mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling

We need to talk about the role of zooplankton in marine food webs

Zooplankton are the key intermediary between primary production and the fish community and a cornerstone of marine food webs, but they are often poorly represented in models that tend to focus on fish, charismatic top predators, or ocean biogeochemistry. In this study, we use an intermediate complexity end-to-end food web model of the North Sea with explicit two-way coupling of zooplankton to phytoplankton and higher trophic levels to ask whether this matters. We vary the metabolic rate of omnivorous zooplankton (OZ) as a proxy for uncertainties in our understanding and modeling of zooplankton form and function, and moving beyond previous studies we look at the impacts on the food web in concert with climate warming and fishing. We consider impacts on food web state and time to recover the relevant unfished state after fishing ceases. We also consider potential impacts on pelagic and demersal fishing fleets if we assume that they are constrained by the requirement to allow recovery to an unfished state within a certain period of time as a way of ensuring consistency with Good Environmental Status as required by EU and UK legislation. We find that all three aspects considered are highly sensitive to changes in the treatment of zooplankton, with impacts being larger than for warming of 2 or 4°C across most food web functional groups, particularly for apex predators. We call for a programme of research aimed at improving our understanding of zooplankton ecology and its relationship to the wider food web, and we recommend that improved representations of zooplankton are incorporated in future modeling studies as a priority.

Changes in sea floor productivity are crucial to understanding the impact of climate change in temperate coastal ecosystems according to a new size-based model

The multifaceted effects of climate change on physical and biogeochemical processes are rapidly altering marine ecosystems but often are considered in isolation, leaving our understanding of interactions between these drivers of ecosystem change relatively poor. This is particularly true for shallow coastal ecosystems, which are fuelled by a combination of distinct pelagic and benthic energy pathways that may respond to climate change in fundamentally distinct ways. The fish production supported by these systems is likely to be impacted by climate change differently to those of offshore and shelf ecosystems, which have relatively simpler food webs and mostly lack benthic primary production sources. We developed a novel, multispecies size spectrum model for shallow coastal reefs, specifically designed to simulate potential interactive outcomes of changing benthic and pelagic energy inputs and temperatures and calculate the relative importance of these variables for the fish community. Our model, calibrated using field data from an extensive temperate reef monitoring program, predicts that changes in resource levels will have much stronger impacts on fish biomass and yields than changes driven by physiological responses to temperature. Under increased plankton abundance, species in all fish trophic groups were predicted to increase in biomass, average size, and yields. By contrast, changes in benthic resources produced variable responses across fish trophic groups. Increased benthic resources led to increasing benthivorous and piscivorous fish biomasses, yields, and mean body sizes, but biomass decreases among herbivore and planktivore species. When resource changes were combined with warming seas, physiological responses generally decreased species' biomass and yields. Our results suggest that understanding changes in benthic production and its implications for coastal fisheries should be a priority research area. Our modified size spectrum model provides a framework for further study of benthic and pelagic energy pathways that can be easily adapted to other ecosystems.

Towards vibrant fish populations and sustainable fisheries that benefit all: learning from the last 30 years to inform the next 30 years

A common goal among fisheries science professionals, stakeholders, and rights holders is to ensure the persistence and resilience of vibrant fish populations and sustainable, equitable fisheries in diverse aquatic ecosystems, from small headwater streams to offshore pelagic waters. Achieving this goal requires a complex intersection of science and management, and a recognition of the interconnections among people, place, and fish that govern these tightly coupled socioecological and sociotechnical systems. The World Fisheries Congress (WFC) convenes every four years and provides a unique global forum to debate and discuss threats, issues, and opportunities facing fish populations and fisheries. The 2021 WFC meeting, hosted remotely in Adelaide, Australia, marked the 30th year since the first meeting was held in Athens, Greece, and provided an opportunity to reflect on progress made in the past 30 years and provide guidance for the future. We assembled a diverse team of individuals involved with the Adelaide WFC and reflected on the major challenges that faced fish and fisheries over the past 30 years, discussed progress toward overcoming those challenges, and then used themes that emerged during the Congress to identify issues and opportunities to improve sustainability in the world's fisheries for the next 30 years. Key future needs and opportunities identified include: rethinking fisheries management systems and modelling approaches, modernizing and integrating assessment and information systems, being responsive and flexible in addressing persistent and emerging threats to fish and fisheries, mainstreaming the human dimension of fisheries, rethinking governance, policy and compliance, and achieving equity and inclusion in fisheries. We also identified a number of cross-cutting themes including better understanding the role of fish as nutrition in a hungry world, adapting to climate change, embracing transdisciplinarity, respecting Indigenous knowledge systems, thinking ahead with foresight science, and working together across scales. By reflecting on the past and thinking about the future, we aim to provide guidance for achieving our mutual goal of sustaining vibrant fish populations and sustainable fisheries that benefit all. We hope that this prospective thinking can serve as a guide to (i) assess progress towards achieving this lofty goal and (ii) refine our path with input from new and emerging voices and approaches in fisheries science, management, and stewardship.

