Shark tales: A molecular species-level phylogeny of sharks (Selachimorpha, Chondrichthyes)

Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes

The reproductive diversity of extant cartilaginous fishes (class Chondrichthyes) is extraordinarily broad, reflecting more than 400 million years of evolutionary history. Among their many notable reproductive specialisations are viviparity (live-bearing reproduction) and matrotrophy (maternal provision of nutrients during gestation). However, attempts to understand the evolution of these traits have yielded highly discrepant conclusions. Here, we compile and analyse the current knowledge on the evolution of reproductive diversity in Chondrichthyes with particular foci on the frequency, phylogenetic distribution, and directionality of evolutionary changes in their modes of reproduction. To characterise the evolutionary transformations, we amassed the largest empirical data set of reproductive parameters to date covering nearly 800 extant species and analysed it via a comprehensive molecular-based phylogeny. Our phylogenetic reconstructions indicated that the ancestral pattern for Chondrichthyes is 'short single oviparity' (as found in extant holocephalans) in which females lay successive clutches (broods) of one or two eggs. Viviparity has originated at least 12 times, with 10 origins among sharks, one in batoids, and (based on published evidence) another potential origin in a fossil holocephalan. Substantial matrotrophy has evolved at least six times, including one origin of placentotrophy, three separate origins of oophagy (egg ingestion), and two origins of histotrophy (uptake of uterine secretions). In two clades, placentation was replaced by histotrophy. Unlike past reconstructions, our analysis reveals no evidence that viviparity has ever reverted to oviparity in this group. Both viviparity and matrotrophy have arisen by a variety of evolutionary sequences. In addition, the ancestral pattern of oviparity has given rise to three distinct egg-laying patterns that increased clutch (brood) size and/or involved deposition of eggs at advanced stages of development. Geologically, the ancestral oviparous pattern arose in the Paleozoic. Most origins of viviparity and matrotrophy date to the Mesozoic, while a few that are represented at low taxonomic levels are of Cenozoic origin. Coupled with other recent work, this review points the way towards an emerging consensus on reproductive evolution in chondrichthyans while offering a basis for future functional and evolutionary analyses. This review also contributes to conservation efforts by highlighting taxa whose reproductive specialisations reflect distinctive evolutionary trajectories and that deserve special protection and further investigation.

Revealing Spermatogenesis in Smooth-Hound Sharks Mustelus mustelus: Insights into the Morphological and Macromolecular Composition of Spermatogenic Cells

Elasmobranchs have an ancestral reproductive system, which offers insights into vertebrate reproductive evolution. Despite their unchanged design over 400 million years, they evolved complex mechanisms ensuring reproductive success. However, human activities induced a significant decline in elasmobranch populations worldwide. In the Mediterranean basin, the smooth-hound shark (Mustelus mustelus) is one of the species that are considered vulnerable to human activities. Conservation efforts necessitate a thorough understanding of its reproductive strategy. This study focused on mature male specimens of smooth-hound sharks that were captured in the Adriatic area and successively analyzed to provide, for the first time, a histologically detailed description of testicular development in the species. Seven phases of the spermatogenesis process were identified, along with the macromolecular characterization of cells obtained using Fourier-transform infrared imaging. Histological analysis showed structural and cellular features similar to those documented in the spermatocysts of other elasmobranchs. The examination of the evolution and migration of both germinative and Sertoli cells at each phase revealed their close connection. Furthermore, different expression levels of lipids, proteins, and phosphates (DNA) at each spermatogenesis stage were observed. This research provided new information on spermatogenesis in the common smooth-hound shark, which is crucial for conservation efforts against population decline and anthropogenic pressures.

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.

Genetic identification of three CITES-listed sharks using a paper-based Lab-on-a-Chip (LOC)

Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple "yes" or "no" result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.

Genome mining shows that retroviruses are pervasively invading vertebrate genomes

Endogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.

The importance of the appendicular skeleton for the phylogenetic reconstruction of lamniform sharks (Chondrichthyes: Elasmobranchii)

Lamniform sharks are one of the more conspicuous groups of elasmobranchs, including several emblematic taxa as the white shark. Although their monophyly is well supported, the interrelationships of taxa within Lamniformes remains controversial because of the conflict among various previous molecular-based and morphology-based phylogenetic hypotheses. In this study, we use 31 characters related to the appendicular skeleton of lamniforms and demonstrate their ability to resolve the systematic interrelationships within this shark order. In particular, the new additional skeletal characters resolve all polytomies that were present in previous morphology-based phylogenetic analyses of lamniforms. Our study demonstrates the strength of incorporating new morphological data for phylogenetic reconstructions.

Thermal sensitivity of metabolic rate mirrors biogeographic differences between teleosts and elasmobranchs

Environmental temperature affects physiological functions, representing a barrier for the range expansions of ectothermic species. To understand the link between thermal physiology and biogeography, a key question is whether among-species thermal sensitivity of metabolic rates is mechanistically constrained or buffered through physiological remodeling over evolutionary time. The former conception, the Universal Temperature Dependence hypothesis, predicts similar among- and within-species thermal sensitivity. The latter conception, the Metabolic Cold Adaptation hypothesis, predicts lower among-species thermal sensitivity than within-species sensitivity. Previous studies that tested these hypotheses for fishes overwhelmingly investigated teleosts with elasmobranchs understudied. Here, we show that among-species thermal sensitivity of resting metabolic rates is lower than within-species sensitivity in teleosts but not in elasmobranchs. Further, species richness declines with latitude more rapidly in elasmobranchs than in teleosts. Metabolic Cold Adaptation exhibited by teleosts might underpin their high diversity at high latitudes, whereas the inflexible thermal sensitivity approximated by Universal Temperature Dependence of elasmobranchs might explain their low diversity at high latitudes.

