The appendicular skeleton of the enigmatic shark Leptocharias smithii in comparison with other sharks of the order Carcharhiniformes (Elasmobranchii: Leptochariidae).

Leptocharias smithii has been poorly explored in anatomical terms. This species bears a mosaic of morphological characters and is considered to represent an intermediate condition between other carcharhiniform clades. In the present paper, the anatomy of the appendicular skeleton of the species is thoroughly investigated and compared with other representatives of the order Carcharhiniformes. Leptocharias bears exclusive characteristics, such as the visible separation of the pro- and mesopterygia but it also has an aplesodic pectoral fin, a condition shared with carcharhiniforms placed at the base of the phylogenetic tree and at the same time a chevron-shaped coracoid bar, a condition characteristic of charcharhiniforms placed at the apex of the phylogenetic tree. Additionally, in an attempt to understand the evolution of its appendicular skeleton and of other carcharhiniforms, 20 characters of the paired fins and girdles are explored and discussed in light of two recent phylogenetic hypotheses. Most of these characters were not previously explored and support not only the monophyly of Carcharhiniformes, such as the mesopterygium overlapping the metapterygium in ventral view, but also the monophyly of the less inclusive clade Hemigaleidae + (Galeocerdonidae + (Carcharhinidae+Sphyrnidae)), such as the morphology and arrangement of the distal radials, which are pointed and spaced.

Evolutionary trends in the elasmobranch neurocranium.

The neurocranium (braincase) is one of the defining vertebrate characters. Housing the brain and other key sensory organs, articulating with the jaws and contributing to the shape of the anteriormost portion of the body, the braincase is undoubtedly of great functional importance. Through studying relationships between braincase shape and ecology we can gain an improved understanding of form-function relationships in extant and fossil taxa. Elasmobranchii (sharks and rays) represent an important case study of vertebrate braincase diversity as their neurocranium is simplified and somewhat decoupled from other components of the cranium relative to other vertebrates. Little is known about the associations between ecology and braincase shape in this clade. In this study we report patterns of mosaic cranial evolution in Elasmobranchii that differ significantly from those present in other clades. The degree of evolutionary modularity also differs between Selachii and Batoidea. In both cases innovation in the jaw suspension appears to have driven shifts in patterns of integration and modularity, subsequently facilitating ecological diversification. Our results confirm the importance of water depth and biogeography as drivers of elasmobranch cranial diversity and indicate that skeletal articulation between the neurocranium and jaws represents a major constraint upon the evolution of braincase shape in vertebrates.

Gene expression, evolution, and the genetics of electrosensing in the smalltooth sawfish, Pristis pectinata.

Sawfishes (Pristidae) are large, highly threatened rays named for their tooth-studded rostrum, which is used for prey sensing and capture. Of all five species, the smalltooth sawfish, Pristis pectinata, has experienced the greatest decline in range, currently found in only ~20% of its historic range. To better understand the genetic underpinnings of these taxonomically and morphologically unique animals, we collected transcriptomic data from several tissue types, mapped them to the recently completed reference genome, and contrasted the patterns observed with comparable data from other elasmobranchs. Evidence of positive selection was detected in 79 genes in P. pectinata, several of which are involved in growth factor/receptor tyrosine kinase signaling and body symmetry and may be related to the unique morphology of sawfishes. Changes in these genes may impact cellular responses to environmental conditions such as temperature, dissolved oxygen, and salinity. Data acquired also allow for examination of the molecular components of P. pectinata electrosensory systems, which are highly developed in sawfishes and have likely been influential in their evolutionary success.

Mitogenomic evidence of population differentiation of thorny skate, Amblyraja radiata, in the North Atlantic.

Management of thorny skate (Amblyraja radiata) in the Northwest Atlantic has posed a conservation dilemma for several decades due to the species' lack of response to strong conservation efforts in the US Gulf of Maine and the Canadian Scotian Shelf, confusion over the relationship between two reproductive size morphs of differing life histories that are sympatric in the Northwest Atlantic, and conflicting data on regional population connectivity throughout the species' broader range. To better assess potential A. radiata regional population differentiation and genetic links to life-history variation, we analysed complete mitochondrial genome sequences from 527 specimens collected across the species' North Atlantic geographic range, with particular emphasis on the Northwest Atlantic region. A high level of genetic diversity was evident across the North Atlantic, but significant genetic differentiation was identified between specimens inhabiting the Northwest (Gulf of Maine and Newfoundland) and Northeast (Greenland, Iceland, North Sea, and Arctic Circle) Atlantic. In the Northwest Atlantic, significant differentiation between the Gulf of Maine and Newfoundland regions was revealed; however, the overall level of differentiation was very low. No genetic difference was identified between the large and small reproductive morphs. The results of this study advance our understanding of A. radiata population structure in the North Atlantic but do not resolve all the questions confounding our understanding of the species' biology and evolutionary history.