Metabolic responses of predators to prey density

The metabolic cost of foraging is the dark energy of ecological systems. It is much harder to observe and to measure than its beneficial counterpart, prey consumption, yet it is not inconsequential for the dynamics of prey and predator populations. Here I define the metabolic response as the change in energy expenditure of predators in response to changes in prey density. It is analogous and intrinsically linked to the functional response, which is the change in consumption rate with prey density, as they are both shaped by adjustments in foraging activity. These adjustments are adaptive, ubiquitous in nature, and are implicitly assumed by models of predator–prey dynamics that impose consumption saturation in functional responses. By ignoring the associated metabolic responses, these models violate the principle of energy conservation and likely underestimate the strength of predator–prey interactions. Using analytical and numerical approaches, I show that missing this component of interaction has broad consequences for dynamical stability and for the robustness of ecosystems to persistent environmental or anthropogenic stressors. Negative metabolic responses – those resulting from decreases in foraging activity when more prey is available, and arguably the most common – lead to lower local stability of food webs and a faster pace of change in population sizes, including higher excitability, higher frequency of oscillations, and quicker return times to equilibrium when stable. They can also buffer the effects of press perturbations, such as harvesting, on target populations and on their prey through top-down trophic cascades, but are expected to magnify bottom-up cascades, including the effects of nutrient enrichment or the effects of altering lower trophic levels that can be caused by environmental forcing and climate change. These results have implications for any resource management approach that relies on models of food web dynamics, which is the case of many applications of ecosystem-based fisheries management. Finally, besides having their own individual effects, metabolic responses have the potential to greatly alter, or even invert, functional response-stability relationships, and therefore can be critical to an integral understanding of predation and its influence on population dynamics and persistence.

Temperature impacts on fish physiology and resource abundance lead to faster growth but smaller fish sizes and yields under warming

Resolving the combined effect of climate warming and exploitation in a food web context is key for predicting future biomass production, size-structure and potential yields of marine fishes. Previous studies based on mechanistic size-based food web models have found that bottom-up processes are important drivers of size-structure and fisheries yield in changing climates. However, we know less about the joint effects of 'bottom-up' and physiological effects of temperature; how do temperature effects propagate from individual-level physiology through food webs and alter the size-structure of exploited species in a community? Here, we assess how a species-resolved size-based food web is affected by warming through both these pathways and by exploitation. We parameterize a dynamic size spectrum food web model inspired by the offshore Baltic Sea food web, and investigate how individual growth rates, size-structure, and relative abundances of species and yields are affected by warming. The magnitude of warming is based on projections by the regional coupled model system RCA4-NEMO and the RCP 8.5 emission scenario, and we evaluate different scenarios of temperature dependence on fish physiology and resource productivity. When accounting for temperature-effects on physiology in addition to on basal productivity, projected size-at-age in 2050 increases on average for all fish species, mainly for young fish, compared to scenarios without warming. In contrast, size-at-age decreases when temperature affects resource dynamics only, and the decline is largest for young fish. Faster growth rates due to warming, however, do not always translate to larger yields, as lower resource carrying capacities with increasing temperature tend to result in decline in the abundance of larger fish and hence spawning stock biomass. These results suggest that to understand how global warming affects the size structure of fish communities, both direct metabolic effects and indirect effects of temperature via basal resources must be accounted for.