A Synoptic Review of the Cartilaginous Fishes (Chondrichthyes: Holocephali, Elasmobranchii) from the Upper Jurassic Konservat-Lagerstätten of Southern Germany: Taxonomy, Diversity, and Faunal Relationships

The Late Jurassic-Early Cretaceous (164-100 Ma) represents one of the main transitional periods in life history. Recent studies unveiled a complex scenario in which abiotic and biotic factors and drivers on regional and global scales due to the fragmentation of Pangaea resulted in dramatic faunal and ecological turnovers in terrestrial and marine environments. However, chondrichthyan faunas from this interval have received surprisingly little recognition. The presence of numerous entire skeletons of chondrichthyans preserved in several localities in southern Germany, often referred to as Konservat-Lagerstätten (e.g., Nusplingen and the Solnhofen Archipelago), provides a unique opportunity of to study the taxonomic composition of these assemblages, their ecological distributions and adaptations, and evolutionary histories in detail. However, even after 160 years of study, the current knowledge of southern Germany's Late Jurassic chondrichthyan diversity remains incomplete. Over the last 20 years, the systematic study and bulk sampling of southern Germany's Late Jurassic deposits significantly increased the number of known fossil chondrichthyan genera from the region (32 in the present study). In the present work, the fossil record, and the taxonomic composition of Late Jurassic chondrichthyans from southern Germany are reviewed and compared with several contemporaneous assemblages from other sites in Europe. Our results suggest, inter alia, that the Late Jurassic chondrichthyans displayed extended distributions within Europe. However, it nevertheless also is evident that the taxonomy of Late Jurassic chondrichthyans is in urgent need of revision.

Morphology and phylogenetic significance of the pelvic articular region in elasmobranchs (Chondrichthyes)

The morphology of paired fins is commonly overlooked in morphological studies, particularly the pelvic girdle and fins. Consequently, previous phylogenetic studies incorporating morphological data used few skeletal characters from this complex. In this paper, the phylogenetic significance of pelvic articular characters for elasmobranchs is discussed in light of the morphological variation observed in 130 species, the most comprehensive study exploring the morphology of the pelvic girdle done so far. The 10 morphological characters proposed herein for the pelvic articulation were incorporated into a molecular matrix of NADH2 sequences and submitted to an analysis of maximum parsimony employing extended implied weighting. The most stable tree was selected based on the distortion coefficients, SPR distances (subtree pruning and regrafting) and fit values. Some of the striking synapomorphies recovered within elasmobranchs include the presence of an articular surface for the first enlarged pelvic radial supporting Elasmobranchii and the pelvic articular region for the basipterygium extending from the posterolatral margin of the pelvic girdle over its lateral surface in Echinorhinus + Hexanchiformes. Additionally, the proposed characters and their distributions are discussed considering the relationships recovered and also compared with previous morphological and molecular phylogenetic hypotheses.

Global impact and selectivity of the Cretaceous-Paleogene mass extinction among sharks, skates, and rays

The Cretaceous-Paleogene event was the last mass extinction event, yet its impact and long-term effects on species-level marine vertebrate diversity remain largely uncharacterized. We quantified elasmobranch (sharks, skates, and rays) speciation, extinction, and ecological change resulting from the end-Cretaceous event using >3200 fossil occurrences and 675 species spanning the Late Cretaceous-Paleocene interval at global scale. Elasmobranchs declined by >62% at the Cretaceous-Paleogene boundary and did not fully recover in the Paleocene. The end-Cretaceous event triggered a heterogeneous pattern of extinction, with rays and durophagous species reaching the highest levels of extinction (>72%) and sharks and nondurophagous species being less affected. Taxa with large geographic ranges and/or those restricted to high-latitude settings show higher survival. The Cretaceous-Paleogene event drastically altered the evolutionary history of marine ecosystems.

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.

Characterization of 35 new microsatellite markers for the blacktip reef shark (Carcharhinus melanopterus) and cross-species amplification in eight other shark species

BACKGROUND

Shark species are overfished at a global scale, as they are poached for the finning industry or are caught as bycatch. Efficient conservation measures require fine-scale spatial and temporal studies to characterize shark habitat use, infer migratory habits, analyze relatedness, and detect population genetic differentiation. Gathering these types of data is costly and time-consuming, especially when it requires collection of shark tissue samples.

METHODS AND RESULTS

Genetic tools, such as microsatellite markers, are the most economical sampling method for collecting genetic data, as they enable the estimation of genetic diversity, population structure and parentage relationships and are thus an efficient way to inform conservation strategies. Here, a set of 45 microsatellite loci was tested on three blacktip reef shark (Carcharhinus melanopterus) populations from three Polynesian islands: Moorea, Morane and Tenararo. The set was composed of 10 previously published microsatellite markers and 35 microsatellite markers that were developed specifically for C. melanopterus as part of the present study. The 35 novel and 10 existing loci were cross-amplified on eight additional shark species (Carcharhinus amblyrhynchos, C. longimanus, C. sorrah, Galeocerdo cuvier, Negaprion acutidens, Prionacea glauca, Rhincodon typus and Sphyrna lewini). These species had an average of 69% of successful amplification, considered if at least 50% of the individual samples being successfully amplified per species and per locus.

CONCLUSIONS

This novel microsatellite marker set will help address numerous knowledge gaps that remain, concerning genetic stock identification, shark behavior and reproduction via parentage analysis.

