Considerable effort has been devoted to the estimation of species interaction strengths. This effort has focused primarily on statistical significance testing and obtaining point estimates of parameters that contribute to interaction strength magnitudes, leaving the characterization of uncertainty associated with those estimates unconsidered. We consider a means of characterizing the uncertainty of a generalist predator’s interaction strengths by formulating an observational method for estimating a predator’s prey-specific per capita attack rates as a Bayesian statistical model. This formulation permits the explicit incorporation of multiple sources of uncertainty. A key insight is the informative nature of several so-called non-informative priors that have been used in modeling the sparse data typical of predator feeding surveys. We introduce to ecology a new neutral prior and provide evidence for its superior performance. We use a case study to consider the attack rates in a New Zealand intertidal whelk predator, and we illustrate not only that Bayesian point estimates can be made to correspond with those obtained by frequentist approaches, but also that estimation uncertainty as described by 95% intervals is more useful and biologically realistic using the Bayesian method. In particular, unlike in bootstrap confidence intervals, the lower bounds of the Bayesian posterior intervals for attack rates do not include zero when a predator–prey interaction is in fact observed. We conclude that the Bayesian framework provides a straightforward, probabilistic characterization of interaction strength uncertainty, enabling future considerations of both the deterministic and stochastic drivers of interaction strength and their impact on food webs.
Wolf, C., M. Novak, and A. I. Gitelman. 2017. Bayesian characterization of uncertainty in species interaction strengths. Oecologia 184:327-339.
As evidenced by the rate at which Bolnick et al. 2003 and 2011 are getting cited, the study of intraspecific variation is booming, particularly with respect to individual diet specialization. In his first dissertation paper (that just came out in Ecology), Kyle has shown how many of these studies will have been biased towards the overestimation of diet specialization. That’s because current methods for quantifying diet specialization using inter-individual or individual-to-population comparisons of the observed frequency (proportions) of items in each individual’s diet are biased by small sample sizes. (They are likelihood-based and hence only unbiased at large sample sizes, which very few studies obtain.) Kyle’s paper offers the use of the Bayesian framework as a solution, using simulations and real data to evidence its superior performance (along with a new, intuitive metric of specialization).
Coblentz, K. E., Rosenblatt, A. E. and Novak, M. (2017), The application of Bayesian hierarchical models to quantify individual diet specialization. Ecology, 98: 1535–1547. doi:10.1002/ecy.1802
A long-standing debate concerns how functional responses are best described. [Functional responses are important.] Theory suggests that ratio dependence is consistent with many food web patterns left unexplained by the simplest prey-dependent models. [Pattern-matching is a poor test, and one person’s “elegant” model is another person’s “inappropriate” model.] 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. [Empiricists working in species-rich systems need to step it up (and talk to theoreticians)!]
In this paper 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. [Mark gets extremely excited by the discovery that the “observational approach” of Novak & Wootton 2008 is simply a restricted special case (specific to type II functional responses) of an approach that applies to any (?) functional response, and subsequently comforted by the realization that the most general “non-functional” version of the approach has actually been known for many decades.]
We apply the approach to surveys and experiments involving two intertidal whelks and their full suite of potential prey. [Study species (interactions) in nature!] 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. [Have you ever seen AIC model weights of 0.999?!?] It also indicates how, for generalist predators, even the qualitative nature of predator dependence can be prey-specific. [Prey-dependent consumer dependence? Maybe?]
Novak, M., Wolf, C., Coblentz, K. E. and Shepard, I. D. (2017), Quantifying predator dependence in the functional response of generalist predators. Ecol Lett, 20: 761–769. doi:10.1111/ele.12777
I’ve known Jon since my sophomore summer of undergrad at the Shoals Marine Lab where he helped introduce me to underwater research, so it was a blast to get to collaborate with him on this paper.
The punchline: Using video-monitored experiments that Jon and Franz Smith conducted, we were able to quantify the effect of sharks and sea lions on the rate with which triggerfish selectively consume pencil versus green urchins (and how they thereby influence benthic algal abundances), and how ‘kleptoparasitic’ interference by hogfish affects triggerfish feeding rates as well. In other words, the paper’s about (1) how un-manipulatable ‘top-predators’ can affect a trophic cascade even in a diverse tropical food web, (2) how behavioral interaction modify the strength of cascades, and (3) how important species-identity (triggerfish vs. hogfish, pencil vs. green urchins) at different levels of the food chain can be for cascades to occur.
