Showing papers by "William W. L. Cheung published in 2021"

Protecting the global ocean for biodiversity, food and climate

Abstract: The ocean contains unique biodiversity, provides valuable food resources and is a major sink for anthropogenic carbon. Marine protected areas (MPAs) are an effective tool for restoring ocean biodiversity and ecosystem services1,2, but at present only 2.7% of the ocean is highly protected3. This low level of ocean protection is due largely to conflicts with fisheries and other extractive uses. To address this issue, here we developed a conservation planning framework to prioritize highly protected MPAs in places that would result in multiple benefits today and in the future. We find that a substantial increase in ocean protection could have triple benefits, by protecting biodiversity, boosting the yield of fisheries and securing marine carbon stocks that are at risk from human activities. Our results show that most coastal nations contain priority areas that can contribute substantially to achieving these three objectives of biodiversity protection, food provision and carbon storage. A globally coordinated effort could be nearly twice as efficient as uncoordinated, national-level conservation planning. Our flexible prioritization framework could help to inform both national marine spatial plans4 and global targets for marine conservation, food security and climate action. Using a globally coordinated strategic conservation framework to plan an increase in ocean protection through marine protected areas can yield benefits for biodiversity, food provisioning and carbon storage.

Global decline in capacity of coral reefs to provide ecosystem services

Abstract: Summary Coral reefs worldwide are facing impacts from climate change, overfishing, habitat destruction, and pollution. The cumulative effect of these impacts on global capacity of coral reefs to provide ecosystem services is unknown. Here, we evaluate global changes in extent of coral reef habitat, coral reef fishery catches and effort, Indigenous consumption of coral reef fishes, and coral-reef-associated biodiversity. Global coverage of living coral has declined by half since the 1950s. Catches of coral-reef-associated fishes peaked in 2002 and are in decline despite increasing fishing effort, and catch-per-unit effort has decreased by 60% since 1950. At least 63% of coral-reef-associated biodiversity has declined with loss of coral extent. With projected continued degradation of coral reefs and associated loss of biodiversity and fisheries catches, the well-being and sustainable coastal development of human communities that depend on coral reef ecosystem services are threatened.

Enabling conditions for an equitable and sustainable blue economy

Abstract: The future of the global ocean economy is currently envisioned as advancing towards a ‘blue economy’—socially equitable, environmentally sustainable and economically viable ocean industries1,2. However, tensions exist within sustainable development approaches, arising from differing perspectives framed around natural capital or social equity. Here we show that there are stark differences in outlook on the capacity for establishing a blue economy, and on its potential outcomes, when social conditions and governance capacity—not just resource availability—are considered, and we highlight limits to establishing multiple overlapping industries. This is reflected by an analysis using a fuzzy logic model to integrate indicators from multiple disciplines and to evaluate their current capacity to contribute to establishing equitable, sustainable and viable ocean sectors consistent with a blue economy approach. We find that the key differences in the capacity of regions to achieve a blue economy are not due to available natural resources, but include factors such as national stability, corruption and infrastructure, which can be improved through targeted investments and cross-scale cooperation. Knowledge gaps can be addressed by integrating historical natural and social science information on the drivers and outcomes of resource use and management, thus identifying equitable pathways to establishing or transforming ocean sectors1,3,4. Our results suggest that policymakers must engage researchers and stakeholders to promote evidence-based, collaborative planning that ensures that sectors are chosen carefully, that local benefits are prioritized, and that the blue economy delivers on its social, environmental and economic goals. The capacity to create an equitable and sustainable ‘blue economy’ from ocean resources will be determined by addressing social conditions, governance and infrastructure, not just resource availability, as shown by a fuzzy logic model incorporating multidisciplinary criteria.

Next-generation ensemble projections reveal higher climate risks for marine ecosystems.

Abstract: Projections of climate change impacts on marine ecosystems have revealed long-term declines in global marine animal biomass and unevenly distributed impacts on fisheries. Here we apply an enhanced suite of global marine ecosystem models from the Fisheries and Marine Ecosystem Model Intercomparison Project (Fish-MIP), forced by new-generation Earth system model outputs from Phase 6 of the Coupled Model Intercomparison Project (CMIP6), to provide insights into how projected climate change will affect future ocean ecosystems. Compared with the previous generation CMIP5-forced Fish-MIP ensemble, the new ensemble ecosystem simulations show a greater decline in mean global ocean animal biomass under both strong-mitigation and high-emissions scenarios due to elevated warming, despite greater uncertainty in net primary production in the high-emissions scenario. Regional shifts in the direction of biomass changes highlight the continued and urgent need to reduce uncertainty in the projected responses of marine ecosystems to climate change to help support adaptation planning.