Preliminary study of shark microbiota at a unique mix-species shark aggregation site, in the Eastern Mediterranean Sea

Sharks, as apex predators, play an essential ecological role in shaping the marine food web and maintaining healthy and balanced marine ecosystems. Sharks are sensitive to environmental changes and anthropogenic pressure and demonstrate a clear and rapid response. This designates them a "keystone" or "sentinel" group that may describe the structure and function of the ecosystem. As a meta-organism, sharks offer selective niches (organs) for microorganisms that can provide benefits for their hosts. However, changes in the microbiota (due to physiological or environmental changes) can turn the symbiosis into a dysbiosis and may affect the physiology, immunity and ecology of the host. Although the importance of sharks within the ecosystem is well known, relatively few studies have focused on the microbiome aspect, especially with long-term sampling. Our study was conducted at a site of coastal development in Israel where a mixed-species shark aggregation (November-May) is observed. The aggregation includes two shark species, the dusky (Carcharhinus obscurus) and sandbar (Carcharhinus plumbeus) which segregate by sex (females and males, respectively). In order to characterize the bacterial profile and examine the physiological and ecological aspects, microbiome samples were collected from different organs (gills, skin, and cloaca) from both shark species over 3 years (sampling seasons: 2019, 2020, and 2021). The bacterial composition was significantly different between the shark individuals and the surrounding seawater and between the shark species. Additionally, differences were apparent between all the organs and the seawater, and between the skin and gills. The most dominant groups for both shark species were Flavobacteriaceae, Moraxellaceae, and Rhodobacteraceae. However, specific microbial biomarkers were also identified for each shark. An unexpected difference in the microbiome profile and diversity between the 2019-2020 and 2021 sampling seasons, revealed an increase in the potential pathogen Streptococcus. The fluctuations in the relative abundance of Streptococcus between the months of the third sampling season were also reflected in the seawater. Our study provides initial information on shark microbiome in the Eastern Mediterranean Sea. In addition, we demonstrated that these methods were also able to describe environmental episodes and the microbiome is a robust measure for long-term ecological research.

The Nursehound Scyliorhinus stellaris Mitochondrial Genome—Phylogeny, Relationships among Scyliorhinidae and Variability in Waters of the Balearic Islands

The complete mitochondrial DNA sequence of the Nursehound Scyliorhinus stellaris has been determined for the first time and compared with congeneric species. The mitogenome sequence was 16,684 bp in length. The mitogenome is composed of 13 PCGs, 2 rRNAs, 22 transfer RNA genes and non-coding regions. The gene order of the newly sequenced mitogenome is analogous to the organization described in other vertebrate genomes. The typical conservative blocks in the control region were indicated. The phylogenetic analysis revealed a monophyletic origin of the Scyliorhininae subfamily, and within it, two subclades were identified. A significant divergence of Scyliorhinus spp. together with Poroderna patherinum in relation to the group of Cephaloscyllium spp. was observed, except for Scyliorhinus torazame, more related to this last cited clade. A hypothesis of a divergent evolution consequent to a selective pressure in different geographic areas, which lead to a global latitudinal diversity gradient, has been suggested to explain this phylogenetic reconstruction. However, convergent evolution on mitochondrial genes could also involve different species in some areas of the world.

Evolutionary analysis of swimming speed in early vertebrates challenges the 'New Head Hypothesis'

The ecological context of early vertebrate evolution is envisaged as a long-term trend towards increasingly active food acquisition and enhanced locomotory capabilities culminating in the emergence of jawed vertebrates. However, support for this hypothesis has been anecdotal and drawn almost exclusively from the ecology of living taxa, despite knowledge of extinct phylogenetic intermediates that can inform our understanding of this formative episode. Here we analyse the evolution of swimming speed in early vertebrates based on caudal fin morphology using ancestral state reconstruction and evolutionary model fitting. We predict the lowest and highest ancestral swimming speeds in jawed vertebrates and microsquamous jawless vertebrates, respectively, and find complex patterns of swimming speed evolution with no support for a trend towards more active lifestyles in the lineage leading to jawed groups. Our results challenge the hypothesis of an escalation of Palaeozoic marine ecosystems and shed light into the factors that determined the disparate palaeobiogeographic patterns of microsquamous versus macrosquamous armoured Palaeozoic jawless vertebrates. Ultimately, our results offer a new enriched perspective on the ecological context that underpinned the assembly of vertebrate and gnathostome body plans, supporting a more complex scenario characterized by diverse evolutionary locomotory capabilities reflecting their equally diverse ecologies.

Grouping behaviour impacts on the parasitic pressure and squamation of sharks

The evolution of grouping behaviour involves a complex trade-off of benefits and costs. Among the latter, an increase in the risk of parasitic transmission is a well-documented phenomenon that has likely promoted the evolution of defensive mechanisms in aquatic vertebrates. Here, we explore the relationship between grouping behaviour, parasitic richness (∼parasitic pressure), and the evolution of potential defensive traits in the squamation of sharks through phylogenetic, standard and zero-inflation regression models. Our results demonstrate that sharks that frequently aggregate show increased parasitic pressure, which may constitute an agent of selection. Accordingly, their squamation is characterized by large-scale crown insertion angles and low-scale coverage, which are interpreted as traits that compromise parasite attachment and survival. These traits are less evident in regions of the body and ecological groups that are subjected to high abrasive stress or increased drag. Thus, the squamation of sharks responds to a compromise between various functions, where protective and hydrodynamic roles prevail over the rest (e.g. ectoparasitic defence and bioluminescence aiding). This work establishes a quantitative framework for inferring parasitic pressure and social interaction from squamation traits and provides an empirical basis from which to explore these phenomena through early vertebrate and chondrichthyan evolution.