Witman, J. D., F. Smith, and M. Novak. 2017. Experimental demonstration of a trophic cascade in the Galápagos rocky subtidal: Effects of consumer identity and behavior. PLoS ONE 12:e0175705.
Kyle Coblentz’s DDIG proposal has been “recommended for funding”!!!!
Predator foraging behavior and the stability of ecosystems
Here’s the layman’s version of his abstract:
Ecosystems are constantly being disturbed, whether it be by natural threats, changes in the environment, or human activities. In spite of these disturbances, most ecosystems remain more or less stable. However, those ecosystems that do become unstable can lead to massive economic and environmental costs. Therefore, ecologists have had a long term interest in understanding exactly what causes ecosystems to be stable. One explanation has to do with the behavior of consumers in food webs, which describe how energy flows through the species in an ecosystem. The idea is that consumer’s preferences for different foods can change depending on how disturbances affect their food items. If a disturbance causes one food species to greatly increase, the consumer can switch its attention to that species and prevent it from disrupting the rest of the food web. On the other hand, if a disturbance causes a food species to decrease to low levels, the consumer will switch its attention to other food species preventing the extinction of the species affected by the disturbance. While mathematical models have shown strong support for this process stabilizing ecosystems, it is only one mode by which consumers might forage and whether this process leads to stability in real world ecosystems is still an open question. The researchers will perform experiments to find out how actual consumers’ preferences change with disturbances to their food species and if those changes make the ecosystem more stable. The information gathered by the researchers will help scientists to understand why ecosystems are stable and may help managers prevent the costs that come along with a loss of ecosystem stability.
This research uses a predatory whelk on the Oregon coast to examine how different possible foraging strategies of generalist predators influence the stability of rocky intertidal communities. The researchers will use whelks trained on different prey in the laboratory to replicate different methods of generalist foraging in the field (constant prey preferences, adaptive foraging, etc.). The whelks will be exposed to two natural pulse recruitment perturbations in the field. The researchers will use the changes in species densities following the perturbations to determine the resilience and resistance stability of the communities. This will allow the researchers to examine the role that generalists play in promoting community stability and what forms of generalist foraging are the most likely to stabilize communities.
Here’s the abstract: The community matrix is among ecology’s most important mathematical abstractions, formally encapsulating the interconnected network of effects that species have on one another’s populations. Despite its importance, the term “community matrix” has been applied to multiple types of matrices that have differing interpretations. This has hindered the application of theory for understanding community structure and perturbation responses. Here, we clarify the correspondence and distinctions among the Interaction matrix, the Alpha matrix, and the Jacobian matrix, terms that are frequently used interchangeably as well as synonymously with the term “community matrix.” We illustrate how these matrices correspond to different ways of characterizing interaction strengths, how they permit insights regarding different types of press perturbations, and how these are related by a simple scaling relationship. Connections to additional interaction strength characterizations encapsulated by the Beta matrix, the Gamma matrix, and the Removal matrix are also discussed. Our synthesis highlights the empirical challenges that remain in using these tools to understand actual communities.
Novak, M., J. Yeakel, A. E. Noble, D. F. Doak, M. Emmerson, J. A. Estes, U. Jacob, M. T. Tinker, and J. T. Wootton. 2016. Characterizing species interactions to understand press perturbations: What is the community matrix? Annual Review of Ecology, Evolution, and Systematics 47:409-432.
Congratulations to (Dr.) Kurt Ingeman who joined the ranks of the PhD’d last month and shortly thereafter started a visiting assistant professor position at Pacific University! You can read his two published thesis chapters in MEPS (2015 and forthcoming). Keep an eye out for a third (“Effects of predator novelty on intraguild predation with adaptive prey defense”).
