Henning Winker

• PhD Fisheries Sciences
• Researcher at European Commission

13 Identifying species at risk of extinction is necessary to prioritise conservation efforts. The International 14 Union for Conservation of Nature's (IUCN) Red List of Threatened Species is the global standard for 15 quantifying extinction risk, with many species categorised according to population reduction thresholds. 16 We introduce the Bayesia...

The natural mortality rate (M) of a fish stock is typically highly influential on the outcome of age-structured stock assessment models, but at the same time extremely difficult to estimate. In data-limited stock assessments, M usually relies on a range of empirically or theoretically derived M estimates, which can vary vastly. This article aims at...

Overfishing is the primary cause of marine defaunation, yet declines in and increasing extinction risks of individual species are difficult to measure, particularly for the largest predators found in the high seas. Here we calculate two well-established indicators to track progress towards Aichi Biodiversity Targets and Sustainable Development Goal...

Integrated analysis has increasingly been the preferred approach for conducting stock assessments and providing the basis for management advice for fish and invertebrate stocks around the world. Many decisions are required when developing integrated stock assessments. For example, the analyst needs to decide whether the model fits the data, if the...

Here, we summarise the extinction risk of the sharks and rays endemic to coastal, shelf, and slope waters of the southwest Indian Ocean and adjacent waters (SWIO+, Namibia to Kenya, including SWIO islands). This region is a hotspot of endemic and evolutionarily distinct sharks and rays. Nearly one-fifth (n = 13 of 70, 18.6%) of endemic sharks and r...

This report presents the most up-to-date information and analyses of the status of marine fishery resources in South Africa at the time of compilation. The number of fish stocks covered has increased steadily from 43 in 2012 to 77 in the current report (Figure I). Among the species included for the first time are a further six sharks (bronze whaler...

1. In the face of biodiversity loss worldwide, it is paramount to quantify species’ extinction risk to guide conservation efforts. The International Union for the Conservation of Nature (IUCN)’s Red List is considered the global standard for evaluating extinction risks. IUCN criteria also inform national extinction risk assessments. Bayesian models...

Overfishing is the most significant threat facing sharks and rays. Given the growth in consumption of seafood, combined with the compounding effects of habitat loss, climate change, and pollution, there is a need to identify recovery paths, particularly in poorly managed and poorly monitored fisheries. Here, we document conservation through fisheri...

The main objective of the workshop was to review the recommendations of WKREF1 and consider how these might feed into a new reference points framework and guidelines for ICES. There were a number of presentations on the wider issues of best practice for reference points, the Allee effect, density dependence and the WKIRISH approach. The starting po...

This ad hoc report first reviews the technical details of the Generalised Linear Mixed effects Model (GLMM) approach that is applied to estimate model-based indicators for the performance of the Common Fisheries Policy. It then presents the results a suitability study of applying the Bayesian State-Space model ‘JARA’ as an alternative to the curren...

The southwest Indian Ocean (SWIO) is a hotspot of endemic and evolutionarily distinct sharks and rays. We summarise the extinction risk of the sharks and rays endemic to coastal, shelf, and slope waters of the SWIO and adjacent waters (Namibia to Kenya, including SWIO islands). Thirteen of 70 species (19%) are threatened: one is Critically Endanger...

Management Strategy Evaluation of small pelagic stocks of the Adriatic. MSE carried out for Sardines and Anchovies in GSA17/18. Harvest control rules tuned and evaluated against robustness test. Work carried out in the FLR framework.

The fine-scale movement of Mustelus mustelus in relation to environmental conditions was investigated at various temporal scales with acoustic telemetry and temperature–depth transmitters inside a coastal marine protected area in South Africa. Twenty-four sharks were equipped with acoustic tags and logged by an array of 28 acoustic receivers from N...

The southwest Indian Ocean (SWIO) is a hotspot of endemic and evolutionarily distinct sharks and rays. We summarise the extinction risk of the sharks and rays endemic to coastal, shelf, and slope waters of the SWIO and adjacent waters (Namibia to Kenya, including SWIO islands). Thirteen of 70 species (19%) are threatened: one is Critically Endanger...

This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Abstract This study evaluates the relationship between both commercial and scientific spatial fisheries data and a new satellite-based estimate o...

Supplementary Information of : Mesoscale productivity fronts and local fishing opportunities in the European Seas. Fish and Fisheries, 00, 1–21. https://doi.org/10.1111/faf.12585

This publication is a Science for Policy report by the Joint Research Centre (JRC), the European Commission’s science and knowledge service. It aims to provide evidence-based scientific support to the European policymaking process. The scientific output expressed does not imply a policy position of the European Commission. Neither the European Comm...

The adoption of the Precautionary Approach requires providing advice that is robust to uncertainty. Therefore, when conducting stock assessment alternative, model structures and data sets are commonly considered. The primary diagnostics used to compare models are to examine residuals patterns to check goodness-of-fit and to conduct retrospective an...

