arXiv subjects

Justin D. Yeakel

Publications and source records attributed to Justin D. Yeakel.

16 recordsLinked to original sources

arXiv2025

Functional Motifs in Foodwebs and Networks

When studying a complex system it is often useful to think of the system as a network of interacting units. One can then ask if some properties of the entire network are already explained by a small part of the network - a network motif. A famous example of an ecological motif is competitive exclusion in foodwebs, where the presence of two species competing for a shared resource precludes the existence of a stable equilibrium for the whole system. However, other examples of motifs with such direct impacts on stability are not known. Here we explain why small motifs that allow conclusions on systemic stability are rare. Moreover, we show that another dynamical property, reactivity, is naturally rooted in motifs. Computing the reactivity in motifs can reveal which parts of a network are prone to respond violently to perturbations. This highlights motif reactivity as a useful property to measure in real-world systems to understand likely modes of systemic failure in foodwebs, epidemics, supply chains and other applications.

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arXiv2025

Bioenergetic trophic trade-offs determine mass-dependent extinction thresholds across the Cenozoic

Body size drives the energetic demands of organisms, constraining trophic interactions between species and playing a significant role in shaping the feasibility of species' populations in a community. On macroevolutionary timescales, these demands feed back to shape the selective landscape driving the evolution of body size and diet. We develop a theoretical framework for a three-level trophic food chain -- typical for terrestrial mammalian ecosystems -- premised on bioenergetic trade-offs to explore mammalian population dynamics. Our results show that interactions between predators, prey, and external subsidies generate instabilities linked to body size extrema, corresponding to observed limits of predator size and diet. These instabilities generate size-dependent constraints on coexistence and highlight a feasibility range for carnivore size between 40 to 110 kg, encompassing the mean body size of terrestrial Cenozoic hypercarnivores. Finally, we show that predator dietary generalization confers a selective advantage to larger carnivores, which then declines at megapredator body sizes, aligning with diet breadth estimates for contemporary and Pleistocene species. Our framework underscores the importance of understanding macroevolutionary constraints through the lens of ecological pressures, where the selective forces shaping and reshaping the dynamics of communities can be explored.

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arXiv2025

Coarse-Graining Cascades Within Food Webs

Quantifying population dynamics is a fundamental challenge in ecology and evolutionary biology, particularly for species that are cryptic, microscopic, or extinct. Traditional approaches rely on continuous representations of population size, but in many cases, the precise number of individuals is unknowable. Here, we present a coarse-grained population model that simplifies population dynamics to binary states - high or low - determined by the balance of bottom-up resource availability and top-down predation pressure. This Boolean framework provides a minimal yet analytically tractable alternative to traditional Lotka-Volterra-based models, enabling direct insights into the role of food web structure in shaping community stability. Using this approach, we investigate how trophic interactions influence population persistence, cyclic dynamics, and extinction risk across model food webs. We find that top-down effects are a primary driver of cycling, aligning with theoretical expectations from traditional population models, and that trophic position strongly influences extinction risk, with higher-trophic species more prone to persistent low-population states. Additionally, we explore the role of trophic short-circuits -- direct interactions between apex predators and low-trophic prey -- and find that they can buffer cascades and alter extinction patterns in ways that are often overlooked in classical models. By simplifying population dynamics to a two-state system, this framework provides a powerful tool for disentangling the structural drivers of community stability. These results highlight the potential of coarse-grained approaches to complement existing models, offering new insights into trophic interactions, extinction risks, and the susceptibility of species to trophic cascades.

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arXiv2023

On the dynamics of mortality and the ephemeral nature of mammalian megafauna

Energy flow through consumer-resource interactions is largely determined by body size. Allometric relationships govern the dynamics of populations by impacting rates of reproduction, as well as alternative sources of mortality, which have differential impacts on smaller to larger organisms. Here we derive and investigate the timescales associated with four alternative sources of mortality for terrestrial mammals: mortality from starvation, mortality associated with aging, mortality from consumption by predators, and mortality introduced by anthropogenic subsidized harvest. The incorporation of these allometric relationships into a minimal consumer-resource model illuminates central constraints that may contribute to the structure of mammalian communities. Our framework reveals that while starvation largely impacts smaller-bodied species, the allometry of senescence is expected to be more difficult to observe. In contrast, external predation and subsidized harvest have greater impacts on the populations of larger-bodied species. Moreover, the inclusion of predation mortality reveals mass thresholds for mammalian herbivores, where dynamic instabilities may limit the feasibility of megafaunal populations. We show how these thresholds vary with alternative predator-prey mass relationships, which are not well understood within terrestrial systems. Finally, we use our framework to predict the harvest pressure required to induce mass-specific extinctions, which closely align with previous estimates of anthropogenic megafaunal exploitation in both paleontological and historical contexts. Together our results underscore the tenuous nature of megafaunal populations, and how different sources of mortality may contribute to their ephemeral nature over evolutionary time.

