An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure

The species richness (diversity) of local plant and animal assemblages-biological communities-balances regional processes of species formation and geographic dispersal, which add species to communities, against processes of predation, competitive exclusion, adaptation, and stochastic variation, which may promote local extinction. During the past three decades, ecologists have sought to explain differences in local diversity by the influence of the physical environment on local interactions among species, interactions that are generally believed to limit the number of coexisting species. But diversity of the biological community often fails to converge under similar physical conditions, and local diversity bears a demonstrable dependence upon regional diversity. These observations suggest that regional and historical processes, as well as unique events and circumstances, profoundly influence local community structure. Ecologists must broaden their concepts of community processes and incorporate data from systematics, biogeography, and paleontology into analyses of ecological patterns and tests of community theory.

The central themes of community ecology-distribution, abundance, and diversity-display strongly marked and very general patterns. These include the log-normal distribution of abundance, the relation between range and abundance, the species-area law, and the turnover of species composition. Each pattern is the subject of a large literature that interprets it in terms of ecological processes, typically involving the sorting of differently specialized species onto heterogeneous landscapes. All of these patterns can be shown to arise, however, from neutral community models in which all individuals have identical properties, as the consequence of local dispersal alone. This implies, at the least, that functional interpretations of these patterns must be reevaluated. More fundamentally, neutral community models provide a general theory for biodiversity and conservation biology capable of predicting the fundamental processes and patterns of community ecology.

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.