No abstract

The difficulty of experimentally quantifying non-trophic species interactions has long troubled ecologists. Increasingly, a new application of the classic "checkerboard distribution" approach is used to infer interactions by examining the pairwise frequency at which species are found to spatially co-occur. However, the link between spatial associations, as estimated from observational co-occurrence, and species interactions has not been tested. Here we used nine common statistical methods to estimate associations from surveys of rocky intertidal communities in the Northeast Pacific Ocean. We compared those inferred associations with a new data set of experimentally determined net and direct species interactions. Although association methods generated networks with aggregate structure similar to previously published interaction networks, each method detected a different set of species associations from the same data set. Moreover, although association methods generally performed better than a random model, associations rarely matched empirical net or direct species interactions, with high rates of false positives and true positives, and many false negatives. Our findings cast doubt on studies that equate species co-occurrences to species interactions and highlight a persistent, unanswered question: how do we interpret spatial patterns in communities? We suggest future research directions to unify the observational and experimental study of species interactions, and discuss the need for community standards and best practices in association analysis.

CW contributed to method development, KC and IS performed the caging experi-7 ment, and MN conceived of the study, carried out the fieldwork and analyses, and 8 wrote the manuscript. (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/082115 doi: bioRxiv preprint first posted online Oct. 20, 2016

A long-standing debate concerns how functional responses are best described. Theory suggests that ratio dependence is consistent with many food web patterns left unexplained by the simplest prey-dependent models. However, for logistical reasons, ratio dependence and predator dependence more generally have seen infrequent empirical evaluation and then only so in specialist predators, which are rare in nature. Here we develop an approach to simultaneously estimate the prey-specific attack rates and predator-specific interference (facilitation) rates of predators interacting with arbitrary numbers of prey and predator species in the field. We apply the approach to surveys and experiments involving two intertidal whelks and their full suite of potential prey. Our study provides strong evidence for predator dependence that is poorly described by the ratio dependent model over manipulated and natural ranges of species abundances. It also indicates how, for generalist predators, even the qualitative nature of predator dependence can be prey-specific.

A scientific understanding of the biological world arises when ideas about how nature works are formalized, tested, refined, and then tested again. Although the benefits of feedback between theoretical and empirical research are widely acknowledged by ecologists, this link is still not as strong as it could be in ecological research. This is in part because theory, particularly when expressed mathematically, can feel inaccessible to empiricists who may have little formal training in advanced math. To address this persistent barrier, we provide a general and accessible guide that covers the basic, step-by-step process of how to approach, understand, and use ecological theory in empirical work. We first give an overview of how and why mathematical theory is created, then outline four specific ways to use both mathematical and verbal theory to motivate empirical work, and finally present a practical tool kit for reading and understanding the mathematical aspects of ecological theory. We hope that empowering empiricists to embrace theory in their work will help move the field closer to a full integration of theoretical and empirical research.

Abstract. Endophytic fungi live symbiotically in the tissues of plants. Although a large amount of evidence suggests a mutualistic role for vertically transmitted endophytic fungi in agronomic grasses, the role of horizontally transmitted endophytic fungi as mutualists has been challenged. Recent studies, however, have shown that horizontally transmitted endophytic fungi can act as mutualists to their plant hosts by providing defense against pathogens and defoliators. In particular, several experimental studies have shown that endophytic fungi interact negatively with leaf-cutting ants and their fungal cultivar, but these studies were performed under laboratory conditions. Using field colonies of Atta colombica in Central Panama, we measured the fungal endophyte content in the forage material of leaf-cutting ants and compared it to ambient endophyte levels. We then used the collected data to model the area of plant material containing endophytes that enters a mature colony daily. We found that mature colonies collect leaf material that is 20% lower in endophyte abundance than surrounding leaves. A similar pattern was observed for newly emerged colonies. Our model suggests that via ant foraging preferences, leaf-cutting ants reduce the possible area of material containing endophytes entering the colony by 33%. Our results provide further evidence for a negative interaction between leaf-cutting ants and horizontally transmitted endophytes, suggesting that fungal endophytes have a defensive role in tropical plants by influencing leafcutting ant foraging preferences.

Intraspecific variation in ecologically relevant traits is widespread. In generalist predators in particular, individual diet specialization is likely to have important consequences for food webs. Understanding individual diet specialization empirically requires the ability to quantify individual diet preferences accurately. Here we compare the currently used frequentist maximum likelihood approach, which infers individual preferences using the observed prey proportions to Bayesian hierarchical models that instead estimate these proportions. Using simulated and empirical data, we find that the approach of using observed prey proportions consistently overestimates diet specialization relative to the Bayesian hierarchical approach when the number of prey observations per individual is low or the number of prey observations vary among individuals, two common features of empirical data. Furthermore, the Bayesian hierarchical approach permits the estimation of point estimates for both prey proportions and their variability within and among levels of organization (i.e., individuals, experimental treatments, populations), while also characterizing the uncertainty of these estimates in ways inaccessible to frequentist methods. The Bayesian hierarchical approach provides a useful framework for improving the quantification and understanding of intraspecific variation in diet specialization studies.

Predator feeding rates (described by their functional response) must saturate at high prey densities. Although thousands of manipulative functional response experiments show feeding rate saturation at high densities under controlled conditions, it remains unclear how saturated feeding rates are at natural prey densities. The general degree of feeding rate saturation has important implications for the processes determining feeding rates and how they respond to changes in prey density. To address this, we linked two databases—one of functional response parameters and one on mass–abundance scaling—through prey mass to calculate a feeding rate saturation index. We find that: (1) feeding rates may commonly be unsaturated and (2) the degree of saturation varies with predator and prey taxonomic identities and body sizes, habitat, interaction dimension and temperature. These results reshape our conceptualisation of predator–prey interactions in nature and suggest new research on the ecological and evolutionary implications of unsaturated feeding rates.