Mineral texture classification using deep convolutional neural networks: An application to zircons from porphyry copper deposits

The texture and morphology of igneous zircon indicates magmatic conditions during zircon crystallization and can be used to constrain provenance. Zircons from porphyry copper deposits are typically prismatic, euhedral, and strongly oscillatory zoned which may differentiate them from zircons associated with unmineralized igneous systems. Here, cathodoluminescence images of zircons from the Quellaveco porphyry copper district, Southern Peru, were collected to compare zircon textures between the premineralization Yarabamba Batholith and the Quellaveco porphyry copper deposit. Quellaveco porphyry zircons are prismatic, euhedral, and strongly oscillatory zoned, whereas the batholith zircons are subhedral-anhedral with weaker zoning. We adopt a deep convolutional neural network (CNN) approach to demonstrate that a CNN can classify Quellaveco porphyry zircons with high success. We trial several CNN architectures to classify zircon images: LeNet-5, AlexNet and VGG, including a transfer learning approach where we used the weights of a VGG model pretrained on the ImageNet data set. The VGG model with transfer learning is the most effective approach, with accuracy and receiver operating characteristic-area under curve (ROC-AUC) scores of 0.86 and 0.93, indicating that a Quellaveco porphyry zircon CL image can be ranked higher than a batholith zircon with 93% probability. Visualizing model layer outputs demonstrates that the CNN models can recognize crystal edges, zoning, and mineral inclusions. We trial implementing trained CNN models as unsupervised feature extractors, which can empirically quantify crystal textures and morphology. Therefore, deep learning provides a tool for the extraction of information from large, imaged-based petrographic data sets which can facilitate petrologic and provenance studies

Exercise intensity while hooked is associated with physiological status of longline-captured sharks

Some shark populations face declines owing to targeted capture and by-catch in longline fisheries. Exercise intensity during longline capture and physiological status may be associated, which could inform management strategies aimed at reducing the impacts of longline capture on sharks. The purpose of this study was to characterize relationships between exercise inten- sity and physiological status of longline-captured nurse sharks (Ginglymostoma cirratum) and Caribbean reef sharks (Carcharhinus perezi). Exercise intensity of longline-captured sharks was quantified with digital cameras and accelerometers, which was paired with blood-based physiological metrics from samples obtained immediately post-capture. Exercise intensity was associated with physiological status following longline capture. For nurse sharks, blood pH increased with capture dur- ation and the proportion of time exhibiting low-intensity exercise. Nurse sharks also had higher blood glucose and plasma potassium concentrations at higher sea surface temperatures. Associations between exercise intensity and physiological sta- tus for Caribbean reef sharks were equivocal; capture duration had a positive relation with blood lactate concentrations and a negative relationship with plasma chloride concentrations. Because Caribbean reef sharks did not appear able to influence blood pH through exercise intensity, this species was considered more vulnerable to physiological impairment. While both species appear quite resilient to longline capture, it remains to be determined if exercise intensity during capture is a useful tool for predicting mortality or tertiary sub-lethal consequences. Fisheries management should consider exercise during cap- ture for sharks when developing techniques to avoid by-catch or reduce physiological stress associated with capture

Classification and characterisation of magmatic-hydrothermal tourmaline by combining field observations and microanalytical techniques

Tourmaline from the St. Byron lobe of the Land’s End granite, SW England, was assessed by macroscopic, optical and quantitative microanalytical methods. In total, seven types of tourmaline were distinguished. The seven types reflect different crystallisation environments and stages in the magmatic-hydrothermal transition. Types 1-3 are interpreted to represent a gradual transition from tourmaline crystallising from a silicate melt to precipitation from magmatic aqueous fluids. Types 5-7 crystallised at subsolidus conditions from a different fluid generation than types 1-3. These fluids may be magmatic or mixed with other fluids (e.g., meteoric or formation waters). The Sn-mineralisation in the area is mostly related to the latter fluid generation, and the mineralising potential is reflected by the tourmaline composition.This is an open access article, available to all readers online, published under a creative commons licensing Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Published under licence by IOP Publishing Lt

The future of recreational fisheries: Advances in science, monitoring, management, and practice

