Estimating age composition for multiple years when there are gaps in the ageing data: the case of western Atlantic bluefin tuna

Age–length key (ALK) methods generally perform well when length samples and age samples are representative of the underlying population. It is unclear how well these methods perform when lengths are representative but age samples are sparse (i.e. age samples are small or missing in many years, and some length groups do not have any age observations). With western Atlantic bluefin tuna, the available age data are sparse and have been, for the most part, collected opportunistically. We evaluated two methods capable of accommodating sparse age data: a novel hybrid ALK (combining forward ALKs and cohort slicing) and the combined forward-inverse ALK. Our goal was to determine if the methods performed better than cohort slicing, which has traditionally been used to obtain catch-at-age for Atlantic bluefin tuna, given the data limitations outlined above. Simulation results indicated that the combined forward-inverse ALK performed much better than the other methods. When applied to western Atlantic bluefin tuna data, the combined forward-inverse ALK approach was able to track cohorts and identified an inconsistency in the ageing of some samples

Identifying trade-offs and reference points in support of ecosystem approaches to managing Gulf of Mexico menhaden

Gulf menhaden (Brevoortia patronus) support the largest fishery by yield in the Gulf of Mexico (GoM) and are a key forage species for many marine predators. While menhaden stock assessments indicated that overfishing was not likely to have occurred in the past, concerns have been raised regarding the possible effects of menhaden fishing on their predators. In this study, we used a US Gulfwide Ecopath with Ecosim (EwE) model to explore the predicted effects of increased menhaden harvest on the GoM ecosystem and focused our analyses on Gulf menhaden predators. Key menhaden predators identified included king mackerel (Scomberomorus cavalla), Spanish mackerel (Scomberomorus maculatus), sea trout (Cynoscion spp.), red drum (Sciaenops ocellatus), and pelagic coastal piscivores [e.g., bluefish (Pomatomus saltatrix)]. As expected, these predators exhibited reduced biomass in response to increased Gulf menhaden harvest, with a predicted 11% decrease in predator biomass at simulated fishing levels near historical highs. Our results indicate strong relationships between the effects of menhaden fishing and the predator fishing mortality for king mackerel and intermediate relationships for Spanish mackerel, blacktip shark (Carcharhinus limbatus), red drum, large coastal sharks, and pelagic coastal piscivores. Biomass of predator groups such as demersal coastal invertebrate feeders [e.g., drums and croakers (Sciaenidae)] are more affected by menhaden harvest (through trophodynamics interactions and bycatch removal) compared to the isolated effect of their fishing mortality. For almost all the groups examined in the trade-off analysis, with the exception of sea trout, current biomass (2016) was higher than their target biomass representing 75% of their biomass at maximum sustainable yield. In comparison to the time series of fishing mortality rates estimated by the most recent Gulf menhaden stock assessment, the mean ecological reference point (ERP) of 0.862 was exceeded in all but 1 year from 1977 to 2007; however, neither the target nor threshold upper ERP value has been exceeded since 2008. The observed Gulf menhaden landings from 2003 to the present were generally within the range of the projected equilibrium landings (i.e., within confidence intervals) at both the ERP target and threshold values except for three recent years

Evaluating Atlantic bluefin tuna harvest strategies that use conventional genetic tagging data

An individual tagging model was implemented within the spatial, seasonal, multi-stock, multi-fleet operating models of the peer-reviewed Management Strategy Evaluation (MSE) framework for Atlantic bluefin tuna to evaluate the benefits of a harvest strategy that utilizes conventional gene tagging. A multi-year Brownie estimator was developed to test the accuracy and precision of exploitation rate estimates arising from gene tagging programs with various scenarios for spatial release distribution, release numbers and fishery exploitation rates. Harvest strategies that used the Brownie estimator were tested to evaluate yield and resource conservation performance relative to idealized management using perfect information. For the eastern stock, releasing 1,000 fish throughout the Atlantic and genotyping 27% of all landed fish at an estimated cost of US$2M was sufficient to obtain estimates of exploitation rate with a coefficient of variation of 20$2.5M. Harvest strategies using the gene tagging data provided expected yield and resource conservation performance that was not substantially lower than a harvest strategy assuming using perfect information regarding vulnerable biomass. Reducing the number of releases most strongly affected the worst-case ‘lower-tail’ outcomes for West area yield and eastern stock biomass. Conventional gene tagging harvest strategies offer a promising basis for calculating management advice for Atlantic bluefin tuna that may be cheaper, simpler, and more robust than the current conventional stock assessment paradigm

