Identification of Cartilaginous Fish Endogenous Foamy Virus Rooting to Vertebrate Counterparts.

Foamy viruses (FVs) are ideal models for studying the long-term evolutionary history between viruses and their hosts. Currently, FVs have been documented in nearly all major taxa of vertebrates, but evidence is lacking for true FV infiltration in cartilaginous fish, the most basal living vertebrates with jaws. Here, we screened 11 available genomes and 10 transcriptome sequence assemblies of cartilaginous fish and revealed a novel endogenous foamy virus, termed cartilaginous fish endogenous foamy virus (CFEFV), in the genomes of sharks and rays. Genomic analysis of CFEFVs revealed feature motifs that were retained among canonical FVs. Phylogenetic analysis using polymerase sequences revealed the rooting nature of CFEFVs to vertebrate FVs, indicating their deep origin. Interestingly, three viral lineages were found in a shark (Scyliorhinus torazame), one of which was clustered with ray-finned fish foamy-like viruses, indicating that multiple episodes of viral infiltrations had occurred in this species. These findings fill a major gap in the Spumaretrovirinae taxon and reveal the aquatic origin of FVs found in terrestrial vertebrates. IMPORTANCE Although foamy viruses (FVs) have been found in major branches of vertebrates, the presence of these viruses in cartilaginous fish, the most basal living vertebrates with jaws, remains to be explored. This study revealed a collection of cartilaginous endogenous FVs in sharks and rays through in silico genomic mining. These viruses were rooted in the polymerase (POL) phylogeny, indicating the ancient aquatic origin of FVs. However, their envelope (ENV) protein grouped with those of amphibian FVs, suggesting different evolutionary histories of different FV genes. Overall, we provide the last missing gap for the taxonomic investigation of Spumaretrovirinae and provide concrete support for the aquatic origin of FVs.

Fishing profile and commercial landings of shark and batoids in a global elasmobranchs conservation hotspot.

This paper describes the fishing profile and the temporal variation in the commercial landings of elasmobranchs in a global hotspot for their conservation and investigates the variables that influenced the landings. Census data on commercial catches were obtained between April 2008 and October 2010 from nine landing sites in Bragança (Pará, northern Brazil). Five vessel types, four fishing gears, and eight fishing techniques engaged with elasmobranch capture were identified. A total of 2,357 landings were recorded, with a total production of 354 t. The highest yields were recorded in 2009, with sharks being harvested mostly by small and medium-sized vessels, and batoids, by small vessels and canoes. Drifting nets and longlines played a prominent role in elasmobranch fisheries. The results show that the landings were influenced by days at sea, which is common in tropical fisheries. The elasmobranch data series is discontinuous as statistics are absent for most fishing sites albeit imperative for proper management, as well as relevant for decision-makers focusing on their conservation.

Can denticle morphology help identify southeastern Australian elasmobranchs?

Elasmobranchs are covered in scale-like structures called dermal denticles, comprising dentine and enameloid. These structures vary across the body of an individual and between species, and are frequently shed and preserved in marine sediments. With a good understanding of denticle morphology, current and historical elasmobranch diversity and abundance might be assessed from sediment samples. Here, replicate samples of denticles from the bodies of several known (deceased) shark species were collected and characterized for morphology before being assigned morphotypes. These data were used to expand the established literature describing denticles and to investigate intra- and interspecific variability, with the aim of increasing the viability of using sediment samples to assess elasmobranch diversity and abundance. Denticle morphology was influenced more by life-history traits than by species, where demersal species were largely characterized by generalized function and defense denticles, whereas pelagic and benthopelagic species were characterized by drag-reduction denticles. Almost all species possessed abrasion strength or defense denticles on the snout, precluding their utility for separating species. In a separate manipulative experiment, samples of denticles were collected from sediments in two aquaria with known elasmobranchs to determine their utility for reliably separating species. Visual examination of denticles, morphometric measurements, scaled photographs, and reference collections allowed for some precise identification, but not always to the species level. Ongoing work to develop denticle reference collections could help to identify past and present families and, in some cases, species.

Diet of the critically endangered blackchin guitarfish Glaucostegus cemiculus revealed using DNA metabarcoding.