Recreational fisheries (RF) are complex social-ecological systems that play an important role in aquatic environments while generating significant social and economic benefits around the world. The nature of RF is diverse and rapidly evolving, including the participants, their priorities and behaviors, and the related ecological impacts and social and economic benefits. RF can lead to negative ecological impacts, particularly through overexploitation of fish populations and spread of non-native species and genotypes through stocking. Hence, careful management and monitoring of RF is essential to sustain these ecologically and socioeconomically important resources. This special issue on recreational fisheries contains diverse research, syntheses, and perspectives that highlight the advances being made in RF research, monitoring, management, and practice, which we summarize here. Co-management actions are rising, often involving diverse interest groups including government and non-government organizations; applying collaborative management practices can help balance social and economic benefits with conservation targets. Technological and methodological advances are improving the ability to monitor biological, social, and economic dynamics of RF, which underpin the ability to maximize RF benefits through management actions. To ensure RF sustainability, much research focuses on the ecological aspects of RF, as well as the development of management and angling practices that reduce negative impacts on fish populations. For example, angler behavior can be influenced to conform to conservation-minded angling practices through regulations, but is often best accomplished through growing bottom-up social change movements. Anglers can also play an important role in fisheries monitoring and conservation, including providing data on fish abundance and assemblages (i.e., citizen science). The increasing impacts that growing human populations are having on the global environment are threatening many of the natural resources and ecosystem services they provide, including valuable RF. However, with careful development of research initiatives, monitoring and management, sustainable RF can generate positive outcomes for both society and natural ecosystems and help solve allocation conflicts with commercial fisheries and conservation

The future of recreational fisheries: Advances in science, monitoring, management, and practice

Recreational fisheries (RF) are complex social-ecological systems that play an important role in aquatic environments while generating significant social and economic benefits around the world. The nature of RF is diverse and rapidly evolving, including the participants, their priorities and behaviors, and the related ecological impacts and social and economic benefits. RF can lead to negative ecological impacts, particularly through overexploitation of fish populations and spread of non-native species and genotypes through stocking. Hence, careful management and monitoring of RF is essential to sustain these ecologically and socioeconomically important resources. This special issue on recreational fisheries contains diverse research, syntheses, and perspectives that highlight the advances being made in RF research, monitoring, management, and practice, which we summarize here. Co-management actions are rising, often involving diverse interest groups including government and non-government organizations; applying collaborative management practices can help balance social and economic benefits with conservation targets. Technological and methodological advances are improving the ability to monitor biological, social, and economic dynamics of RF, which underpin the ability to maximize RF benefits through management actions. To ensure RF sustainability, much research focuses on the ecological aspects of RF, as well as the development of management and angling practices that reduce negative impacts on fish populations. For example, angler behavior can be influenced to conform to conservation-minded angling practices through regulations, but is often best accomplished through growing bottom-up social change movements. Anglers can also play an important role in fisheries monitoring and conservation, including providing data on fish abundance and assemblages (i.e., citizen science). The increasing impacts that growing human populations are having on the global environment are threatening many of the natural resources and ecosystem services they provide, including valuable RF. However, with careful development of research initiatives, monitoring and management, sustainable RF can generate positive outcomes for both society and natural ecosystems and help solve allocation conflicts with commercial fisheries and conservation

Influence of magmatic and magmatic-hydrothermal processes on the lithium endowment of micas in the Cornubian Batholith (SW England)

This is the final version. Available on open access from Springer via the DOI in this recordThe Cornubian Batholith (SW England) is an archetypal Variscan rare metal granite with potential for Li-mica mineralization. We present a petrographic, trace element and multivariate statistical study of micas from the Cornubian Batholith granite series and related hydrothermally altered units to assess the role of magmatic vs subsolidus processes and of fluxing elements (F and B) on the Li cycle during the evolution of the system. The mica types are as follows: (1) magmatic, which include Fe-biotite, protolithionite I and phengite-muscovite from the most primitive granites, and zinnwaldite I from more fractionated lithologies; (2) subsolidus, which encompass high-temperature autometasomatic Li-micas and low-temperature hydrothermal muscovite-phengite. Autometasomatic species include protolithionite II, zinnwaldite II and lepidolite, which were observed in the most fractionated and hydrothermally altered units, and occur as replacements of magmatic micas. Low-temperature hydrothermal Li-poor micas formed via alteration of magmatic and autometasomatic micas or as replacement of feldspars, and albeit occur in all studied lithologies they are best represented by the granite facies enriched in metasomatic tourmaline. The evolution of micas follows two major trends underlining a coupling and decoupling between the Li(F) and B fluxes. These include as follows: (1) a Li(F)-progressive trend explaining the formation of protolithionite I and zinnwaldite I, which fractionate Li along with Cs, Nb and Sn during the late-magmatic stages of crystallization, and of zinnwaldite II and lepidolite forming from the re-equilibration of primary micas with high-temperature Li-B-W-Tl-Cs-Mn-W-rich autometasomatic fluids; (2) a Li(F)-retrogressive trend explaining the low-temperature hydrothermal muscovitization, which represents the main Li depletion process. Trace element geochemistry and paragenesis of late muscovite-phengite support that muscovitization is a district-scale process that affected the upper parts of the granite cupolas through acidic and B(Fe-Sn)-saturated hydrothermal fluids associated with metasomatic tourmalinization, which were mixed with a low Eh meteoric component.Natural Environment Research Council (NERC)Ministry of Science and Higher Education of the Republic of Kazakhsta

Integrating network analysis, sensor tags, and observation to understand shark ecology and behavior