Managing fisheries for maximum nutrient yield

Wild-caught fish are a bioavailable source of nutritious food that, if managed strategically, could enhance diet quality for billions of people. However, optimising nutrient production from the sea has not been a priority, hindering development of nutrition-sensitive policies. With fisheries management increasingly effective at rebuilding stocks and regulating sustainable fishing, we can now begin to integrate nutritional outcomes within existing management frameworks. Here, we develop a conceptual foundation for managing fisheries for multispecies Maximum Nutrient Yield (mMNY). We empirically test our approach using size-based models of North Sea and Baltic Sea fisheries and show that mMNY is predicted by the relative contribution of nutritious species to total catch and their vulnerability to fishing, leading to trade-offs between catch and specific nutrients. Simulated nutrient yield curves suggest that vitamin D, which is deficient in Northern European diets, was underfished at fishing levels that returned maximum catch weights. Analysis of global catch data shows there is scope for nutrient yields from most of the world's marine fisheries to be enhanced through nutrient-sensitive fisheries management. With nutrient composition data now widely available, we expect our mMNY framework to motivate development of nutrient-based reference points in specific contexts, such as data-limited fisheries. Managing for mMNY alongside policies that promote access to fish could help close nutrient gaps for coastal populations, maximising the contribution of wild-caught fish to global food and nutrition security.

Using Food Webs and Metabolic Theory to Monitor, Model, and Manage Atlantic Salmon—A Keystone Species Under Threat

Populations of Atlantic salmon are crashing across most of its natural range: understanding the underlying causes and predicting these collapses in time to intervene effectively are urgent ecological and socioeconomic priorities. Current management techniques rely on phenomenological analyses of demographic population time-series and thus lack a mechanistic understanding of how and why populations may be declining. New multidisciplinary approaches are thus needed to capitalize on the long-term, large-scale population data that are currently scattered across various repositories in multiple countries, as well as marshaling additional data to understand the constraints on the life cycle and how salmon operate within the wider food web. Here, we explore how we might combine data and theory to develop the mechanistic models that we need to predict and manage responses to future change. Although we focus on Atlantic salmon—given the huge data resources that already exist for this species—the general principles developed here could be applied and extended to many other species and ecosystems.

Refocusing multiple stressor research around the targets and scales of ecological impacts

Ecological communities face a variety of environmental and anthropogenic stressors acting simultaneously. Stressor impacts can combine additively or can interact, causing synergistic or antagonistic effects. Our knowledge of when and how interactions arise is limited, as most models and experiments only consider the effect of a small number of non-interacting stressors at one or few scales of ecological organization. This is concerning because it could lead to significant underestimations or overestimations of threats to biodiversity. Furthermore, stressors have been largely classified by their source rather than by the mechanisms and ecological scales at which they act (the target). Here, we argue, first, that a more nuanced classification of stressors by target and ecological scale can generate valuable new insights and hypotheses about stressor interactions. Second, that the predictability of multiple stressor effects, and consistent patterns in their impacts, can be evaluated by examining the distribution of stressor effects across targets and ecological scales. Third, that a variety of existing mechanistic and statistical modelling tools can play an important role in our framework and advance multiple stressor research.

From data compilation to model validation: comparing three ecosystem models of the Tasman and Golden Bays, New Zealand

The Tasman and Golden Bays (TBGB) are a semi-enclosed embayment system in New Zealand that supports numerous commercial and recreational activities. We present three ecosystem models of the TBGB ecosystem with varying levels of complexity, aimed at contributing as tools to aid in understanding this ecosystem and its responses to anthropogenic and natural pressures. We describe the process of data compilation through to model validation and analyse the importance of knowledge gaps with respect to model dynamics and results. We compare responses in all three models to historical fishing, and analyse similarities and differences in the dynamics of the three models. We assessed the most complex of the models against initialisation uncertainty and sensitivity to oceanographic variability and found it most sensitive to the latter. We recommend that scenarios relating to ecosystem dynamics of the TBGB ecosystem include sensitivities, especially oceanographic uncertainty, and compare responses across all three models where it is possible to do so.

