The Bayesian optimization algorithm (BOA) uses Bayesian networks to learn linkages between the decision variables of an optimization problem. This paper studies the influence of different selection and replacement methods on the accuracy of linkage learning in BOA. Results on concatenated m-k deceptive trap functions show that the model accuracy depends on a large extent on the choice of selection method and to a lesser extent on the replacement strategy used. Specifically, it is shown that linkage learning in BOA is more accurate with truncation selection than with tournament selection. The choice of replacement strategy is important when tournament selection is used, but it is not relevant when using truncation selection. On the other hand, if performance is our main concern, tournament selection and restricted tournament replacement should be preferred. These results aim to provide practitioners with useful information about the best way to tune BOA with respect to structural model accuracy and overall performance.