Managing fisheries for human and food security

We evaluate the current status of the global marine fisheries using the frameworks of conflict, food security and vulnerability. Existing trends suggest that there is likely to be greater food insecurity and fisheries conflicts due to issues such as: declining fishery resources; a North–South divide in investment; changing consumption patterns; increasing reliance on fishery resources for coastal communities; and inescapable poverty traps creating by low net resource productivity and few alternatives. Consequently, managing fisheries from a food security perspective will become increasingly necessary, and we therefore briefly review fisheries from the perspective of food security and evaluate it using a vulnerability framework. Specifically, we describe three key components of vulnerability (exposure, sensitivity and adaptive capacity) for selected fisheries. This is followed by proposals to build the adaptive capacity of fisheries and recommendations to avoid future conflicts. Adaptive capacity attributes include assets, social flexibility and organization attributes, and learning. We present some key ways to build these aspects of the fishery to reduce the many potential environmental and social threats that increase the vulnerability of fisheries. Recommendations include fewer subsidies, reduced capital investment, precautionary management to minimize risks of ecosystem collapse, conservation of remaining resources, diversified portfolios of production and markets, and greater equity in contracts and distribution. Further, we recommend a contextual diagnostic and environmental justice framework to assess a range of options for fishery governance.     

Measuring and monitoring compliance in no‐take marine reserves

No‐take marine reserves are increasingly popular tools for conservation and fisheries management. While much attention has been paid to evaluating the effects of design aspects (size, location, etc.) in achieving reserve objectives, less emphasis has been placed on the role of stakeholder compliance. Therefore, the first aim of this study was to evaluate the state of compliance literature and examine the methods used to measure compliance in reserves. The state of compliance literature is limited, although publications with compliance information have increased sixfold in the last decade. However, most studies containing compliance information (63%) fail to provide quantitative estimates. Furthermore, most (95%) quantitative estimates of compliance were reported using a single method, which is problematic because each method has biases and limited applicability. Methods used to indicate compliance include (i) direct observation; (ii) indirect observation; (iii) law enforcement records; (iv) direct questioning; (v) expert opinion; and (vi) modelling. Our second aim was to empirically demonstrate the critical role of compliance in reserve outcomes by comparing a mixed‐effects model on compliance data synthesized from 63 marine reserves to that of a null model. The model of best fit demonstrated a negative relationship between non‐compliance and target species biomass response ratios. Thus, without incorporating any aspects of reserve design, compliance data predicted reserve response ratios of fish biomass. Accordingly, researchers should explore ways to better understand and measure non‐compliance. Therefore, future research should triangulate multiple sources of quantitative compliance data collected using standardized techniques and conduct baseline surveys before reserve implementation.     

High‐resolution ecological niche modelling of threatened freshwater mussels in east Texas,USA

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Translating the terrestrial mitigation hierarchy to marine megafauna by‐catch

In terrestrial and coastal systems, the mitigation hierarchy is widely and increasingly used to guide actions to ensure that no net loss of biodiversity ensues from development. We develop a conceptual model which applies this approach to the mitigation of marine megafauna by‐catch in fisheries, going from defining an overarching goal with an associated quantitative target, through avoidance, minimization, remediation to offsetting. We demonstrate the framework's utility as a tool for structuring thinking and exposing uncertainties. We draw comparisons between debates ongoing in terrestrial situations and in by‐catch mitigation, to show how insights from each could inform the other; these are the hierarchical nature of mitigation, out‐of‐kind offsets, research as an offset, incentivizing implementation of mitigation measures, societal limits and uncertainty. We explore how economic incentives could be used throughout the hierarchy to improve the achievement of by‐catch goals. We conclude by highlighting the importance of clear agreed goals, of thinking beyond single species and individual jurisdictions to account for complex interactions and policy leakage, of taking uncertainty explicitly into account and of thinking creatively about approaches to by‐catch mitigation in order to improve outcomes for conservation and fishers. We suggest that the framework set out here could be helpful in supporting efforts to improve by‐catch mitigation efforts and highlight the need for a full empirical application to substantiate this.     

