Functional diversity (FD) has the potential to address many ecological questions, from impacts of global change on biodiversity to ecological restoration. There are several methods estimating the different components of FD. However, most of these methods can only be computed at limited spatial scales and cannot account for intraspecific trait variability (ITV), despite its significant contribution to FD. Trait probability density (TPD) functions (which explicitly account for ITV) reflect the probabilistic nature of niches. By doing so, the TPD approach reconciles existing methods for estimating FD within a unifying framework, allowing FD to be partitioned seamlessly across multiple scales (from individuals to species, and from local to global scales), and accounting for ITV. We present methods to estimate TPD functions at different spatial scales and probabilistic implementations of several FD concepts, including the primary components of FD (functional richness, evenness, and divergence), functional redundancy, functional rarity, and solutions to decompose beta FD into nested and unique components. The TPD framework has the potential to unify and expand analyses of functional ecology across scales, capturing the probabilistic and multidimensional nature of FD. The R package TPD (https://CRAN.R-project.org/package=TPD) will allow users to achieve more comparative results across regions and case studies.

1. Plant invasions can drastically change the structure of native communities, but it is not fully understood whether alien species occupy phylogenetic and functional space within the range occupied by natives, or provide a novel set of evolutionary origins and traits to the invaded communities.2. Here, we evaluated this open question with data on a large number of plant communities from different terrestrial habitats. We used ~27,000 vegetation plots from 26 terrestrial habitats in the Czech Republic and compared phylogenetic and functional diversity (PD and FD, respectively) and community trait means in invaded and non-invaded plots. We tested for differences (1) between invaded vs. non-invaded plots, (2) among natives in invaded vs. non-invaded plots, and (3) in invaded plots only, with and without aliens. To minimize habitat filtering effects on PD and FD, we ran these tests within the habitat-specific species pools of the 26 vegetation types.3. In general, PD, FD and trait mean values changed with invasion, with changes being rather consistent across the habitats considered. Invaded plots were less phylogenetically, but more functionally diverse than non-invaded plots. The greater FD in invaded plots, compared to non-invaded ones, was due to greater dissimilarity between natives. In fact, native species in invaded plots showed higher PD and FD than native species in non-invaded plots, while alien species reduced PD and FD in invaded plots. Changes in the trait means with invasion were due to differences in native species in invaded and non-invaded plots, rather than to an effect of alien species. Within most habitats, the trait means and variance of all aliens were similar to those of all natives, while in some habitats, the variability in traits was greater between aliens that belonged to phylogenetically closer clades. Synthesis.Our results suggest that alien species more often occupy a phylogenetic and functional space within the range formed by the native species in a community. They do so either by filling empty gaps or by excluding natives from the | 2231Journal of Ecology LOIOLA et AL.

The use of functional analyses in ecology has grown exponentially over the past two decades, broadening our understanding of biological diversity and its change across space and time. Virtually all ecological sub-disciplines recognize the critical value of looking at species and communities from a functional perspective, and this has led to a proliferation of methods for estimating contrasting dimensions of functional diversity. Differences between these methods and their development generated terminological inconsistencies and confusion about the selection of the most appropriate approach for addressing any particular ecological question, hampering the potential for comparative studies and meta-analyses. We show that two general mathematical frameworks for estimating functional diversity are prevailing: those based on dissimilarity matrices (e.g., Rao entropy, functional dendrograms) and those relying on multidimensional spaces, constructed as either binary (convex hulls) or probabilistic hypervolumes. We review these frameworks, discuss their strengths and weaknesses, and provide an overview of the main R packages allowing to perform these calculations. In parallel, we propose a ‘periodic table’ of functional diversity metrics quantifying the richness, divergence, and regularity of species or individuals under each framework. Therefore, this overview offers a roadmap for confidently approaching functional diversity analyses both theoretically and practically.

Functional and phylogenetic diversity (FD and PD respectively) of the resident community are expected to exert a key role in community resistance to colonization by surrounding species, and their establishment success. However, few studies have explored this topic experimentally or evaluated the interactive effects of these diversity measures. We implemented a diversity experiment to disentangle the role of FD and PD by sowing mixtures of 6 species, drawn from a pool of 19 species naturally coexisting in central European mesic meadows. The mixtures were designed to cover four independent combinations of high and low FD and PD. Species covers were estimated in spring and late summer over two growing seasons. We then assessed the establishment success of colonizers as a function of their mean traits and phylogenetic distance to the resident (i.e. sown) communities, as well as the resistance of the resident communities to natural colonizers as a function of their functional and phylogenetic structure. Results generally indicated a temporal shift regarding which trait values made a colonizer successful, from an acquisitive strategy in early stages to a more conservative trait syndrome in later stages. FD decreased community resistance to natural colonization. However, PD tempered this effect: with high PD, FD was not significant, suggesting complementary information between these two components of biodiversity. On average, colonizing species were more functionally distant from the resident species in sown communities with high functional diversity, i.e. those that were more colonized. Synthesis. Our results confirm an interplay between FD and PD during community assembly processes, namely resistance to colonizers, suggesting that these two descriptors of biodiversity only partially overlap in their contribution to the overall ecological structure of a community. The hypothesis that higher FD increases resistance through a more complete use of resources was challenged. Results rather suggested that greater FD could provide an unsaturated functional trait space allowing functionally unique species to occupy it.