Publications

 

Authors
Year
Title
Journal
 
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Novak & Tinkerin pressOecologia
Beas-Luna, Novak, Carr, Tinker, Black, Caselle, Hoban, Malone, Ilesin pressAn online database for informing ecological network models: http://kelpforest.ucsc.eduPLOS ONE
Novak2013Proceedings of the Royal Society B280: 20131415request
SOM
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Kenner, Estes, Tinker, Bodkin, Cowen, Harrold, Hatfield, Novak, Rassweiler & Reed2013Ecology (Data paper)94(11): 2654pdflink
Yeakel, Guimarães, Novak, Fox-Dobbs & Koch2012Journal of the Royal Society Interface9: 3219-3228pdf SOMlink
Twardochleb, Novak & Moore2012
Ecological Applications
Cover image
22(4): 1162–1171pdflink
Tinker, Guimarães, Novak, Marquitti, Bodkin, Staedler, Bentall & Estes2012Ecology Letters15(5): 475-483pdf SOMlink
Novak, Moore & Leidy2011Global Change Biology17: 3714-3723pdflink
Yeakel, Novak, Guimarães, Dominy, Koch, Ward, Moore & Semmens2011PLoS One6(7): e22015pdflink
Novak, Wootton, Doak, Emmerson, Estes & Tinker2011Ecology (Concepts & Synthesis)
Highlighted by F1000
92(4): 836-846pdflink
Yeakel, Stiefs, Novak & Gross2011Theoretical Ecology
Highlighted by F1000
4(2): 179-194pdflink
Bolnick, Amarasekare, Araújo, Bürger, Levine, Novak, Schreiber, Urban & Vasseur 2011Trends in Ecology & Evolution26(4): 183-191pdflink
DeAngelis, Wolkowicz, Lou, Jian, Novak, Svanbäck, Araújo, Jo & Cleary2011The American Naturalist178(1): 15-29pdflink
Novak2010Ecology91(8): 2394-2405pdflink
Novak & Wootton2010Oikos119: 1057-1063pdf
erratum
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Novak & Wootton2008Ecology (Report)89(8): 2083-2089pdflink
Doak, Estes, Halpern, Jacob, Lindberg, Lovvorn, Monson, Tinker, Williams, Wootton, Carroll, Emmerson, Micheli & Novak2008Ecology (Concepts & Synthesis)89(4): 952-961pdflink
Novak2004Crustaceana77(5): 603-620pdflink

 
 

Dissertations

Author
Year
Title
School
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Novak2008UChicagopdf

The patterns of diel activity of four large decapod species in the shallow subtidal of the Isles of Shoals, Gulf of Maine, U. S. A. were investigated. During the summer of 1999 the diel abundance and size distribution of active decapod individuals were surveyed at three depth ranges at a sheltered site on Appledore Island. Densities of active American lobsters, Homarus americanus H. Milne Edwards, 1837, were, as expected, highest at night. The crabs Cancer borealis Stimpson, 1859 and Carcinus maenas (L., 1758), however, were almost exclusively active during the day. Cancer irroratus Say, 1817 were equally active during the day and the night, but the mean size of individuals was significantly larger during the day. Surveys at additional sites in 2003 confirmed that these same patterns of diel activity were present throughout the Isles of Shoals. An extensive review of the literature suggests that such diurnal activity is not only unusual for the three crab species of this study, but for the whole genus Cancer as well.
Ecological surprises, substantial and unanticipated changes in the abundance of one or more species that result from previously unsuspected processes, are a common outcome of both experiments and observations in community and population ecology. Here, we give examples of such surprises along with the results of a survey of well-established field ecologists, most of whom have encountered one or more surprises over the course of their careers. Truly surprising results are common enough to require their consideration in any reasonable effort to characterize nature and manage natural resources. We classify surprises as dynamic-, pattern-, or intervention-based, and we speculate on the common processes that cause ecological systems to so often surprise us. A long-standing and still growing concern in the ecological literature is how best to make predictions of future population and community dynamics. Although most work on this subject involves statistical aspects of data analysis and modeling, the frequency and nature of ecological surprises imply that uncertainty cannot be easily tamed through improved analytical procedures, and that prudent management of both exploited and conserved communities will require precautionary and adaptive management approaches.
