The use of functional traits to elucidate the causes and consequences of biological diversity.

The rapid and global rise in species extinctions has prompted much research into the causes and consequences of biodiversity loss. In the past two decades, efforts have expanded beyond characterizing diversity through numbers of species -- or species richness -- and integrated additional information on how species interact with one another and their environment via functional traits. Functional traits permit a more nuanced exploration of patterns in community structure and composition, and provide a mechanistic basis to link community diversity to ecosystem processes. In this dissertation, I apply functional traits to observational surveys and a small-scale experimental manipulation to understand and explain patterns in diversity, and to link functional diversity to ecosystem functioning. In all three cases, I show that functional traits yield substantial additional insight into ecological patterns and processes beyond what can be gained via richness alone.;In the first chapter, I use functional traits and two newly-derived phylogenies to understand the role of biotic interactions in determining how local communities of reef fishes assemble from the available pool of species. to address this question, I utilized data from the Reef Life Survey network, a global citizen science program that has conducted visual censuses of reef fish communities at nearly 2,000 sites across the globe. to rigorously disentangle the biotic and abiotic drivers of assembly, I aimed to factor out the effect of environment by grouping species based on their fine-scale habitat requirements, then tested for significant patterns in functional and phylogenetic diversity of local communities relative to the regional species pool. I found that most communities were functionally and phylogenetically clustered relative to the regional pool, meaning that species found in these communities were more functionally- and phylogenetically-similar than expected by chance. This clustering increased with increasing latitude independent of several major axes of environmental variation. I propose several non-mutually exclusive explanations for this pattern, including: (1) increased competition at higher latitudes, potentially driven by variability in resources; (2) higher mobility of fishes at high latitudes reducing trait and evolutionary composition at any given site relative to what could be observed there (i.e., high turnover), and; (3) reduced richness at high latitudes reducing the probability of capturing functionally and phylogenetically unique species. This chapter is one of the first studies to unite a macroecological perspective on assembly with functional biogeography across global gradients, particularly for vertebrates.;In the second chapter, I utilized data from a 15-year observational survey of an eelgrass Zostera marina L. bed in the York River Estuary, Chesapeake Bay, USA to test the relative strength of top-down and bottom-up control and the role of species richness and functional diversity in mediating trophic processes. I united biological data on eelgrass, microalgal epiphyte, and invertebrate grazer biomass, and predator abundances with physical data on temperature, light, turbidity, and nutrients using structural equation modeling. Across spring, summer, and fall seasons, biological variables appeared to be largely controlled by temperature and turbidity. However, there was weaker but statistically significant evidence for top-down control in the spring and summer, changing over to bottom-up control in the fall. In contrast to evidence from small-scale experiments, there was no effect of diversity on ecosystem properties such as standing stock biomass of eelgrass, grazers, and predators, which may have been a consequence of the overall low diversity and high functional redundancy present in this system. This chapter reveals a small but significant role for biology in the face of strong, long-term natural variation in abiotic parameters in a temperate eelgrass bed.;In the third and final chapter, I experimentally manipulated functional trait diversity of estuarine mesograzers and predators within multiple levels of species richness to test the relative predictive ability of functional diversity and species richness on ecosystem functioning. I found that multivariate functional diversity based on 8 traits was a better predictor and explained more variation in standing stock biomass of predator, grazer, and recruiting invertebrates than did species richness. Aggregating across all 8 traits in a multivariate index of functional diversity improved prediction accuracy relative to any individual trait. I then used structural equation modeling to show that the positive effects of community-level functional diversity were a consequence of both predator and grazer functional diversity, although predator effects were much stronger. I also modeled the contributions of each individual species to show that different functions were driven by different species with unique combinations of traits, suggestive of functional complementarity. Together, these results suggest that functional diversity is a powerful alternative to species richness in predicting the ecosystem consequences of species loss. This chapter is one of the first studies to conduct an a priori manipulation of functional traits using consumers, and the first to manipulate traits across multiple levels of a realistic food web