Dental pathologies in lamniform and carcharhiniform sharks with comments on the classification and homology of double tooth pathologies in vertebrates

Double tooth pathologies are important indicators of trauma, disease, diet, and feeding biomechanics, and are widely documented in mammals. However, diagnosis of double tooth pathologies in extinct non-mammalian vertebrates is complicated by several compounding factors including: a lack of shared terminology reflecting shared etiology, inconsistencies in definitions and key features within and outside of mammals (e.g., gemination, fusion, twinning, concrescence); differences in tooth morphology, heterodonty, regeneration, and implantation between mammals and non-mammalian vertebrates; and the unmet need for diagnostic criteria that can be applied to isolated teeth, which are common in the fossil record. Here we report on double tooth pathologies in the lamniform and carcharhiniform Cenozoic sharks Otodus megalodon (NCSM 33639) and Carcharhinus leucas (NCSM 33640, 33641). All three teeth bear a singular bifid crown with mirrored halves and abnormal internal microstructure-a single, bifurcating pulp cavity in C. leucas and a more than tripling of vessels in O. megalodon (from two to seven main ascending canals). We identify these abnormalities as likely examples of gemination due to their symmetry, which rules out fusion of tooth buds in one tooth file in different developmental stages in polyphyodont taxa; however, we note that incomplete forms of mesiodistal tooth fusion can be morphologically indistinguishable from gemination, and thus fusion cannot be rejected. We further compile and recategorize, when possible, the diversity of tooth pathologies in sharks. The identification of double tooth pathologies in O. megalodon and C. leucas has paleobiological implications. Such pathologies in sharks are largely hypothesized to stem from trauma to developing tooth buds. Carcharhinus leucas is known to feed on prey documented to cause feeding-related oral traumas (e.g., rays, sawfish, spiny fish, and sea urchins). However, O. megalodon, is considered to have largely fed on marine mammals, and perhaps turtles and/or fish, raising the possibility that the dietary diversity of this species is, as of yet, underappreciated. The genetic underpinnings of tooth morphogenesis and regeneration is highly conserved throughout vertebrate evolution, suggesting a homologous framework can be established. However, more research is needed to link developmental, paleobiological, and/or paleoenvironmental factors to gemination/fusion in polyphyodont taxa. We argue that the definitions and diagnostic criteria for dental pathologies in vertebrates require standardization in order to advance macroevolutionary studies of feeding trauma in deep time.

Combined phylogeny and new classification of catsharks (Chondrichthyes: Elasmobranchii: Carcharhiniformes)

This is the first study to combine morphological and molecular characters to infer the phylogenetic relationships among catsharks. All currently valid genera classified in the family Scyliorhinidae s.l. and representatives of other carcharhinoid families plus one lamnoid and two orectoloboids were included as terminal taxa. A total of 143 morphological characters and 44 NADH2 sequences were analysed. Parsimony analyses under different weighting schemes and strengths were used to generate hypotheses of phylogenetic relationships. The phylogenetic analysis of 78 terminal taxa, using the combined dataset and weighting each column separately (SEP; k = 3) resulted in one most-parsimonious cladogram of 4441 steps with the greatest internal resolution of clades and strongest support. The main changes in nomenclature and classification are the revised definition and scope of Scyliorhinidae, Apristurus and Pentanchus and the revalidation of Atelomycteridae. The monophyly of Pentanchidae is supported, as is that of most catshark genera. Two new subfamilies of the family Pentanchidae are defined: Halaelurinae subfam. nov. and Galeinae subfam. nov. Our analysis emphasizes the relevance of morphological characters in the inference of evolutionary history of carcharhinoids and sheds light on the taxonomic status of some genera in need of further exploration.

Shark spiral intestines may operate as Tesla valves

Looking to nature for inspiration has led to many diverse technological advances. The spiral valve intestine of sharks has provided the opportunity to observe the efficiency of different valve systems. It is supposed that the spiral intestine present in sharks, skates and rays slows the transit rate of digesta through the gut and provides increased surface area for the absorption of nutrients. In this investigation, we use a novel technique-creating three-dimensional reconstructions from CT scans of spiral intestines-to describe the morphology of the spiral intestine of at least one species from 22 different shark families. We discuss the morphological data in an evolutionary, dietary and functional context. The evolutionary analyses suggest that the columnar morphology is the ancestral form of the spiral intestine. Dietary analyses reveal no correlation between diet type and spiral intestine morphology. Flow rate was slowed significantly more when the two funnel-shaped spiral intestines were subjected to flow in the posterior to anterior direction, indicating their success at producing unidirectional flow, similar to a Tesla valve. These data are available to generate additional three-dimensional morphometrics, create computational models of the intestine, as well as to further explore the function of the gastrointestinal tract of sharks in structural and physiological contexts.

The published complete mitochondrial genome of the milk shark (Rhizoprionodon acutus) is a misidentified Pacific spadenose shark (Scoliodon macrorhynchos) (Chondrichthyes: Carcharhiniformes)

The recently published mitogenome of milk shark Rhizoprionodon acutus (MN602076/NC_046016) was fully resolved in an unexpected phylogenetic position in the original mitogenome announcement, which rendered the genus Scoliodon paraphyletic. Here, we show that this mitogenome is actually that of a misidentified Pacific spadenose shark (Scoliodon macrorhynchos). The error is documented to avoid the perpetuation of erroneous sequence information in the literature.

Description of the chondrocranium of the silky shark Carcharhinus falciformis with comments on the cranial terminology and phylogenetic implications in carcharhinids (Chondrichthyes, Carcharhiniformes, Carcharhinidae)

The definition and scope of the genus Carcharhinus has undergone several changes over the years and recent molecular studies have questioned its monophyly by the inclusion of other carcharhinid genera. Although many descriptions of chondrocranium are available for Carcharhinus species, some inconsistences and divergences are found in the literature, mainly regarding the foramina of the orbital region. In this study, the chondrocranium of the silky shark, Carcharhinus falciformis, from specimens caught at the Brazilian coast and the terminology of its components is revised has been described. Chondrocrania of other Carcharhinus species and carcharhinid genera are also examined in order to investigate the phylogenetic significance of chondrocranial morphology. Three new anatomical terms and nine chondrocrania characters are proposed and described in detail. The chondrocranial morphology varies widely among Carcharhinus species mainly regarding the rostrum and nasal capsules. The chondrocrania of Prionace, Nasolamia, and Negaprion are similar to Carcharhinus species and reveal the need to further explore the relationships among these genera. Characters potentially informative for systematics are the shape of rostral node, the preorbital process, and the subethmoidal fossa, and the occurrence of an epiphyseal notch and foramen, and must be included in phylogenetic studies encompassing other carcharhiniforms.

Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs

Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.

Functional Morphology of the Feeding Apparatus of the Snaggletooth Shark, Hemipristis elongata (Carcharhiniformes: Hemigaleidae)

The anatomy of the feeding apparatus of the snaggletooth shark, Hemipristis elongata (Klunzinger, 1871) is illustrated in detail from the dissection of three heads. Two new muscles are described: the Adductor mandibularis internus and the Levator mandibularis. A subdivision of the Levator palatoquadrati is described and named the Pronator subdivision of the Levator palatoquadrati. Also, eight new anatomical features associated with the mandibular arch and with the chondrocranium (CR) are described. Three are cartilages: the suprapalatine cartilages, the craniopalatoquadrate cartilage and the calcified Meckelian dental fold. The remaining five features are processes: the Pronator process of the palatoquadrate (PQ), the Levator palatoquadrati alpha process, the proquadrate process, the ectorbital process (ECP) and the Meckelian Intermandibularis ridge. Some of them are not restricted to H.elongata. The function of these new muscles and anatomical features is discussed and a hypothesis about the functional morphology of the feeding apparatus of the snaggletooth shark is proposed. The extent and the assumptive importance of the pronation of the mandibular arch in the snaggletooth shark feeding behaviour is described and discussed. An alternative for the main function of the Levator palatoquadrati as hypothesized by Motta et al. (1997) and Wilga et al. (2001) is proposed for the families Hemigaleidae, Carcharhinidae and Sphyrnidae. We anticipate this muscle is more involved in the pronation rather than in the protrusion of the mandibular arch.

Behavioural thermoregulation linked to foraging in blue sharks

Large pelagic fishes often dive and surface repeatedly as if they were airbreathers, raising a question about the functions of these movements. Some species (e.g., bigeye tuna, ocean sunfish) apparently alternate foraging in deep cold waters and rewarming in shallow warm waters. However, it is unclear how prevalent this pattern is among species. Blue sharks are the widest-ranging pelagic shark with expanded vertical niches, providing a model for studying foraging-thermoregulation associations. We used electronic tags, including video cameras, to record the diving behaviour, muscle temperature, and foraging events of two blue sharks. During repeated deep dives (max. 422 m), muscle temperature changed more slowly than ambient water temperature. Sharks shifted between descents and ascents before muscle temperature reached ambient temperature, leading to a narrower range (8 °C) of muscle temperature than ambient temperature (20 °C). 2.5-h video footage showed a shark catching a squid, during which a burst swimming event was recorded. Similar swimming events, detected from the entire tag data (20 - 22 h), occurred over a wide depth range (5 - 293 m). We conclude that, instead of alternating foraging and rewarming, blue sharks at our study site forage and thermoregulate continuously in the water column. Furthermore, our comparative analyses showed that the heat exchange rates of blue sharks during the warming and cooling process were not exceptional among fishes for their body size. Thus, behavioural thermoregulation linked to foraging, rather than enhanced abilities to control heat exchange rates, is likely key to the expanded thermal niches of this ectothermic species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00227-021-03971-3.

Visual Opsin Diversity in Sharks and Rays

The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.

The intraspecific diversity of tooth morphology in the large-spotted catshark Scyliorhinus stellaris: insights into the ontogenetic cues driving sexual dimorphism

Teeth in sharks are shed and replaced throughout their lifetime. Morphological dental changes through ontogeny have been identified in several species and have been correlated with shifts in diet and the acquisition of sexual maturity. However, these changes were rarely quantified in detail along multiple ontogenetic stages, which makes it difficult to infer the developmental processes responsible for the observed plasticity. In this work, we use micro-computed tomography and 3D geometric morphometrics to describe and analyze the tooth size and shape diversity across three ontogenetic stages (hatchling, juvenile, and sexually mature) in the large-spotted catshark Scyliorhinus stellaris (Linnaeus, 1758). We first describe the intra-individual variation of tooth form for each sex at each ontogenetic stage. We provide a tooth morphospace for palatoquadrate and Meckelian teeth and identify dental features, such as relative size and number of cusps, involved in the range of variation of the observed morphologies. We then use these shape data to draw developmental trajectories between ontogenetic stages and for each tooth position within the jaw to characterize ontogenetic patterns of sexual dimorphism. We highlight the emergence of gynandric heterodonty between the juvenile and mature ontogenetic stages, with mature females having tooth morphologies more similar to juveniles' than mature males that display regression in the number of accessory cusps. From these data, we speculate on the developmental processes that could account for such developmental plasticity in S. stellaris.

Comparative morphology of shark pectoral fins

Sharks vary greatly in morphology, physiology, and ecology. Differences in whole body shape, swimming style, and physiological parameters have previously been linked to varied habitat uses. Pectoral fin morphology has been used to taxonomically classify species and hypotheses on the functional differences in shape are noted throughout the literature; however, there are limited comparative datasets that quantify external and skeletal morphology. Further, fins were previously categorized into two discrete groups based on the amount of skeletal support present: (a) aplesodic, where less than half of the fin is supported and (b) plesodic where greater than half of the fin is supported. These discrete classifications have been used to phylogenetically place species, though the methodology of classification is infrequently described. In this study, we sampled fins from 18 species, 6 families, and 3 orders, which were also grouped into five ecomorphotype classifications. We examined the external morphology, extent of skeletal support, and cross-sectional shape of individual cartilaginous elements. Using phylogenetic comparative methods, we show that fin shape does not differ significantly between ecomorphotypes, suggesting there may be some mechanical constraint. However, we find that the internal anatomy of the fin does vary significantly between ecomorphotypes, especially the extent and distribution of calcification of skeletal support, suggesting that the superficial similarity of fin shapes across ecomorphotypes may belie differences in function. Finally, we find that a number of morphological variables such as number of radials, radial calcification and shape, and fin taper all correlate with the extent of skeletal support. Within these morphospaces, we also describe that some orders/families tend to occupy certain areas with limited overlap. While we demonstrate that there is some mechanical constraint limiting external variations in shark pectoral fin morphology, there are compounding differences in skeletal anatomy that occur within ecomorphotypes which we propose may affect function.

