Play behavior in ectothermic vertebrates

Until a few decades ago, play was considered a behavior unique to birds and mammals. Although play in other vertebrates is still a neglected research subject, data on it has been slowly accumulating, and are reviewed here. Now we know that animals as diverse as stingrays, cichlid fishes, monitor lizards, softshell turtles, and crocodiles can be unexpectedly playful. This knowledge has implications to broader theoretical problems, but much more research attention is needed to utilize its potential.

Mitigating elasmobranch fin trade: A market analysis for made-to-measure interventions

The unsustainable trade in elasmobranch products, particularly fins, contributes to the decline of elasmobranch populations worldwide. Designing and implementing context-appropriate solutions to mitigate unsustainable trade requires a thorough analysis of markets. Here we assess the market component of the elasmobranch fin trade in the Bay of Bengal, Bangladesh, using a framework designed to analyse wildlife markets. Using a mixed-method approach, we characterised the market to identify the components contributing to unsustainable practices. By-catch retention levels were high leading to the development of a solid market. Trade on fins was prevalent due to a high price, lack of awareness, actors' limited ability to adhere to regulations, and no strategies and incentives to limit fishing mortality. An imbalanced power and financial structure between actors were revealed, with some actors accessing unequal benefits from the market. Impediments for adopting conservation measures by low-access actors (e.g., fishers) with limited decision-making power or resources were evident. We also identified challenges to enforcement primarily due to limited reporting and issues identifying species and products. Fishers noted several socio-ecological, technical, and enforcement issues (e.g., policing instead of meaningful monitoring, punitive measures without facilitating compliance), that will require adequate time and resources to change practices. Lack of opportunities and information to adhere to regulations and increased enforcement has led to conflicts, non-compliance and unwillingness to report catches. The study has significantly strengthened the current understanding of Bangladesh's complex elasmobranch product market while highlighting critical knowledge gaps that must be addressed to inform and improve management decisions. Based on the findings, we recommend targeted actions to respond to the current market for mitigating elasmobranch product trade and moving towards establishing sustainable and ethical trade. Our work has both regional and global significance, given the role of the Bay of Bengal nations in the worldwide elasmobranch product market.

Smart sharks: a review of chondrichthyan cognition

450 million years of evolution have given chondrichthyans (sharks, rays and allies) ample time to adapt perfectly to their respective everyday life challenges and cognitive abilities have played an important part in that process. The diversity of niches that sharks and rays occupy corresponds to matching diversity in brains and behaviour, but we have only scratched the surface in terms of investigating cognition in this important group of animals. The handful of species that have been cognitively assessed in some detail over the last decade have provided enough data to safely conclude that sharks and rays are cognitively on par with most other vertebrates, including mammals and birds. Experiments in the lab as well as in the wild pose their own unique challenges, mainly due to the handling and maintenance of these animals as well as controlling environmental conditions and elimination of confounding factors. Nonetheless, significant advancements have been obtained in the fields of spatial and social cognition, discrimination learning, memory retention as well as several others. Most studies have focused on behaviour and the underlying neural substrates involved in cognitive information processing are still largely unknown. Our understanding of shark cognition has multiple practical benefits for welfare and conservation management but there are obvious gaps in our knowledge. Like most marine animals, sharks and rays face multiple threats. The effects of climate change, pollution and resulting ecosystem changes on the cognitive abilities of sharks and stingrays remain poorly investigated and we can only speculate what the likely impacts might be based on research on bony fishes. Lastly, sharks still suffer from their bad reputation as mindless killers and are heavily targeted by commercial fishing operations for their fins. This public relations issue clouds people's expectations of shark intelligence and is a serious impediment to their conservation. In the light of the fascinating results presented here, it seems obvious that the general perception of sharks and rays as well as their status as sentient, cognitive animals, needs to be urgently revisited.

Essential and non-essential trace element concentrations in muscle and liver of a pregnant Munk's pygmy devil ray (Mobula munkiana) and its embryo

During gestation, essential and non-essential trace elements are transferred from the pregnant females to embryos. This study aimed to determine and compare the concentrations of seven essential trace elements (Fe, Zn, Se, Cu, Mn, Cr, Co) and six non-essential trace elements (As, Cd, V, U, Tl, Ag) in the muscle and the liver of a Munk's pygmy devil ray pregnant female, Mobula munkiana, and its embryo. Transfer evidence of essential and non-essential trace elements was detected in M. munkiana tissues. Arsenic was found in elevated concentrations in the pregnant female and the embryo tissues. Elevated levels of Cd, V, U, and Ag were found in the pregnant female liver, but were minimal in the embryo tissue. This is the first study to investigate maternal transfer of essential and non-essential trace elements in these species and their reproductive strategy.

MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data

The development of third-generation sequencing technology has brought significant changes and influences on genomics. Compared to the second-generation sequencing methods, the third-generation technologies produce around 100 times longer reads to reveal new genomic variations that complete long-term gaps in the human reference genome. However, these reads' excessive length and high error rate severely increase the amount of data and alignment cost. The traditional data analysis platform and serial sequence alignment method can not effectively deal with large-scale long read alignment. There is a critical need for a novel data analysis platform that can deliver fast alignment of large-scale sequences to solve the problem of long read alignment. High-performance computing platforms and efficient, scalable algorithms based on these platforms have significant potential to impact sequence analysis approaches. This paper presented minimapR, a multi-level parallel long-read alignment tool based on minimap2, a popular third-generation read aligner. MinimapR is developed based on the new high-performance distributed framework Ray. Ray fully integrates with the Python environment and can be easily installed with pip. MinimapR can utilize the power of multiple computing nodes, significantly accelerating alignment speeds without sacrificing sensitivity. The minimapR tool was tested on 64 nodes and demonstrated a 50 fold increase in speed with 78 % parallel efficiency. The source code and user manual of minimapR are freely available at https://github.com/Geehome/minimapR.

Polypocephalus barsami sp. nov., a New Species of Polypocephalidae Meggitt, 1924 (Lecanicephalidea) from the Persian Gulf

INTRODUCTION

Although many batoid species, known as final hosts of lecanicephalidean cestodes, exist in the Persian Gulf, no knowledge regarding this cestode order is available for this region. This study is the first one focusing on this order in the Persian Gulf.

METHODS

A total of 11 cowtail stingrays, Pastinachus sephen (Forsskål), were collected from the north eastern Persian Gulf. Isolated cestodes were fixed in 10% seawater-buffered formalin and stored in 70% ethanol. For morphological examinations, worms were stained using acetic carmine; a subset was prepared for SEM.

RESULTS

A new species of Polypocephalus Braun, 1878 was described. Polypocephalus barsami sp. nov. is the only species within its genus reported outside the waters of Japan, India, Sri Lanka, and Egypt in the Indian Ocean. Since the microtriches were not described in the generic diagnosis of Polypocephalus, the description of the microtriches is added based on the standardised terminology. Furthermore, the characteristics of this new species were discussed and compared within Polypocephalus, many species of which have poor descriptions.

CONCLUSIONS

Polypocephalus barsami sp. nov. is the first report of the genus Polypocephalus in the Persian Gulf and the 15th valid species of its genus.

Hypermobility in Hallux Valgus

The interaction between hypermobility and hallux valgus remains both contemporary and incendiary. The difficulty in setting clinical and radiological parameters to diagnose and the complexity of questions that circumnutate the philosophy among etiology and denouement, fires up the debate regarding these conditions. Outcomes among procedures that address or neglect ray instability are still used as argument for any group of believers or nonbelievers. Through proving the true existence of hypermobility and its relationship with bunions, our colleges and professors have produced an incredible amount of excellent data that helped us better comprehend the hallux valgus syndrome in a general manner.

Indications, functional results and patient satisfaction after isolated second ray resection following traumatic injury: A retrospective review of 25 patients

Amputation of the second ray is a surgical treatment option when reconstruction and/or reimplantation fail. The aim of our study was to review the outcomes after transmetacarpal resection of the second ray following a post-traumatic injury and to assess indications, functional outcomes, and patient satisfaction. Between January 2003 and December 2013, 25 patients (6 women and 19 men with a mean age of 51 years) underwent transmetacarpal resection of their second ray after a post-traumatic injury. Sixteen patients were right-handed and 9 were left-handed. Injuries involved the dominant hand in 14 cases (60%). In order to differentiate patients with preserved index finger length preoperatively from those with a shorter, amputated index finger stump, patients were divided into 2 groups. Group 1 included those with an "intact finger" and Group 2 included patients with an "amputated stump". Data collection, including patient satisfaction and functional outcomes, was performed at 83 months postoperative on average. Average length of follow-up was 7.0±1.0 years (range 5-12 years). Group 1 (intact finger) and 2 (amputated stump) included 15 and 10 patients, respectively. Six patients (24%) had primary ray amputation and 19 (76%) had secondary ray amputation. No surgical revision was necessary. In Group 1, the indications were purely functional in all but two cases, whereas aesthetic indications played a role in all patients in Group 2. The average total time off work was 3 months. There was no difference between Group 1 and 2 (P>0.05). However, patients with primary ray resection averaged 10 weeks of lost work compared to 17 weeks for secondary amputation. There was no functional difference between Groups 1 and 2. Scores for cosmetic appearance and patient satisfaction were higher in Group 2. In certain specific situations after complex hand trauma, transmetacarpal amputation of the second ray is indicated as soon as possible, in order to reduce the time off work. Patient satisfaction following this surgical procedure is high, especially in groups with amputated stumps. A 30% decrease in pinch and grip strength is the rule. No secondary surgery is normally required.

Patients Allergic to Fish Tolerate Ray Based on the Low Allergenicity of Its Parvalbumin

Background

Clinical reactions to bony fish species are common in patients with allergy to fish and are caused by parvalbumins of the β-lineage. Cartilaginous fish such as rays and sharks contain mainly α-parvalbumins and their allergenicity is not well understood.

