The analysis of the phylogenetic structure of communities can help reveal contemporary ecological interactions, as well as link community ecology with biogeography and the study of character evolution. The number of studies employing this broad approach has increased to the point where comparison of their results can now be used to highlight successes and deficiencies in the approach, and to detect emerging patterns in community organization. We review studies of the phylogenetic structure of communities of different major taxa and trophic levels, across different spatial and phylogenetic scales, and using different metrics and null models. Twenty-three of 39 studies (59%) find evidence for phylogenetic clustering in contemporary communities, but terrestrial and/or plant systems are heavily over-represented among published studies. Experimental investigations, although uncommon at present, hold promise for unravelling mechanisms underlying the phylogenetic community structure patterns observed in community surveys. We discuss the relationship between metrics of phylogenetic clustering and tree balance and explore the various emerging biases in taxonomy and pitfalls of scale. Finally, we look beyond one-dimensional metrics of phylogenetic structure towards multivariate descriptors that better capture the variety of ecological behaviours likely to be exhibited in communities of species with hundreds of millions of years of independent evolution.

Understanding the contribution of ecological interactions to the origin and maintenance of diversity is a fundamental challenge for ecologists and evolutionary biologists, and one that is currently receiving a great deal of attention. Natural enemies (e.g., predators, parasites, and herbivores) are ubiquitous in food webs and are predicted to have significant impacts on phenotypic diversity and on speciation, and extinction rates of their prey. Spurred by the development of a theoretical framework beginning in the late 1970s, there is now a growing body of literature that addresses the effects of enemy–prey interactions on the evolution of prey. A number of theoretical models predict that enemies can produce phenotypic divergence between closely related species, even in the absence of interspecific competition for resources. Effects on diversification of prey are more variable, and enemies may either enhance or depress speciation and extinction rates of their prey. Empirical evidences from a number of study systems, notably those involving predators and prey in aquatic environments and interactions between insects and flowering plants, confirm both predictions. There is now considerable evidence for the role of enemies, especially those that are size-selective or use visual cues when identifying suitable prey, on phenotypic divergence of sympatric and allopatric taxa. Enemies may spur diversification rates in certain groups under some circumstances, and hinder diversification rates in other cases. I suggest that further research should focus on the role of enemies in diversification of prey, with significant insights likely to be the product of applying traditional experimental approaches and emerging comparative phylogenetic methods.

Ecological character displacement is common in nature but the mechanisms causing divergence are not well understood. The contributions of ecological interactions other than competition have received little attention. We conducted a pond experiment to explore the contribution of both competition and predation to character divergence in threespine stickleback species. We estimated the strength of divergent selection on a morphologically intermediate target population between competition treatments under two alternate predation treatments. Divergent selection on the target population tended to be stronger in the predatoraddition treatment than in the predator-reduction treatment, a difference that approached significance (P ‫؍‬ 0.09). This trend occurred even though competition was strongest in the predatorreduction treatment. Overall, the strength of divergent selection was best predicted by stickleback mortality (P ‫؍‬ 0.025) being strongest where mortality was highest. These results indicate that predation and other agents of mortality can enhance the rate of change in competition per unit of phenotypic divergence and, thereby, divergent selection, even as they lower the overall strength of competition. In this way, predation and other agents of mortality may facilitate, rather than hinder, character displacement.

Elucidating factors associated with diversification have been attempted in lineages as diverse as birds, mammals and angiosperms, yet has met with limited success. In flowering plants, the ambiguity of associations between traits and diversification has sparked debate since Darwin's description of angiosperm diversification as an 'abominable mystery'. Recent work has found that diversification is often diversity-dependent, suggesting that species richness depends on geographical area available more than on traits or the time available to accumulate species. Here, we undertake phylogenetic generalized least squares analyses that jointly examine the effects of age, ecoregion area and four ecological traits on diversification in 409 angiosperm families. Area explained the most variation, dwarfing the effect of traits and age, suggesting that diversity-dependent diversification is controlled by ecological limits. Within the context of area, however, traits associated with biotic pollination (zygomorphy) exhibited the greatest effect, possibly through the evolution of specialization.

Although it is implicit that interactions between species depend on their traits, studies on the probability of finding related species in a community are in their infancy. Community composition and species richness of predaceous diving beetles (Dytiscidae: Coleoptera) have been used as indicators of freshwater ecosystem function yet no incorporation of phylogenetic relationships of coexisting dytiscids has been attempted to date. Improved knowledge of phylogenetic relationships and phylogenetic community structure analysis methods may provide additional insight into the relationships between community composition and species richness, thus impacting our interpretation of aquatic indicator species metrics. Here, we use museum records of dytiscid beetles in 53 lakes of Alberta, Canada to: (1) compile a supertree of dytiscid beetles that live in the province, (2) examine whether coexisting dytiscids tend to be more or less related than expected by chance, and (3) examine whether phylogenetic structuring depends on species richness or mean size of coexisting species. We find that, although the majority of dytiscid assemblages exhibited phylogenetic clustering, the extent to which this occurred depended on the mean size of dytiscids. We discuss the potential mechanisms and implications of the observed patterns in phylogenetic clustering, along with data that would further improve our understanding of community dynamics in dytiscid beetles.