The complete mitogenome of the Critically Endangered smalltooth sand tiger shark, Odontaspis ferox (Lamniformes: Odontaspididae)

Here, we report the first complete mitochondrial genome for the smalltooth sand tiger shark, Odontaspis ferox (Risso, 1810). The circular mitochondrial genome was found to be 16,682 bp in length and contains 37 genes, a control region and the replication origin of the L-strand (O_L). The base composition of this mitogenome is 32.6% A, 23.3% C, 12.8% G, and 31.3% T. Phylogenetic analysis of Lamniformes indicates that O. ferox did not group with Carcharias taurus and so the taxonomic classification of Odontaspididae needs to be revised. This study promotes conservation genetics for this poorly studied shark species which is listed critically endangered in the Mediterranean Sea.

Evolutionary trends of the conserved neurocranium shape in angel sharks (Squatiniformes, Elasmobranchii)

Elasmobranchii (i.e., sharks, skates, and rays) forms one of the most diverse groups of marine predators. With a fossil record extending back into the Devonian, several modifications in their body plan illustrate their body shape diversity through time. The angel sharks, whose fossil record dates back to the Late Jurassic, some 160 Ma, have a dorsoventrally flattened body, similar to skates and rays. Fossil skeletons of this group show that the overall morphology was well established earlier in its history. By examining the skull shape of well-preserved fossil material compared to extant angel sharks using geometric morphometric methods, within a phylogenetic framework, we were able to determine the conservative skull shape among angel sharks with a high degree of integration. The morphospace occupation of extant angel sharks is rather restricted, with extensive overlap. Most of the differences in skull shape are related to their geographic distribution patterns. We found higher levels of disparity in extinct forms, but lower ones in extant species. Since angel sharks display a highly specialized prey capture behaviour, we suggest that the morphological integration and biogeographic processes are the main drivers of their diversity, which might limit their capacity to display higher disparities since their origin.

Discovery of a new mode of oviparous reproduction in sharks and its evolutionary implications

Two modes of oviparity are known in cartilaginous fishes, (1) single oviparity where one egg case is retained in an oviduct for a short period and then deposited, quickly followed by another egg case, and (2) multiple oviparity where multiple egg cases are retained in an oviduct for a substantial period and deposited later when the embryo has developed to a large size in each case. Sarawak swellshark Cephaloscyllium sarawakensis of the family Scyliorhinidae from the South China Sea performs a new mode of oviparity, which is named “sustained single oviparity”, characterized by a lengthy retention of a single egg case in an oviduct until the embryo attains a sizable length. The resulting fecundity of the Sarawak swellshark within a season is quite low, but this disadvantage is balanced by smaller body, larger neonates and quicker maturation. The Sarawak swellshark is further uniquely characterized by having glassy transparent egg cases, and this is correlated with a vivid polka-dot pattern of the embryos. Five modes of lecithotrophic (yolk-dependent) reproduction, i.e. short single oviparity, sustained single oviparity, multiple oviparity, yolk-sac viviparity of single pregnancy and yolk-sac viviparity of multiple pregnancy were discussed from an evolutionary point of view.

Was the Devonian placoderm Titanichthys a suspension feeder?

Large nektonic suspension feeders have evolved multiple times. The apparent trend among apex predators for some evolving into feeding on small zooplankton is of interest for understanding the associated shifts in anatomy and behaviour, while the spatial and temporal distribution gives clues to an inherent relationship with ocean primary productivity and how past and future perturbations to these may impact on the different tiers of the food web. The evolution of large nektonic suspension feeders-'gentle giants'-occurred four times among chondrichthyan fishes (e.g. whale sharks, basking sharks and manta rays), as well as in baleen whales (mysticetes), the Mesozoic pachycormid fishes and at least twice in radiodontan stem group arthropods (Anomalocaridids) during the Cambrian explosion. The Late Devonian placoderm Titanichthys has tentatively been considered to have been a megaplanktivore, primarily due to its gigantic size and narrow, edentulous jaws while no suspension-feeding apparatus have ever been reported. Here, the potential for microphagy and other feeding behaviours in Titanichthys is assessed via a comparative study of jaw mechanics in Titanichthys and other placoderms with presumably differing feeding habits (macrophagy and durophagy). Finite-element models of the lower jaws of Titanichthys termieri in comparison to Dunkleosteus terrelli and Tafilalichthys lavocati reveal considerably less resistance to von Mises stress in this taxon. Comparisons with a selection of large-bodied extant taxa of similar ecological diversity reveal similar disparities in jaw stress resistance. Our results, therefore, conform to the hypothesis that Titanichthys was a suspension feeder with jaws ill-suited for biting and crushing but well suited for gaping ram feeding.

Body forms in sharks (Chondrichthyes: Elasmobranchii) and their functional, ecological, and evolutionary implications

Sharks are among the oldest vertebrate lineages in which their success has been attributed to their diversity in body shape and locomotor design. In this study, we investigated the diversity of body forms in extant sharks using landmark-based geometric morphometric analyses on nearly all the known (ca. 470) extant sharks. We ran three different analyses: the 'full body,' 'precaudal body,' and 'caudal fin' analyses. Our study suggests that there are two basic body forms in sharks, a 'shallow-bodied' form (Group A) and 'deep-bodied' form (Group B), where all sharks essentially have one basic caudal fin design of a heterocercal tail despite some specializations. We found that swimming modes in sharks are highly correlated with body forms where Group A sharks are predominantly anguilliform swimmers and Group B sharks are represented by carangiform and thunniform swimmers. The majority of Group A sharks are found to be benthic whereas pelagic forms are relatively common among Group B sharks. Each of the two superorders of sharks, Squalomorphii and Galeomorphii, must have gone through complex evolutionary history where each superorder contains both Group A sharks and Group B sharks, possibly involving parallel evolution from one group to the other or at least one episode of evolutionary reversal.

