Jonathan S. Lefcheck

piecewiseSEM: Piecewise structural equation modelling in r for ecology, evolution, and systematics

Summary Ecologists and evolutionary biologists rely on an increasingly sophisticated set of statistical tools to describe complex natural systems. One such tool that has gained significant traction in the biological sciences is structural equation models (SEM), a form of path analysis that resolves complex multivariate relationships among a suite of interrelated variables. Evaluation of SEMs has historically relied on covariances among variables, rather than the values of the data points themselves. While this approach permits a wide variety of model forms, it limits the incorporation of detailed specifications. Recent developments have allowed for the simultaneous implementation of non-normal distributions, random effects and different correlation structures using local estimation, but this process is not yet automated and consequently, evaluation can be prohibitive with complex models. Here, I present a fully documented, open-source package piecewiseSEM, a practical implementation of confirmatory path analysis for the r programming language. The package extends this method to all current (generalized) linear, (phylogenetic) least-square, and mixed effects models, relying on familiar r syntax. I also provide two worked examples: one involving random effects and temporal autocorrelation, and a second involving phylogenetically independent contrasts. My goal is to provide a user-friendly and tractable implementation of SEM that also reflects the ecological and methodological processes generating data.

Integrating abundance and functional traits reveals new global hotspots of fish diversity

Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao’s Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites (‘community evenness’), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.

Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats

The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversitys effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversitys effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups.

Investigating the relationship between biodiversity and ecosystem multifunctionality: challenges and solutions

Summary Extensive research shows that more species-rich assemblages are generally more productive and efficient in resource use than comparable assemblages with fewer species. But the question of how diversity simultaneously affects the wide variety of ecological functions that ecosystems perform remains relatively understudied. It presents several analytical and empirical challenges that remain unresolved. In particular, researchers have developed several disparate metrics to quantify multifunctionality, each characterizing different aspects of the concept and each with pros and cons. We compare four approaches to characterizing multifunctionality and its dependence on biodiversity, quantifying (i) magnitudes of multiple individual functions separately, (ii) the extent to which different species promote different functions, (iii) the average level of a suite of functions and (iv) the number of functions that simultaneously exceeds a critical threshold. We illustrate each approach using data from the pan-European BIODEPTH experiment and the R multifunc package developed for this purpose, evaluate the strengths and weaknesses of each approach and implement several methodological improvements. We conclude that an extension of the fourth approach that systematically explores all possible threshold values provides the most comprehensive description of multifunctionality to date. We outline this method and recommend its use in future research.

Biodiversity mediates top–down control in eelgrass ecosystems: a global comparative‐experimental approach

Nutrient pollution and reduced grazing each can stimulate algal blooms as shown by numerous experiments. But because experiments rarely incorporate natural variation in environmental factors and biodiversity, conditions determining the relative strength of bottom-up and top-down forcing remain unresolved. We factorially added nutrients and reduced grazing at 15 sites across the range of the marine foundation species eelgrass (Zostera marina) to quantify how top-down and bottom-up control interact with natural gradients in biodiversity and environmental forcing. Experiments confirmed modest top-down control of algae, whereas fertilisation had no general effect. Unexpectedly, grazer and algal biomass were better predicted by cross-site variation in grazer and eelgrass diversity than by global environmental gradients. Moreover, these large-scale patterns corresponded strikingly with prior small-scale experiments. Our results link global and local evidence that biodiversity and top-down control strongly influence functioning of threatened seagrass ecosystems, and suggest that biodiversity is comparably important to global change stressors.