Congratulations to Isaac and Julia for completing and successfully defending two fantastic honors theses! It’s crazy to think how quickly the last four years have gone by (Julia and Isaac were the very first to join “the lab” in their freshman year), and it’s equally impressive to see how much they both accomplished in that time!
To briefly summarize what they did:
Isaac focused on Nucella ostrina and its prey to assess the consistency of two methods for inferring the `strength’ of trophic species interactions: stable isotopes (analyzed via mixing models to estimate the proportional contribution of prey to a focal predator) and an observational approach (which uses field surveys to estimate predator feeding rates). Interestingly, he found only a very weak correlation between the two.
Julia focused her efforts on characterizing the spatial and temporal variation of various life history attributes of Pollicipes polymerus Gooseneck barnacles along the Oregon coast. This species is starting to become of interest to local seafood markets (and could easily go the way of its over-harvested sister-species Pollicipes pollicipes on the Iberian Peninsula), yet very little of its basic population biology has been studied.
To read more, check out the PDF’s of their theses which are posted at the bottom of our Publications page. You can also find a poster of Julia’s project here.
Where are they off to next? While Isaac is off to grad school at the University of Maine to work with Hamish Greig, Julia is pursuing more Gooseneck barnacle work at OIMB (for which she and her collaborators got funding from Oregon Sea Grant).
An important goal for ecology is to predict the effects of long-term, sustained perturbations, such as climate change, pollution, and harvesting on species abundances. Nature’s complexity is perceived as a major obstacle to this endeavor because perturbations can propagate along many pathways through the tangled food web of interactions that connect species to each other. Intuition and previous theory (including our own previous work) suggest that, because of food web complexity, even predictions of whether a particular species will increase or decrease in abundance following a perturbation elsewhere in its food web are highly sensitive to uncertainty in the strengths of each species’ pairwise interactions.
Our new work published in The American Naturalist suggests a mechanism that could actually result in more complex networks becoming more predictable than previously assumed. This mechanism is rooted in fundamental metabolic constraints – universal to all species – that govern how species’ body sizes affect their rates of feeding and growth.
Our simulations suggest that the distribution of interaction strengths that emerges when metabolic constraints are considered becomes increasingly skewed as food web complexity increases. The strongest interactions become stronger while weak interactions become more prevalent and weaker. The result is that fewer interactions drive the propagation of a perturbation through the food web, and that more interactions attenuate its effects along most potential pathways. Thus, as complexity increases, species responses become more predictably tied to the dynamics of fewer species.
The skewed distribution of species interaction strengths has been noted in many empirical food webs. That the extent of this skew is itself dependent on complexity is a new hypothesis that, if verified, suggests a fundamentally different way of approaching nature’s complexity in order to predict and manage its dynamics.
Wendy has been awarded an undergraduate SURE Science grant! She and Leah (whose PhD work is focusing on crayfish predator-prey interactions) will be investigating the competitive interactions between Signal crayfish (which are native to Oregon) and Ringed crayfish (which have recently been detected in Oregon). Way to go, Wendy!
It’s been quite the quarter for Tamara: 3 awards for 3 proposals! She and Dan are developing a new research direction for our lab — investigating the influence of trait-mediated effects on the interactions of crayfish and Juga snails — that ties into the work we’ve been doing on the food web dynamics of our local streams. Way to go, Tamara!
What a start to the spring quarter, with both Zach and Shannon receiving NSF Graduate Research Fellowships plus Shannon receiving an additional ARCS fellowship from the Advancing Science in America foundation. (Is it a problem when a lab PI is intimidated by his/her own graduate students?!? The lab as a whole is 5-for-5 so far!!!)
Developed largely by Dan Preston, this workshop’s focus was on food webs in the context of global change (with a bunch of `the scientific process’ thrown in). Students learned about classifying and identifying aquatic macro-invertebrates, and how they and their foods webs respond nutrient pollution and non-native species.
Gooseneck barnacles, Pollicipes spp., are overharvested under insufficient and belated management in Spain, Portugal and British Columbia. Julia has been investigating the life history of P. polymerus along the Oregon coast to inform sustainable management before harvesting takes off here too (as it is already threatening to do). Her honors work — which she recently presented at the Western Society of Naturalists meeting and won Best Undergraduate Poster for (!) — focuses on describing seasonal and regional variation in the reproduction, growth, recruitment & abundance of the species. Here’s a pdf of her poster.