Group living in animals is a well-studied phenomenon, having been documented extensively in a wide range of terrestrial, freshwater, and marine species. Although social dynamics are complex across space and time, recent technological and analytical advances enable deeper understanding of their nature and ecological implications. While for some taxa, a great deal of information is known regarding the mechanistic underpinnings of these social processes, knowledge of these mechanisms in elasmobranchs is lacking. Here, we used an integrative and novel combination of direct observation, accelerometer biologgers, and recent advances in network analysis to better understand the mechanistic bases of individual-level differences in sociality (leadership, network attributes) and diel patterns of locomotor activity in a widespread marine predator, the lemon shark (Negaprion brevirostris). We found that dynamic models of interaction based on Markov chains can accurately predict juvenile lemon shark social behavior and that lemon sharks did not occupy consistent positions within their network. Lemon sharks did however preferentially associate with specific group members, by sex as well as by similarity or nonsimilarity for a number of behavioral (nonsimilarity: leadership) and locomotor traits (similarity: proportion of time swimming "fast," mean swim duration; nonsimilarity: proportion of swimming bursts/transitions between activity states). Our study provides some of the first information on the mechanistic bases of group living and personality in sharks and further, a potential experimental approach for studying fine-scale differences in behavior and locomotor patterns in difficult-to-study organisms

Spatial Connectivity and Drivers of Shark Habitat Use Within a Large Marine Protected Area in the Caribbean, The Bahamas Shark Sanctuary

Marine protected areas (MPAs) have emerged as potentially important conservation tools for the conservation of biodiversity and mitigation of climate impacts. Among MPAs, a large percentage has been created with the implicit goal of protecting shark populations, including 17 shark sanctuaries which fully protect sharks throughout their jurisdiction. The Commonwealth of the Bahamas represents a long-term MPA for sharks, following the banning of commercial longlining in 1993 and subsequent designation as a shark sanctuary in 2011. Little is known, however, about the longterm behavior and space use of sharks within this protected area, particularly among reef-associated sharks for which the sanctuary presumably offers the most benefit. We used acoustic telemetry to advance our understanding of the ecology of such sharks, namely Caribbean reef sharks (Carcharhinus perezi) and tiger sharks (Galeocerdo cuvier), over two discrete islands (New Providence and Great Exuma) varying in human activity level, over 2 years. We evaluated which factors influenced the likelihood of detection of individuals, analyzed patterns of movement and occurrence, and identified variability in habitat selection among species and regions, using a dataset of 23 Caribbean reef sharks and 15 tiger sharks which were passively monitored in two arrays with a combined total of 13 acoustic receivers. Caribbean reef sharks had lower detection probabilities than tiger sharks, and exhibited relatively low habitat connectivity and high residency, while tiger sharks demonstrated wider roaming behavior across much greater space. Tiger sharks were associated with shallow seagrass habitats where available, but frequently transited between and connected different habitat types. Our data support the notion that large MPAs afford greater degrees of protection for highly resident species such as Caribbean reef sharks, shark, acoustic telemetry, marine protected area, MPA, seagrass, coral reef, Bahamas, Caribbea

Inter-rater reliability of categorical versus continuous scoring of fish vitality: does it affect the utility of the reflex action mortality predictor (RAMP) approach?

Scoring reflex responsiveness and injury of aquatic organisms has gained popularity as predictors of discard survival. Given this method relies upon the individual interpretation of scoring criteria, an evaluation of its robustness is done here to test whether protocol-instructed, multiple raters with diverse backgrounds (research scientist, technician, and student) are able to produce similar or the same reflex and injury score for one of the same flatfish (European plaice, Pleuronectes platessa) after experiencing commercial fishing stressors. Inter-rater reliability for three raters was assessed by using a 3-point categorical scale (‘absent’, ‘weak’, ‘strong’) and a tagged visual analogue continuous scale (tVAS, a 10 cm bar split in three labelled sections: 0 for ‘absent’, ‘weak’, ‘moderate’, and ‘strong’) for six reflex responses, and a 4-point scale for four injury types. Plaice (n = 304) were sampled from 17 research beam-trawl deployments during four trips. Fleiss kappa (categorical scores) and intra-class correlation coefficients (ICC, continuous scores) indicated variable inter-rater agreement by reflex type (ranging between 0.55 and 0.88, and 67% and 91% for Fleiss kappa and ICC, respectively), with least agreement among raters on extent of injury (Fleiss kappa between 0.08 and 0.27). Despite differences among raters, which did not significantly influence the relationship between impairment and predicted survival, combining categorical reflex and injury scores always produced a close relationship of such vitality indices and observed delayed mortality. The use of the continuous scale did not improve fit of these models compared with using the reflex impairment index based on categorical scores. Given these findings, we recommend using a 3-point categorical over a continuous scale. We also determined that training rather than experience of raters minimised inter-rater differences. Our results suggest that cost-efficient reflex impairment and injury scoring may be considered a robust technique to evaluate lethal stress and damage of this flatfish species on-board commercial beam-trawl vessels