_2 0.7993 0.9231 0.8239 0.8664
compute H2P_1_2 0.6020 0.0315 (*) 0.9975 (**) 0.7193
parameter DAS_S_1 0.1329 0.2298 0.4582 0.2639
posterior DAS_S_2 0.1099 0.0559 0.1681 0.0816
distributions DAS_1_2 0.3402 1.0000 (***) 0.0001 (***) 0.2529

Evolutionary scenarios 1, 2 and 3 are detailed in Figure 3. The single "pseudo-observed" test data set analyzed here was simulated under scenario 3. The probability (tsimulated <tobserved) given for each test quantities (t) was computed from 10,000 data sets simulated from the posterior distributions of parameters obtained under a given scenario. Corresponding tail-area probabilities, or p-values, of the test quantities (t) can be easily obtained as Prob(tsimulated <tobserved) and 1.0 - Prob (tsimulated <tobserved) for Prob (tsimulated <tobserved) ≤ 0.5 and > 0.5, respectively [22]. The test quantities correspond to the summary statistics used to discriminate among scenarios and compute the posterior distributions of parameters or to other statistics. NAL_i = mean number of alleles in population i, HET_i = mean expected heterozygosity in population i [38], MGW_i = mean ratio of the number of alleles over the range of allele sizes [54], FST_i_j = FST value between populations i and j [39], VAR_i = mean allelic size variance in population i, LIK_i_j = mean individual assignment likelihoods of population i assigned to population j [22], H2P_i_j = mean expected heterozygosity pooling samples from populations i and j, DAS_i_j = shared allele distance between populations i and j [55]. Populations i and j correspond to populations S, 1 or 2 in Figure 3. *, **, *** = tail-area probability < 0.05, < 0.01 and < 0.001, respectively. Significant tail-area probabilities after applying the false discovery rate correction method of Benjamini and Hochberg [43] are given in bold italic characters.