Efforts to estimate the strength of species interactions in species-rich, reticulate food webs have been hampered by the multitude of direct and indirect interactions such systems exhibit and have been limited by an assumption that pairwise interactions display linear functional forms. Here we present a new method for directly measuring, on a per capita basis, the nonlinear strength of trophic species interactions within such food webs. This is an observation-based method, requiring three pieces of information: (1) species abundances, (2) predator and prey-specific handling times, and (3) data from predator-specific feeding surveys in which the number of individuals observed feeding on each of the predator's prey species has been tallied. The method offers a straightforward way to assess the completeness of one's sampling effort in accurately estimating interaction strengths through the construction of predator-specific prey accumulation curves. The method should be applicable to a variety of systems in which empirical estimates of direct interaction strengths have thus far remained elusive.
Few methods for demonstrating the effects of species interactions rival that of the manipulative experiment. The now commonly performed removal or addition of predators, competitors, or mutualists to experimen- tally replicated populations of recipient species has irrefutably shown that species can have important effects on each other’s populations, and that the strengths of these effects can vary considerably across environmental contexts and species identi- ties. A large body of research is directed towards understanding this variation to forecast community dynamics and dissect how species interactions regulate community structure. It has frequently been pointed out that progress in this field will require more explicit connections between ecological theory and the realities of nature. This requires that interaction strengths measured experimentally be appropriate to the biology of our study systems and the mathematical abstractions we ascribe to them.
Here we clarify some of the assumptions made in the application of the two most commonly used indices for measur- ing the strengths of species interactions with manipulative removal/addition experiments: Paine’s index and the dynamic index. We explain how the values these indices are intended to measure – the per capita interaction strength between two species – are typically not estimated in common currencies. We then introduce extensions to these indices that alleviate a subset of previously made assumptions and limitations. These include a reformulation of Paine’s index appropriate for an open-recruitment system, and an extension of the dynamic index applicable to interactions of a particular nonlinear form. While we focus our language on predator–prey interactions, our discussions are pertinent to the measurement of species effects in other types of interactions as well.
The complexity of food webs poses a significant hurdle for our growing understanding of the structure and dynamics of ecological communities. Empirical methods that measure the per capita strengths of trophic species interactions offer a means to identify keystone species and bridge mathematical models and data to synthesize our knowledge of population dynamics and predator feeding behaviors. Many such methods have been proposed, but few have seen independent validation of their estimates or underlying assumptions. This is particularly so with respect to the nonlinear functional responses by which predators often respond to their prey. Here I describe an empirical test of a recently proposed observational method for estimating the nonlinear strength of predator–prey interactions in the field. By applying the method to two populations of a predatory intertidal whelk, Haustrum scobina, I estimated its per capita attack rates on all nine of its observed prey species. These spanned two orders of magnitude in per capita strength. Concurrent experimental manipulations of the two predator populations provided population time series for the response of a mussel prey species, Xenostrobus pulex. I obtained independent interaction strength estimates for this focal interaction by fitting a sequence of hypothesized predator–prey models to these time series. Overall, site-specific models assuming linear functional responses performed better than all others. A direct comparison of the attack-rate estimates from the observational method with those of the best-performing nonlinear model nevertheless revealed high concordance between the two methods. The results of this study therefore support the use of the observational method in larger and more complex food webs and suggest that trophic interactions in the range of mean prey densities observed in nature are approximately linear.