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arXiv2019

Caching in or falling back at the Sevilleta

Foraging in uncertain environments requires balancing the risks associated with finding alternative resources against potential gains. In aridland environments characterized by extreme variation in the amount and seasonal timing of primary production, consumer communities must weigh the risks associated with foraging for preferred seeds that can be cached against fallback foods of low nutritional quality (e.g., leaves) that must be consumed immediately. Here we explore the influence of resource-scarcity, body size, and seasonal uncertainty on the expected foraging behaviors of caching rodents in the northern Chihuahaun Desert by integrating these elements with a Stochastic Dynamic Program (SDP) to determine fitness-maximizing foraging strategies. We demonstrate that resource-limited environments promote dependence on fallback foods, reducing the likelihood of starvation while increasing future risk exposure. Our results point to a qualitative difference in the use of fallback foods and the fitness benefits of caching at the threshold body size of 50 g. Above this threshold the fitness benefits are greater for consumers with smaller caches, affirming empirical observations of cache use among rodents in such dynamic environments. This suggests that larger-bodied consumers with larger caches may be less sensitive to the future uncertainties in monsoonal onset predicted by global climate scenarios.

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arXiv2019

Diverse interactions and ecosystem engineering stabilize community assembly

The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact not only with each other but indirectly through environmental effects, however the role of these ecosystem engineers has not yet been considered in models of ecological networks. Here we explore the dynamics of ecosystem assembly, where the colonization and extinction of species within a community depends on the constraints imposed by trophic, service, and engineering dependencies. We show that our assembly model reproduces many key features of ecological systems, such as the role of generalists during assembly, realistic maximum trophic levels, and increased nestedness with higher frequencies of mutualisms. We find that ecosystem engineering has large and nonlinear effects on extinction rates, facilitating robustness by creating niche space, but at the same time increasing the magnitude of extinction cascades. We emphasize the importance of redundancies in engineered effects and show that such redundancy lowers the barriers to colonization, promoting community diversity. Together, our results suggest that ecological engineers may enhance community diversity while increasing persistence by facilitating colonization and limiting competitive exclusion.

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arXiv2019

Scaling of the risk landscape drives optimal life history strategies and the evolution of grazing

Consumers face numerous risks that can be minimized by incorporating different life-history strategies. How much and when a consumer adds to its energetic reserves or invests in reproduction are key behavioral and physiological adaptations that structure much of how organisms interact. Here we develop a theoretical framework that explicitly accounts for stochastic fluctuations of an individual consumer's energetic reserves while foraging and reproducing on a landscape with resources that range from uniformly distributed to highly clustered. First, we show that optimal life-history strategies vary in response to changes in the mean productivity of the resource landscape, where depleted environments promote reproduction at lower energetic states, greater investment in each reproduction event, and smaller litter sizes. We then show that if resource variance scales with body size due to landscape clustering, consumers that forage for clustered foods are susceptible to strong Allee effects, increasing extinction risk. Finally, we show that the proposed relationship between consumer body size, resource clustering, and Allee effect-induced population instability offers key ecological insights into the evolution of large-bodied grazing herbivores from small-bodied browsing ancestors.

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arXiv2017

The dynamics of starvation and recovery

The eco-evolutionary dynamics of species are fundamentally linked to the energetic constraints of its constituent individuals. Of particular importance is the interplay between reproduction and the dynamics of starvation and recovery. To elucidate this interplay, we introduce a nutritional state-structured model that incorporates two classes of consumer: nutritionally replete, reproducing consumers, and undernourished, non-reproducing consumers. We obtain strong constraints on starvation and recovery rates by deriving allometric scaling relationships and find that population dynamics are typically driven to a steady state. Moreover, these rates fall within a 'refuge' in parameter space, where the probability of population extinction is minimized. We also show that our model provides a natural framework to predict maximum mammalian body size by determining the relative stability of an otherwise homogeneous population to a competing population with altered percent body fat. This framework provides a principled mechanism for a selective driver of Cope's rule.