Much of the focus in evolutionary biology has been on the adaptive differentiation among organisms. It is equally important to understand the processes that result in similarities of structure among systems. Here, we discuss examples of similarities occurring at different ecological scales, from predator–prey relations (attack rates and handling times) through communities (food-web structures) to ecosystem properties. Selection among systemic configurations or patterns that differ in their intrinsic stability should lead generally to increased representation of relatively stable structures. Such nonadaptive, but selective processes that shape ecological communities offer an enticing mechanism for generating widely observed similarities, and have sparked new interest in stability properties. This nonadaptive systemic selection operates not in opposition to, but in parallel with, adaptive evolution.
Knowing how time is distributed within a fossil record is fundamental to paleobiology. Time-averaging (the degree to which non-contemporaneous skeletal specimens are combined within the depositional layers of a fossil record) establishes the temporal scales at which questions can be addressed and dictates appropriate sampling and analytical frameworks. In this new paper, Rebecca Terry and I present a new model of how “time” (i.e. the frequency distribution of fossil ages) gets distributed across the layers of a fossil record by the processes of specimen decay, mixing and burial. The predictions of our model are supported by the age-frequency distributions of AMS 14C-dated small mammal specimens collected from four different strata within the Homestead Cave record.
An increasing number of studies are seeking to quantify the degree to which individuals within natural predator populations are specialized in their diets. How the time-scale implicit in one’s investigation alters inferences regarding this variation has not been considered, yet is important because the two most common methods for assessing diet specialization — stable isotope ratios and snapshot stomach contents — represent extremes along a spectrum of time-scales. In this paper that just came out in Oecologia, Tim Tinker and I use data from two well-studied sea otter populations to show how the time-scale of one’s study alters (i) the apparent magnitude of individual variation and (ii) the degree to which individuals appear to be temporally consistent in their diet choices (the two key ingredients of individual specialization). Our analyses also reveal some really interesting seasonality and switching behaviour in individual sea otter diets. Check out the rest of the Special Issue for even more papers on the topic of individual specialization.
Daniel Preston arrived this week, joining us for a postdoc from Pieter Johnson‘s lab at the University of Colorado. Dan completed his undergrad in our department, so we’re not the only ones who are happy to have him here!
Since giving his talk at ESA, Kurt’s research on the density-(in)dependence of lionfish effects on native prey populations has been making the news! Listen to his interviews with NPR station WLRN Miami or with the AAAS Science Update podcast, or read about it in the South Florida Sun Sentinel.
As part of our recent NSF award, we’re teaming up OSU’s Science & Math Investigative Learning Experiences program (SMILE) to develop lessons and activities for elementary school teachers from around Oregon to use in their after school clubs. Joined by the Terry lab, this first round of lessons focused on food webs and predator diet diversity (thinking about the pros and cons of being a generalist versus a specialist predator), motivated by activities involving owls and their prey (e.g., pellet dissections).
Isaac Shepard just found out that his proposal to OSU’s Undergraduate Research, Innovation, Scholarship and Creativity (URISC) program has been funded! His proposed project — Using Stable Isotopes as a Measure of Interaction Strength — will form the basis of his honors thesis research. Way to go, Isaac!
Novak M (2013) Data from: Trophic omnivory across a productivity gradient: intraguild predation theory and the structure and strength of species interactions. Dryad Digital Repository. doi:10.5061/dryad.6k144
The Ecolé polytechnique fédérale de Lausanne, Switzerland, is hosting a series workshops on the “role of mathematics and computer science in ecological theory” this year. Here’s the poster for one of them…. Non-adaptive selection: explaining macroscopic laws in ecology and evolution.
