Aim
The Hutchinsonian hypervolume is the conceptual foundation for many lines of ecological and evolutionary inquiry, including functional morphology, comparative biology, community ecology and niche theory. However, extant methods to sample from hypervolumes or measure their geometry perform poorly on high-dimensional or holey datasets.

Innovation
We first highlight the conceptual and computational issues that have prevented a more direct approach to measuring hypervolumes. Next, we present a new multivariate kernel density estimation method that resolves many of these problems in an arbitrary number of dimensions.

Main conclusions
We show that our method (implemented as the ‘hypervolume’ R package) can match several extant methods for hypervolume geometry and species distribution modelling. Tools to quantify high-dimensional ecological hypervolumes will enable a wide range of fundamental descriptive, inferential and comparative questions to be addressed.

The n‐dimensional hypervolume

Environmental filtering, where the environment selects against certain species, is thought to be a major mechanism structuring communities. However, recent criticisms cast doubt on our ability to accurately infer filtering because competition can give rise to patterns identical to those caused by environmental filtering. While experiments can distinguish mechanisms, observational patterns are especially problematic. The environment determines community composition not only directly via survival, but also by influencing competition. If species population growth rates covary with environmental gradients, then outcomes of competitive exclusion will also vary with the environment. Here, we argue that observational studies remain valuable, but inferences about the importance of the environment cannot rely on compositional data alone, and that species abundances, population growth, or traits must be correlated with the environment.

Should Environmental Filtering be Abandoned

The subdiscipline of 'community phylogenetics' is rapidly growing and influencing thinking regarding community assembly. In particular, phylogenetic dispersion of co-occurring species within a community is commonly used as a proxy to identify which community assembly processes may have structured a particular community: phylogenetic clustering as a proxy for abiotic assembly, that is habitat filtering, and phylogenetic overdispersion as a proxy for biotic assembly, notably competition. We challenge this approach by highlighting (typically) implicit assumptions that are, in reality, only weakly supported, including (i) phylogenetic dispersion reflects trait dispersion; (ii) a given ecological function can be performed only by a single trait state or combination of trait states; (iii) trait similarity causes enhanced competition; (iv) competition causes species exclusion; (v) communities are at equilibrium with processes of assembly having been completed; (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter; and (vii) observed phylogenetic dispersion is driven predominantly by local and present-day processes. Moreover, technical sophistication of the phylogenetic-patterns-as-proxy approach trades off against sophistication in alternative, potentially more pertinent approaches to directly observe or manipulate assembly processes. Despite concerns about using phylogenetic dispersion as a proxy for community assembly processes, we suggest there are underappreciated benefits of quantifying the phylogenetic structure of communities, including (i) understanding how coexistence leads to the macroevolutionary diversification of habitat lineage-pools (i.e. phylogenetic-patterns-as-result approach); and (ii) understanding the macroevolutionary contingency of habitat lineage-pools and how it affects present-day species coexistence in local communities (i.e. phylogenetic-patterns-as-cause approach). We conclude that phylogenetic patterns may be little useful as proxy of community assembly. However, such patterns can prove useful to identify and test novel hypotheses on (i) how local coexistence may control macroevolution of the habitat lineage-pool, for example through competition among close relatives triggering displacement and diversification of characters, and (ii) how macroevolution within the habitat lineage-pool may control local coexistence of related species, for example through origin of close relatives that can potentially enter in competition. 2015 British Ecological Society.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2435.12425

Phylogenetic patterns are not proxies of community assembly mechanisms (they are far better)

Summary 1. Theory predicts that the processes generating biodiversity after disturbance will change during succession. Comparisons of phylogenetic and functional (alpha and beta) diversity with taxonomic diversity can provide insights into the extent to which community assembly is driven by deterministic or stochastic processes, but comparative approaches have yet to be applied to successional systems. 2. We characterized taxonomic, phylogenetic and functional plant (alpha and beta) diversity within and between four successional stages in a > 270-year-long arable-to-grassland chronosequence. Null models were used to test whether functional and phylogenetic turnover differed from random expectations, given the levels of species diversity. 3. The three facets of diversity showed different patterns of change during succession. Between early and early-mid succession, species richness increased but there was no increase in functional or phylogenetic diversity. Higher than predicted levels of functional similarity between species within the early and early-mid successional stages, indicate that abiotic filters have selected for sets of functionally similar species within sites. Between late-mid and late succession, there was no further increase in species richness, but a significant increase in functional alpha diversity, suggesting that functionally redundant species were replaced by functionally more dissimilar species. Functional turnover between stages was higher than predicted, and higher than within-stage turnover, indicating that different assembly processes act at different successional stages. 4. Synthesis. Analysis of spatial and temporal turnover in different facets of diversity suggests that deterministic processes generate biodiversity during post-disturbance ecosystem development and that the relative importance of assembly processes has changed over time. Trait-mediated abiotic filtering appears to play an important role in community assembly during the early and early-mid stages of arable-to-grassland succession, whereas the relative importance of competitive exclusion appears to have increased towards the later successional stages. Phylogenetic diversity provided a poor reflection of functional diversity and did not contribute to inferences about underlying assembly processes. Functionally deterministic assembly suggests that it may be possible to predict future post-disturbance changes in biodiversity, and associated ecosystem attributes, on the basis of species’ functional traits but not phylogeny.

/pdf/contrasting-changes-in-taxonomic-phylogenetic-and-functional-t483wkzotl.pdf

Contrasting changes in taxonomic, phylogenetic and functional diversity during a long‐term succession: insights into assembly processes

Summary Phylogenetic niche conservatism (PNC) is the tendency of lineages to retain their niche-related traits through speciation events. A recent surge in the availability of well-sampled molecular phylogenies has stimulated phylogenetic approaches to understanding ecological processes at large geographical scales and through macroevolutionary time. We stress that PNC is a pattern, nota process,and is foundonly in sometraits andsomelineages. Atthesimplest level, apattern ofPNCisan inevitableconsequenceofevolution-descentwithmodificationand divergenceof lineages - but several intrinsic causes, including physicochemical, developmental and genetic constraints, can lead directly to a marked pattern of PNC. A pattern of PNC can also be caused indirectly, as a by-product of other causes, such as extinction, dispersal limitation, competition and predation. Recognition of patterns of PNC can contribute to understanding macroevolu- tionaryprocesses:forexample,releasefromconstraintintraitshasbeenhypothesizedtotrigger adaptive radiations such as that of the angiosperms. Given the multiple causes of patterns of PNC, tests should address explicit questions about hypothesized processes. We conclude that PNC is a scientifically useful concept with applications to the practice of ecological research.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2012.04298.x

Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

1 Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes 2 Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities 3 We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana Trait variation was summarized into two ordination axes that reflect species niche overlap 4 We also generated a dated molecular phylogenetic tree based on DNA sequencing of two plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the plots 5 We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance 6 We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities 7 Synthesis We provide the most comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems

https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1365-2745.2012.01966.x

Mailyn-Adriana Gonzalez

Papers

Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities