Shannon awarded Oregon Shell Club scholarship

The Oregon Shell Club has awarded Shannon a fellowship to support her thesis work on individual diet variation in whelks (“Canalization of individual whelk prey preference”).  She’ll be taking to the lab to ask whether whelk hatchlings raised on different diets exhibit different foraging behaviors (ie. recognition and handling times); whether diet soon after emergence affects an individual’s ability to subsequently switch prey, and if so, whether there are certain prey species that are more likely to elicit diet specialization; and whether different whelk populations along with coast having different prey communities differ in their prey preferences and their ability to switch prey species.

Drivers of feeding rates in a generalist predator

Preston, D. L., Henderson, J. S., Falke, L. P., Segui, L. M., Layden, T. J. and Novak, M. (2018), What drives interaction strengths in complex food webs? A test with feeding rates of a generalist stream predator. Ecology, 99: 1591-1601. doi:10.1002/ecy.2387

[Note: Dan’s working on a follow-up paper that incorporates two additional seasons of surveys.  We plan to post the whole data set along with it.]

Describing the mechanisms that drive variation in species interaction strengths is central to understanding, predicting, and managing community dynamics. Multiple factors have been linked to trophic interaction strength variation, including species densities, species traits, and abiotic factors. Yet most empirical tests of the relative roles of multiple mechanisms that drive variation have been limited to simplified experiments that may diverge from the dynamics of natural food webs. Here, we used a field‐based observational approach to quantify the roles of prey density, predator density, predator‐prey body‐mass ratios, prey identity, and abiotic factors in driving variation in feeding rates of reticulate sculpin (Cottus perplexus). We combined data on over 6,000 predator‐prey observations with prey identification time functions to estimate 289 prey‐specific feeding rates at nine stream sites in Oregon. Feeding rates on 57 prey types showed an approximately log‐normal distribution, with few strong and many weak interactions. Model selection indicated that prey density, followed by prey identity, were the two most important predictors of prey‐specific sculpin feeding rates. Feeding rates showed a positive relationship with prey taxon densities that was inconsistent with predator saturation predicted by current functional response models. Feeding rates also exhibited four orders‐of‐magnitude in variation across prey taxonomic orders, with the lowest feeding rates observed on prey with significant anti‐predator defenses. Body‐mass ratios were the third most important predictor variable, showing a hump‐shaped relationship with the highest feeding rates at intermediate ratios. Sculpin density was negatively correlated with feeding rates, consistent with the presence of intraspecific predator interference. Our results highlight how multiple co‐occurring drivers shape trophic interactions in nature and underscore ways in which simplified experiments or reliance on scaling laws alone may lead to biased inferences about the structure and dynamics of species‐rich food webs.

SMILE Field Day

We had a fantastic time hosting ~100 SMILE students this weekend. What can be more fun than a hall full of kids foraging for algal (chocolate) resources while avoiding being eaten themselves (think dodge ball), and then repeating the experiments with crayfish feeding on snails and stonefly prey?!?  (Other than seeing the variety of expressions that a real crayfish can elicit:

And check out the awesome t-shirt logo that Shannon designed and drew!

Thanks to the Terry lab and a bunch of other IB grad students for helping out with parallel activities!



Kurt receives a Smith Fellowship!

Kurt is becoming a Smith Fellow!  The Society of Conservation Biology just announced the class of 2018:

His project, “Ecosystem-based recovery: Coordinating predator-prey management to optimize conservation outcomes and accelerate restoration of marine food webs” is going to follow up on some work that Jameal Samhouri (at NOAA) spearheaded with Shannon last year.  His postdoc mentors on the project will be Adrian Stier (at UCSB), Jameal, and Jodie Toft (at The Nature Conservancy).

Prey detection times for inferring fish feeding rates

The typical way to infer the “importance” of a generalist predator’s prey species is to calculate the (proportional) occurrence in the average predator individual’s stomach contents, either by frequency counts, volume or mass.  These are indices of importance.

What we’d really like to know, however, is how important a particular prey item is in terms of the rate at which predator individuals consume them, either in terms of prey numbers per time or prey mass per time.  (Clearly, if you know both prey counts per time and the mass of an average prey individual you can also estimate prey mass per time.)