A key assumption of the ideal free distribution (IFD) is that there are no costs in moving between habitat patches. However, because many populations exhibit more or less continuous population movement between patches and traveling cost is a frequent factor, it is important to determine the effects of costs on expected population movement patterns and spatial distributions. We consider a food chain (tritrophic or bitrophic) in which one species moves between patches, with energy cost or mortality risk in movement. In the two-patch case, assuming forced movement in one direction, an evolutionarily stable strategy requires bidirectional movement, even if costs during movement are high. In the N-patch case, assuming that at least one patch is linked bidirectionally to all other patches, optimal movement rates can lead to source-sink dynamics where patches with negative growth rates are maintained by other patches with positive growth rates. As well, dispersal between patches is not balanced (even in the two-patch case), leading to a deviation from the IFD. Our results indicate that cost-associated forced movement can have important consequences for spatial metapopulation dynamics. Relevance to marine reserve design and the study of stream communities subject to drift is discussed.
Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution.
Over the past 7 years, several authors have used the approach of generalized modeling to study the dynamics of food chains and food webs. Generalized models come close to the efficiency of random matrix models, while being as directly interpretable as conventional differential-equation-based models. Here, we present a pedagogical introduction to the approach of generalized modeling. This introduction places more emphasis on the underlying concepts of generalized modeling than previous publications. Moreover, we propose a shortcut that can significantly accelerate the formulation of generalized models and introduce an iterative procedure that can be used to refine existing generalized models by integrating new biological insights.
How best to predict the effects of perturbations to ecological communities has been a long-standing goal for both applied and basic ecology. This quest has recently been revived by new empirical data, new analysis methods, and increased computing speed, with the promise that ecologically important insights may be obtainable from a limited knowledge of community interactions. We use empirically based and simulated networks of varying size and connectance to assess two limitations to predicting perturbation responses in multispecies communities: (1) the inaccuracy by which species interaction strengths are empirically quantified and (2) the indeterminacy of species responses due to indirect effects associated with network size and structure. We find that even modest levels of species richness and connectance (25 pairwise interactions) impose high requirements for interaction strength estimates because system indeterminacy rapidly overwhelms predictive insights. Nevertheless, even poorly estimated interaction strengths provide greater average predictive certainty than an approach that uses only the sign of each interaction. Our simulations provide guidance in dealing with the trade-offs involved in maximizing the utility of network approaches for predicting dynamics in multispecies communities.
Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.
Many factors contribute to the nonrandom processes of extinctions and invasions that are changing the structure of ecological communities worldwide. These factors include the attributes of the species, their abiotic environment, and the interactions and feedbacks between them. The relative importance of these factors has been difficult to quantify. We used nested subset theory and a novel permutation-based extension of gradient analysis to disentangle the direct and indirect pathways by which these factors affect the metacommunity structure of freshwater fishes inhabiting the streams tributary to the San Francisco Bay. Our analyses provide quantitative measures of how species and stream attributes may influence extinction vulnerability and invasion risk, highlight the need for considering the multiple interacting drivers of community change concurrently, and indicate that the ongoing disassembly and assembly of Bay Area freshwater fish communities are not fully symmetric processes. Fish communities are being taken apart and put back together in only partially analogous trajectories of extinction and invasion for which no single explanatory hypothesis is sufficient. Our study thereby contributes to the forecasting of continued community change and its effects on the functioning of freshwater ecosystems.
Studies of consumer-resource interactions suggest that individual diet specialisation is empirically widespread and theoretically important to the organisation and dynamics of populations and communities. We used weighted networks to analyze the resource use by sea otters, testing three alternative models for how individual diet specialisation may arise. As expected, individual specialisation was absent when otter density was low, but increased at high-otter density. A high-density emergence of nested resource-use networks was consistent with the model assuming individuals share preference ranks. However, a density-dependent emergence of a non-nested modular network for ‘core’ resources was more consistent with the ‘competitive refuge’ model. Individuals from different diet modules showed predictable variation in rank-order prey preferences and handling times of core resources, further supporting the competitive refuge model. Our findings support a hierarchical organisation of diet specialisation and suggest individual use of core and marginal resources may be driven by different selective pressures.