Vision in sharks and rays: Opsin diversity and colour vision

The visual sense of elasmobranch fishes is poorly studied compared to their bony cousins, the teleosts. Nevertheless, the elasmobranch eye features numerous specialisations that have no doubt facilitated the diversification and evolutionary success of this fascinating taxon. In this review, I highlight recent discoveries on the nature and phylogenetic distribution of visual pigments in sharks and rays. Whereas most rays appear to be cone dichromats, all sharks studied to date are cone monochromats and, as a group, have likely abandoned colour vision on multiple occasions. This situation in sharks mirrors that seen in other large marine predators, the pinnipeds and cetaceans, which leads us to reassess the costs and benefits of multiple cone pigments and wavelength discrimination in the marine environment.

The retinal pigments of the whale shark (Rhincodon typus) and their role in visual foraging ecology

The spectral tuning properties of the whale shark (Rhincodon typus) rod (rhodopsin or Rh1) and long-wavelength-sensitive (LWS) cone visual pigments were examined to determine whether these retinal pigments have adapted to the broadband light spectrum available for surface foraging or to the narrowband blue-shifted light spectrum available at depth. Recently published whale shark genomes have identified orthologous genes for both the whale shark Rh1 and LWS cone opsins suggesting a duplex retina. Here, the whale shark Rh1 and LWS cone opsin sequences were examined to identify amino acid residues critical for spectral tuning. Surprisingly, the predicted absorbance maximum (λmax) for both the whale shark Rh1 and LWS visual pigments is near 500 nm. Although Rh1 λmax values near 500 nm are typical of terrestrial vertebrates, as well as surface foraging fish, it is uncommon for a vertebrate LWS cone pigment to be so greatly blue-shifted. We propose that the spectral tuning properties of both the whale shark Rh1 and LWS cone pigments are most likely adaptations to the broadband light spectrum available at the surface. Whale shark melanopsin (Opn4) deactivation kinetics was examined to better understand the underlying molecular mechanisms of the pupillary light reflex. Results show that the deactivation rate of whale shark Opn4 is similar to the Opn4 deactivation rate from vertebrates possessing duplex retinae and is significantly faster than the Opn4 deactivation rate from an aquatic rod monochromat lacking functional cone photoreceptors. The rapid deactivation rate of whale shark Opn4 is consistent with a functional cone class and would provide the animal with an exponential increase in the number of photons required for photoreceptor signaling when transitioning from photopic to scotopic light conditions, as is the case when diving.

'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market

Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.

Asymmetric paralog evolution between the "cryptic" gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4

The vertebrate gene repertoire is characterized by “cryptic” genes whose identification has been hampered by their absence from the genomes of well-studied species. One example is the Bmp16 gene, a paralog of the developmental key genes Bmp2 and -4. We focus on the Bmp2/4/16 group of genes to study the evolutionary dynamics following gen(om)e duplications with special emphasis on the poorly studied Bmp16 gene. We reveal the presence of Bmp16 in chondrichthyans in addition to previously reported teleost fishes and reptiles. Using comprehensive, vertebrate-wide gene sampling, our phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remnants of a gene quartet that originated during the two rounds of whole-genome duplication (2R-WGD) early in vertebrate evolution. We confirm that Bmp16 genes were lost independently in at least three lineages (mammals, archelosaurs and amphibians) and report that they have elevated rates of sequence evolution. This finding agrees with their more “flexible” deployment during development; while Bmp16 has limited embryonic expression domains in the cloudy catshark, it is broadly expressed in the green anole lizard. Our study illustrates the dynamics of gene family evolution by integrating insights from sequence diversification, gene repertoire changes, and shuffling of expression domains.

Role of elasmobranchs and holocephalans in understanding peptide evolution in the vertebrates: Lessons learned from gonadotropin releasing hormone (GnRH) and corticotropin releasing factor (CRF) phylogenies

The cartilaginous fishes (Class Chondrichthyes) comprise two morphologically distinct subclasses; Elasmobranchii and Holocephali. Evidence indicates early divergence of these subclasses, suggesting monophyly of their lineage. However, such a phylogenetic understanding is not yet developed within two highly conserved peptide lineages, GnRH and CRF. Various GnRH forms exist across the Chondrichthyes. Although 4-7 immunoreactive forms have been described in Elasmobranchii, only one has been elucidated in Holocephali. In contrast, Chondrichthyan CRF phylogeny follows a pattern more consistent with vertebrate evolution. For example, three forms are expressed within the lamprey, with similar peptides present within the genome of the Callorhinchus milii, a holocephalan. Although these findings are consistent with recent evidence regarding the phylogenetic age of Chondrichthyan lineages, CRF evolution in vertebrates remains elusive. Assuming that the Elasmobranchii and Holocephali are part of a monocladistic clade within the Chondrichthyes, we interpret the findings of GnRH and CRF to be products of their respective lineages.