In this paper we show how that can be done:  it requires knowing how long a prey item remains identifiable (i.e. present, detectable, and identifiable to an observer) in a predator individual’s stomach.  Because prey items are either identifiable or not (i.e. the data are binary) and the transition point between the two cannot be directly observed (i.e. because it occurs inside the fish!), we use Survival models to estimate detection times.

In this paper we use experiments on Reticulate sculpins (Cottus perplexus) to show that detection times can be estimated and that they vary with prey identity, predator and prey size, and temperature (similar to what we’d shown previously for intertidal whelks).

We also show that, for sculpins, detection times can vary across prey species by over an order-of-magnitude!  That means that prior inferences of prey “importance” have likely been off by over an order-of-magnitude as well!!!!

Preston, Henderson, Falke & Novak (2017) Using Survival Models to Estimate Invertebrate Prey Identification Times in a Generalist Stream Fish.  Transactions of the American Fisheries Society Vol. 146(6): 1303-1314.

Homage to Yodzis 1988: [Exact probabilities for] the indeterminacy of ecological interactions [complex networks] as perceived through press perturbations

Picture a food web of species labelled A thru Z with each species affecting all others via a (complex) network of interactions.  How accurately must we estimate the direct links between all pairs of species in the network to predict even just the qualitative (increase vs. decrease) net effect with which species Z will respond to a change imposed on species A?  

That’s the question that Yodzis 1988 asked using simulations of the so-called “Community matrix”.  His simulations entailed a qualitative comparison of the inverse of the community matrix (i.e. the “Net Effects matrix”) to the inverse of the same to which an order-of-magnitude error (estimation uncertainty) had been added, a process he repeated for many different networks.

These computations required weeks of VAX 11/780 CPU cycles, so it would have been impracticable to increase the sample size much above 100.” 
– Yodzis 1988

His conclusion was that even qualitative predictions would be next to impossible in real food webs.

By 2011, when I tried to ask the follow-up question of how much better our predictive capacity would be if we could estimate interactions with less than an order-of-magnitude uncertainty, my equivalent simulations took mere minutes to run on a standard laptop (Novak et al. 2011). (Nonetheless, I still managed to crash an NCEAS server when I naively implemented a set of related “Loop Analysis” calculations over too large a set of networks.)  Last year, Alison Iles and I took the simulations a step further to incorporate allometric constraints on the interaction strengths (Iles & Novak 2016).

But this is why it pays to collaborate with mathematicians:  David Koslicki (OSU Dept. of Mathematics) has now made our use of simulations for asking such questions obsolete, showing (among other things) that

“an error to the direct effect of species l on species k will cause a qualitatively incorrect prediction to be made for the net effect of any jth species on any ith species if and only if the ratio of: 1. the product of the error and the net effects of k on i and of j on l, and 2. the net effect of j on i times one plus the product of the error and the net effect of k on l, is greater than 1.”

That’s a mouthful, yes, but it means that we can calculate exactly and without resorting to simulations the probability of making incorrect qualitative predictions for any range and magnitude of estimation uncertainties.

I wonder what Yodzis could have done with such analytically powerful simplicity.

Koslicki & Novak (2017) Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations. Journal of Mathematical Biology

Here’s a pdf with the ecological interpretations of the math highlighted.

Lab talks & posters at ESA in Portland.

Jeremy Henderson – Buried alive: the direct effects of disturbance increase the potential for proliferation in Zostera japonica, an invasive seagrass species, by eliciting a tradeoff in resource allocation
Scheduled: Aug 7, 2017, 16:30 to 18:30
Location: Exhibit Hall, Oregon Convention Center

Landon Falke – Dietary overlap among three sympatric predators in Western Oregon stream communities
Scheduled: Aug 8, 2017, 16:30 to 18:30
Location: Exhibit Hall A, Oregon Convention Center

Tamara Layden – Trematode parasite biomass exceeds aquatic insect biomass in Oregon streams
Scheduled: Aug 8, 2017, 16:30 to 18:30
Location: Exhibit Hall A, Oregon Convention Center

Zach Randell – Influence of habitat variation on 36 years of subtidal community structure at San Nicolas Island
Scheduled: Aug 10, 2017, 16:30 to 18:30
Location: Exhibit Hall A, Oregon Convention Center