Predators sometimes provide biotic resistance against invasions by nonnative prey. Understanding and predicting the strength of biotic resistance remains a key challenge in invasion biology. A predator's functional response to nonnative prey may predict whether a predator can provide biotic resistance against nonnative prey at different prey densities. Surprisingly, functional responses have not been used to make quantitative predictions about biotic resistance. We parameterized the functional response of signal crayfish (Pacifastacus leniusculus) to invasive New Zealand mud snails (Potamopyrgus antipodarum; NZMS) and used this functional response and a simple model of NZMS population growth to predict the probability of biotic resistance at different predator and prey densities. Signal crayfish were effective predators of NZMS, consuming more than 900 NZMS per predator in a 12 hour period, and Bayesian model fitting indicated their consumption rate followed a type 3 functional response to NZMS density. Based on this functional response and associated parameter uncertainty, we predict that NZMS will be able to invade new systems at low crayfish densities (<0.2 crayfish m-2) regardless of NZMS density. At intermediate to high crayfish densities (>0.2 crayfish m-2), we predict that low densities of NZMS will be able to establish in new communities; however, once NZMS reach a threshold density of approximately 2000 NZMS m-2, predation by crayfish will drive negative NZMS population growth. Further, at very high densities, NZMS overwhelm predation by crayfish and invade. Thus, interacting thresholds of propagule pressure and predator densities define the probability of biotic resistance. Quantifying the shape and uncertainty of predator functional responses to non-native prey may help predict the outcomes of invasions.
Patterns of species interactions affect the dynamics of food webs. An important component of species interactions that is rarely considered with respect to food webs is the strengths of interactions, which may affect both structure and dynamics. In natural systems, these strengths are variable, and can be quantified as probability distributions. We examined how variation in strengths of interactions can be described hierarchically, and how this variation impacts the structure of species interactions in predator–prey networks, both of which are important components of ecological food webs. The stable isotope ratios of predator and prey species may be particularly useful for quantifying this variability, and we show how these data can be used to build probabilistic predator–prey networks. Moreover, the distribution of variation in strengths among interactions can be estimated from a limited number of observations. This distribution informs network structure, especially the key role of dietary specialization, which may be useful for predicting structural properties in systems that are difficult to observe. Finally, using three mammalian predator–prey networks (two African and one Canadian) quantified from stable isotope data, we show that exclusion of link-strength variability results in biased estimates of nestedness and modularity within food webs, whereas the inclusion of body size constraints only marginally increases the predictive accuracy of the isotope-based network. We find that modularity is the consequence of strong link-strengths in both African systems, while nestedness is not significantly present in any of the three predator–prey networks.
San Nicolas Island is surrounded by broad areas of shallow subtidal habitat, characterized by dynamic kelp forest communities that undergo dramatic and abrupt shifts in community composition. Although these reefs are fished, the physical isolation of the island means that they receive less impact from human activities than most reefs in Southern California, making San Nicolas an ideal place to evaluate alternative theories about the dynamics of these communities. Here we present monitoring data from seven sampling stations surrounding the island, including data on fish, invertebrate, and algal abundance. These data are unusual among subtidal monitoring data sets in that they combine relatively frequent sampling (twice per year) with an exceptionally long time series (since 1980). Other outstanding qualities of the data set are the high taxonomic resolution captured and the monitoring of permanent quadrats and swaths where the history of the community structure at specific locations has been recorded through time. Finally, the data span a period that includes two of the strongest ENSO events on record, a major shift in the Pacific decadal oscillation, and the reintroduction of sea otters to the island in 1987 after at least 150 years of absence. These events provide opportunities to evaluate the effects of bottom-up forcing, top- down control, and physical disturbance on shallow rocky reef communities.