Energy Flow Through Marine Ecosystems: Confronting Transfer Efficiency

Abstract: Transfer efficiency is the proportion of energy passed between nodes in food webs. It is an emergent, unitless property that is difficult to measure, and responds dynamically to environmental and ecosystem changes. Because the consequences of changes in transfer efficiency compound through ecosystems, slight variations can have large effects on food availability for top predators. Here, we review the processes controlling transfer efficiency, approaches to estimate it, and known variations across ocean biomes. Both process-level analysis and observed macroscale variations suggest that ecosystem-scale transfer efficiency is highly variable, impacted by fishing, and will decline with climate change. It is important that we more fully resolve the processes controlling transfer efficiency in models to effectively anticipate changes in marine ecosystems and fisheries resources.

A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

Abstract: Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify novel species and understand their potential functions in a dynamic ecosystem. Many computational tools have been developed to construct and annotate MAGs from metagenomic sequencing, however, there is a prominent gap to comprehensively introduce their background and practical performance. In this paper, we have thoroughly investigated the computational tools designed for both upstream and downstream analyses, including metagenome assembly, metagenome binning, gene prediction, functional annotation, taxonomic classification, and profiling. We have categorized the commonly used tools into unique groups based on their functional background and introduced the underlying core algorithms and associated information to demonstrate a comparative outlook. Furthermore, we have emphasized the computational requisition and offered guidance to the users to select the most efficient tools. Finally, we have indicated current limitations, potential solutions, and future perspectives for further improving the tools of MAG construction and annotation. We believe that our work provides a consolidated resource for the current stage of MAG studies and shed light on the future development of more effective MAG analysis tools on metagenomic sequencing.

Marine high temperature extremes amplify the impacts of climate change on fish and fisheries.

Abstract: Extreme temperature events have occurred in all ocean basins in the past two decades with detrimental impacts on marine biodiversity, ecosystem functions, and services. However, global impacts of t...

Identifying uncertainties in scenarios and models of socio-ecological systems in support of decision-making

Abstract: There are many sources of uncertainty in scenarios and models of socio-ecological systems, and understanding these uncertainties is critical in supporting informed decision-making about the management of natural resources. Here, we review uncertainty across the steps needed to create socio-ecological scenarios, from narrative storylines to the representation of human and biological processes in models and the estimation of scenario and model parameters. We find that socio-ecological scenarios and models would benefit from moving away from “stylized” approaches that do not consider a wide range of direct drivers and their dependency on indirect drivers. Indeed, a greater focus on the social phenomena is fundamental in understanding the functioning of nature on a human-dominated planet. There is no panacea for dealing with uncertainty, but several approaches to evaluating uncertainty are still not routinely applied in scenario modeling, and this is becoming increasingly unacceptable. However, it is important to avoid uncertainties becoming an excuse for inaction in decision-making when facing environmental challenges.

Compound climate risks threaten aquatic food system benefits

Abstract: Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and cultures of billions of people worldwide, but climate-related hazards may compromise their ability to provide these benefits. Here, we estimate national-level aquatic food system climate risk using an integrative food systems approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes. We show that without mitigation, climate hazards pose high risks to nutritional, social, economic and environmental outcomes worldwide—especially for wild-capture fisheries in Africa, South and Southeast Asia, and Small Island Developing States. For countries projected to experience compound climate risks, reducing societal vulnerabilities can lower climate risk by margins similar to meeting Paris Agreement mitigation targets. System-level interventions addressing dimensions such as governance, gender equity and poverty are needed to enhance aquatic and terrestrial food system resilience and provide investments with large co-benefits towards meeting the Sustainable Development Goals. The nutritional, economic and livelihood contributions provided by aquatic food systems are threatened by climate change. Building climate resilience requires systemic interventions that reduce social vulnerabilities.

