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Numerous hypotheses have been proposed to explain the shape of occupancy frequency distributions (distributions of the numbers of species occupying different numbers of areas). Artefactual effects include sampling characteristics, whereas biological mechanisms include organismal, niche-based and meta-population models. To date, there has been little testing of these models. In addition, although empirically derived occupancy distributions encompass an array of taxa and spatial scales, comparisons between them are often not possible because of differences in sampling protocol and method of construction. In this paper, the effects of sampling protocol (grain, sample number, extent, sampling coverage and intensity) on the shape of occupancy distributions are examined, and approaches for minimising artefactual effects recommended. Evidence for proposed biological determinants of the shape of occupancy distributions is then examined. Good support exists for some mechanisms (habitat and environmental heterogeneity), little for others (dispersal ability), while some hypotheses remain untested (landscape productivity, position in geographic range, range size frequency distributions), or are unlikely to be useful explanations for the shape of occupancy distributions 'species specificity and adaptation to habitat, extinction-colonization dynamics). The presence of a core (class containing species with the highest occupancy) mode in occupancy distributions is most likely to be associated with larger sample units, and small homogenous sampling areas positioned well within and towards the range centers of a sufficient proportion of the species in the assemblage. Satellite (class with species with the lowest occupancy) modes are associated with sampling large, heterogeneous areas that incorporate a large proportion of the assemblage range. However, satellite modes commonly also occur in the presence of a core mode, and rare species effects are likely to contribute to the presence of a satellite mode at most sampling scales. In most proposed hypotheses, spatial scale is an important determinant of the shape of the observed occupancy distribution. Because the attributes of the mechanisms associated with these hypotheses change with spatial scale, their predictions for the shape of occupancy distributions also change. To understand occupancy distributions and the mechanisms underlying them, a synthesis of pattern documentation and model testing across scales is thus needed. The development of null models, comparisons of occupancy distributions across spatial scales and taxa, documentation of the movement of individual species between occupancy classes with changes in spatial scale, as well as further testing of biological mechanisms are all necessary for an improved understanding of the distribution of species and assemblages within their geographic ranges.