Objective

To investigate the allergenicity of cartilaginous fish and their α-parvalbumins in individuals allergic to bony fish.

Methods

Sensitization to cod, salmon, and ray among patients allergic to cod, salmon, or both (n = 18) was explored by prick-to-prick testing. Clinical reactivity to ray was assessed in 11 patients by food challenges or clinical workup. IgE-binding to β-parvalbumins (cod, carp, salmon, barramundi, tilapia) and α-parvalbumins (ray, shark) was determined by IgE-ELISA. Basophil activation tests and skin prick tests were performed with β-parvalbumins from cod, carp, and salmon and α-parvalbumins from ray and shark.

Results

Tolerance of ray was observed in 10 of 11 patients. Prick-to-prick test reactions to ray were markedly lower than to bony fish (median wheal diameter 2 mm with ray vs 11 mm with cod and salmon). IgE to α-parvalbumins was lower (median, 0.1 kU/L for ray and shark) than to β-parvalbumins (median, ≥1.65 kU/L). Furthermore, α-parvalbumins demonstrated a significantly reduced basophil activation capacity compared with β-parvalbumins (eg, ray vs cod, P < .001; n = 18). Skin prick test further demonstrated lower reactivity to α-parvalbumins compared with β-parvalbumins.

Conclusions

Most patients allergic to bony fish tolerated ray, a cartilaginous fish, because of low allergenicity of its α-parvalbumin. A careful clinical workup and in vitro IgE-testing for cartilaginous fish will improve patient management and may introduce an alternative to bony fish into patients’ diet.

Complex flow in the nasal region of guitarfishes

Scent detection in an aquatic environment is dependent on the movement of water. We set out to determine the mechanisms for moving water through the olfactory organ of guitarfishes (Rhinobatidae, Chondrichthyes) with open nasal cavities. We found at least two. In the first mechanism, which we identified by observing dye movement in the nasal region of a life-sized physical model of the head of Rhinobatos lentiginosus mounted in a flume, olfactory flow is generated by the guitarfish's motion relative to water, e.g. when it swims. We suggest that the pressure difference responsible for motion-driven olfactory flow is caused by the guitarfish's nasal flaps, which create a region of high pressure at the incurrent nostril, and a region of low pressure in and behind the nasal cavity. Vortical structures in the nasal region associated with motion-driven flow may encourage passage of water through the nasal cavity and its sensory channels, and may also reduce the cost of swimming. The arrangement of vortical structures is reminiscent of aircraft wing vortices. In the second mechanism, which we identified by observing dye movement in the nasal regions of living specimens of Glaucostegus typus, the guitarfish's respiratory pump draws flow through the olfactory organ in a rhythmic (0.5-2 Hz), but continuous, fashion. Consequently, the respiratory pump will maintain olfactory flow whether the guitarfish is swimming or at rest. Based on our results, we propose a model for olfactory flow in guitarfishes with open nasal cavities, and suggest other neoselachians which this model might apply to.

Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra

The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products.

DNA barcoding unveils skate (Chondrichthyes: Rajidae) species diversity in 'ray' products sold across Ireland and the UK

Skates are widely consumed across the globe, but many large species are subject to considerable concern regarding their conservation and management. Within Europe such issues have recently driven policy changes so that, for the first time, reports of skate landings now have to be made under species-specific names. Total allowable catches have also been established for many groups, which have been set to zero for a number of the most vulnerable species (e.g., Dipturus batis, Raja undulata and Rostoraja alba). Whilst accurate species identification has become an important issue for landings, the sale of skates is still usually made under a blanket term of “skate” or “ray”. The matter of identifying species of skate is further complicated by their morphologically conservative nature and the fact that they are commercially valued for their wings. Thus, before sale their bodies are usually discarded (i.e., “winged”) and often skinned, making morphological identification impossible. For the first time, DNA barcoding (of the mitochondrial COI gene) was applied to samples of skate wings from retail outlets across the British Isles, providing insight into which species are sold for consumption. A total of 98 wing samples were analysed, revealing that six species were sold; blonde ray (Raja brachyura), spotted ray (Raja montagui), thornback ray (Raja clavata), cuckoo ray (Leucoraja naevus) small-eyed ray (Raja microocellata) and shagreen ray (Leucoraja fullonica). Statistical testing demonstrated that there were significant differences in the species sold in the distinct retail groups which suggests complex drivers behind the patterns of sale in skates. The results also indicate that endangered species are not commonly being passed on to consumers. In addition, the practice of selling skate wings under ambiguous labels is highlighted as it makes it extremely difficult for consumers to exercise a right to avoid species of conservation concern. Interestingly, a single retailer chain labelled their wings as originating from three smaller-growing species (generally to be considered of lower conservation concern); of the six samples analysed from this company a third were mislabelled and originated from the thornback ray (a larger species that is currently undergoing population declines).