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

Faunal Communities Are Invariant to Fragmentation in Experimental Seagrass Landscapes

Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4-400 m(2) in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused mesopredators and epifaunal communities using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the number of patches and the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at more realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities

BioTIME: A database of biodiversity time series for the Anthropocene

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km(2) (158 cm(2)) to 100 km(2) (1,000,000,000,000 cm(2)). Time period and grainBio: TIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates

Squidpops: A Simple Tool to Crowdsource a Global Map of Marine Predation Intensity

We present a simple, standardized assay, the squidpop, for measuring the relative feeding intensity of generalist predators in aquatic systems. The assay consists of a 1.3-cm diameter disk of dried squid mantle tethered to a rod, which is either inserted in the sediment in soft-bottom habitats or secured to existing structure. Each replicate squidpop is scored as present or absent after 1 and 24 hours, and the data for analysis are proportions of replicate units consumed at each time. Tests in several habitats of the temperate southeastern USA (Virginia and North Carolina) and tropical Central America (Belize) confirmed the assay’s utility for measuring variation in predation intensity among habitats, among seasons, and along environmental gradients. In Belize, predation intensity varied strongly among habitats, with reef\u3eseagrass = mangrove\u3eunvegetated bare sand. Quantitative visual surveys confirmed that assayed feeding intensity increased with abundance and species richness of fishes across sites, with fish abundance and richness explaining up to 45% and 70% of the variation in bait loss respectively. In the southeastern USA, predation intensity varied seasonally,being highest during summer and declining in late autumn. Deployments in marsh habitats generally revealed a decline in mean predation intensity from fully marine to tidal freshwater sites. The simplicity, economy, and standardization of the squidpop assay should facilitate engagement of scientists and citizens alike, with the goal of constructing high-resolution maps of how top-down control varies through space and time in aquatic ecosystems, and addressing a broad array of long-standing hypotheses in macro- and community ecolog

Restoration of seagrass habitat leads to rapid recovery of coastal ecosystem services

There have been increasing attempts to reverse habitat degradation through active restoration, but few largescale successes are reported to guide these efforts. Here, we report outcomes from a unique and very successful seagrass restoration project: Since 1999, over 70 million seeds of a marine angiosperm, eelgrass (Zostera marina), have been broadcast into mid-western Atlantic coastal lagoons, leading to recovery of 3612 ha of seagrass. Well-developed meadows now foster productive and diverse animal communities, sequester substantial stocks of carbon and nitrogen, and have prompted a parallel restoration for bay scallops (Argopecten irradians). Restored ecosystem services are approaching historic levels, but we also note that managers value services differently today than they did nine decades ago, emphasizing regulating in addition to provisioning services. Thus, this study serves as a blueprint for restoring and maintaining healthy ecosystems to safeguard multiple benefits, including co-benefits that may emerge as management priorities over time

Abundance and local - scale processes contribute to multi-phyla gradients in global marine diversity

Among themost enduring ecological challenges is an integrated theory explaining the latitudinal biodiversity gradient, including discrepancies observed at different spatial scales. Analysis of Reef Life Survey data for 4127 marine species at 2406 coral and rocky sites worldwide confirms that the total ecoregion richness peaks in low latitudes, near +15°N and −15°S. However, although richness at survey sites ismaximal near the equator for vertebrates, it peaks at high latitudes for large mobile invertebrates. Site richness for different groups is dependent on abundance, which is in turn correlated with temperature for fishes and nutrients for macroinvertebrates. We suggest that temperature-mediated fish predation and herbivory have on strained mobile macroinvertebrate diversity at the site scale across the tropics. Conversely, at the ecoregion scale, richness responds positively to coral reef area, highlighting potentially huge global biodiversity losses with coral decline. Improved conservation outcomes require management frameworks, informed by hierarchical monitoring, that cover differing site- and regional-scale processes across diverse taxa, including attention to invertebrate species, which appear disproportionately threatened by warming seas

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 biodiversity\u27s 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 biodiversity\u27s 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