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1. NetworkExtinction : An R package to simulate extinction propagation and rewiring potential in ecological networks

   https://doi.org/10.1111/2041-210X.14126  

   Ávila‐Thieme, M. Isidora ; Kusch, Erik ; Corcoran, Derek ; Castillo, Simón P. ; Valdovinos, Fernanda S. ; Navarrete, Sergio A. ; Marquet, Pablo A. ( June 2023 , Methods in Ecology and Evolution)

   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 nullmore »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.

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2. The role of inputs of marine wrack and carrion in sandy‐beach ecosystems: a global review

   https://doi.org/10.1111/brv.12886  

   Hyndes, Glenn A. ; Berdan, Emma L. ; Duarte, Cristian ; Dugan, Jenifer E. ; Emery, Kyle A. ; Hambäck, Peter A. ; Henderson, Christopher J. ; Hubbard, David M. ; Lastra, Mariano ; Mateo, Miguel A. ; et al ( August 2022 , Biological Reviews)

   Sandy beaches are iconic interfaces that functionally link the ocean with the landviathe flow of organic matter from the sea. These cross‐ecosystem fluxes often comprise uprooted seagrass and dislodged macroalgae that can form substantial accumulations of detritus, termed ‘wrack’, on sandy beaches. In addition, the tissue of the carcasses of marine animals that regularly wash up on beaches form a rich food source (‘carrion’) for a diversity of scavenging animals. Here, we provide a global review of how wrack and carrion provide spatial subsidies that shape the structure and functioning of sandy‐beach ecosystems (sandy beaches and adjacent surf zones), which typically have littlein situprimary production. We also examine the spatial scaling of the influence of these processes across the broader land‐ and seascape, and identify key gaps in our knowledge to guide future research directions and priorities. Large quantities of detrital kelp and seagrass can flow into sandy‐beach ecosystems, where microbial decomposers and animals process it. The rates of wrack supply and its retention are influenced by the oceanographic processes that transport it, the geomorphology and landscape context of the recipient beaches, and the condition, life history and morphological characteristics of the macrophyte taxa that are the ultimate sourcemore »of wrack. When retained in beach ecosystems, wrack often creates hotspots of microbial metabolism, secondary productivity, biodiversity, and nutrient remineralization. Nutrients are produced during wrack breakdown, and these can return to coastal waters in surface flows (swash) and aquifers discharging into the subtidal surf. Beach‐cast kelp often plays a key trophic role, being an abundant and preferred food source for mobile, semi‐aquatic invertebrates that channel imported algal matter to predatory invertebrates, fish, and birds. The role of beach‐cast marine carrion is likely to be underestimated, as it can be consumed rapidly by highly mobile scavengers (e.g. foxes, coyotes, raptors, vultures). These consumers become important vectors in transferring marine productivity inland, thereby linking marine and terrestrial ecosystems. Whilst deposits of organic matter on sandy‐beach ecosystems underpin a range of ecosystem functions and services, they can be at variance with aesthetic perceptions resulting in widespread activities, such as ‘beach cleaning and grooming’. This practice diminishes the energetic base of food webs, intertidal fauna, and biodiversity. Global declines in seagrass beds and kelp forests (linked to global warming) are predicted to cause substantial reductions in the amounts of marine organic matter reaching many beach ecosystems, likely causing flow‐on effects for food webs and biodiversity. Similarly, future sea‐level rise and increased storm frequency are likely to alter profoundly the physical attributes of beaches, which in turn can change the rates at which beaches retain and process the influxes of wrack and animal carcasses. Conservation of the multi‐faceted ecosystem services that sandy beaches provide will increasingly need to encompass a greater societal appreciation and the safeguarding of ecological functions reliant on beach‐cast organic matter on innumerable ocean shores worldwide.

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3. Global Connectivity of Southern Ocean Ecosystems

   https://doi.org/10.3389/fevo.2021.624451  

   Murphy, Eugene J. ; Johnston, Nadine M. ; Hofmann, Eileen E. ; Phillips, Richard A. ; Jackson, Jennifer A. ; Constable, Andrew J. ; Henley, Sian F. ; Melbourne-Thomas, Jessica ; Trebilco, Rowan ; Cavanagh, Rachel D. ; et al ( August 2021 , Frontiers in Ecology and Evolution)

