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Effective population size as a parameter closely correlating with the genetic and genotypic diversity of the seed orchard output is an important indicator of seed orchard functioning. It is determined by the variation of male and female gametic contributions of parental genotypes (including those outside the seed orchard), influenced by the variation in male and female gamete production, reproductive phenology, pollen dispersal within seed orchard and other factors. We assessed male and female fecundity, as well as temporal course of male and female flowering in two seed orchards of Pinus nigra Arnold and Fraxinus excelsior L. / F. angustifolia Vahl. in Slovakia. In both cases, male and female gametic contributions of plus-tree clones were modeled on the basis of fecundity and flowering phenology, and were used to calculate status number as an estimator of effective population size. In the seed orchard of Pinus nigra, marker-aided verification of clonal fidelity revealed unexpectedly high proportion of misplaced ramets (29.9%) and alien genotypes (44.4%). Monitoring of reproductive processes in 2002 and 2003 showed high variation in both male and female fecundity, and pollen shedding preceding female receptivity in Pinus nigra. All these factors contributed to a very low relative status effective number, representing 8.6% to 38.6% of the population census (depending from the management option in relation to misplaced and alien genotypes). In the mixed seed orchard of Fraxinus excelsior and F. angustifolia, the proportion of misplaced and alien genotypes was much lower (22.4% and 12.3%, respectively). However, a high fecundity variation and protogyny resulted in a low relative status number (18.8% to 29.5% of the census number of clones) also in this seed orchard. Practical implications of these findings are shortly discussed and practical management options are proposed. [ABSTRACT FROM AUTHOR]