Embryonic development in the bonnethead (Sphyrna tiburo), a viviparous hammerhead shark.

BACKGROUND: The hammerhead sharks (family Sphyrnidae) are an immediately recognizable group of sharks due to their unique head shape. Though there has long been an interest in hammerhead development, there are currently no explicit staging tables published for any members of the group. The bonnethead Sphyrna tiburo is the smallest member of Sphyrnidae and is abundant in estuarine and nearshore waters in the Gulf of Mexico and Western North Atlantic Ocean. Due to their relative abundance, close proximity to shore, and brief gestation period, it has been possible to collect and document multiple embryonic specimens at progressive stages of development. RESULTS: We present the first comprehensive embryonic staging series for the Bonnethead, a viviparous hammerhead shark. Our stage series covers a period of development from stages that match the vertebrate phylotypic period, from Stage 23, through stages of morphological divergence to complete development at birth-Stage 35). Notably, we use a variety of techniques to document crucial stages that lead to their extreme craniofacial diversity, resulting in the formation of one of the most distinctive characters of any shark species, the cephalofoil or hammer-like head. CONCLUSION: Documenting the development of hard-to-access vertebrates, like this viviparous shark species, offers important information about how new and diverse morphologies arise that otherwise may remain poorly studied. This work will serve as a platform for future comparative developmental research both within sharks and across the phylogeny of vertebrates, underpinning the extreme potential of craniofacial development and morphological diversity in vertebrate animals.

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.

Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionally low cancer rates. These two features could be explained by a low nuclear mutation rate. Here, we provide a direct estimate of the nuclear mutation rate in the epaulette shark (Hemiscyllium ocellatum). We generate a high-quality reference genome, and resequence the whole genomes of parents and nine offspring to detect de novo mutations. Using stringent criteria, we estimate a mutation rate of 7×10-10 per base pair, per generation. This represents one of the lowest directly estimated mutation rates for any vertebrate clade, indicating that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by a low mutation rate.

Revision of the Western Indian Ocean Angel Sharks, Genus Squatina (Squatiniformes, Squatinidae), with Description of a New Species and Redescription of the African Angel Shark Squatina africana Regan, 1908.

Sampling efforts on the Saya de Malha Bank (part of the Mascarene Plateau, western Indian Ocean) unveiled three unusual small juvenile angel shark specimens, that were a much paler color than the only known western Indian Ocean species, Squatina africana Regan, 1908. However, it took many years before further specimens, including adults of both sexes, and tissue samples were collected. The present manuscript contains a redescription of S. africana based on the holotype and additional material, as well as the formal description of the new species of Squatina. All specimens of the new species, hereafter referred to as Squatina leae sp. nov., were collected in the western Indian Ocean off southwestern India and on the Mascarene Plateau at depths of 100-500 m. The new species differs from S. africana in a number of characteristics including its coloration when fresh, smaller size at birth, size at maturity, and adult size, genetic composition, and distribution. Taxonomic characteristics include differences in the morphology of the pectoral skeleton and posterior nasal flap, denticle arrangement and morphology, vertebral counts, trunk width, pectoral-pelvic space, and clasper size. A key to the species of Squatina in the Indian Ocean is provided.

Systematics and Phylogenetic Interrelationships of the Enigmatic Late Jurassic Shark Protospinax annectans Woodward, 1918 with Comments on the Shark-Ray Sister Group Relationship.