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

The Robustness of Brownie Tag Return Models to Complex Spatiotemporal Dynamics Evaluated through Simulation Analysis

The development of a reliable tagging program requires simulation testing the experimental design. However, the potential for model misspecification, particularly in the underlying spatiotemporal dynamics, is often ignored. A continuous time, spatially-explicit, age-structured, capture-recapture operating model was developed to better emulate real-world population dynamics typically overlooked in spatially-aggregated or discrete time tagging models. Various spatiotemporal model parametrizations, including case studies with Atlantic bluefin and yellowfin tunas, were explored to evaluate the bias associated with Brownie tag return estimation models. Simulations demonstrated that accounting for connectivity was essential for obtaining unbiased parameter estimates, and that migration rates could be reliably estimated without the correlation associated with other parameters (e.g., between tag reporting and mortality). Mortality parameter estimates were particularly sensitive to the temporal dynamics of the tagging and fishing seasons, but accounting for the seasonality in tag releases and fishery recaptures allowed for relatively unbiased estimation. Our results indicate that parameter bias and uncertainty can be severely underestimated when discrete time or spatially-aggregated operating models are used to determine optimal experimental design of tagging studies.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

On Making Statistical Inferences Regarding the Relationship between Spawners and Recruits and the Irresolute Case of Western Atlantic Bluefin Tuna (Thunnus thynnus).

Forecasts of the future abundance of western Atlantic bluefin tuna (Thunnus thynnus) have, for nearly two decades, been based on two competing views of future recruitment potential: (1) a "low" recruitment scenario based on hockey-stick (two-line) curve where the expected level of recruitment is set equal to the geometric mean of the recruitment estimates for the years after a supposed regime-shift in 1975, and (2) a "high" recruitment scenario based on a Beverton-Holt curve fit to the time series of spawner-recruit pairs beginning in 1970. Several investigators inferred the relative plausibility of these two scenarios based on measures of their ability to fit estimates of spawning biomass and recruitment derived from stock assessment outputs. Typically, these comparisons have assumed the assessment estimates of spawning biomass are known without error. It is shown here that ignoring error in the spawning biomass estimates can predispose model-choice approaches to favor the regime-shift hypothesis over the Beverton-Holt curve with higher recruitment potential. When the variance of the observation error approaches that which is typically estimated for assessment outputs, the same model-choice approaches tend to favor the single Beverton-Holt curve. For this and other reasons, it is argued that standard model-choice approaches are insufficient to make the case for a regime shift in the recruitment dynamics of western Atlantic bluefin tuna. A more fruitful course of action may be to move away from the current high/low recruitment dichotomy and focus instead on adopting biological reference points and management procedures that are robust to these and other sources of uncertainty

Spawning stock biomass (t) and recruitment estimates (in number) from the 2014 stock assessment (note that results for the last three years were not included in the AICc computations because they were considered to be poorly determined by the assessment working group).

<p>Spawning stock biomass (t) and recruitment estimates (in number) from the 2014 stock assessment (note that results for the last three years were not included in the AICc computations because they were considered to be poorly determined by the assessment working group).</p

Parameter estimates for the Beverton-Holt, three-line regime shift and Beverton-Holt regime shift models fitted to the spawning stock biomass and recruitment estimates from the 2014 assessment of western Atlantic bluefin tuna.

<p>Parameter estimates for the Beverton-Holt, three-line regime shift and Beverton-Holt regime shift models fitted to the spawning stock biomass and recruitment estimates from the 2014 assessment of western Atlantic bluefin tuna.</p

Structure and estimation framework for Atlantic Bluefin tuna operating models.

A preliminary spatial, multi-stock statistical catch-at-length assessment model is developed as a basis for defining operating models for Atlantic bluefin tuna. The modifiable multi-stock model (M3) aims to improve upon previous multi-stock models such as MAST (Taylor et al. 2011) in three core areas. The first iteration of the model: (1) makes use of indices of abundance specific to time-area strata (e.g. for a given ocean area and month of the year), (2) does not use conventional tagging data to inform exploitation rates, (3) is fitted to samples of length composition data and therefore avoids established problems related to ageing individuals based on a growth curve and length data only. In this paper we provide a full account of preliminary M3 model equations and discuss the results of simulation evaluations of model estimation performance. Limitations of the current approach and future areas for model development are also discussed