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Journal ArticleDOI

A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients

TL;DR: It is demonstrated that a reliable test for changes in assembly processes along stress gradients requires functional diversity indices measuring either functional richness or functional divergence, which provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.
Abstract: Question Which functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress gradients? Is their power affected by stochastic processes and variations in species richness along stress gradients? Methods We used a simple community assembly model to explore the power of functional diversity indices across a wide range of ecological contexts. The model assumes that with declining stress the influence of niche complementarity on species fitness increases while that of environmental filtering decreases. We separately incorporated two trait-independent stochastic processes – mass and priority effects – in simulating species occurrences and abundances along a hypothetical stress gradient. We ran simulations where species richness was constant along the gradient, or increased, decreased or varied randomly with declining stress. We compared observed values for two indices of functional richness – total functional dendrogram length (FD) and convex hull volume (FRic) – with a matrix-swap null model (yielding indices SESFD and SESFRic) to remove any trivial effects of species richness. We also compared two indices that measure both functional richness and functional divergence – Rao quadratic entropy (Rao) and functional dispersion (FDis) – with a null model that randomizes abundances across species but within communities. This converts them to pure measures of functional divergence (SESRao and SESFDis). Results When mass effects operated, only SESRao and SESFDis gave reasonable power, irrespective of how species richness varied along the stress gradient. FD, FRic, Rao and FDis had low power when species richness was constant, and variation in species richness greatly influenced their power. SESFRic and SESFD were unaffected by variation in species richness. When priority effects operated, FRic, SESFRic, Rao and FDis had good power and were unaffected by variation in species richness. Variation in species richness greatly affected FD and SESFD. SESRao and SESFDis had low power in the priority effects model but were unaffected by variation in species richness. Conclusions Our results demonstrate that a reliable test for changes in assembly processes along stress gradients requires functional diversity indices measuring either functional richness or functional divergence. We recommend using SESFRic as a measure of functional richness and either SESRao or SESFDis (which are very closely related mathematically) as a measure of functional divergence. Used together, these indices of functional richness and functional divergence provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.
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Journal ArticleDOI
13 Feb 2015-Science
TL;DR: An updated and extended analysis of the planetary boundary (PB) framework and identifies levels of anthropogenic perturbations below which the risk of destabilization of the Earth system (ES) is likely to remain low—a “safe operating space” for global societal development.
Abstract: The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system into a new state should they be substantially and persistently transgressed.

7,169 citations


Additional excerpts

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Journal ArticleDOI
TL;DR: This work provides a unified method of decomposing these diversities and constructing normalized taxonomic, phylogenetic, and functional similarity and differentiation measures, including N-assemblage phylogenetic or functional generalizations of species diversity.
Abstract: Hill numbers or the effective number of species are increasingly used to quantify species diversity of an assemblage. Hill numbers were recently extended to phylogenetic diversity, which incorporates species evolutionary history, as well as to functional diversity, which considers the differences among species traits. We review these extensions and integrate them into a framework of attribute diversity (the effective number of entities or total attribute value) based on Hill numbers of taxonomic entities (species), phylogenetic entities (branches of unit-length), or functional entities (species-pairs with unit-distance between species). This framework unifies ecologists' measures of species diversity, phylogenetic diversity, and distance-based functional diversity. It also provides a unified method of decomposing these diversities and constructing normalized taxonomic, phylogenetic, and functional similarity and differentiation measures, including N-assemblage phylogenetic or functional generalizations of...

521 citations

01 Jan 2014
TL;DR: In this paper, the authors present a taxonomic, phylogenetic, and functional framework for attribute diversity, which unifies ecologists' measures of species diversity,phylogenetic diversity, and distance-based functional diversity.
Abstract: Hillnumbersortheeffectivenumberofspeciesareincreasinglyusedtoquan- tify species diversity of an assemblage. Hill numbers were recently extended to phylogenetic diversity, which incorporates species evolutionary history, as well as to functional diversity, which considers the differences among species traits. We review these extensions and integrate them into a frame- work of attribute diversity (the effective number of entities or total attribute value) based on Hill numbers of taxonomic entities (species), phylogenetic entities (branches of unit-length), or functional entities (species-pairs with unit-distance between species). This framework unifies ecologists' measures of species diversity,phylogeneticdiversity,anddistance-basedfunctional di- versity. It also provides a unified method of decomposing these diversities and constructing normalized taxonomic, phylogenetic, and functional sim- ilarity and differentiation measures, including N-assemblage phylogenetic or functional generalizations of the classic Jaccard, Sorensen, Horn, and Morisita-Horn indexes. A real example shows how this framework extracts ecological meaning from complex data.