The Late Jurassic elasmobranch Protospinax annectans is often regarded as a key species to our understanding of crown group elasmobranch interrelationships and the evolutionary history of this group. However, since its first description more than 100 years ago, its phylogenetic position within the Elasmobranchii (sharks and rays) has proven controversial, and a closer relationship between Protospinax and each of the posited superorders (Batomorphii, Squalomorphii, and Galeomorphii) has been proposed over the time. Here we revise this controversial taxon based on new holomorphic specimens from the Late Jurassic Konservat-Lagerstätte of the Solnhofen Archipelago in Bavaria (Germany) and review its skeletal morphology, systematics, and phylogenetic interrelationships. A data matrix with 224 morphological characters was compiled and analyzed under a molecular backbone constraint. Our results indicate a close relationship between Protospinax, angel sharks (Squatiniformes), and saw sharks (Pristiophoriformes). However, the revision of our morphological data matrix within a molecular framework highlights the lack of morphological characters defining certain groups, especially sharks of the order Squaliformes, hampering the phylogenetic resolution of Protospinax annectans with certainty. Furthermore, the monophyly of modern sharks retrieved by molecular studies is only weakly supported by morphological data, stressing the need for more characters to align morphological and molecular studies in the future.

From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator.

The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.

Revision of the genus Centrophorus (Squaliformes: Centrophoridae): Part 3Redescription of Centrophorus uyato (Rafinesque) with a discussion of its complicated nomenclatural history.

Centrophorus uyato (Rafinesque, 1810) has a complicated nomenclatural history which has led to multiple scientific names being ascribed to this species. In the Mediterranean Sea, and elsewhere in its range, this species was previously referred to as C. granulosus (Bloch Schneider, 1801). The first paper in this revision series clarified that C. granulosus refers to a much larger species of gulper shark which attains at least 1.7 m length and is absent from the Mediterranean Sea. Further complicating the nomenclature of this species is the fact that the original description clearly refers to a Squalus species, and not a Centrophorus species. In this third part of the revision of the genus Centrophorus, this problematic species is redescribed. A detailed synonymy is provided and it is confirmed that C. machiquensis, C. bragancae and C. zeehaani are junior synonyms of this species. To preserve nomenclatural stability within the genus, the name Centrophorus uyato is retained for this species with a neotype from close to the original type locality off Italy being designated. Intraspecific variation within Centrophorus uyato is also discussed, particularly relating to denticle morphology and body morphology.

Tiger Shark Attack on a Scuba Diver in New Caledonia.

Herein we report an unprovoked shark attack on a scuba diver in New Caledonia. The species responsible for the attack was identified as a tiger shark (Galeocerdo cuvier), based on both the victim's testimony and forensic examination. The victim suffered significant loss of soft tissues from one thigh, which resulted in hemorrhagic shock. Even though the event occurred at a remote location, miles away from the nearest hospital, appropriate first aid, immediate deployment of an alert system, and prompt helicopter transfer by an emergency rescue team allowed the victim to be transferred to an intensive care unit in stable condition and to undergo surgery within 4 h of being bitten. Early coverage of exposed bone was performed, followed up with negative pressure dressing, antibiotic treatment, hyperbaric oxygen therapy, and a split skin graft. In spite of the massive muscular loss incurred, the victim was able to regain her ability to walk within 6 wk of the incident. Shark attacks on scuba divers are rare and seldom reported, especially in New Caledonia.

The Phylogeny of Rays and Skates (Chondrichthyes: Elasmobranchii) Based on Morphological Characters Revisited.

Elasmobranchii are relatively well-studied. However, numerous phylogenetic uncertainties about their relationships remain. Here, we revisit the phylogenetic evidence based on a detailed morphological re-evaluation of all the major extant batomorph clades (skates and rays), including several holomorphic fossil taxa from the Palaeozoic, Mesozoic and Cenozoic, and an extensive outgroup sampling, which includes sharks, chimaeras and several other fossil chondrichthyans. The parsimony and maximum-likelihood analyses found more resolved but contrasting topologies, with the Bayesian inference tree neither supporting nor disfavouring any of them. Overall, the analyses result in similar clade compositions and topologies, with the Jurassic batomorphs forming the sister clade to all the other batomorphs, whilst all the Cretaceous batomorphs are nested within the remaining main clades. The disparate arrangements recovered under the different criteria suggest that a detailed study of Jurassic taxa is of utmost importance to present a more consistent topology in the deeper nodes, as issues continue to be present when analysing those clades previously recognized only by molecular analyses (e.g., Rhinopristiformes and Torpediniformes). The consistent placement of fossil taxa within specific groups by the different phylogenetic criteria is promising and indicates that the inclusion of more fossil taxa in the present matrix will likely not cause loss of resolution, therefore suggesting that a strong phylogenetic signal can be recovered from fossil taxa.

