LETTER A framework for metacommunity analysis of phylogenetic structure Vale ´ rio D. Pillar* and Leandro d. S. Duarte Department of Ecology, Laboratory of Quantitative Ecology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil *Correspondence: E-mail: vpillar@ufrgs.br Abstract It is well known that species evolutionary history plays a crucial role in community assembly. Here, we offer a formal analytical framework to integrate in metacommunity analysis the speciesÕ phylogeny with their functional traits and abundances. We define phylogenetic structure of a community as phylogenetically weighted species composition. This is used to reveal patterns of phylogenetic community variation and to measure and test by specified null models the phylogenetic signal at the metacommunity level, which we distinguish from phylogenetic signal at the species pool level. The former indicates that communities more similar in their phylogenetic structure are also similar in their average trait values, which may indicate speciesÕ niche conservation for the given traits. We apply this framework to an example from grassland communities and find that traits with significant phylogenetic signal at the metacommunity level exhibit ecological filtering along the resource gradient, but since both mechanisms act independently on traits, niche conservatism is not supported. Keywords Assembly rules, disturbance, ecological gradient, functional traits, niche conservatism, phylogenetic signal, phylogeny, soil nitrogen, trait convergence, trait divergence. Ecology Letters (2010) 13: 587–596 INTRODUCTION The problem of how communities are structured over space and time is a central issue in ecology. In general terms, community assembly is driven by niche-based habitat, environmental filtering and biotic interactions (e.g. Cornwell & Ackerly 2009). From the niche perspective, community assembly involves two paradoxical trends: species colonizing a site with a particular set of environmental conditions will tend to exhibit similarity for certain phenotypic traits, leading to trait convergence (Keddy 1992; Weiher et al. 1998). Nonetheless, ecological similarity may limit species coexistence within a local community; in this case, limiting similarity (MacArthur & Levins 1967) is likely to lead to phenotypic trait divergence. A given set of traits may express both trends simultaneously (Pillar et al. 2009). Furthermore, community assembly is also likely to result from spatial dispersal limitation and evolutionary events involving species which make up the regional species pool (Hubbell 2001). Independently of which factor (niche vs. neutral) predominates as the major driver of community assembly process, a topic exhaustively debated by ecologists (Bell et al. 2006; Gravel et al. 2006; Clark 2008, among many others), the role of the evolutionary history of species in community assembly is crucial for understanding how communities are structured over different spatial and temporal scales, as the regional abundance of species is largely determined by historical factors related to biogeo- graphical and macro-evolutionary processes (Webb et al. 2002; Cavender-Bares et al. 2009). Together, niche, neutral and historical factors are expected to determine which species will constitute the species pool over a geographical range (c diversity), as well as the composition of local communities within it (a diversity), and the unevenness of species distribution between communities (b diversity). Disentangling the interplay among these multiple mecha- nisms in determining biological diversity constitutes a major challenge of ecology. Studies addressing the spatial variation of species distribution have broadened their scope to encompass phylogenetic aspects of community assembly (Brooks 1985; Losos 1996), and have attracted special interest of ecologists over the last decade (Ackerly 2000; Webb 2000; Silvertown et al. 2001; Webb et al. 2002; Cavender-Bares et al. 2004; Ecology Letters, (2010) 13: 587–596 doi: 10.1111/j.1461-0248.2010.01456.x Ó 2010 Blackwell Publishing Ltd/CNRS