We present the first assessment of the diet of the blackchin guitarfish Glaucostegus cemiculus (Geoffroy Saint-Hilaire, 1817) for West Africa using DNA metabarcoding on stomach contents of individuals captured in the Bijagós Archipelago, Guinea-Bissau. The diet was dominated by crustaceans, particularly caramote prawn Penaeus kerathurus (frequency of occurrence [FO] = 74%, numerical frequency [NF] = 54%) and fiddler crab Afruca tangeri (FO = 74%, NF = 12%). Bony fishes were present in 30% of the stomachs. We highlight the importance of conservation action for intertidal habitats and their associated benthic invertebrates for the survival of the critically endangered blackchin guitarfish.

Two new species of Scyphophyllidium (Cestoda: Phyllobothriidea) from Chaenogaleus macrostoma (Bleeker) (Elasmobranchii: Carcharhiniformes) from the Persian Gulf, Iran.

Two new species of Scyphophyllidium Woodland, 1927 are described from the Hooktooth shark, Chaenogaleus macrostoma (Bleeker), from the Persian Gulf, Iran. Scyphophyllidium hormuziense n. sp. is assigned to morphological category 2 of its genus because it possesses bothridial marginal loculi and an apical sucker on each flat bothridium, and lacks bothridial facial loculi. Within category 2, it is distinguished from its congeners, except for S. janineae (Ruhnke, Healy and Shapero, 2006), by possessing, rather than lacking, a prominent cephalic peduncle. It differs from S. janineae in the distribution of the vitelline follicles. Scyphophyllidium iraniense n. sp. is assigned to morphological category 5 because its bothridia are essentially flat and lack proximal apertures, marginal loculi, facial loci and semi-circular muscle bands, and bears weakly serrate gladiate spinitriches on its distal bothridial surfaces. Within its morphological category, the presence of a long cephalic peduncle distinguishes S. iraniense n. sp. from its congeners lacking this structure or possessing a short cephalic peduncle. It further differs from S. arnoldi (Ruhnke and Thompson, 2006) and S. typicum (Subhapradha, 1955) in total length, from S. paulum (Linton, 1897) in lacking a conspicuous band of muscles along the locular periphery of the bothridia, and from S. kirstenae (Ruhnke, Healy and Shapero, 2006) in the distribution of the vitelline follicles. This study brings the number of the valid Scyphophyllidium species of the Persian Gulf to five.

Pandarus Leach, 1816 (Copepoda: Siphonostomatoida: Pandaridae) species collected from elasmobranchs off South Africa with the description of Pandarus echinifer n. sp.

Eight species of Pandarus Leach, 1816 collected from hosts caught off South Africa are reported. These species include P. bicolor Leach, 1816, P. niger Kirtisinghe, 1950 and P. carcharhini Ho, 1963 belonging to the "bicolor" group and P. cranchii Leach, 1819, P. satyrus Dana, 1849, P. smithii Rathbun, 1886 and P. sinuatus Say, 1818 belonging to the "cranchii" group. Notes on previous and new distinguishing features are provided with illustrations, specifically the relative lengths of the dorsal plates and caudal rami as well as the structure of the distomedial spine on the second segment of leg 1 exopod. Additionally, illustrated re-descriptions are provided for P. satyrus and P. sinuatus. Furthermore, a new species Pandarus echinifer n. sp., also belonging to the "cranchii" group, collected from the snaggletooth shark Hemipristis elongata (Klunzinger) is described. This species is most similar to P. sinuatus but can be distinguished from it by the heavily spinulated distomedial spine on the last segment of the first leg exopod. Molecular analysis of the cytochrome oxidase I partial gene is used to calculate sequence divergences amongst different individuals and species. According to the results (as well as based on morphological characters) P. rhincodonicus Norman, Newbound & Knott, 2000 is a synonym of P. cranchii. New hosts and geographic localities from South Africa (and Ningaloo Park, Western Australia) are reported.

DEVELOPING A THROMBOELASTOGRAPHY ASSAY IN ELASMOBRANCHS.

