Forage fish interactions: A symposium on creating the tools for ecosystem-based management of marine resources

Forage fish (FF) have a unique position within marine foodwebs and the development of sustainable harvest strategies for FF will be a critical step in advancing and implementing the broader, ecosystem-based management of marine systems. In all, 70 scientists from 16 nations gathered for a symposium on 12–14 November 2012 that was designed to address three key questions regarding the effective management of FF and their ecosystems: (i) how do environmental factors and predator–prey interactions drive the productivity and distribution of FF stocks across ecosystems worldwide, (ii) what are the economic and ecological costs and benefits of different FF management strategies, and (iii) do commonalities exist across ecosystems in terms of the effective management of FF exploitation

The Canadian context for evidence-based conservation and environmental management

Canada has strong institutional capacity for science-based decision-making related to natural resource conservation and environmental management. Yet, the concept of using systematic reviews (conducted in accordance with established guidelines) to support evidence-based conservation and environmental management in Canada is in its infancy. Here we discuss the Canadian context for implementing more rigorous evidence-based approaches using systematic reviews. Of particular relevance to Canada is its vast size, broad diversity of ecosystems and heavy economic reliance on natural resources that vary widely in the type and scale of their environmental effects. These factors result in a wide variety of environmental monitoring needs over an extensive area that pose challenges to the scientific community charged with overseeing wise use of the environment. In addition, there are diverse and engaged user groups (e.g., hunters, trappers, fishers, bird watchers, foresters) and indigenous peoples that have constitutional rights to their natural resources. Traditional environmental knowledge is a complementary source of evidence in the Canadian environmental impact assessment process and therefore must be a part of evidence synthesis. Systematic reviews are not intended to replace local field studies, but rather have the opportunity to draw upon a broader suite of evidence that can be interfaced with local perspectives. The existing institutional structures in Canada could easily incorporate systematic reviews into their science advice and decision-making frameworks but to date, there are few examples of where this has occurred. Drawing on the expertise of a growing global collaboration for environmental evidence synthesis, Canadian institutions (federal, provincial and NGO) are poised to more broadly incorporate systematic reviews once their benefits are fully realized and the capacity to undertake such systematic reviews is fully developed. Systematic reviews offer a consolidated view of the available scientific literature on a given question. The results may offer significant value when working with stakeholders and decision makers contributing other sources of information to the question. For example, mechanisms to capture and integrate scientific knowledge with stakeholder and traditional knowledge may benefit from the scientific sources being filtered, interpreted and summarized for discussion. In other cases, wher

The CBD Post‐2020 biodiversity framework: People's place within the rest of nature

Recognizing two decades of failure to achieve global goals and targets, parties to the Convention on Biological Diversity are in the final phase of negotiating a Post-2020 Global Biodiversity Framework for the conservation, sustainable use and benefit sharing of biodiversity. The framework attempts to set out pathways, goals and targets for the next decade to achieve positive biodiversity change. This perspective intends to help that framework set people firmly as part of nature, not apart from it. Despite work done so far through four meetings, new thinking and focus is still needed on ‘what’ changes must be conceptualized and implemented, and ‘how’ those changes are to be delivered. To help achieve that new thinking, as a broad range of people, many with a focus on aquatic systems, we highlight six key foci that offer potential to strengthen delivery of the framework and break the ‘business as usual’ logjam. These foci are as follows: (i) a reframing of the narrative of ‘people's relationship with the rest of nature’ and emphasize the crucial role of Indigenous Peoples and Local Communities in delivering positive biodiversity change; (ii) moving beyond a focus on species and places by prioritizing ecosystem function and resilience; (iii) supporting a diversity of top-down and bottom-up governance processes; (iv) embracing new technologies to make and measure progress; (v) linking business more effectively with biodiversity and (vi) leveraging the power of international agencies and programmes. Given they are linked to a greater or lesser degree, implementing these six foci together will lead to a much-needed broadening of the framework, especially those of business and broader urban civil society, as well as those of Indigenous Peoples and Local Communities. Read the free Plain Language Summary for this article on the Journal blog

Developing priority variables ("ecosystem Essential Ocean Variables" — eEOVs) for observing dynamics and change in Southern Ocean ecosystems

