Most components of an organism's phenotype can be viewed as the expression of multiple traits. Many of these traits operate as complexes, where multiple subsidiary parts function and evolve together. As trait complexity increases, so does the challenge of describing complexity in intuitive, biologically meaningful ways. Traditional multivariate analyses ignore the phenomenon of individual complexity and provide relatively abstract representations of variation among individuals. We suggest adopting well-known diversity indices from community ecology to describe phenotypic complexity as the diversity of distinct subsidiary components of a trait. Using a hierarchical framework, we illustrate how total trait diversity can be partitioned into within-individual complexity (α diversity) and between-individual components (β diversity). This approach complements traditional multivariate analyses. The key innovations are (i) addition of individual complexity within the same framework as between-individual variation and (ii) a group-wise partitioning approach that complements traditional level-wise partitioning of diversity. The complexity-as-diversity approach has potential application in many fields, including physiological ecology, ecological and community genomics, and transcriptomics. We demonstrate the utility of this complexity-as-diversity approach with examples from chemical and microbial ecology. The examples illustrate biologically significant differences in complexity and diversity that standard analyses would not reveal.

Abstract. Beta diversity is an important metric in ecology quantifying differentiation or disparity in composition among communities, ecosystems, or phenotypes. To compare systems with different sizes (N, number of units within a system), beta diversity is often converted to related indices such as turnover or local/regional differentiation. Here we use simulations to demonstrate that these naive measures of dissimilarity depend on sample size and design. We show that when N is the number of sampled units (e.g., quadrats) rather than the "true" number of communities in the system (if such exists), these differentiation measures are biased estimators. We propose using average pairwise dissimilarity as an intuitive solution. That is, instead of attempting to estimate an N-community measure, we advocate estimating the expected dissimilarity between any random pair of communities (or sampling units)-especially when the "true" N is unknown or undefined. Fortunately, measures of pairwise dissimilarity or overlap have been used in ecology for decades, and their properties are well known. Using the same simulations, we show that average pairwise metrics give consistent and unbiased estimates regardless of the number of survey units sampled. We advocate pairwise dissimilarity as a general standardization to ensure commensurability of different study systems.

The global biodiversity crisis has invigorated the search for generalized patterns in most disciplines within the natural sciences. Studies based on organismal functional traits attempt to broaden implications of results by identifying the response of functional traits, instead of taxonomic units, to environmental variables. Determining the functional trait responses enables more direct comparisons with, or predictions for, communities of different taxonomic composition. The North American freshwater fish fauna is both diverse and increasingly imperiled through human mediated disturbances, including climate change. The Tennessee River, USA, contains one of the most diverse assemblages of freshwater fish in North America and has more imperiled species than other rivers, but there has been no trait-based study of community structure in the system. We identified 211 localities in the upper Tennessee River that were sampled by the Tennessee Valley Authority between 2009 and 2011 and compiled fish functional traits for the observed species and environmental variables for each locality. Using fourth corner analysis, we identified significant correlations between many fish functional traits and environmental variables. Functional traits associated with an opportunistic life history strategy were correlated with localities subject to greater land use disturbance and less flow regulation, while functional traits associated with a periodic life history strategy were correlated with localities subject to regular disturbance and regulated flow. These are patterns observed at the continental scale, highlighting the generalizability of trait-based methods. Contrary to studies that found no community structure differences when considering riparian buffer zones, we found that fish functional traits were correlated with different environmental variables between analyses with buffer zones vs. entire catchment area land cover proportions. Using existing databases and fourth corner analysis, our results support the broad application potential for trait-based methods and indicate trait-based methods can detect environmental filtering by riparian zone land cover.

Abstract. Increasing rates of anthropogenic nitrogen (N) enrichment to soils often lead to the dominance of nitrophilic plant species and reduce plant diversity in natural ecosystems. Yet, we lack a framework to predict which species will be winners or losers in soil N enrichment scenarios, a framework that current literature suggests should integrate plant phylogeny, functional tradeoffs, and nutrient co-limitation. Using a controlled fertilization experiment, we quantified biomass responses to N enrichment for 23 forest tree species within the genus Eucalyptus that are native to Tasmania, Australia. Based on previous work with these species' responses to global change factors and theory on the evolution of plant resource-use strategies, we hypothesized that (1) growth responses to N enrichment are phylogenetically structured, (2) species with more resource-acquisitive functional traits have greater growth responses to N enrichment, and (3) phosphorus (P) limits growth responses to N enrichment differentially across species, wherein P enrichment increases growth responses to N enrichment more in some species than others. We built a hierarchical Bayesian model estimating effects of functional traits (specific leaf area, specific stem density, and specific root length) and P fertilization on species' biomass responses to N, which we then compared between lineages to determine whether phylogeny explains variation in responses to N. In concordance with literature on N limitation, a majority of species responded strongly and positively to N enrichment. Mean responses ranged three-fold, from 6.21 (E. pulchella) to 16.87 (E. delegatensis) percent increases in biomass per g NÁm À2 Áyr À1 added. We identified a strong difference in responses to N between two phylogenetic lineages in the Eucalyptus subgenus Symphyomyrtus, suggesting that shared ancestry explains variation in N limitation. However, our model indicated that after controlling for phylogenetic non-independence, eucalypt responses to N were not associated with functional traits (although post-hoc analyses show a phylogenetic pattern in specific root length similar to that of responses to N), nor were responses differentially limited by P. Overall, our model results suggest that phylogeny is a powerful predictor of winners and losers in anthropogenic N enrichment scenarios in Tasmanian eucalypts, which may have implications for other species.