Thromboelastography (TEG) is a hemostatic assay evaluating clot initiation time, kinetics, strength, and extent of fibrinolysis. Hemostatic assays in nonmammalian species have been less extensively studied because of lack of taxon-specific reagents and unique physiology. Hemostatic or hemorrhagic disease has been described postmortem in elasmobranchs, but antemortem detection of coagulopathies is limited in this taxon. The study aimed to establish an elasmobranch TEG protocol to improve hemostatic evaluation and facilitate advanced treatment options for animals under human care. Multiple clotting initiators were assessed for efficacy with frozen-thawed citrated plasma, fresh citrated plasma, and fresh whole citrated blood: RapidTEGTM, citrated kaolin, Reptilase®, and species brain-derived thromboplastin prepared by two different methods. Initial evaluation found plasma samples clot inconsistently, but TEG analyses using fresh whole blood consistently led to measurable TEG reactions using multiple clotting initiators. The most reliable elasmobranch TEG results were observed using citrated fresh whole blood and the RapidTEG clot initiation reagent.

Energetic connectivity of diverse elasmobranch populations - implications for ecological resilience.

Understanding the factors shaping patterns of ecological resilience is critical for mitigating the loss of global biodiversity. Throughout aquatic environments, highly mobile predators are thought to serve as important vectors of energy between ecosystems thereby promoting stability and resilience. However, the role these predators play in connecting food webs and promoting energy flow remains poorly understood in most contexts. Using carbon and nitrogen isotopes, we quantified the use of several prey resource pools (small oceanic forage, large oceanics, coral reef, and seagrass) by 17 species of elasmobranch fishes (n = 351 individuals) in The Bahamas to determine their functional diversity and roles as ecosystem links. We observed remarkable functional diversity across species and identified four major groups responsible for connecting discrete regions of the seascape. Elasmobranchs were responsible for promoting energetic connectivity between neritic, oceanic and deep-sea ecosystems. Our findings illustrate how mobile predators promote ecosystem connectivity, underscoring their functional significance and role in supporting ecological resilience. More broadly, strong predator conservation efforts in developing island nations, such as The Bahamas, are likely to yield ecological benefits that enhance the resilience of marine ecosystems to combat imminent threats such as habitat degradation and climate change.

Diversity and evolution of serotonergic cells in taste buds of elasmobranchs and ancestral actinopterygian fish.

A subset of gustatory cells are serotonin immunoreactive (ir) in the mammalian taste bud. In the taste bud of lamprey, elongated gustatory-like cells are also serotonin-ir. In contrast, flattened serotonin-ir cells are located only in the basal region of the taste buds in the teleosts and amphibians. These serotonin-ir cells are termed as basal cells. To evaluate the evolution and diversity of serotonergic cells in the taste bud of amniote animals, we explored the distribution and morphology of serotonin-ir cells in the taste buds of ancestral actinopterygian fish (spotted gar, sturgeon, Polypterus senegalus) and elasmobranch (stingray). In all examined animals, the taste buds contained serotonin-ir cells in their basal part. The number of serotonin-ir basal cells in each taste bud was different between these fish species. They were highest in the stingray and decreased in the order of the Polypterus, sturgeon, and gar. While serotonin immunoreactivity was observed only in the basal cells in the taste buds of the ancestral actinopterygian fish, some elongated cells were also serotonin-ir in addition to the basal cells in the stingray taste buds. mRNA of tryptophan hydroxylase 1 (tph1), a rate-limiting enzyme of the serotonin synthesis, is expressed in both the elongated and basal cells of stingray taste buds, indicating that these cells synthesize the serotonin by themselves. These results suggest that the serotonin-ir basal cells arose from the ancestor of the cartilaginous fish, and serotonin-ir cells in the elasmobranch taste bud exhibit an intermediate aspect between the lamprey and actinopterygian fish.

Measures and models of visual acuity in epipelagic and mesopelagic teleosts and elasmobranchs.