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arXiv2017

Eco-evolutionary dynamics and collective dispersal: implications for salmon metapopulation robustness

The spatial dispersal of individuals is known to play an important role in the dynamics of populations, and is central to metapopulation theory. At the same time, local adaptation to environmental conditions creates a geographic mosaic of evolutionary forces, where the combined drivers of selection and gene flow interact. Although the dispersal of individuals from donor to recipient populations provides connections within the metapopulation, promoting demographic and evolutionary rescue, it may also introduce maladapted individuals into habitats host to different environmental conditions, potentially lowering the fitness of the recipient population. Here we explore a model of the eco-evolutionary dynamics between two populations connected by dispersal, where the productivity of each is defined by a trait complex that is subject to local selection. Although general in nature, our model is inspired by salmon metapopulations, where dispersal between populations is defined in terms of the straying rate, which has been shown to be density-dependent. The results of our model reveal that increased straying between evolving populations leads to alternative stable states, which has large and nonlinear effects on two measures of metapopulation robustness: the portfolio effect and the time to recovery following an induced disturbance. We show that intermediate levels of straying result in large gains in robustness, and that increased habitat heterogeneity promotes robustness when straying rates are low, and erodes robustness when straying rates are high. Finally, we show that density-dependent straying promotes robustness, particularly when the aggregate biomass is low and straying is correspondingly high, which has important ramifications for the conservation of salmon metapopulations facing both natural and anthropogenic disturbances.

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arXiv2017

Revealing biases in the sampling of ecological interaction networks

The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the links between nodes). These issues may affect the accuracy of empirically constructed ecological networks. We explore the properties of sampled ecological networks by simulating large-scale ecological networks with predetermined topologies, and sampling them with different mathematical procedures. Several types of modular networks were generated, intended to represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different sampling designs that may be encountered in field experiments. The observed networks generated by each sampling process were analyzed with respect to number and size of components. We show that the sampling effort needed to estimate underlying network properties depends both on the sampling design and on network topology. Networks with random or scale-free modules require more complete sampling compared to networks whose modules are nested or bipartite. Overall, the structure of nested modules was the easiest to detect, regardless of sampling design. Sampling according to species degree was consistently found to be the most accurate strategy to estimate network structure. Conversely, sampling according to module results in an accurate view of certain modules, but fails to provide a global picture of the underlying network. We recommend that these findings are incorporated into the design of projects aiming to characterize large networks of species interactions in the field, to reduce sampling biases. The software scripts developed to construct and sample networks are provided for further explorations of network structure and comparisons to real interaction data.

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arXiv2016

Exploring the isotopic niche: isotopic variance, physiological incorporation, and the temporal dynamics of foraging

Consumer foraging behaviors are dynamic, changing in response to prey availability, seasonality, competition, and even the consumer's physiological state. The isotopic composition of a consumer is a product of these factors as well as the isotopic 'landscape' of its prey, i.e. the isotopic mixing space. Here we build a mechanistic framework that links the ecological and physiological processes of an individual consumer to the isotopic distribution that describes its diet, and ultimately to the isotopic composition of its own tissues, defined as its 'isotopic niche'. By coupling these processes, we systematically investigate under what conditions the isotopic niche of a consumer changes as a function of both the geometric properties of its mixing space and foraging strategies that may be static or dynamic over time. Results of our derivations reveal general insight into the conditions impacting isotopic niche width as a function of consumer specialization on prey, as well as the consumer's ability to transition between diets over time. We show analytically that moderate specialization on isotopically unique prey can serve to maximize a consumer's isotopic niche width, while temporally dynamic diets will tend to result in peak isotopic variance during dietary transitions. We demonstrate the relevance of our theoretical findings by examining a marine system composed of nine invertebrate species commonly consumed by sea otters. In general, our analytical framework highlights the complex interplay of mixing space geometry and consumer dietary behavior in driving expansion and contraction of the isotopic niche. Because this approach is established on ecological mechanism, it is well-suited for enhancing the ecological interpretation, and uncovering the root causes, of observed isotopic data.