Evolution and functional impact of rare coding variation from deep sequencing of human exomes

As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding genes to an average median depth of 111× in 2440 individuals of European (n = 1351) and African (n = 1088) ancestry. We identified over 500,000 single-nucleotide variants (SNVs), the majority of which were rare (86% with a minor allele frequency less than 0.5%), previously unknown (82%), and population-specific (82%). On average, 2.3% of the 13,595 SNVs each person carried were predicted to affect protein function of ~313 genes per genome, and ~95.7% of SNVs predicted to be functionally important were rare. This excess of rare functional variants is due to the combined effects of explosive, recent accelerated population growth and weak purifying selection. Furthermore, we show that large sample sizes will be required to associate rare variants with complex traits.     

Description and efficacy of a response-based “QUAD” cyclical hypofractionated palliative-intent radiation protocol in dogs with macroscopic solid tumours: 108 cases

Palliative-intent radiation therapy can alleviate pain and clinical signs in dogs with cancer, but optimal fractionation scheme is unknown. The objective of this retrospective case series is to evaluate clinical benefit, objective response, adverse effects, and outcomes in 108 dogs with macroscopic solid tumours treated with a cyclical “QUAD” hypofractionated palliative-intent radiation therapy protocol. Median QUAD dose was 14 Gy (14–16 Gy). Median total dose was 28 Gy (14–48 Gy). Clinical benefit rate was 93%, with median onset of subjective palliation 21 days after the first QUAD, lasting a median of 134 days. Tumour volumetric objective response was assessed with CT prior to the third QUAD in 36 dogs, with stable disease in 24 dogs (67%) and partial response in 9 dogs (25%). Sinonasal and oral were the most common tumour locations in 32 and 30 dogs, respectively. Median progression-free survival was 153 days (95% CI 114–200). Median overall survival was 212 days (95% CI 152–259). Number of QUAD cycles completed, clinical benefit achieved, anti-inflammatory received, total radiation dose, time to maximum clinical benefit, and response duration were positively associated with progression-free and overall survival. Acute toxicities were observed in 15 dogs (14%) with 3 high-grade (grade 3) toxicities (3%). Low-grade (grade 1 and 2) late skin and ocular toxicities were observed in 31 dogs (29%), predominantly leukotrichia, alopecia, keratoconjunctivitis sicca, and cataracts. This report demonstrates that QUAD radiation is an alternative protocol to be considered for palliation of dogs with inoperable or advanced stage solid tumours.     

Retrospective investigation of perioperative risk factors for immediate postoperative corneal erosions in dogs undergoing phacoemulsification

Objective

To characterize the incidence, contributing risk factors, and healing characteristics of immediate postoperative corneal erosions (IPCE) in dogs undergoing routine phacoemulsification.

Animals Studied

Medical records of 313 canine eyes (159 dogs) undergoing routine phacoemulsification surgery.

Procedures

Medical records of dogs undergoing planned cataract surgery at UW Veterinary Care were retrospectively reviewed. Patient-related variables including age, skull conformation, diabetes status, and cataract stage at the time of surgery were recorded. Intraoperative variables per eye were also recorded including surgical technique, surgeon expertise level, average phacoemulsification power, and phacoemulsification time. Diagnosis of IPCE ≤ 24 h after completion of surgery and time to IPCE healing were recorded where follow-up data were available.

Results

Immediate postoperative corneal erosions were observed in 48/313 (15.3%) operated eyes. The presence of diabetes mellitus or brachycephalic skull conformation, preoperative Schirmer tear test (STT) value, surgical technique and surgeon experience level, phacoemulsification time, and absolute phacoemulsification time were not statistically significant risk factors for IPCE. Average phacoemulsification power was associated with IPCE (RR 1.52, p = .001). Time to IPCE healing was similar in diabetic and non-diabetic dogs (median [IQR] 8 [6–11] days and 8 [6–15] days, respectively). Diabetes mellitus, brachycephaly, and phacoemulsification parameters were not associated with IPCE healing at 7 or 14 days postoperatively.