Persistent Uncertainties in Ocean Net Primary Production Climate Change Projections at Regional Scales Raise Challenges for Assessing Impacts on Ecosystem Services

Abstract: Ocean net primary production (NPP) results from CO2 fixation by marine phytoplankton, catalysing the transfer of organic matter and energy to marine ecosystems, supporting most marine food webs and fisheries production as well as stimulating ocean carbon sequestration. Thus, alterations to ocean NPP in response to climate change, as quantified by Earth system model experiments conducted as part of the 5th and 6th Coupled Model Intercomparison Project (CMIP5 and CMIP6) efforts, are expected to alter key ecosystem services. Despite reductions in inter-model variability since CMIP5, the ocean components of CMIP6 models disagree roughly 2-fold in the magnitude and spatial distribution of NPP in the contemporary era, due to incomplete understanding and insufficient observational constraints. Projections of NPP change in absolute terms show large uncertainty in CMIP6, most notably in the North Atlantic and the Indo-Pacific regions, with the latter explaining over two-thirds of the total inter-model uncertainty. While the Indo-Pacific has previously been identified as a hotspot for climate impacts on biodiversity and fisheries, the increased inter-model variability of NPP projections further exacerbates the uncertainties of climate risks on ocean-dependent human communities. Drivers of uncertainty in NPP changes at regional scales integrate different physical and biogeochemical factors that require more targeted mechanistic assessment in future studies. Globally, inter-model uncertainty in the projected changes in NPP has increased since CMIP5, which amplifies the challenges associated with the management of associated ecosystem services. Notably, this increased regional uncertainty in the projected NPP change in CMIP6 has occurred despite reduced uncertainty in the regional rates of NPP for historical period. Improved constraints on the magnitude of ocean NPP and the mechanistic drivers of its spatial variability would improve confidence in future changes. It is unlikely that the CMIP6 model ensemble samples the complete uncertainty in NPP, with the inclusion of additional mechanistic realism likely to widen projections further in the future, especially at regional scales. This has important consequences for assessing ecosystem impacts. Ultimately, we need an integrated mechanistic framework that considers how NPP and marine ecosystems respond to impacts of not only climate change, but also the additional non-climate drivers.

DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data.

Abstract: Single-cell RNA sequencing has enabled to capture the gene activities at single-cell resolution, thus allowing reconstruction of cell-type-specific gene regulatory networks (GRNs). The available algorithms for reconstructing GRNs are commonly designed for bulk RNA-seq data, and few of them are applicable to analyze scRNA-seq data by dealing with the dropout events and cellular heterogeneity. In this paper, we represent the joint gene expression distribution of a gene pair as an image and propose a novel supervised deep neural network called DeepDRIM which utilizes the image of the target TF-gene pair and the ones of the potential neighbors to reconstruct GRN from scRNA-seq data. Due to the consideration of TF-gene pair's neighborhood context, DeepDRIM can effectively eliminate the false positives caused by transitive gene-gene interactions. We compared DeepDRIM with nine GRN reconstruction algorithms designed for either bulk or single-cell RNA-seq data. It achieves evidently better performance for the scRNA-seq data collected from eight cell lines. The simulated data show that DeepDRIM is robust to the dropout rate, the cell number and the size of the training data. We further applied DeepDRIM to the scRNA-seq gene expression of B cells from the bronchoalveolar lavage fluid of the patients with mild and severe coronavirus disease 2019. We focused on the cell-type-specific GRN alteration and observed targets of TFs that were differentially expressed between the two statuses to be enriched in lysosome, apoptosis, response to decreased oxygen level and microtubule, which had been proved to be associated with coronavirus infection.

Climate change impacts on living marine resources in the Eastern Tropical Pacific

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2020 The Authors. Diversity and Distributions published by John Wiley & Sons Ltd. 1Changing Ocean Research Unit, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, Canada 2Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San José, Costa Rica 3Smithsonian Tropical Research Institute, Balboa, Panamá 4Centro de Estudios del Mar y Acuicultura, Universidad de San Carlos de Guatemala, Guatemala, Guatemala 5Museo de Zoología, Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica 6Centro Oceanográfico de Vigo, Instituto Español de Oceanografia, Madrid, Spain

Climate-induced decrease in biomass flow in marine food webs may severely affect predators and ecosystem production.