Should we account for mesozooplankton reproduction and ontogenetic growth in biogeochemical modeling?

Mesozooplankton play a key role in marine ecosystems as they modulate the transfer of energy from phytoplankton to large marine organisms. In addition, they directly influence the oceanic cycles of carbon and nutrients through vertical migrations, fecal pellet production, respiration, and excretion. Mesozooplankton are mainly made up of metazoans, which undergo important size changes during their life cycle, resulting in significant variations in metabolic rates. However, most marine biogeochemical models represent mesozooplankton as protists-like organisms. Here, we study the potential caveats of this simplistic representation by using a chemostat-like zero-dimensional model with four different Nutrient-Phytoplankton-Zooplankton configurations in which the description of mesozooplankton ranges from protist-type organisms to using a size-based formulation including explicit reproduction and ontogenetic growth. We show that the size-based formulation strongly impacts mesozooplankton. First, it generates a delay of a few months in the response to an increase in food availability. Second, the increase in mesozooplankton biomass displays much larger temporal variations, in the form of successive cohorts, because of the dependency of the ingestion rate to body size. However, the size-based formulation does not affect smaller plankton or nutrient concentrations. A proper assessment of these top-down effects would require implementing our size-resolved approach in a 3-dimensional biogeochemical model. Furthermore, the bottom-up effects on higher trophic levels resulting from the significant changes in the temporal dynamics of mesozooplankton could be estimated in an end-to-end model coupling low and high trophic levels.

Interacting forces of predation and fishing affect species' maturation size

Fishing is a strong selective force and is supposed to select for earlier maturation at smaller body size. However, the extent to which fishing-induced evolution is shaping ecosystems remains debated. This is in part because it is challenging to disentangle fishing from other selective forces (e.g., size-structured predation and cannibalism) in complex ecosystems undergoing rapid change.Changes in maturation size from fishing and predation have previously been explored with multi-species physiologically structured models but assumed separation of ecological and evolutionary timescales. To assess the eco-evolutionary impact of fishing and predation at the same timescale, we developed a stochastic physiologically size-structured food-web model, where new phenotypes are introduced randomly through time enabling dynamic simulation of species' relative maturation sizes under different types of selection pressures.Using the model, we carried out a fully factorial in silico experiment to assess how maturation size would change in the absence and presence of both fishing and predation (including cannibalism). We carried out ten replicate stochastic simulations exposed to all combinations of fishing and predation in a model community of nine interacting fish species ranging in their maximum sizes from 10 g to 100 kg. We visualized and statistically analyzed the results using linear models.The effects of fishing on maturation size depended on whether or not predation was enabled and differed substantially across species. Fishing consistently reduced the maturation sizes of two largest species whether or not predation was enabled and this decrease was seen even at low fishing intensities (F = 0.2 per year). In contrast, the maturation sizes of the three smallest species evolved to become smaller through time but this happened regardless of the levels of predation or fishing. For the four medium-size species, the effect of fishing was highly variable with more species showing significant and larger fishing effects in the presence of predation.Ultimately our results suggest that the interactive effects of predation and fishing can have marked effects on species' maturation sizes, but that, at least for the largest species, predation does not counterbalance the evolutionary effect of fishing. Our model also produced relative maturation sizes that are broadly consistent with empirical estimates for many fish species.

LeMaRns: A Length-based Multi-species analysis by numerical simulation in R

Fish stocks interact through predation and competition for resources, yet stocks are typically managed independently on a stock-by-stock basis. The need to take account of multi-species interactions is widely acknowledged. However, examples of the application of multi-species models to support management decisions are limited as they are often seen as too complex and lacking transparency. Thus there is a need for simple and transparent methods to address stock interactions in a way that supports managers. Here we introduce LeMaRns, a new R-package of a general length-structured fish community model, LeMans, that characterises fishing using fleets that can have different gears and species catch preferences. We describe the model, package implementation, and give three examples of use: determination of multi-species reference points; modelling of mixed-fishery interactions; and examination of the response of community indicators to dynamical changes in fleet effort within a mixed-fishery. LeMaRns offers a diverse array of options for parameterisation. This, along with the speed, comprehensive documentation, and open source nature of the package makes LeMans newly accessible, transparent, and easy to use, which we hope will lead to increased uptake by the fisheries management community.