Physiological effects of diet mixing on consumer fitness: a meta‐analysis

The degree of dietary generalism among consumers has important consequences for population, community, and ecosystem processes, yet the effects on consumer fitness of mixing food types have not been examined comprehensively. We conducted a meta-analysis of 161 peer-reviewed studies reporting 493 experimental manipulations of prey diversity to test whether diet mixing enhances consumer fitness based on the intrinsic nutritional quality of foods and consumer physiology. Averaged across studies, mixed diets conferred significantly higher fitness than the average of single-species diets, but not the best single prey species. More than half of individual experiments, however, showed maximal growth and reproduction on mixed diets, consistent with the predicted benefits of a balanced diet. Mixed diets including chemically defended prey were no better than the average prey type, opposing the prediction that a diverse diet dilutes toxins. Finally, mixed-model analysis showed that the effect of diet mixing was stronger for herbivores than for higher trophic levels. The generally weak evidence for the nutritional benefits of diet mixing in these primarily laboratory experiments suggests that diet generalism is not strongly favored by the inherent physiological benefits of mixing food types, but is more likely driven by ecological and environmental influences on consumer foraging.

Biodiversity enhances reef fish biomass and resistance to climate change

Significance Marine fisheries provide a major global source of protein, feeding billions of people, but they face destabilization in many regions from overexploitation and climate change. Using the most comprehensive dataset of fish diversity and abundance, encompassing over 4,500 surveys from nearshore habitats around the world, we show that biodiversity is among the strongest predictors of reef fish community biomass, comparable in importance to global temperature gradients and human impacts. Importantly, diverse fish communities were more resistant to rising and variable temperature, suggesting that high biodiversity also buffers against changing climate. Maintaining taxonomically and functionally diverse fish communities can thus stabilize fisheries’ yields in a changing ocean. Fishes are the most diverse group of vertebrates, play key functional roles in aquatic ecosystems, and provide protein for a billion people, especially in the developing world. Those functions are compromised by mounting pressures on marine biodiversity and ecosystems. Because of its economic and food value, fish biomass production provides an unusually direct link from biodiversity to critical ecosystem services. We used the Reef Life Survey’s global database of 4,556 standardized fish surveys to test the importance of biodiversity to fish production relative to 25 environmental drivers. Temperature, biodiversity, and human influence together explained 47% of the global variation in reef fish biomass among sites. Fish species richness and functional diversity were among the strongest predictors of fish biomass, particularly for the large-bodied species and carnivores preferred by fishers, and these biodiversity effects were robust to potentially confounding influences of sample abundance, scale, and environmental correlations. Warmer temperatures increased biomass directly, presumably by raising metabolism, and indirectly by increasing diversity, whereas temperature variability reduced biomass. Importantly, diversity and climate interact, with biomass of diverse communities less affected by rising and variable temperatures than species-poor communities. Biodiversity thus buffers global fish biomass from climate change, and conservation of marine biodiversity can stabilize fish production in a changing ocean.

Multitrophic functional diversity predicts ecosystem functioning in experimental assemblages of estuarine consumers

The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on generalized linear mixed-effects models. Combining inferences from eight traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.

Choosing and using multiple traits in functional diversity research

Species are different, but they are not equally different. Yet many indices of biodiversity assume species vary to identical degrees. This notion does not meet with intuition: some species vary greatly in terms of their morphology, behaviour and ecology, while others vary only a little. One way to reconcile the dissimilarity between species is by collecting information on their functional traits (FTs), descriptors of how organisms interact with their environment and each other. Functional diversity (FD) is the total variation in one or more FTs across all species within a community, and provides a powerful complement to species diversity. There are several challenges facing the application of FD to conservation science, including lack of rigorous trait data for many organisms, and sparse details on how to select available traits to generate meaningful inferences for the various summary metrics of FD. This Comment provides a brief discussion on choosing and using FTs, and recommendations for best practice. Ultimately, researchers need to consider using a variety of traits when hypotheses are multifaceted or could potentially evolve, at the same time thinking critically about trait selection to avoid redundant information.

Multifunctionality does not imply that all functions are positively correlated

The recent publication by Bradford et al. (1) argues that indices of ecosystem multifunctionality—the simultaneous performance of multiple ecosystem functions (2)—are only useful if all component functions “respond to community change in a positive correlated fashion.” We contend that this argument fundamentally misinterprets the concept of ecosystem multifunctionality.