Development and evolution of tooth renewal in neoselachian sharks as a model for transformation in chondrichthyan dentitions

A defining feature of dentitions in modern sharks and rays is the regulated pattern order that generates multiple replacement teeth. These are arranged in labio-lingual files of replacement teeth that form in sequential time order both along the jaw and within successively initiated teeth in a deep dental lamina. Two distinct adult dentitions have been described: alternate, in which timing of new teeth alternates between two adjacent files, each erupting separately, and the other arranged as single files, where teeth of each file are timed to erupt together, in some taxa facilitating similarly timed teeth to join to form a cutting blade. Both are dependent on spatiotemporally regulated formation of new teeth. The adult Angel shark Squatina (Squalomorphii) exemplifies a single file dentition, but we obtained new data on the developmental order of teeth in the files of Squatina embryos, showing alternate timing of tooth initiation. This was based on micro-CT scans revealing that the earliest mineralised teeth at the jaw margin and their replacements in file pairs (odd and even jaw positions) alternate in their initiation timing. Along with Squatina, new observations from other squalomorphs such as Hexanchus and Chlamydoselachus, together with representatives of the sister group Galeomorphii, have established that the alternate tooth pattern (initiation time and replacement order) characterises the embryonic dentition of extant sharks; however, this can change in adults. These character states were plotted onto a recent phylogeny, demonstrating that the Squalomorphii show considerable plasticity of dental development. We propose a developmental-evolutionary model to allow change from the alternate to a single file alignment of replacement teeth. This establishes new dental morphologies in adult sharks from inherited alternate order.

DNA barcoding reveals the diversity of sharks in Guyana coastal markets

ABSTRACT A fundamental challenge for both sustainable fisheries and biodiversity protection in the Neotropics is the accurate determination of species identity. The biodiversity of the coastal sharks of Guyana is poorly understood, but these species are subject to both artisanal fishing as well as harvesting by industrialized offshore fleets. To determine what species of sharks are frequently caught and consumed along the coastline of Guyana, we used DNA barcoding to identify market specimens. We sequenced the mitochondrial co1 gene for 132 samples collected from six markets, and compared our sequences to those available in the Barcode of Life Database (BOLD) and GenBank. Nearly 30% of the total sample diversity was represented by two species of Hammerhead Sharks (Sphyrna mokarran and S. lewini), both listed as Endangered by the International Union for Conservation of Nature (IUCN). Other significant portions of the samples included Sharpnose Sharks (23% - Rhizoprionodon spp.), considered Vulnerable in Brazilian waters due to unregulated gillnet fisheries, and the Smalltail Shark (17% - Carcharhinus porosus). We found that barcoding provides efficient and accurate identification of market specimens in Guyana, making this study the first in over thirty years to address Guyana’s coastal shark biodiversity.

Ecomorphological inferences in early vertebrates: reconstructing Dunkleosteus terrelli (Arthrodira, Placodermi) caudal fin from palaeoecological data

Our knowledge about the body morphology of many extinct early vertebrates is very limited, especially in regard to their post-thoracic region. The prompt disarticulation of the dermo-skeletal elements due to taphonomic processes and the lack of a well-ossified endoskeleton in a large number of groups hinder the preservation of complete specimens. Previous reconstructions of most early vertebrates known from partial remains have been wholly based on phylogenetically closely related taxa. However, body design of fishes is determined, to a large extent, by their swimming mode and feeding niche, making it possible to recognise different morphological traits that have evolved several times in non-closely related groups with similar lifestyles. Based on this well-known ecomorphological correlation, here we propose a useful comparative framework established on extant taxa for predicting some anatomical aspects in extinct aquatic vertebrates from palaeoecological data and vice versa. For this, we have assessed the relationship between the locomotory patterns and the morphological variability of the caudal region in extant sharks by means of geometric morphometrics and allometric regression analysis. Multivariate analyses reveal a strong morphological convergence in non-closely related shark species that share similar modes of life, enabling the characterization of the caudal fin morphology of different ecological subgroups. In addition, interspecific positive allometry, affecting mainly the caudal fin span, has been detected. This phenomenon seems to be stronger in sharks with more pelagic habits, supporting its role as a compensation mechanism for the loss of hydrodynamic lift associated with the increase in body size, as previously suggested for many other living and extinct aquatic vertebrates. The quantification of shape change per unit size in each ecological subgroup has allowed us to establish a basis for inferring not only qualitative aspects of the caudal fin morphology of extinct early vertebrates but also to predict absolute values of other variables such as the fin span or the hypocercal and heterocercal angles. The application of this ecomorphological approach to the specific case of Dunkleosteus terrelli has led to a new reconstruction of this emblematic placoderm. Our proposal suggests a caudal fin with a well-developed ventral lobe, narrow peduncle and wide span, in contrast to classical reconstructions founded on the phylogenetic proximity with much smaller placoderms known from complete specimens. Interestingly, this prediction gains support with the recent discovery of fin distal elements (ceratotrichia) in a well preserved D. terrelli, which suggests a possible greater morphological variability in placoderm caudal fins than previously thought.

Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.

Assessing the relationships between phylogenetic and functional singularities in sharks (Chondrichthyes)

The relationships between diversity and ecosystem functioning have become a major focus of science. A crucial issue is to estimate functional diversity, as it is intended to impact ecosystem dynamics and stability. However, depending on the ecosystem, it may be challenging or even impossible to directly measure ecological functions and thus functional diversity. Phylogenetic diversity was recently under consideration as a proxy for functional diversity. Phylogenetic diversity is indeed supposed to match functional diversity if functions are conservative traits along evolution. However, in case of adaptive radiation and/or evolutive convergence, a mismatch may appear between species phylogenetic and functional singularities. Using highly threatened taxa, sharks, this study aimed to explore the relationships between phylogenetic and functional diversities and singularities. Different statistical computations were used in order to test both methodological issue (phylogenetic reconstruction) and overall a theoretical questioning: the predictive power of phylogeny for function diversity. Despite these several methodological approaches, a mismatch between phylogeny and function was highlighted. This mismatch revealed that (i) functions are apparently nonconservative in shark species, and (ii) phylogenetic singularity is not a proxy for functional singularity. Functions appeared to be not conservative along the evolution of sharks, raising the conservational challenge to identify and protect both phylogenetic and functional singular species. Facing the current rate of species loss, it is indeed of major importance to target phylogenetically singular species to protect genetic diversity and also functionally singular species in order to maintain particular functions within ecosystem.