Larvae of the pipevine swallowtail, Battus philenor, feed on plants in the genus Aristolochia, which contains aristolochic acids, toxic alkaloids unique to the Aristolochiaceae. Pipevine swallowtails sequester these compounds and, as a consequence, are chemically defended against many natural enemies. In California, the primary aristolochic acid present in the butterfly is aristolochic acid I. Newly eclosed adult females possess greater amounts of these sequestered toxins compared to males. However, over the course of the flight season, the aristolochic acid content of females in the population declines, whereas male aristolochic acid content remains relatively constant. Transference of sequestered aristolochic acids to eggs by females might explain the decline of these sequestered chemical defenses observed over time. We found no evidence that males transfer aristolochic acids to females via the spermatophore. The possibility that females at the end of the flight season may be automimics of males is discussed. Temporal variation in the aristolochic acid defenses exhibited by this pipevine swallowtail population is both age- and sex-dependent.

Specialized plant-insect interactions are a defining feature of life on earth, yet we are only beginning to understand the factors that set limits on host ranges in herbivorous insects. To better understand the recent adoption of alfalfa as a host plant by the Melissa blue butterfly, we quantified arthropod assemblages and plant metabolites across a wide geographic region while controlling for climate and dispersal inferred from population genomic variation. The presence of the butterfly is successfully predicted by direct and indirect effects of plant traits and interactions with other species. Results are consistent with the predictions of a theoretical model of parasite host range in which specialization is an epiphenomenon of the many barriers to be overcome rather than a consequence of trade-offs in developmental physiology.

For small sedentary herbivores that inhabit seaweeds, choosing a host that provides adequate nutrition and refuge should be favored by natural selection. Yet, the relative importance of seaweed nutritional value versus habitat quality in driving mesograzer host choice remains poorly understood for most herbivores. Previous work in coastal North Carolina, USA, and 2 tropical locations suggests that amphipods often utilize host seaweeds that offer superior refuge from both omnivorous and carnivorous consumers. Our study was conducted in New Zealand, where carnivores alone are the major consumers of seaweed-dwelling amphipods. We show that the herbivorous amphipod Aora typica preferentially utilizes the dictyotalean seaweed Dictyota kunthii over a dominant canopy-forming kelp, Ecklonia radiata, and that this preferred seaweed host provides a superior refuge from predators in both laboratory and field experiments. There was no difference in A. typica feeding preference between D. kunthii and E. radiata, but A. typica grew faster when reared on E. radiata. These results suggest that seaweed refuge quality, not nutritional quality, drives A. typica host preference and distribution in this system. KEY WORDS: Amphipod · Enemy-free space · Fitness · Plant−herbivore interaction · New Zealand · SeaweedResale or republication not permitted without written consent of the publisher

Recently there have been major theoretical advances in the quantification and partitioning of diversity within and among communities, regions, and ecosystems. However, applying those advances to real data remains a challenge. Ecologists often end up describing their samples rather than estimating the diversity components of an underlying study system, and existing approaches do not easily provide statistical frameworks for testing ecological questions. Here we offer one avenue to do all of the above using a hierarchical Bayesian approach. We estimate posterior distributions of the underlying "true" relative abundances of each species within each unit sampled. These posterior estimates of relative abundance can then be used with existing formulae to estimate and partition diversity. The result is a posterior distribution of diversity metrics describing our knowledge (or beliefs) about the study system. This approach intuitively leads to statistical inferences addressing biologically motivated hypotheses via Bayesian model comparison. Using simulations, we demonstrate that our approach does as well or better at approximating the "true" diversity of a community relative to naïve or ad-hoc bias-corrected estimates. Moreover, model comparison correctly distinguishes between alternative hypotheses about the distribution of diversity within and among samples. Finally, we use an empirical ecological dataset to illustrate how the approach can be used to address questions about the makeup and diversities of assemblages at local and regional scales.