Intraguild predation theory centres on two predictions: (i) for an omnivore and an intermediate predator (IG-prey) to coexist on shared resources, the IG-prey must be the superior resource competitor, and (ii) increasing resource productivity causes the IG-prey's equilibrium abundance to decline. I tested these predictions with a series of species-rich food webs along New Zealand's rocky shores, focusing on two predatory whelks, Haustrum haustorium, a trophic omnivore, and Haustrum scobina, the IG-prey. In contrast to theory, the IG-prey's abundance increased with productivity. Furthermore, feeding rates and allometric considerations indicate a competitive advantage for the omnivore when non-shared prey are considered, despite the IG-prey's superiority for shared prey. Nevertheless, clear and regular cross-gradient changes in network structure and interaction strengths were observed that challenge the assumptions of current theory. These insights suggest that the consideration of consumer-dependent functional responses, non-equilibrium dynamics, the dynamic nature of prey choice and non-trophic interactions among basal prey will be fruitful avenues for theoretical development.
Many populations consist of individuals that differ substantially in their diets. Quantification of the magnitude and temporal consistency of such intraspecific diet variation is needed to understand its importance, but the extent to which different approaches for doing so reflect instantaneous versus time-aggregated measures of individual diets may bias inferences. We used direct observations of sea otter individuals (Enhydra lutris nereid) to assess how (i) the time-scale of sampling, (ii) under-sampling, and (iii) the incidence- versus frequency-based consideration of prey species affects the inferred strength and consistency of intraspecific diet variation. Analyses of feeding observations aggregated over hourly to annual intervals revealed a substantial bias associated with time-aggregation that decreases the inferred magnitude of specialization and increases the inferred consistency of individuals’ diets. Time-aggregation also made estimates of specialization more sensitive to the consideration of prey frequency, which decreased estimates relative to the use of prey incidence,. Time-aggregation did not affect the extent to which under-sampling contributed to its overestimation. Our analyses demonstrate the importance of studying intraspecific diet variation with an explicit consideration of time and thereby suggest guidelines for future empirical efforts. Failure to consider time will likely produce inconsistent predictions regarding the effects of intraspecific variation on predator-prey interactions.
Two elements of food webs add significantly to their complexity: The presence of trophic omnivores and the nonlinear nature of predator-prey interactions. I introduce a new observational method for estimating the strengths of species interactions that accounts for the indeterminacy of omnivorous indirect effects and the saturating functional responses that predators exhibit. I present an empirical support for the method’s accuracy by applying it to two populations of the predatory whelk, Haustrum (= Lepsiella) scobina, that is common to the rocky intertidal shores of New Zealand, and comparing these interaction strength estimates with those derived from experimental manipulations of H. scobina’s populations.
I then test two key predictions of intraguild predation theory by investigating how species abundances, food web structure and species interactions strengths change across six omnivorous food webs along a gradient of productivity present around New Zealand’s coastline. I find that the intermediate predator, H. scobina, is the superior competitor for shared prey, as predicted by theory. Counter to theory, however, I show that it is the omnivorous whelk, H. haustorium, that is the superior competitor when all prey are considered, and that H. scobina’s abundance increases with increasing productivity. My analyses reveal clear and regular cross-gradient shifts in interactions that can be incorporated into future modeling efforts.
Finally, I ask to what degree whelk feeding rates are saturated with respect to prey densities and, by extending and parameterizing the classic Rosenzweig-MacArthur model, ask whether empirical interactions are nonlinear enough to affect the stability of whelk-prey dynamics. Results indicate that feeding rates are not strongly saturated and that increasing diet richness has a non-additive effect on a predator’s saturation such that alternative prey have a stabilizing effect on whelk-prey dynamics. I thereby offer a new mechanism by which generalist predators stabilize the dynamics of their species-rich food webs.
My dissertation brings empirical data to bear on the importance of omnivory and the nonlinear nature of trophic interactions. Furthering our understanding of these food web features can contribute much to both the conceptual and applied goals of ecology.