Catch-only models (COMs) have been the focus of ongoing research into data-poor stock assessment methods. Two of the most recent models that are especially promising are (i) CMSY+, the latest refined version of CMSY that has progressed from Catch-MSY, and (ii) SRA+ (Stock Reduction Analysis Plus), one of the latest developments in the field. Compar...

Red list assessment of Dasyatis chrysonata

Mustelus mustelus from the Langebaan Marine Protected Area (LMPA) has been largely protected from fishing activities for the past 30 years; therefore, its biology represents those of an unfished stock. The reproductive biology, diet, growth and maturity of M. mustelus was studied in the Langebaan Lagoon region in the south-western Cape Coast of Sou...

CMSY++ is an advanced state-space Bayesian method for stock assessment that estimates fisheries reference points (MSY, Fmsy, Bmsy) as well as status or relative stock size (B/Bmsy) and fishing pressure or exploitation (F/Fmsy) from catch and (optionally) abundance data, a prior for resilience or productivity (r), and broad priors for the ratio of b...

Phenotypic plasticity in life-history traits in response to heterogeneous environments has been observed in a number of fishes. Conversely, genetic structure has recently been detected in even the most wide ranging pelagic teleost fish and shark species with massive dispersal potential, putting into question previous expectations of panmixia. Shall...

Soupfin sharks (Galeorhinus galeus), globally referred to as tope, are medium sized sharks that are globally distributed in temperate waters. Soupfin sharks were the first shark species to be commercially harvested in South Africa and remains one of the top five most commercially valuable shark species. The species is currently caught in the demers...

This workshop is the third in a series of workshops on guidelines for developing Management Strategy Evaluations (MSEs) within ICES, and was intended to explore some of the issues that arose out of workshops that actually developed MSEs for a range of ICES stocks since the second MSE guidelines workshop was held in early 2019. It is intended that r...

Managing coastal fisheries is challenging as the status of many fish stocks caught in these fisheries remains unknown. In the South African linefishery, regular comprehensive assessments of the status of most linefish stocks are unattainable owing to a scarcity of reliable long-term data. Length-based analysis remains the only option to determine s...

To further implement an ecosystem approach to management of the small pelagic fishery in South Africa, we attempted to develop functional relationships between spatialised time-series of the biomass of three small pelagic fish species and the catch per unit effort (CPUE) of four linefish species (i.e. species caught on hook and line, excluding long...

Albacore, Thunnus alalunga, is the main target of the South African tuna pole-line (baitboat) fleet operating along the west and south west coast of South Africa. The South African catch is the second largest in the region with annual landings of around 4000 t. A standardization of the CPUE of the South African baitboat fleet for the time series 20...

Bayesian State-Space Surplus Production Models were fitted to South Atlantic albacore (Thunnus alalunga) catch and CPUE data using the 'JABBA' R package. In accordance with the 2019 SCRS work plan (update of the 2016 assessment), this document presents four preliminary scenarios that explore two production functions (Schaefer or Fox) as well as two...

This paper presents a new, updated, temporally dynamic Ecosim model for the Southern Benguela (1978–2015) by capturing recent advancements in our understanding of the dynamics and newly available data series from an additional decade of research in the region. The paper documents the model development and the thinking behind incorporating a newly a...

Bayesian State-Space Surplus Production Models were fitted to Mediterranean swordfish (Xiphias gladius) catch and CPUE data using the 'JABBA' R package. For the 'Reference' model we used a Schaefer model with an existing r prior, while for the 'ASEM' model we developed a Pella-Tomlinson model based on priors derived from an Age-structured Equilibri...

Understanding changes in abundance is crucial for conservation, but population growth rates often vary over space and time. We use 40 years of count data (1979–2019) and Bayesian state‐space models to assess the African penguin Spheniscus demersus population under IUCN Red List Criterion A. We deconstruct the overall decline in time and space to id...

This contribution presents the detailed responses to the peer-review of Froese et al. (2019) "Estimating stock status from relative abundance and resilience" (ICES J. Mar. Sci. 2019) which outlined a method called "AMSY" for inferring biomass trends for stocks for which only catch-per-unit-effort and limited ancillary ('priors') data are available....

African Penguin Spheniscus demersus numbers have declined steadily over three generations, resulting in a loss of nearly 60% since of 1989. The breeding population reached an historic low of ~20,850 pairs in 2019. We use count data and JARA, a generalized Bayesian state-space tool for estimating extinction risk estimates under IUCN Red List Criteri...

Bayesian State-Space Surplus Production Models were fitted to Atlantic blue marlin (Kajikia albida) catch and CPUE data using the open-source stock assessment tool JABBA. The three scenarios (S1-sensitivity run 1, S2-sensitivity run 2 and S3-base case model) were based on sensitivity analysis of the initial runs, which corresponded to a 'steepness-...