Eyes in low-light environments typically must balance sensitivity and spatial resolution. Vertebrate eyes with large "pixels" (e.g., retinal ganglion cells with inputs from many photoreceptors) will be sensitive but provide coarse vision. Small pixels can render finer detail, but each pixel will gather less light, and thus have poor signal relative-to-noise, leading to lower contrast sensitivity. This balance is particularly critical in oceanic species at mesopelagic depths (200-1000 m) because they experience low light and live in a medium that significantly attenuates contrast. Depending on the spatial frequency and inherent contrast of a pattern being viewed, the viewer's pupil size and temporal resolution, and the ambient light level and water clarity, a visual acuity exists that maximizes the distance at which the pattern can be discerned. We develop a model that predicts this acuity for common conditions in the open ocean, and compare it to visual acuity in marine teleost fishes and elasmobranchs found at various depths in productive and oligotrophic waters. Visual acuity in epipelagic and upper mesopelagic species aligned well with model predictions, but species at lower mesopelagic depths (> 600 m) had far higher measured acuities than predicted. This is consistent with the prediction that animals found at lower mesopelagic depths operate in a visual world consisting primarily of bioluminescent point sources, where high visual acuity helps localize targets of this kind. Overall, the results suggest that visual acuity in oceanic fish and elasmobranchs is under depth-dependent selection for detecting either extended patterns or point sources.

Progesterone receptors in extratesticular ducts of the Amazonian stingray Potamotrygon wallacei: A potential role in sperm maturation and aggregate formation.

In cururu stingray (Potamotrygon wallacei Carvalho, Rosa and Araújo 2016) males, plasma progesterone (P4) levels appear to be associated with spermiation events. However, the specific contribution of P4 in sperm maturation via extratesticular ducts in this stingray species is unknown. With the aim of filling this knowledge gap, this study examined the morphology and the presence of progesterone receptors (PR) in the ducts, and analyzed the relationship of progesterone (P4) with sperm maturation and formation of aggregates. Morphological analysis showed that a columnar pseudostratified epithelium with stereocilia lined all the attached ducts. In active males, the secretory cells of the epididymis and the Leydig glands presented PR; however, these receptors were not found in the distal region of the epididymis (essential for nurturing and capacitation events) of regressing males. In the seminal vesicles of active males, the spermatozoa are parallelly aligned and embedded in a matrix to form the spermatozeugmata. The matrixes are formed by proteins secreted by the ducts and Sertoli cell cytoplasts. These structures presented PR, which suggests that P4 engages in sperm metabolism during storage. Our findings allude to the potential role of P4 in regulating the development and function of the attached ducts in different reproductive phases. Furthermore, P4 seems to be an essential component for regulating sperm progress, protein secretion, aggregate formation, and maintenance of sperm during storage in this freshwater stingray.

Nitrogen transporters along the intestinal spiral valve of cloudy catshark (Scyliorhinus torazame): Rhp2, Rhbg, UT.

As part of their osmoregulatory strategy, marine elasmobranchs retain large quantities of urea to balance the osmotic pressure of the marine environment. The main source of nitrogen used to synthesize urea comes from the digestion and absorption of food across the gastrointestinal tract. In this study we investigated possible mechanisms of nitrogen movement across the spiral valve of the cloudy catshark (Scyliorhinus torazame) through the molecular identification of two Rhesus glycoprotein ammonia transporters (Rhp2 and Rhbg) and a urea transporter (UT). We used immunohistochemistry to determine the cellular localizations of Rhp2 and UT. Within the spiral valve, Rhp2 was expressed along the apical brush border membrane, and UT was expressed along the basolateral membrane and the blood vessels. The mRNA abundance of Rhp2 was significantly higher in all regions of the spiral valve of fasted catsharks compared to fed catsharks. The mRNA abundance of UT was significantly higher in the anterior spiral valve of fasted catsharks compared to fed. The mRNA transcript of four ornithine urea cycle (OUC) enzymes were detected along the length of the spiral valve and in the renal tissue, indicating the synthesis of urea via the OUC occurs in these tissues. The presence of Rhp2, Rhbg, and UT along the length of the spiral valve highlights the importance of ammonia and urea movement across the intestinal tissues, and increases our understanding of the mechanisms involved in maintaining whole-body nitrogen homeostasis in the cloudy catshark.

Southward range extension and transboundary movements of reef manta rays Mobula alfredi along the east African coastline.