Mark Novak – Quantifying predator dependence in the functional response of generalist predators
Scheduled: Aug 8, 2017, 08:00 to 08:20
Location: C122, Oregon Convention Center

Kyle Coblentz – Quantifying individual diet specialization using Bayesian hierarchical models
Scheduled: Aug 10, 2017, 09:20 to 09:40
Location: D133-134, Oregon Convention Center

Kurt E. Ingeman – Predator novelty alters coexistence boundaries and modulates energy pathways in an intraguild predation system
Scheduled: Aug 10, 2017, 13:30 to 13:50
Location: D136, Oregon Convention Center

Isaac Shepard – Estimating predator diets using observational methods: A comparison of stable isotope and feeding survey methods
Scheduled: Aug 10, 2017, 14:50 to 15:10
Location: D139, Oregon Convention Center

Alison C. Iles – Complexity increases predictability in allometrically constrained food webs
Scheduled: Aug 10, 2017, 16:40 to 17:00
Location: Portland Blrm 258, Oregon Convention Center

Chris Wolf – Range Contractions of the World’s Large Carnivores
Scheduled: Aug 11, 2017, 08:00 to 08:20

Daniel L. Preston – Predator-prey densities, body size ratios, and environmental drivers of feeding rates in a freshwater sculpin
Scheduled: Aug 11, 2017, 09:20 to 09:40
Location: D139, Oregon Convention Center

Kyle’s Evolution talk on YouTube

I’m still amazed by this, but this year’s Evolution meeting organizers recorded over 400 of the talks, and posted them to YouTube.  

Here is Kyle’s talk on The effects of consumer satiation and interference on the strength of disruptive selection

Bayesian characterization of uncertainty in species interaction strengths

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.



Prey-dependent consumer dependence(!?!)

Abstract [and interpretation]:

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

Code available on GitHub:
Data available from the Dryad Digital Repository:

Isaac and Kyle surveying whelks in the experimental cages.


Trophic cascade and consumer interference in the Galápagos subtidal

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.

Data available here:

Leah awarded NSF/NOAA GRIP *and* NSF GROW awards!

Yup, you read that right.  Leah’s not only pulled in an award from the NSF Graduate Research Internship Program (GRIP) to conduct research at NOAA, but her kick-ass proposal to the NSF Graduate Research Opportunities Worldwide (GROW) program has also been funded!  Both programs are restricted to students with existing NSF Graduate Research Fellowships Program (GRFP) awards.  The GROW award will be taking her to Uppsala, Sweden for a few months to work with Richard Svanbäck.  The only downside:  she’s had to decline the GRIP award in order to capitalize on the GROW award.  

Long-Term Studies Contribute Disproportionately to Ecology and Policy

Our paper — the result of a multi-year collaboration between our lab, the Menge lab, and the Raimondi-Carr lab at UCSC — is out in in BioScience, and we got the cover!

Abstract: As the contribution for long-term ecological and environmental studies (LTEES) to our understanding of how species and ecosystems respond to a changing global climate becomes more urgent, the relative number and investment in LTEES are declining. To assess the value of LTEES to advancing the field of ecology, we evaluated relationships between citation rates and study duration, as well as the representation of LTEES with the impact factors of 15 ecological journals. We found that the proportionate representation of LTEES increases with journal impact factor and that the positive relationship between citation rate and study duration is stronger as journal impact factor increases. We also found that the representation of LTEES in reports written to inform policy was greater than their representation in the ecological literature and that their authors particularly valued LTEES. We conclude that the relative investment in LTEES by ecologists and funders should be seriously reconsidered for advancing ecology and its contribution to informing environmental policy.

Hughes, B. B., R. Beas-Luna, A. K. Barner, K. Brewitt, D. R. Brumbaugh, E. B. Cerny-Chipman, S. L. Close, K. E. Coblentz, K. L. de Nesnera, S. T. Drobnitch, J. D. Figurski, B. Focht, M. Friedman, J. Freiwald, K. K. Heady, W. N. Heady, A. Hettinger, A. Johnson, K. A. Karr, B. Mahoney, M. M. Moritsch, A.-M. K. Osterback, J. Reimer, J. Robinson, T. Rohrer, J. M. Rose, M. Sabal, L. M. Segui, C. Shen, J. Sullivan, R. Zuercher, P. T. Raimondi, B. A. Menge, K. Grorud-Colvert, M. Novak, and M. H. Carr. 2017. Long-Term Studies Contribute Disproportionately to Ecology and Policy. Bioscience 67:271-281.