Dome patterns in pelagic size spectra reveal strong trophic cascades

In ecological communities, especially the pelagic zones of aquatic ecosystems, certain body-size ranges are often over-represented compared to others. Community size spectra, the distributions of community biomass over the logarithmic body-mass axis, tend to exhibit regularly spaced local maxima, called “domes”, separated by steep troughs. Contrasting established theory, we explain these dome patterns as manifestations of top-down trophic cascades along aquatic food chains. Compiling high quality size-spectrum data and comparing these with a size-spectrum model introduced in this study, we test this theory and develop a detailed picture of the mechanisms by which bottom-up and top-down effects interact to generate dome patterns. Results imply that strong top-down trophic cascades are common in freshwater communities, much more than hitherto demonstrated, and may arise in nutrient rich marine systems as well. Transferring insights from the general theory of non-linear pattern formation to domes patterns, we provide new interpretations of past lake-manipulation experiments.

An important question in ecology is how much species at higher trophic levels affect lower levels through top-down cascades. Here the authors show through analyses of pelagic size spectra that such cascades are strong in freshwater systems and can also arise in nutrient rich marine systems.

Early warning signals of recovery in complex systems

Early warning signals (EWSs) offer the hope that patterns observed in data can predict the future states of ecological systems. While a large body of research identifies such signals prior to the collapse of populations, the prediction that such signals should also be present before a system’s recovery has thus far been overlooked. We assess whether EWSs are present prior to the recovery of overexploited marine systems using a trait-based ecological model and analysis of real-world fisheries data. We show that both abundance and trait-based signals are independently detectable prior to the recovery of stocks, but that combining these two signals provides the best predictions of recovery. This work suggests that the efficacy of conservation interventions aimed at restoring systems which have collapsed may be predicted prior to the recovery of the system, with direct relevance for conservation planning and policy.

While several studies have documented early warning signals of population collapse, the use of such signals as indicators of population recovery has not been investigated. Here the authors use models and empirical fisheries data to show that there are statistical indicators preceding recovery of cod populations.

A size-structured matrix model to simulate dynamics of marine community size spectrum

Several types of size-based models have been developed to model the size spectra of marine communities, in which abundance scales strongly with body size, using continuous differential equations. In this study, we develop a size-structured matrix model, which can be seen as a discretization of the Mckendrick-von Foerster equation, to simulate the dynamics of marine communities. The developed model uses a series of simple body size power functions to describe the basic processes of predator–prey interactions, reproduction, metabolism, and non-predation mortality based on the principle of mass balance. Linear size spectra with slopes of approximately –1 are successfully reproduced by this model. Several examples of numerical simulations are provided to demonstrate the model’s behavior. Size spectra with cut-offs and/or waves are also found for certain parameter values. The matrix model is flexible and can be freely manipulated by users to answer different questions and is executed over a shorter numerical calculation running time than continuous models.

High fishery catches through trophic cascades in China

Indiscriminate and intense fishing has occurred in many marine ecosystems around the world. Although this practice may have negative effects on biodiversity and populations of individual species, it may also increase total fishery productivity by removing predatory fish. We examine the potential for this phenomenon to explain the high reported wild catches in the East China Sea-one of the most productive ecosystems in the world that has also had its catch reporting accuracy and fishery management questioned. We show that reported catches can be approximated using an ecosystem model that allows for trophic cascades (i.e., the depletion of predators and consequent increases in production of their prey). This would be the world's largest known example of marine ecosystem "engineering" and suggests that trade-offs between conservation and food production exist. We project that fishing practices could be modified to increase total catches, revenue, and biomass in the East China Sea, but single-species management would decrease both catches and revenue by reversing the trophic cascades. Our results suggest that implementing single-species management in currently lightly managed and highly exploited multispecies fisheries (which account for a large fraction of global fish catch) may result in decreases in global catch. Efforts to reform management in these fisheries will need to consider system wide impacts of changes in management, rather than focusing only on individual species.