Opportunistic in-water and aerial surveys in South Africa and the analysis of contributed citizen science data have extended the known range of reef manta rays Mobula alfredi along the eastern coast of Africa by 140 km (to Mdumbi Beach) and verified the first transboundary movements for the species. Additionally, six new long-range dispersal records have provided evidence of connectivity with the M. alfredi population off the Inhambane coastline of Mozambique. Five of these records captured one-way movements, the longest of which was an individual that travelled 505 km from Praia do Tofo to Sodwana Bay with 301 days between sightings. A single individual made a return trip between Závora, Mozambique and Sodwana Bay, South Africa (a total distance of ~870 km). These findings support the Convention on Migratory Species listing for the species, suggesting regional transboundary management units are warranted for this wide-ranging elasmobranch.

Smooth muscle "microsphincters" in the gastric mucosa of stingrays (Elasmobranchii, Dasyatidae).

The occurrence of smooth muscle sphincters around gastric gland tubules in the cardiac stomach of some elasmobranch species is reported for the first time. These "microsphincters" took the form of a twisted torus, approximately 12-16 muscle fibres thick, that could fully constrict the gland tubules. However, their inconsistent positioning does not suggest a role in partitioning the tubules from the stomach lumen or in modulating secretory activity. Further research is required to ascertain the full taxonomic occurrence of these structures across the Elasmobranchii and to elucidate their function.

Localization and Characterization of Major Neurogenic Niches in the Brain of the Lesser-Spotted Dogfish Scyliorhinus canicula.

Adult neurogenesis is defined as the ability of specialized cells in the postnatal brain to produce new functional neurons and to integrate them into the already-established neuronal network. This phenomenon is common in all vertebrates and has been found to be extremely relevant for numerous processes, such as long-term memory, learning, and anxiety responses, and it has been also found to be involved in neurodegenerative and psychiatric disorders. Adult neurogenesis has been studied extensively in many vertebrate models, from fish to human, and observed also in the more basal cartilaginous fish, such as the lesser-spotted dogfish, Scyliorhinus canicula, but a detailed description of neurogenic niches in this animal is, to date, limited to the telencephalic areas. With this article, we aim to extend the characterization of the neurogenic niches of S. canicula in other main areas of the brain: we analyzed via double immunofluorescence sections of telencephalon, optic tectum, and cerebellum with markers of proliferation (PCNA) and mitosis (pH3) in conjunction with glial cell (S100ß) and stem cell (Msi1) markers, to identify the actively proliferating cells inside the neurogenic niches. We also labeled adult postmitotic neurons (NeuN) to exclude double labeling with actively proliferating cells (PCNA). Lastly, we observed the presence of the autofluorescent aging marker, lipofuscin, contained inside lysosomes in neurogenic areas.

The challenge of implementing environmental DNA metabarcoding to detect elasmobranchs in a resource-limited marine protected area.

Elasmobranchs are threatened and eDNA metabarcoding is a powerful tool that can help efforts to better understand and conserve them. Nevertheless, the inter-calibration between optimal methodological practices and its implementation in resource-limited situations is still an issue. Based on promising results from recent studies, the authors applied a cost-effective protocol with parameters that could be easily replicated by any conservationist. Nonetheless, the results with fewer elasmobranchs detected than expected reveal that endorsed primers and sampling strategies still require further optimization, especially for applications in resource-limited conservation programmes.

Birth and growth of the shortnose guitarfish Zapteryx brevirostris (Müller & Henle, 1841) (Chondrichthyes, Rhinobatidae) in captivity.

Endemic to the south-west Atlantic Ocean, the shortnose guitarfish (Zapteryx brevirostris) is a small species, classified as endangered by the IUCN. Although reproduction in captivity has been successful for some species, a range of factors can limit the success of captive breeding programmes for elasmobranchs. In Brazil, the Ubatuba Aquarium was the first public aquarium to reproduce small-sized elasmobranchs. Since 2018, at least five parturition events have been recorded for Z. brevirostris at the institution. From a total of 13 live neonates that rearing was attempted, the mean ± standard error of weight, total length (TL) and disc width at birth were 17.47 ± 1.6 g, 13.25 ± 0.7 cm and 6.53 ± 0.2 cm, respectively. The mean weight as well as mean TL were higher for females at all births, with 26.15 g and 15.07 cm for females in comparison with 17.09 g and 13.94 cm for males. Considering the increasing risk of extinction that the species is facing, age and growth studies are fundamental for the success of conservation, improving the knowledge of Z. brevirostris life cycle so that a more efficient and sustainable management can be carried out. This study provides important data, as well as directions for captive breeding of the species.