A fundamental question in ecology is how the interactions between species cause some species to exhibit cyclic fluctuations over time while for other species they do not. Our understanding of these mechanisms predicates our ability to forecast how species and their ecosystems will respond to environmental perturbations, including habitat deterioration and climate change. Current theory is rooted in the more logistically-tractable study of specialist predator species that feed on only one or a few prey species. However, most species in nature are generalists embedded in complex networks of species interactions. This limitation is widely acknowledged as a significant problem in the development of resource management and conservation practices. With funding from the NSF (Award#1353827), we’re going to build on the approach of Novak & Wootton (2008) to develop a new class of methods enabling the interactions of generalist predators to be measured in species-rich communities, including cases involving intra- and inter-specific predator interference and adaptive foraging. We plan to apply these methods in local stream communities to evaluate support for several theory-motivated hypotheses regarding the propensity of generalist versus specialist predator-prey interactions to cycle. These empirical results will be integrated into abstracted mathematical models to investigate the degree to which the interactions of generalists alter conclusions about ecosystem stability derived from the study of specialists.
Although Leah has been with us for more than a month and Kyle has been here all summer, the start of the new school year makes their PhD student status official! Kyle joins us from Tulane and Leah joins us from San Diego State (with a few stops along the way, including some time at the Environmental Defense Fund). And both were awarded NSF Graduate Research Fellowships! Way to go guys!
The 3-species intraguild predation module is a common motif in food webs that combines the processes of predation and competition. As a result, a lot of theory has been produced concerning IGP’s effects on community structure and dynamics. More recent work has also begun to extend the theory to 5 species, but its general utility in nature’s species-rich food webs, where IGP interactions may be more diffuse, has largely been untested. In this paper that just came out in Proceedings B, I tested two of IGP theory’s central predictions using a series of omnivorous food webs located around along a strong productivity gradient around New Zealand’s coastline. The predictions weren’t supported, but perhaps for a very interesting reason: food web structure and interaction strengths changed (in a consistent and potentially predictable manner) along the productivity gradient. Most theory, in contrast, has assumed that these remain constant.
The spring quarter has been a busy one with a veritable slew of people joining the lab: Alison Iles joins us from the Menge lab. She will be focusing her postdoc on the development and application of allometry-informed network models to help our CAMEO group investigate the effects of otters and MPAs on kelp forests ecosystems. Kurt Ingeman (co-advised by Mark Hixon) is studying the impacts of invasive lionfish in the Caribbean for his Ph.D., and will be using models and a meta-analysis to better understand non-native predator effects. Trevor Bark joins us with an interest in theoretical ecology and networks of microbial species interactions, and is contributing to our Kelp forest species’ life histories and interactions database. And, last but not least, Julia Bingham and Isaac Shephard have joined us us to develop their honors college research projects on species interactions in the rocky intertidal.
Our proposal to investigate how kelp forest ecosystems from around the world are responding to climate change has been accepted!
Jarrett Byrnes, Sean Connell and I are going to be leading a new NCEAS working group this fall. We’re bringing together an international team of kelp forest researchers to collate our existing data sets and synthesize what we already know about how kelp forest ecosystems are responding to environmental changes. The goal is, of course, to understand and forecast how these valuable communities will continue to change in the future. In the process, we hope to jumpstart a global network of kelp forest researchers to better coordinate ongoing efforts.
I’m several months behind in announcing this one (it’s been available online for several months now), but with this paper Justin Yeakel has finally brought us into the world of quantifying species “interaction strengths” the way it ought to be done: with a recognition that they are best described in a probabilistic manner, not just by a specific estimate with some measurement error around it. The paper will be coming out in the Journal of the Royal Society Interface, hopefully in print some time soon!
Laura’s paper — assessing the potential for signal crayfish to provide biotic resistance to the invasion of New Zealand mud snails — just came out in Ecological Applications. And they made it the feature article! Well done Laura!
Novak, Moore & Leidy. 2011. Nestedness patterns and the dual nature of community reassembly in California streams: a multivariate permutation-based approach. Global Change Biology 17:3714-3723.
Leidy, R. A. 1999. Fish survey 1992-1998. Bay area stream fishes. Version 1.2.
Leidy, R. A. 2007. Ecology, assemblage structure, distribution, and status of fishes in streams tributary to the San Francisco estuary, California. San Francisco Estuary Institute, U. S. Environmental Protection Agency 530:198. (part 1, part 2, part 3, part 4, part 5)