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Abstract The allometric trophic network (ATN) framework for modeling population dynamics has provided numerous insights into ecosystem functioning in recent years. Herein we extend ATN modeling of the intertidal ecosystem off central Chile to include empirical data on pelagic chlorophyll-a concentration. This intertidal community requires subsidy of primary productivity to support its rich ecosystem. Previous work models this subsidy using a constant rate of phytoplankton input to the system. However, data shows pelagic subsidies exhibit highly variable, pulse-like behavior. The primary contribution of our work is incorporating this variable input into ATN modeling to simulate how this ecosystem may respond to pulses of pelagic phytoplankton. Our model results show that: (1) closely related sea snails respond differently to phytoplankton variability, which is explained by the underlying network structure of the food web; (2) increasing the rate of pelagic-intertidal mixing increases fluctuations in species’ biomasses that may increase the risk of local extirpation; (3) predators are the most sensitive species to phytoplankton biomass fluctuations, putting these species at greater risk of extirpation than others. Finally, our work provides a straightforward way to incorporate empirical, time-series data into the ATN framework that will expand this powerful methodology to new applications. 

Abstract The Peruvian Province, from 6° S in Peru to 42° S in Chile, is a highly productive coastal marine region whose biology and fossil record have long been studied separately but never integrated. To understand how past events and conditions affected today's species composition and interactions, we examined the role of extinction, colonization, geologic changes to explain previously unrecognized peculiar features of the biota and to compare the Peruvian Province's history to that of other climatically similar temperate coasts. We synthesized all available data on the benthic (or benthically feeding) biota, with emphasis on fossilizable taxa, for the interval from the Miocene (23–5.4 Ma) and Pliocene (5.4–2.5 Ma) to the present. We outline the history of ecological guilds including primary producers, herbivores, predators, and suspension‐feeders and document patterns of extinction, colonization, and geographic restriction. We identify twelve unusual attributes of the biota, most of which are the result of repeated episodes of extinction. Several guilds present during the Miocene and Pliocene are not represented in the province today, while groups such as kelps and perhaps intertidal predatory sea stars are relative newcomers. Guilds on soft bottoms and in sheltered habitats were severely affected by extinction, whereas those on hard bottoms were most affected by colonists and held their own in diversity. The Peruvian Province has not served as a biogeographic refuge, in contrast to the coasts of Australasia and Argentina, where lineages no longer present in the Peruvian Province survive. The loss of sheltered habitats since the Pliocene explains many of the present‐day peculiarities of the biota. The history of the province's biota explains its unique attributes. High productivity, a rich Southern Hemisphere heritage, and colonization from the north account for the present‐day composition and unusual characteristics of the biota. 

Abstract Earth's biosphere is undergoing drastic reorganization due to the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, leading to secondary extinctions and exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for directly simulating and quantifying extinction cascades and creating novel interactions (i.e. rewiring) remains absent.Here, we presentNetworkExtinction—a novel R package which we have developed to explore the propagation of species extinction sequences through ecological networks and quantify the effects of rewiring potential in response to primary species extinctions. WithNetworkExtinction, we integrate ecological theory and computational simulations to develop functionality with which users may analyse and visualize the structure and robustness of ecological networks. The core functions introduced withNetworkExtinctionfocus on simulations of sequential primary extinctions and associated secondary extinctions, allowing user‐specified secondary extinction thresholds and realization of rewiring potential.With the packageNetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In‐built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can estimate the network's degree distribution by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analysing a Chilean coastal marine food web.NetworkExtinctionis a compact and easy‐to‐use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds and rewiring potential. Therefore, this package is particularly useful for evaluating ecosystem responses to anthropogenic and environmental perturbations that produce nonrandom and sometimes targeted, species extinctions. 

Comparative studies suggest remarkable similarities among food webs across habitats, including systematic changes in their structure with diversity and complexity (scale-dependence). However, historic aboveground terrestrial food webs (ATFWs) have coarsely grouped plants and insects such that these webs are generally small, and herbivory is disproportionately under-represented compared to vertebrate predator–prey interactions. Furthermore, terrestrial herbivory is thought to be structured by unique processes compared to size-structured feeding in other systems. Here, we present the richest ATFW to date, including approximately 580 000 feeding links among approximately 3800 taxonomic species, sourced from approximately 27 000 expert-vetted interaction records annotated as feeding upon one of six different resource types: leaves, flowers, seeds, wood, prey and carrion. By comparison to historical ATFWs and null ecological hypotheses, we show that our temperate forest web displays a potentially unique structure characterized by two properties: (i) a large fraction of carnivory interactions dominated by a small number of hyper-generalist, opportunistic bird and bat predators; and (ii) a smaller fraction of herbivory interactions dominated by a hyper-rich community of insects with variably sized but highly specific diets. We attribute our findings to the large-scale, even resolution of vertebrate, insect and plant guilds in our food web. This article is part of the theme issue ‘Connected interactions: enriching food web research by spatial and social interactions’. 

This theme issue features 18 papers exploring ecological interactions, encompassing metabolic, social, and spatial connections alongside traditional trophic networks. This integration enriches food web research, offering insights into ecological dynamics. By examining links across organisms, populations, and ecosystems, a hierarchical approach emerges, connecting horizontal effects within organizational levels vertically across biological organization levels. The inclusion of interactions involving humans is a key focus, highlighting the need for their integration into ecology given the complex interactions between human activities and ecological systems in the Anthropocene. The comprehensive exploration in this theme issue sheds light on the interconnectedness of ecological systems and the importance of considering diverse interactions in understanding ecosystem dynamics. This article is part of the theme issue ‘Connected interactions: enriching food web research by spatial and social interactions’. 

Ecosystem-based fisheries management (EBFM) has emerged as a promising framework for understanding and managing the long-term interactions between fisheries and the larger marine ecosystems in which they are nested. However, successful implementation of EBFM has been elusive because we still lack a comprehensive understanding of the network of interacting species in marine ecosystems (the food web) and the dynamic relationship between the food web and the humans who harvest those ecosystems. Here, we advance such understanding by developing a network framework that integrates the complexity of food webs with the economic dynamics of different management policies. Specifically, we generate hundreds of different food web models with 20–30 species, each harvested by five different fishers extracting the biomass of a target and a bycatch species, subject to two different management scenarios and exhibiting different information in terms of avoiding bycatch when harvesting the target species. We assess the different ecological and economic consequences of these policy alternatives as species extinctions and profit from sustaining the fishery. We present the results of different policies relative to a benchmark open access scenario where there are no management policies in place. The framework of our network model would allow policymakers to evaluate different management approaches without compromising on the ecological complexities of a fishery. This article is part of the theme issue ‘Connected interactions: enriching food web research by spatial and social interactions’.