AbstractAimsUnderstanding how historical and ecological (species interactions) factors affect species and shape community structure is a fundamental goal in ecology. However, these two components are difficult to disentangle and are often confounded. We address the influence of these factors in governing the structure of bird assemblages.LocationSoutheastern Australia.TaxonThe Meliphagoidea superfamily.MethodsBy adopting a semi‐experimental approach (i.e. high vs low interference competition), we examine the influence of a genus (Manorina) of honeyeater species that is well known for its hyper‐aggressiveness and strong competitive capacity on the phylogenetic and functional structure of local assemblages across three different habitats (eucalypt woodlands, mallee and cleared habitat). We applied a model that explicitly incorporates the effects of neutral colonization and local extinction in shaping community structure and estimated the contributions of niche‐based and neutral processes to community assembly using the STEPCAM technique.ResultsCommunities with the presence of Manorina species were characterized by faster rates of colonization and local extinction and exhibited a higher degree of phylogenetic clustering than communities without these despotic species, which suggests that this model not only mirrors habitat preferences, but also unintendedly accounts for the effect of biotic interactions. Stochastic processes had a lower contribution in the presence of Manorina species, whereas the role of filtering tended to be higher. We observed habitat differences in terms of functional (but not phylogenetic) structure, with more functionally clustered assemblages in the cleared habitat.Main ConclusionsAlthough recent studies have suggested that neutral‐species processes are sufficient to explain local assemblage phylogenetic structure, our capacity to isolate them from contemporary ecological processes is still limited. This study also reinforces the idea that biotic interactions can also lead to patterns of underdispersion and thus, assumptions behind null model approaches for community assembly should be carefully considered in each case.