Reliable statements about variability and change in marine ecosystems and their underlying causes are needed to report on their status and to guide management. Here we use the Framework on Ocean Observing (FOO) to begin developing ecosystem Essential Ocean Variables (eEOVs) for the Southern Ocean Observing System (SOOS). An eEOV is a defined biological or ecological quantity, which is derived from field observations, and which contributes significantly to assessments of Southern Ocean ecosystems. Here, assessments are concerned with estimating status and trends in ecosystem properties, attribution of trends to causes, and predicting future trajectories. eEOVs should be feasible to collect at appropriate spatial and temporal scales and are useful to the extent that they contribute to direct estimation of trends and/or attribution, and/or development of ecological (statistical or simulation) models to support assessments. In this paper we outline the rationale, including establishing a set of criteria, for selecting eEOVs for the SOOS and develop a list of candidate eEOVs for further evaluation. Other than habitat variables, nine types of eEOVs for Southern Ocean taxa are identified within three classes: state (magnitude, genetic/species, size spectrum), predator–prey (diet, foraging range), and autecology (phenology, reproductive rate, individual growth rate, detritus). Most candidates for the suite of Southern Ocean taxa relate to state or diet. Candidate autecological eEOVs have not been developed other than for marine mammals and birds. We consider some of the spatial and temporal issues that will influence the adoption and use of eEOVs in an observing system in the Southern Ocean, noting that existing operations and platforms potentially provide coverage of the four main sectors of the region — the East and West Pacific, Atlantic and Indian. Lastly, we discuss the importance of simulation modelling in helping with the design of the observing system in the long term. Regional boundary: south of 30°S

Generation of Priority Research Questions to Inform Conservation Policy and Management at a National Level

Integrating knowledge from across the natural and social sciences is necessary to effectively address societal tradeoffs between human use of biological diversity and its preservation. Collaborative processes can change the ways decision makers think about scientific evidence, enhance levels of mutual trust and credibility, and advance the conservation policy discourse. Canada has responsibility for a large fraction of some major ecosystems, such as boreal forests, Arctic tundra, wetlands, and temperate and Arctic oceans. Stressors to biological diversity within these ecosystems arise from activities of the country's resource-based economy, as well as external drivers of environmental change. Effective management is complicated by incongruence between ecological and political boundaries and conflicting perspectives on social and economic goals. Many knowledge gaps about stressors and their management might be reduced through targeted, timely research. We identify 40 questions that, if addressed or answered, would advance research that has a high probability of supporting development of effective policies and management strategies for species, ecosystems, and ecological processes in Canada. A total of 396 candidate questions drawn from natural and social science disciplines were contributed by individuals with diverse organizational affiliations. These were collaboratively winnowed to 40 by our team of collaborators. The questions emphasize understanding ecosystems, the effects and mitigation of climate change, coordinating governance and management efforts across multiple jurisdictions, and examining relations between conservation policy and the social and economic well-being of Aboriginal peoples. The questions we identified provide potential links between evidence from the conservation sciences and formulation of policies for conservation and resource management. Our collaborative process of communication and engagement between scientists and decision makers for generating and prioritizing research questions at a national level could be a model for similar efforts beyond Canada

Challenges for Implementing an Ecosystem Approach to Fisheries Management

The ecosystem approach is being promoted as the foundation of solutions to the unsustainability of fisheries. However, because the ecosystem approach is broadly inclusive, the science for its implementation is often considered to be overly complex and difficult. When the science needed for an ecosystem approach to fisheries is perceived this way, science products cannot keep pace with fisheries critics, thus encouraging partisan political interference in fisheries management and proliferation of “faith-based solutions. In this paper we argue that one way to effectively counter politicization of fisheries decision-making is to ensure that new ecosystem-based approaches in fisheries are viewed only as an emergent property of innovation in science and policy. We organize our essay using three major themes to focus the discussion: empirical, jurisdictional, and societal challenges. We undertake at least partial answers to the following questions: (1) has conventional fisheries management really failed?; (2) can short-comings in conventional fisheries management be augmented with new tools, such as allocation of rights?; (3) is the Ecosystem Approach to Fisheries (EAF) equivalent to Ecosystem-Based Management?; and (4) is restoration of degraded ecosystems a necessary component of an EAF

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations. Ubiquitinpathway genes tend to be upregulated in cancermediated by diverse mechanisms. By integratingpan-cancer multiomic data, we identify a group oftumor samples that exhibit worse prognosis. Thesesamples are consistently associated with the upre-gulation of cell-cycle and DNA repair pathways, char-acterized by mutatedTP53,MYC/TERTamplifica-tion, andAPC/PTENdeletion. Our analysishighlights the importance of the ubiquitin pathwayin cancer development and lays a foundation fordeveloping relevant therapeutic strategies

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead