Abstract Background Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance/progeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained. Commonly, the provenance effect is fitted as a fixed term or can be implemented as a contemporary group in the pedigree. Results The use of a provenance effect, either as a fixed term or as the same contemporary groups in both maternal and paternal sides of the pedigree, resulted in fairly similar precision of genetic parameters in our case. However, when we developed a phantom contemporary group for the paternal side of the pedigree that considered a different genetic quality of pollen compared with the maternal contribution from trees in the local environment, the model fit and accuracy of breeding values increased. Conclusion Consideration of the mating dynamics and the vector of gene flow are important factors in modelling contemporary genetic groups, particularly when implementing pedigrees within a mixed model framework to obtain unbiased estimates of genetic parameters. This approach is especially important in traits involved in local adaptation.
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