Integrated Taxonomy Revealed Genetic Differences in Morphologically Similar and Non-Sympatric Scoliodon macrorhynchos and S. laticaudus.

Previous examination of the mitochondrial NADH2 gene and morphological characteristics led to the resurrection of Scoliodon macrorhynchos as a second valid species in the genus, in addition to S. laticaudus. This study applied an integrated taxonomic approach to revisit the classification of the genus Scoliodon based on new materials from the Malaysian Peninsula, Malaysian Borneo and Eastern Bay of Bengal. Mitochondrial DNA data suggested the possibility of three species of Scoliodon in the Indo-West Pacific, while the nuclear DNA data showed partially concordant results with a monophyletic clade of S. macrorhynchos and paraphyletic clades of S. laticaudus and S. cf. laticaudus from the Malacca Strait. Morphological, meristic and dental characteristics overlapped between the three putative species. Collective molecular and morphological evidence suggested that the differences that exist among the non-sympatric species of Scoliodon are consistent with isolation by distance, and Scoliodon macrorhynchos remains as a valid species, while S. cf. laticaudus is assigned as S. laticaudus. The Malacca Strait acts as a spatial delineator in separating the Pacific S. macrorhynchos (including South China Sea) from the Northern Indian Ocean S. laticaudus. Future taxonomic work should focus on clarifying the taxonomic status of Scoliodon from the Indonesian waters.

Deciphering reticulate evolution of the largest group of polyploid vertebrates, the subfamily cyprininae (Teleostei: Cypriniformes).

Despite the rarity of polyploidy in animals, some groups with polyploid species exhibit complicated and interesting patterns of reticulate evolution. Here we focus on fishes in the subfamily Cyprininae, the largest polyploid group of vertebrates. The large number of polyploid taxa poses significant challenges for phylogenetic and evolutionary studies on this subfamily. In this study, we cloned and sequenced three single-copy nuclear loci to investigate the evolution of polyploidy in the Cyprininae. Topologies of nuclear gene trees were compared with a newly reconstructed mitochondrial tree. The data provided herein corroborate the hybrid origins of the tribes Torini, Cyprinini, Spinibarbini, Barbini, and also Probarbini. Based on results from this study and previous studies, we hypothesize that at least 13 independent polyploidization events have occurred during the evolution of the Cyprininae. We offer hypotheses on the origin of each polyploid group and show that a diploid group or the diploid ancestor of a polyploid group might have served as progenitor of one or two other polyploid groups. The evolutionary history of Cyprinine (since its first divergence) can be divided into three stages: the "Diploid stage" (69.2-43.4 Ma or million years ago), the "Tetraploidization stage" (43.4-18.9 Ma), and the "Hexaploidization stage" (18.9 Ma to present). The second stage is when all tetraploidization events happened, while the last stage is when all hexaploidization events and most genus- or species-specific polyploidization events occurred. The post-polyploidization dynamics of polyploid groups are complicated and warrant more genomic level studies. We showed that the subfamily Cyprininae may represent a more complicated polyploid system than most, if not all, other vertebrates and some plants, if one or more of the following factors are considered: number of polyploid species, number of different ploidy levels, and number and type of independent polyploidization events.

Morphological and Molecular Evidence Reveals the Longnose Skate Zearaja brevicaudata (Marini, 1933) to be a Senior Synonym of Dipturus lamillai Concha, Caira, Ebert & Pompert 2019.