Bayesian State-Space Surplus Production Models were fitted to yellowfin tuna catch and standardized catch-per-unit-effort (CPUE) data using the open-source stock assessment tool JABBA. Here, we present results from six scenarios (base case model and S1-S5).These scenarios corresponded to combinations of different CPUEs associated with three alterna...

The Law of the Sea and regional and national laws and agreements require exploited populations or stocks to be managed so that they can produce maximum sustainable yields. However, exploitation level and stock status are unknown for most stocks because the data required for full stock assessments are missing. This study presents a new method [abund...

Common smoothhound shark (Mustelus mustelus) are medium sized sharks distributed from the Mediterranean down to the SouthWest Indian Ocean. Commercially it is one of the top five most valuable shark species mainly caught as target or by-catch by the demersal shark longline fishery, commercial linefishery and the inshore trawl fishery. Total catches...

Fish population processes could exhibit non-stationary behaviour as a stochastic biological process with temporal autocorrelation that may be influenced by environmental changes. Here we developed a Bayesian autoregressive state-space surplus production modelling framework to explore potential non-stationarity in population processes. We then evalu...

The Cape Gannet Morus capensis is one of several seabird species endemic to the Benguela upwelling ecosystem (BUS) but whose population has recently decreased, leading to an unfavourable IUCN Red List assessment. Application of ‘JARA’ (‘Just Another Red-List Assessment,’ a Bayesian state-space tool used for IUCN Red List assessments) to updated inf...

The International Union for Conservation of Nature's (IUCN) Red List is the global standard for quantifying extinction risk but assessing population reduction (criterion A) of wide-ranging, long-lived marine taxa remains difficult and controversial. We show how Bayesian state-space models (BSSM), coupled with expert knowledge at IUCN Red List works...

This paper presents a multivariate lognormal (MVLN) Monte-Carlo approach to produce Kobe phase plots and Kobe II projection matrices for range of fixed catch scenarios from the 2018 Indian Ocean yellowfin tuna reference grid of Stock Synthesis models. First, we present Kobe-phase plots for the current stock status that compare within-model uncertai...

The southern mullet Chelon richardsonii (Mugilidae) is the main target species of the inshore net fishery (gillnet and beach-seine) on the west coast of South Africa. The stock has displayed symptoms of overfishing, with a 28% reduction in the standardised catch per unit effort (CPUE) between 2008 and 2016, and a 36.5-mm reduction in mean total len...

Integrated Age-structured models (e.g. Stock Synthesis), and surplus production models (e.g. JABBA) are increasingly run in parallel during stock assessments of tuna and tuna-like species. Yet, the choice of parameterization for the two different model types may not always be compatible, which can violate the validity model comparison and consequen...

The development of a Stock Synthesis model for North Atlantic shortfin mako (Isurus oxyrinchus) in 2017 has resulted in substantially more pessimistic inference about stock status and future projections when compared to previous assessments for this stock. Here, we aim to uncouple the key drivers of the underlying age-structured population dynamics...

Identifying species at risk of extinction is necessary to prioritise conservation efforts. The International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species is the global standard for quantifying extinction risk, with many species categorised on the basis of a reduction in population size. We introduce the Bayesian state-sp...

Assessing the bycatch of seabirds is a key step in understanding the impact of fishing on their populations. In this analysis, we used the seabird risk assessment methodology that was developed in New Zealand to estimate the bycatch of 26 albatross and petrel taxa that breed in the Southern Hemisphere. The bycatch estimates were related to populati...

Climate change and fishery impacts modify the spatial distribution of marine species. Understanding and predicting changes in distribution is important for adaptation by fishers and the management of fishery resources and biodiversity. However, identifying such trends is challenging given the variability inherent in trawl survey data. We apply a no...

For most rare marine species abundance trends are poorly estimated. This uncertainty often translates into disagreement on managment regulations, impeding conservation efforts when they are most urgently required. The world’s largest sea bream, the red steenbras (Petrus rupestris), has been subject to a substantial and widely acknowledged decline d...

Previous stock assessment advice for Atlantic bigeye tuna (Thunnus obesus) originated from a combination of 'A Stock Production Model Incorporating Covariates' (ASPIC) and Stock Synthesis (ss3). This contribution aims to extend the assessment toolbox for this stock by the Bayesian State-Space Surplus Production Model software 'JABBA'. While Bayesia...

There is a recognized need for new methods with modest data requirements to provide preliminary estimates of stock status for data-limited stocks (e.g. Rudd and Thorson, 2018). Froese et al. (2018)provide such a method, which derives estimates of relative stock size from length frequency (LF) data of exploited stocks. They show that their length-ba...

Spatial dependence can obscure relationships between response and explanatory variables because of structuring within the residuals reducing variance and biasing coefficient estimates. Here, we highlight the influence of the spatial component, in the presence of spatial dependence, on abundance trends. This is illustrated using abundance data for a...