Kyle receives NSF DDIG!

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.

What is the community matrix?

I have to admit that this one took several years to put together and have it feel “right”, but our paper Characterizing species interactions to understand press perturbations: What is the community matrix? is finally out in the Annual Reviews of Ecology, Evolution, & Systematics.  This paper was inspired by the first NCEAS working group I participated in as a grad student, experiencing frustration in trying to understand the literature.

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.

Congrats to (Dr.) Ingeman

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”).

SMILE – The value of collections to ecology

Our latest set of lessons and activities developed with the Science & Math Investigative Learning Experiences program (SMILE) focused on the value (and creation and curation) of natural history collections – repositories of biological specimens – for the study of ecology.  In this case we capitalized on the presence of the Oregon State Arthropod Collection on our campus and focused our activities on Oregon’s insect fauna.  You can find a them on SMILE’s blog:

Isaac and Julia defend their honors theses

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).

Complexity increases predictability in allometrically constrained food webs

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.

Iles & Novak (2016) Data from: Complexity Increases Predictability in Allometrically Constrained Food Webs. Dryad Digital Repository.

Wendy awarded SURE Science award

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!

Species coexistence when predators are novel and prey are naïve

Novel predators and naïve prey: modeling suboptimal responses to introduced predators. Kurt just came back from what sounded like a fantastic Gordon Research Conference (Predator-prey interactions: New Frontiers in Understanding Predator-Prey Interactions in a Human-Altered World).  He presented a poster describing some very cool modeling works he’s been doing regarding the influence of prey naïveté and suboptimal defenses on intraguild predation (IGP) species coexistence.

SMILE – Ponds in peril (Global change and food webs)

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.



Julia awarded Best Undergraduate Poster at WSN

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.

Selection on stability across ecological scales.

A paper summarizing the views presented at a workshop held at the Ecolé polytechnique fédérale de Lausanne, Switzerland, last year.

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.

Where does the time go? A new model of time-averaging.

AFD_modelKnowing 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 paperRebecca 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.

Time-scale alters apparent intraspecific diet specialization

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.

SMILE – Magnificent macroinvertebrates

As part of our 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.  After last fall’s lessons on predator-prey relationships and the diet diversity of owls, this spring’s lessons focused on the stream habitats and the distribution and diversity of stream macroinvertebrates.

SMILE – Of Food webs, Diet diversity, and Owl puke

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).

New NSF project: What stabilizes population dynamics in nature?

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.

Welcome Leah and Kyle

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!

An empirical test of intraguild predation theory


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.

We can call ourselves a lab now for sure!

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.

NCEAS: Kelp forest dynamics across the globe!

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.

Probabilistic interaction strengths

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!

Nestedness patterns and the dual nature of community reassembly in California streams

Data from:
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.

The data consist of three matrices and a list of site locations:
(1) site-specific species abundances (from Leidy 1999, 2007),
(2) site-specific abiotic variables (from Leidy 1999, 2007),
(3) species-specific traits/attributes (collated from the literature),
(4) site-specific lat-long (from Leidy 1999, 2007).

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 1part 2part 3part 4part 5)

Estimating interaction strengths in nature: experimental support for an observational approach

Data from:
Novak, M. (2010), Estimating interaction strengths in nature: experimental support for an observational approach. Ecology, 91: 2394–2405

Novak, Mark (2016): Appendix A. Seasonal temperatures, survey frequency, prey counts and accumulation curves, species abundances, and prey handling times.. figshare. 10.6084/m9.figshare.3547674.v1

Novak, Mark (2016): Appendix B. Mixed effects model summary tables.. figshare. 10.6084/m9.figshare.3547671.v1

Novak, Mark (2016): Appendix C. Performance of experimental interaction strength indices.. figshare. 10.6084/m9.figshare.3547668.v1