Distribution of the reef manta ray Mobula alfredi and the oceanic manta ray Mobula birostris in the Philippines: a collaborative effort for conservation.

Little is known about manta ray population size, structure and connectivity in the Philippines. In collaboration with dive operators, non-governmental organizations and authorities, sightings of manta rays were collated into a single national database. Using in-water photographs and videos gathered through citizen science and dedicated research efforts, this study compiled sightings between 2004 and 2020, showing 22 separate sites throughout the archipelago with manta rays present. A total of 392 individual reef manta rays (Mobula alfredi) and 107 oceanic manta rays (Mobula birostris) were identified from the collected footage. Four specific sites in the provinces of Masbate and Palawan together hosted 89% of all identified individuals and accounted for 95% of sightings, highlighting these areas are key aggregation sites. This study also reports the movements of M. birostris within the Philippines, based on photo-identification of three individuals moving 150 km between Cebu and Masbate. Despite the growing number of recreational divers in Daanbantayan and San Jacinto, an 80% decline in M. birostris sightings was observed at these sites. To ensure effective future conservation, it is recommended that efforts focus on the identification and protection of manta ray hotspots and migratory corridors, the creation of a sustainable tourism framework and, most important, the implementation of mitigation strategies to reduce fisheries interactions.

First record of mating behaviour and induced parturition of the Brazilian endemic Lutz's stingray Hypanus berthalutzae.

The recently described Lutz's stingray Hypanus berthalutzae is endemic to the Brazilian Province, including oceanic islands. Although it is expected to have life-history traits similar to the southern stingray H. americanus, little is known about its reproductive biology. Here we present the first observations of courtship behaviour (n = 4), copulation (n = 3) and an induced parturition of H. berthalutzae at the Fernando de Noronha Archipelago, an insular Marine Protected Area from the Equatorial Atlantic Ocean. The mating event records included (1) 'chasing/close following', (2) 'biting/precopulatory biting', (3) 'insertion/copulation' and (4) 'separation'. These results are especially relevant considering that records of reproductive behaviour in the wild are rare for elasmobranchs in general. Mating events occurred in different months, suggesting that the reproductive cycle of H. berthalutzae in this insular system is asynchronous, as observed for other stingray species in regions with favourable environmental conditions and abundant food throughout the year. The opportunistic documentation of the induced parturition allowed for direct nonlethal observation of the two pups at or near full term in late May. Although preliminary, these observations should be considered in future management plans as they provide relevant data about the life-history traits and mating behaviour of this endemic and threatened species.

Use of underwater contactless ultrasonography to elucidate the internal anatomy and reproductive activity of manta and devil rays (family: Mobulidae).

The ability to visualise the internal anatomical structures of fish provides important information on their reproductive status and body condition and has made important contributions to many areas of fish biology. Obtaining information on the internal anatomy of fish has traditionally required euthanasia and dissection. Although ultrasonography is now increasingly used to study internal fish anatomy without the need for euthanasia, traditional techniques still require restraint and contact with the animal, both of which are known to cause stress. This has prompted the development of waterproof, contactless and portable equipment to allow ultrasonographic examinations to be carried out in free-swimming individuals, which also facilitates the application of this tool in wild populations of endangered species. This study reports the validation of this equipment using anatomical examinations of nine manta and devil ray (Mobulidae) specimens landed at fish markets in Sri Lanka. The species studied were Mobula kuhlii (n = 3), Mobula thurstoni (n = 1), Mobula mobular (n = 1), Mobula tarapacana (n = 1) and Mobula birostris (n = 3). The use of this equipment was further validated with ultrasonographic examinations in 55 free-swimming reef manta rays Mobula alfredi, which enabled maturity status to be quantified in 32 females. Structures successfully identified in free-swimming individuals were the liver, spleen, gallbladder, gastrointestinal tract, skeletal structures, developing follicles and uterus. The study demonstrated that ultrasonography provided a reliable method of determining both sexual maturity and gestational status in free-swimming M. alfredi. The methodology induced no detectable signs of disturbance to the animals involved and therefore offers a viable and practical alternative to invasive techniques currently used to study anatomical changes in both captive and wild marine organisms.