Longnose skates have great economic importance in South American fisheries, and in order to preserve them, it is important to have a well-defined taxonomic status of their species. Dipturus lamillai was recently described for Malvinas Islands waters based on morphological and molecular comparisons with Zearaja chilensis. Although D. lamillai has been compared with several congeneric species, it was not properly compared with the morphologically similar Zearaja brevicaudata, the most abundant longnose skate in the Southwest Atlantic. Here, these species were compared by morphological and molecular analyses in order to evaluate their conspecificity. Linear morphometric variables of holotype and paratypes of D. lamillai and 69 specimens of Z. brevicaudata were compared and investigated using Principal Component Analysis. In addition, thorn patterns, denticle distributions, color, and clasper morphology were compared. No body proportions or other single character that could differentiate D. lamillai from Z. brevicaudata were found. Molecular analyses comprised of the comparison of the Cytochrome oxidase subunit I (COI) and the NADH dehydrogenase subunit 2. The results of the Maximum Likelihood (ML) carried out for each molecular marker showed that sequences from D. lamillai clustered together with those of Z. brevicaudata, and the molecular distance determined by Kimura two-parameter were lower than the expected for different species. Additionally, the Automatic Barcode Gap Discovery method and the Bayesian implementation of the Poisson tree processes were carried out with COI sequences to explore species limits, and their results were consistent with ML analyses. In summary, the results obtained showed that there are no morphological or molecular differences between these nominal species of the valid skate genus Zearaja, leading to the conclusion that they are conspecific. Therefore, we designated Z. brevicaudata as a senior synonym of D. lamillai.

Comment on "An early Miocene extinction in pelagic sharks".

Sibert and Rubin (Reports, 4 June 2021, p. 1105) report an early Miocene extinction in pelagic sharks based on the loss of shark denticle diversity in two widely separated deep-sea sediment cores. We assert that the pattern observed is not a consequence of extinction but results from shifting species ranges induced by global current reorganization.

Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae).

After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy.

Towards complete and error-free genome assemblies of all vertebrate species.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Hemitrygon yemenensis sp. nov., a new species of stingray (Myliobatoidea: Dasyatidae) from the northwestern Indian Ocean.

A new stingray, Hemitrygon yemenensis sp. nov., is described from old preserved material collected on the Arabian Sea coast of eastern Yemen. Consistent with other members of the genus, H. yemenensis sp. nov. is a small dasyatid (males mature at ~22 cm disc width), but it is the only Hemitrygon known to occur outside the western Pacific and eastern Indian Oceans. Hemitrygon yemenensis sp. nov. most closely resembles H. bennetti, but H. yemenensis is separable based on several characters including a longer and more narrowly pointed snout, shorter tail, and a longer disc and head. Hemitrygon yemenensis is unknown to science beyond the two type specimens collected nearly 120 years ago.

Revision of the Eocene 'Platyrhina' species from the Bolca Lagerstätte (Italy) reveals the first panray (Batomorphii: Zanobatidae) in the fossil record.

The fossil-Lagerstätte of Bolca (Italy) is well known for the diversity and exquisite preservation of its bony and cartilaginous fishes documenting tropical shallow-water marine environments associated with coral reefs in the western Tethys during the early Eocene. In this study, the taxonomic, systematic and phylogenetic position of two batoid species traditionally assigned to the living thornback ray genus Platyrhina is re-evaluated. †Platyrhina bolcensis Heckel, 1851 is recognized as a separate species of the Platyrhinidae because of its plate-like antorbital cartilage with an irregular outline and a small horn on the nasal capsules. Also, the rostral cartilage does not reach the anterior border of the disc. Support for the placement of this species within the new genus †Eoplatyrhina gen. nov. is based on a combination of morphological and meristic features (e.g. nasal capsules at right angles to the rostrum; large space between the hyomandibulae and mandibular arch; approximately 132 vertebral centra; 15-16 rib pairs; 81-87 pectoral radials; 18-21 pelvic radials; short, straight and stout claspers; 40-50 caudal-fin radials; thorns absent). A second species, †Platyrhina egertoni (De Zigno, 1876), is more closely related to the living panray Zanobatus than Platyrhina and is assigned here to †Plesiozanobatus gen. nov. because of a combination of characters that support its placement within the family Zanobatidae (tail stout and short, distinctly demarcated from disc; two dorsal fins and complete caudal fin; small dermal denticles and scattered thorns covering disc and tail; rostral cartilage absent; nasal capsules without horn-like processes; mesopterygium absent). The systematic position of a third taxon, †Platyrhina gigantea (Blainville, 1818), is currently impossible to establish due to the poor preservation of the only known specimen, and therefore we propose to consider it a nomen dubium. Palaeoecological and biogeographic features of the Eocene platyrhinids and zanobatids from Bolca are also discussed. http://zoobank.org/urn:lsid:zoobank.org:pub:B4C7A979-7972-409B-B489-A6DDD5E35FE5.