Abstract: Climate change impacts on marine life in the world ocean are expected to accelerate over the 21st century, affecting the structure and functioning of food webs. We analyzed a key aspect of this issue, focusing on the impact of changes in biomass flow within marine food webs and the resulting effects on ecosystem biomass and production. We used a modeling framework based on a parsimonious quasi-physical representation of biomass flow through the food web, to explore the future of marine consumer biomass and production at the global scale over the 21st century. Biomass flow is determined by three climate-related factors: primary production entering the food web, trophic transfer efficiency describing losses in biomass transfers from one trophic level (TL) to the next, and flow kinetic measuring the speed of biomass transfers within the food web. Using climate projections of three earth system models, we calculated biomass and production at each TL on a 1° latitude ×1° longitude grid of the global ocean under two greenhouse gas emission scenarios. We show that the alterations of the trophic functioning of marine ecosystems, mainly driven by faster and less efficient biomass transfers and decreasing primary production, would lead to a projected decline in total consumer biomass by 18.5% by 2090-2099 relative to 1986-2005 under the "no mitigation policy" scenario. The projected decrease in transfer efficiency is expected to amplify impacts at higher TLs, leading to a 21.3% decrease in abundance of predators and thus to a change in the overall trophic structure of marine ecosystems. Marine animal production is also projected to decline but to a lesser extent than biomass. Our study highlights that the temporal and spatial projected changes in biomass and production would imply direct repercussions on the future of world fisheries and beyond all services provided by Ocean.

Predicting how climate change threatens the prey base of Arctic marine predators.

Abstract: Arctic sea ice loss has direct consequences for predators. Climate-driven distribution shifts of native and invasive prey species may exacerbate these consequences. We assessed potential changes by modelling the prey base of a widely distributed Arctic predator (ringed seal; Pusa hispida) in a sentinel area for change (Hudson Bay) under high- and low-greenhouse gas emission scenarios from 1950 to 2100. All changes were relatively negligible under the low-emission scenario, but under the high-emission scenario, we projected a 50% decline in the abundance of the well-distributed, ice-adapted and energy-rich Arctic cod (Boreogadus saida) and an increase in the abundance of smaller temperate-associated fish in southern and coastal areas. Furthermore, our model predicted that all fish species declined in mean body size, but a 29% increase in total prey biomass. Declines in energy-rich prey and restrictions in their spatial range are likely to have cascading effects on Arctic predators.

Meeting Paris agreement objectives will temper seabird winter distribution shifts in the North Atlantic Ocean

Abstract: We explored the implications of reaching the Paris Agreement Objective of limiting global warming to <2°C for the future winter distribution of the North Atlantic sea-bird community. We predicted and quantified current and future winter habitats of five North Atlantic Ocean seabird species (Alle alle, Fratercula arctica, Uria aalge, Uria lomvia and Rissa tridactyla) using tracking data for ~1500 individuals through resource selection functions based on mechanistic modeling of seabird energy requirements, and a dynamic bioclimate envelope model of seabird prey. Future winter distributions were predicted to shift with climate change, especially when global warming exceed 2°C under a “no mitigation” scenario, modifying seabird wintering hotspots in the North Atlantic Ocean. Our findings suggest that meeting Paris agreement objectives will limit changes in seabird selected habitat location and size in the North Atlantic Ocean during the 21st century. We thereby provide key information for the design of adaptive marine-protected areas in a changing ocean

Initial recovery of demersal fish communities in coastal waters of Hong Kong, South China, following a trawl ban

Abstract: Fisheries resources in Hong Kong have been overexploited since the 1970s due to intensive bottom trawling and other fishing activities that have depleted stocks and destroyed marine habitat. To rehabilitate depleted fisheries resources, a permanent ban on trawling in Hong Kong territorial waters came into force on December 31, 2012. In order to determine whether the trawl facilitated recovery of fish communities, trawl surveys were conducted at two sites in each of the eastern, southern and western (estuarine) coastal waters of Hong Kong before and three years after the trawl ban. A total of 315 species and 86 families of fishes in nine feeding groups were encountered during the surveys. Mean trophic level of the fish community, abundance and biomass of total fishes and of predatory fishes increased in eastern and western waters after the ban, but no changes or declines in these metrics were observed in southern waters. Although initial recovery in fish community were observed in eastern and western waters, anthropogenic disturbances might hinder the recovery process, including a large-scale reclamation for construction of coastal infrastructures in the west, illegal trawling, and expansion of non-trawling fishing efforts in the southern and eastern waters. Longer term monitoring is needed to evaluate the effects of the trawl ban, and determine whether recovery in the southern waters will continue to be constrained by the anthropogenic disturbances.