Conclusions

Higher average phacoemulsification power may be associated with the development of IPCE in canine eyes. The presence of diabetes mellitus or brachycephaly are not risk factors for the development of IPCE, nor are they factors that influence IPCE healing.     

In vitro study of the ilial anatomic landmarks for safe implant insertion in the first sacral vertebra of the intact canine sacroiliac joint

OBJECTIVE: To define landmarks on the canine ilial wing for accurate, consistent insertion of implants into the 1st sacral (S1) vertebral body when the sacroiliac joint is intact. STUDY DESIGN: Anatomic study. ANIMALS: Intact, cadaveric canine pelves and sacra (n=25). METHODS: Median sections (5 specimens) were drilled from the center of S1 in a lateral direction, exiting on the ilial wing. Landmarks on the ilial wing and shaft used to define this exit point were then used to locate this point on both wings of 20 articulated specimens, positioned and rigidly held so that the dorsal plane of the pelvis was aligned with a plumb line and the median plane of the pelvis was horizontal. A 2 mm hole was drilled from the marked point, parallel to the plumb line, until it exited the contralateral ilial wing. Distance of drill hole position from the geometric center (GC) of S1 was located on median and paramedian plane images derived from plane, computed tomographic (CT) scans. RESULTS: The entire drill hole was located within S1 in 18 specimens. Mean deviation of the hole from GC (ratio of the distance of GC from the closest S1 body border) in median section was 0.40 +/- 0.29 (craniocaudal direction) and 0.29 +/- 0.23 (dorsoventral). CONCLUSIONS: Use of ilial wing landmarks and drilling perpendicular to the median plane will improve accuracy for insertion of implants into S1 when the sacroiliac joint is intact. CLINICAL RELEVANCE: Ilial wing landmarks should be used to improve accuracy of implant insertion into S1.     

Development of allometric leaf area models for intensively managed black walnut (Juglans nigra L.)

? Introduction

Intensive plantation management of high-value hardwoods, such as black walnut (Juglans nigra L.), is focused on maximizing both stem form and growth at the stand and tree level. While significant research has focused on genetic improvement in black walnut, little is known about the production ecology of this species in plantation settings.

? Objectives

The aim of this study is to assess the applicability of nondestructive projected leaf area (PLA) estimation based on the pipe model theory in three single-aged J. nigra plantations representing discrete age classes ranging from 3 to 27?years of age.

? Results

Branch-level PLA was modeled as a function of branch basal cross-sectional area (R ²?=?0.875). Six nondestructive tree-level PLA models were assessed, with four models yielding R ²?>?0.90. Tree-level models performed well across age classes, with model fits comparable to previous studies in coniferous species.

? Conclusion

This study demonstrates that allometric approaches to modeling leaf area distribution in hardwoods are feasible, but future efforts may need to use different sampling approaches and/or quantify variables that have not been significant in conifers. This study represents an important first step into more quantitative analysis of production ecology of deciduous species in the CHFR of the USA.     

Repeatability and contingency in the evolution of a key innovation in phage lambda

The processes responsible for the evolution of key innovations, whereby lineages acquire qualitatively new functions that expand their ecological opportunities, remain poorly understood. We examined how a virus, bacteriophage λ, evolved to infect its host, Escherichia coli, through a novel pathway. Natural selection promoted the fixation of mutations in the virus's host-recognition protein, J, that improved fitness on the original receptor, LamB, and set the stage for other mutations that allowed infection through a new receptor, OmpF. These viral mutations arose after the host evolved reduced expression of LamB, whereas certain other host mutations prevented the phage from evolving the new function. This study shows the complex interplay between genomic processes and ecological conditions that favor the emergence of evolutionary innovations.