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arXiv2014

Collapse of an ecological network in Ancient Egypt

The dynamics of ecosystem collapse are fundamental to determining how and why biological communities change through time, as well as the potential effects of extinctions on ecosystems. Here we integrate depictions of mammals from Egyptian antiquity with direct lines of paleontological and archeological evidence to infer local extinctions and community dynamics over a 6000-year span. The unprecedented temporal resolution of this data set enables examination of how the tandem effects of human population growth and climate change can disrupt mammalian communities. We show that the extinctions of mammals in Egypt were nonrandom, and that destabilizing changes in community composition coincided with abrupt aridification events and the attendant collapses of some complex societies. We also show that the roles of species in a community can change over time, and that persistence is predicted by measures of species sensitivity, a function of local dynamic stability. Our study is the first high-resolution analysis of the ecological impacts of environmental change on predator-prey networks over millennial timescales, and sheds light on the historical events that have shaped modern animal communities.

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arXiv2013

Compensatory dynamics of fish recruitment illuminated by functional elasticities

Models of Stock Recruitment Relationships (SRRs) are often used to predict fish population dynamics. Commonly used SRRs include the Ricker, Beverton-Holt, and Cushing functional forms, which differ primarily by the degree of density dependent effects (compensation). The degree of compensation determines whether recruitment respectively decreases, saturates, or increases at high levels of spawning stock biomass. In 1982 J.G. Shepherd united these dynamics into a single model, where the degree of compensation is determined by a single parameter, however the difficulty in relating this parameter to biological data has limited its usefulness. Here we use a generalized modeling framework to show that the degree of compensation can be related directly to the functional elasticity of growth, which is a general quantity that measures the change in recruitment relative to a change in biomass, irrespective of the specific SRR. We show that the elasticity of growth can be calculated from short-term fluctuations in fish biomass, is robust to observation error, and can be used to determine general attributes of the SRR in both continuous time production models, as well as discrete time age-structured models. This framework may be particularly useful if fisheries time-series data are limited, and not conducive to determining functional relationships using traditional methods of statistical best-fit.

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arXiv2013

Functional morphology, stable isotopes, and human evolution: a model of consilience

Foraging is constrained by the energy within resources and the mechanics of acquisition and assimilation. Thick molar enamel, a character trait differentiating hominins from African apes, is predicted to mitigate the mechanical costs of chewing obdurate foods. The classic expression of hyperthick enamel together with relatively massive molars, termed megadontia, is most evident in {\it Paranthropus}, a lineage of hominins that lived ca. 2.7 to 1.2 million years ago. Among contemporary primates, thicker molar enamel corresponds with the consumption of stiffer, deformation-resistant foods, possibly because thicker enamel can better resist cracking under high compressive loads. Accordingly, plant underground storage organs (USOs) are thought to be a central food resource for hominins such as {\it Paranthropus} due to their abundance, isotopic composition, and mechanical properties. Here, we present a process-based model to investigate foraging constraints as a function of energetic demands and enamel wear among human ancestors. Our framework allows us to determine the fitness benefits of megadontia, and to explore under what conditions stiff foods such as USOs are predicted to be chosen as fallback, rather than preferred, resources. Our model predictions bring consilience to the noted disparity between functional interpretations of megadontia and microwear evidence, particularly with respect to {\it Paranthropus boisei}.

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arXiv2013

The impact of climate change on the structure of Pleistocene mammoth steppe food webs

Species interactions shape predator-prey networks, impacting community structure and, potentially, ecological dynamics. It is likely that global climatic perturbations that occur over long periods of time have a significant impact on species interactions patterns. However, observations of how these patterns change over time are typically limited to extant communities, which is particularly problematic for communities with long-lived species. Here we integrate stable isotope analysis and network theory to reconstruct patterns of trophic interactions for six independent mammalian communities that inhabited mammoth steppe environments spanning western Europe to eastern Alaska during the Pleistocene. We use a Bayesian mixing model to quantify the proportional contribution of prey to the diets of local predators, and assess how the structure of trophic interactions changed across space and the Last Glacial Maximum (LGM), a global climatic event that severely impacted mammoth steppe communities. We find that large felids had diets that were more constrained than other co-occurring predators, and largely influenced by an increase in {\it Rangifer} abundance after the LGM. Moreover, the structural organization of Beringian and European communities strongly differed: compared to Europe, species interactions in Beringian communities before the LGM were highly compartmentalized, or modular. This modularity was lost during the LGM, and partially recovered after the glacial retreat, and we suggest that changes in modularity among predators and prey may have been driven by geographic insularity.

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arXiv2010

Generalized modeling of ecological population dynamics

Over the past 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.

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