Does a Trawl Ban Benefit Commercially Important Decapoda and Stomatopoda in Hong Kong

Abstract: Crustaceans were among the most valuable fishery resources in Hong Kong. However, the unrestricted and intensive use of different fishing gears, especially bottom trawling, has led to the depletion of commercially important crustaceans in Hong Kong since the 1980s. This study investigated whether commercial crustaceans recovered after the implementation of a permanent Hong Kong-wide trawl ban that began on December 31, 2012. Standardized field surveys were conducted using a commercial shrimp trawler at two sites in eastern and western waters of Hong Kong before (2004) and after the trawl ban (2013–2014 and 2015–2016) and two sites in southern waters after the trawl ban. Diversity, mean size, abundance, biomass and level of disturbance of commercial crustaceans from the three periods were investigated. The eastern waters exhibited an increased diversity of crustacean assemblages in Inner Tolo, and a higher abundance and biomass of crabs were detected in Outer Tolo after the trawl ban. Reduced disturbance, higher diversity in crustacean assemblages and greater abundance and biomass of predatory crabs were observed after the trawl ban in the outer estuary of western waters, and increased abundance and biomass of shrimp were detected in the inner estuary of western waters. No temporal or negative changes were detected in the southeast and southern waters of Lamma Island. The various responses of crustacean assemblages in Hong Kong waters revealed the critical role of complex interactions among multiple stresses, such as ongoing reclamation works, illegal trawling activities and increased fishing efforts using other (legal) fishing methods.

Grand challenges in biodiversity-ecosystem functioning research in the era of science-policy platforms require explicit consideration of feedbacks.

Abstract: Feedbacks are an essential feature of resilient socio-economic systems, yet the feedbacks between biodiversity, ecosystem services and human wellbeing are not fully accounted for in global policy e...

Modelling ocean acidification effects with life stage-specific responses alters spatiotemporal patterns of catch and revenues of American lobster, Homarus americanus.

Abstract: Ocean acidification (OA) affects marine organisms through various physiological and biological processes, yet our understanding of how these translate to large-scale population effects remains limited. Here, we integrated laboratory-based experimental results on the life history and physiological responses to OA of the American lobster, Homarus americanus, into a dynamic bioclimatic envelope model to project future climate change effects on species distribution, abundance, and fisheries catch potential. Ocean acidification effects on juvenile stages had the largest stage-specific impacts on the population, while cumulative effects across life stages significantly exerted the greatest impacts, albeit quite minimal. Reducing fishing pressure leads to overall increases in population abundance while setting minimum size limits also results in more higher-priced market-sized lobsters (> 1 lb), and could help mitigate the negative impacts of OA and concurrent stressors (warming, deoxygenation). However, the magnitude of increased effects of climate change overweighs any moderate population gains made by changes in fishing pressure and size limits, reinforcing that reducing greenhouse gas emissions is most pressing and that climate-adaptive fisheries management is necessary as a secondary role to ensure population resiliency. We suggest possible strategies to mitigate impacts by preserving important population demographics.

Author Correction: Protecting the global ocean for biodiversity, food and climate.

Abstract: In this Article, the affiliation of author Cristina Garilao was incorrectly given as ‘Evolutionary Biology and Ecology Laboratory, Albert Ludwigs University, Freiburg, Germany’ (affiliation 8) It should be ‘GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany’ (affiliation 18) The original Article has been corrected online

Ocean Acidification Amplifies Multi-Stressor Impacts on Global Marine Invertebrate Fisheries

Abstract: Elevated atmospheric carbon dioxide (CO2) is causing global ocean changes and drives changes in organism physiology, life-history traits, and population dynamics of natural marine resources. However, our knowledge of the mechanisms and consequences of ocean acidification (OA) – in combination with other climatic drivers (i.e., warming, deoxygenation) – on organisms and downstream effects on marine fisheries is limited. Here, we explored how the direct effects of multiple changes in ocean conditions on organism aerobic performance scales up to spatial impacts on fisheries catch of 210 commercially exploited marine invertebrates, known to be susceptible to OA. Under the highest CO2 trajectory, we show that global fisheries catch potential declines by as much as 12% by the year 2100 relative to present, of which 3.4% was attributed to OA. Moreover, OA effects are exacerbated in regions with greater changes in pH (e.g., West Arctic basin), but are reduced in tropical areas where the effects of ocean warming and deoxygenation are more pronounced (e.g., Indo-Pacific). Our results enhance our knowledge on multi-stressor effects on marine resources and how they can be scaled from physiology to population dynamics. Furthermore, it underscores variability of responses to OA and identifies vulnerable regions and species.