   Southern Ocean ecosystems are globally important. Processes in the Antarctic atmosphere, cryosphere, and the Southern Ocean directly influence global atmospheric and oceanic systems. Southern Ocean biogeochemistry has also been shown to have global importance. In contrast, ocean ecological processes are often seen as largely separate from the rest of the global system. In this paper, we consider the degree of ecological connectivity at different trophic levels, linking Southern Ocean ecosystems with the global ocean, and their importance not only for the regional ecosystem but also the wider Earth system. We also consider the human system connections, including the role of Southern Ocean ecosystems in supporting society, culture, and economy in many nations, influencing public and political views and hence policy. Rather than Southern Ocean ecosystems being defined by barriers at particular oceanic fronts, ecological changes are gradual due to cross-front exchanges involving oceanographic processes and organism movement. Millions of seabirds and hundreds of thousands of cetaceans move north out of polar waters in the austral autumn interacting in food webs across the Southern Hemisphere, and a few species cross the equator. A number of species migrate into the east and west ocean-basin boundary current and continental shelf regions of themore »major southern continents. Human travel in and out of the Southern Ocean region includes fisheries, tourism, and scientific vessels in all ocean sectors. These operations arise from many nations, particularly in the Northern Hemisphere, and are important in local communities as well as national economic, scientific, and political activities. As a result of the extensive connectivity, future changes in Southern Ocean ecosystems will have consequences throughout the Earth system, affecting ecosystem services with socio-economic impacts throughout the world. The high level of connectivity also means that changes and policy decisions in marine ecosystems outside the Southern Ocean have consequences for ecosystems south of the Antarctic Polar Front. Knowledge of Southern Ocean ecosystems and their global connectivity is critical for interpreting current change, projecting future change impacts, and identifying integrated strategies for conserving and managing both the Southern Ocean and the broader Earth system.« less
4. What's going to be on the menu with global environmental changes?

   https://doi.org/10.1111/gcb.16866  

   Hallam, Jane ; Harris, Nyeema C. ( July 2023 , Global Change Biology)

   Ongoing anthropogenic change is altering the planet at an unprecedented rate, threatening biodiversity, and ecosystem functioning. Species are responding to abiotic pressures at both individual and population levels, with changes affecting trophic interactions through consumptive pathways. Collectively, these impacts alter the goods and services that natural ecosystems will provide to society, as well as the persistence of all species. Here, we describe the physiological and behavioral responses of species to global changes on individual and population levels that result in detectable changes in diet across terrestrial and marine ecosystems. We illustrate shifts in the dynamics of food webs with implications for animal communities. Additionally, we highlight the myriad of tools available for researchers to investigate the dynamics of consumption patterns and trophic interactions, arguing that diet data are a crucial component of ecological studies on global change. We suggest that a holistic approach integrating the complexities of diet choice and trophic interactions with environmental drivers may be more robust at resolving trends in biodiversity, predicting food web responses, and potentially identifying early warning signs of diversity loss. Ultimately, despite the growing body of long‐term ecological datasets, there remains a dearth of diet ecology studies across temporal scales, a shortcomingmore »that must be resolved to elucidate vulnerabilities to changing biophysical conditions.

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5. Water column contributions to coral reef productivity: overcoming challenges of context dependence

   https://doi.org/10.1111/brv.12984  

   Shakya, Anjali W. ; Allgeier, Jacob E. ( June 2023 , Biological Reviews)

   Coral reefs are declining at an unprecedented rate. Effective management and conservation initiatives necessitate improved understanding of the drivers of production because the high rates found in these ecosystems are the foundation of the many services they provide. The water column is the nexus of coral reef ecosystem dynamics, and functions as the interface through which essentially all energy and nutrients are transferred to fuel both new and recycled production. Substantial research has described many aspects of water column dynamics, often focusing on specific components because water column dynamics are highly spatially and temporally context dependent. Although necessary, a cost of this approach is that these dynamics are often not well linked to the broader ecosystem or across systems. To help overcome the challenge of context dependence, we provide a comprehensive review of this literature, and synthesise it through the perspective of ecosystem ecology. Specifically, we provide a framework to organise the drivers of temporal and spatial variation in production dynamics, structured around five primary state factors. These state factors are used to deconstruct the environmental contexts in which three water column sub‐food webs mediate ‘new’ and ‘recycled’ production. We then highlight critical pathways by which global change driversmore »are altering coral reefsviathe water column. We end by discussing four key knowledge gaps hindering understanding of the role of the water column for mediating coral reef production, and how overcoming these could improve conservation and management strategies. Throughout, we identify areas of extensive research and those where studies remain lacking and provide a database of 84 published studies. Improved integration of water column dynamics into models of coral reef ecosystem function is imperative to achieve the understanding of ecosystem production necessary to develop effective conservation and management strategies needed to stem global coral loss.

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