268 citations

Journal ArticleDOI
TL;DR: It is shown how biodiversity's role in supporting a safe operating space for humanity may lie primarily in its interactions with other boundaries, suggesting an immediate area of focus for scientists and policymakers.
Abstract: The idea that there is an identifiable set of boundaries, beyond which anthropogenic change will put the Earth system outside a safe operating space for humanity, is attracting interest in the scientific community and gaining support in the environmental policy world. Rockstrom et al. (2009) identify nine such boundaries and highlight biodiversity loss as being the single boundary where current rates of extinction put the Earth system furthest outside the safe operating space. Here we review the evidence to support a boundary based on extinction rates and identify weaknesses with this metric and its bearing on humanity's needs. While changes to biodiversity are of undisputed importance, we show that both extinction rate and species richness are weak metrics for this purpose, and they do not scale well from local to regional or global levels. We develop alternative approaches to determine biodiversity loss boundaries and extend our analysis to consider large-scale responses in the Earth system that could affect its suitability for complex human societies which in turn are mediated by the biosphere. We suggest three facets of biodiversity on which a boundary could be based: the genetic library of life; functional type diversity; and biome condition and extent. For each of these we explore the science needed to indicate how it might be measured and how changes would affect human societies. In addition to these three facets, we show how biodiversity's role in supporting a safe operating space for humanity may lie primarily in its interactions with other boundaries, suggesting an immediate area of focus for scientists and policymakers.

225 citations


Cites background from "A guide for using functional divers..."

  • ...Although there is now a wide variety of functional diversity indices applicable at the local to landscape scales (see for example Mason et al., 2013), currently there are no general metrics that could be used to assess status or trends in functional diversity at broader scales....

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References
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Book
19 Jun 2013
TL;DR: The second edition of this book is unique in that it focuses on methods for making formal statistical inference from all the models in an a priori set (Multi-Model Inference).
Abstract: Introduction * Information and Likelihood Theory: A Basis for Model Selection and Inference * Basic Use of the Information-Theoretic Approach * Formal Inference From More Than One Model: Multi-Model Inference (MMI) * Monte Carlo Insights and Extended Examples * Statistical Theory and Numerical Results * Summary

36,993 citations

Journal ArticleDOI
TL;DR: UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics that provides both utility functions for reading and writing data and manipulating phylogenetic trees.
Abstract: Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

10,818 citations


"A guide for using functional divers..." refers methods in this paper

  • ...Branch lengths were computed following Grafen (1989) using the ‘compute.brlen’ in R package ‘ape’ (Paradis et al. 2004; R Foundation for Statistical Computing, Vienna, AT, Australia)....

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Journal ArticleDOI
TL;DR: Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time.
Abstract: ▪ Abstract The focus of most ideas on diversity maintenance is species coexistence, which may be stable or unstable. Stable coexistence can be quantified by the long-term rates at which community members recover from low density. Quantification shows that coexistence mechanisms function in two major ways: They may be (a) equalizing because they tend to minimize average fitness differences between species, or (b) stabilizing because they tend to increase negative intraspecific interactions relative to negative interspecific interactions. Stabilizing mechanisms are essential for species coexistence and include traditional mechanisms such as resource partitioning and frequency-dependent predation, as well as mechanisms that depend on fluctuations in population densities and environmental factors in space and time. Equalizing mechanisms contribute to stable coexistence because they reduce large average fitness inequalities which might negate the effects of stabilizing mechanisms. Models of unstable coexitence...

5,240 citations


"A guide for using functional divers..." refers background in this paper

  • ...However, we recognize that species’ responses to environmental heterogeneity and interspecific competition may be influenced by different traits inmany instances (Chesson 2000)....

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Journal ArticleDOI
TL;DR: This framework is used to discuss why the metacommunity concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples.
Abstract: The metacommunity concept is an important way to think about linkages between different spatial scales in ecology. Here we review current understanding about this concept. We first investigate issues related to its definition as a set of local communities that are linked by dispersal of multiple potentially interacting species. We then identify four paradigms for metacommunities: the patch-dynamic view, the species-sorting view, the mass effects view and the neutral view, that each emphasizes different processes of potential importance in metacommunities. These have somewhat distinct intellectual histories and we discuss elements related to their potential future synthesis. We then use this framework to discuss why the concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples. As ecologists strive to understand increasingly complex mechanisms and strive to work across multiple scales of spatio-temporal organization, concepts like the metacommunity can provide important insights that frequently contrast with those that would be obtained with more conventional approaches based on local communities alone.

4,266 citations


"A guide for using functional divers..." refers background in this paper

  • ...Mass effects occur when source–sink metapopulation dynamics allow species to occur at low abundance in communities where they are unable to maintain a viable population (Kunin 1998; Leibold et al. 2004)....

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Journal ArticleDOI
TL;DR: Analysis of variance of log K for all 121 traits indicated that behavioral traits exhibit lower signal than body size, morphological, life-history, or physiological traits, and this work presents new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models.
Abstract: The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal α = 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformat...

3,896 citations


"A guide for using functional divers..." refers methods in this paper

  • ...Generating regional species pools and locally optimal trait values Values for a single trait were simulated for 130 indigenous New Zealand herbaceous and woody angiosperm, gymnosperm and fern species following a Brownian motion model of evolution with mean of 0 and SD of 1 (Blomberg et al. 2003)....

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