Table 3.
Posterior mean estimates for overall mean (μ), residual variance (σ2e), the number of QTL (N QTL), the QTL variance (σ2QTL), and heritability (h 2) for the pilot dataset
| Variable | μ | σ2e | N QTL | σ2QTL | h 2 | 2ln (Bayes factor)a | |||
|---|---|---|---|---|---|---|---|---|---|
| 1/0 | 2/1 | 3/2 | 4/3 | ||||||
| Simulation | 0 | 16 | 3 | 3 | 0.16 | ||||
| Modelb | |||||||||
| Prior(N QTL) = 1 | |||||||||
| UNR | 1.1 | 16.6 | 3.3 | 3.9 | 0.19 | na | 26 | 3.7 | 1.7 |
| TIBD | −0.1 | 16.2 | 3.6 | 3.5 | 0.18 | na | na | 29 | 1.7 |
| LAAM | 0.0 | 16.2 | 3.7 | 3.6 | 0.18 | na | na | 28 | 2.3 |
| Prior(N QTL) = 3 | |||||||||
| UNR | 0.9 | 16.5 | 4.8 | 4.2 | 0.20 | na | 9.5 | 3.1 | 1.5 |
| TIBD | 0.0 | 16.1 | 4.6 | 4.0 | 0.20 | na | na | 24 | 1.6 |
| LAAM | 0.1 | 16.1 | 4.9 | 4.4 | 0.21 | na | na | 24 | 2.2 |
| Prior(N QTL) = 5 | |||||||||
| UNR | 0.8 | 16.4 | 6.1 | 4.3 | 0.21 | na | na | 4.1 | 1.6 |
| TIBD | 0.1 | 16.1 | 5.7 | 4.5 | 0.22 | na | na | 21 | 2.0 |
| LAAM | 0.0 | 16.1 | 5.7 | 4.7 | 0.23 | na | na | 21 | 1.6 |
For model selection estimates for twice the natural log of Bayes Factors are given and three values (1, 3 and 5) for the prior mean of number of QTL are used
na not available due to insufficient number of posterior samples from one or both models to estimate Bayes Factor accurately
a2ln(Bayes Factor) : Bayesian statistic representing the evidence for favoring model Mq over Mq−1 where q represents the number of QTL in the model (q = 1, 2, 3, 4)
bModel abbreviations: UNR model with unrelated parents (without Ancestral Classes), TIBD model with ancestral allele classes and Threshold sampling approach, LAAM model with ancestral allele classes and Latent Ancestor Allele approach